U.S. patent application number 16/006572 was filed with the patent office on 2019-10-31 for systems and methods for generating, visualizing and classifying molecular functional profiles.
This patent application is currently assigned to BostonGene Corporation. The applicant listed for this patent is BostonGene Corporation. Invention is credited to Ravshan Ataullakhanov, Alexander Bagaev, Feliks Frenkel, Nikita Kotlov.
Application Number | 20190332744 16/006572 |
Document ID | / |
Family ID | 62779138 |
Filed Date | 2019-10-31 |
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United States Patent
Application |
20190332744 |
Kind Code |
A9 |
Bagaev; Alexander ; et
al. |
October 31, 2019 |
SYSTEMS AND METHODS FOR GENERATING, VISUALIZING AND CLASSIFYING
MOLECULAR FUNCTIONAL PROFILES
Abstract
Various methods, systems, computer readable media, and graphical
user interfaces (GUIs) are presented and described that enable a
subject, doctor, or user to characterize or classify various types
of cancer precisely. Additionally, described herein are methods,
systems, computer readable media, and GUIs that enable more
effective specification of treatment and improved outcomes for
patients with identified types of cancer. Some embodiments of the
methods, systems, computer readable media, and GUIs described
herein comprise obtaining RNA expression data and/or whole exome
sequencing (WES) data for a biological sample; determining a
molecular-functional (MF) profile for a subject using the data;
determining visual characteristics GUI elements using the data;
generating a GUI personalized to the subject using the determined
visual characteristics; and presenting the generated personalized
GUI to a user.
Inventors: |
Bagaev; Alexander; (Moscow,
RU) ; Frenkel; Feliks; (Moscow, RU) ; Kotlov;
Nikita; (Moscow, RU) ; Ataullakhanov; Ravshan;
(Moscow, RU) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BostonGene Corporation |
Lincoln |
MA |
US |
|
|
Assignee: |
BostonGene Corporation
Lincoln
MA
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20180357377 A1 |
December 13, 2018 |
|
|
Family ID: |
62779138 |
Appl. No.: |
16/006572 |
Filed: |
June 12, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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62598440 |
Dec 13, 2017 |
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62518787 |
Jun 13, 2017 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2600/156 20130101;
G16H 50/30 20180101; G16B 5/20 20190201; G16H 70/20 20180101; G16B
5/00 20190201; G16H 50/70 20180101; G06F 17/18 20130101; G16H 20/40
20180101; G06F 16/285 20190101; G16H 50/50 20180101; C12Q 1/6886
20130101; G16H 20/10 20180101; G16H 20/00 20180101; Y02A 90/10
20180101; G16B 20/00 20190201; G16B 40/00 20190201; C12Q 2600/158
20130101; G16H 10/20 20180101; G16B 45/00 20190201; G16H 50/20
20180101; G16B 50/00 20190201 |
International
Class: |
G06F 19/26 20060101
G06F019/26; G06F 19/24 20060101 G06F019/24 |
Claims
1. A system, comprising: at least one computer hardware processor;
and at least one non-transitory computer-readable storage medium
storing processor-executable instructions that, when executed by
the at least one computer hardware processor, cause the at least
one computer hardware processor to perform: obtaining RNA
expression data and/or whole exome sequencing (WES) data for a
biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the tumor properties group; and second gene groups
associated with cancer microenvironment consisting of the
tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group, determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
2. The system of claim 1, wherein determining the first set of
visual characteristics for the first plurality of GUI elements
determining sizes for each of the first plurality of GUI elements
using the gene expression levels determined for the first gene
groups; and wherein determining the second set of visual
characteristics for the first plurality of GUI elements determining
sizes for each of the second plurality of GUI elements using the
gene expression levels determined for the second gene groups.
3. The system of claim 2, wherein determining the MF profile for
the subject comprises determining the gene expression levels for
each of the first gene groups using a gene set enrichment analysis
(GSEA) technique; and wherein determining the MF profile for the
subject comprises determining the gene expression levels for each
of the second gene groups using the gene set enrichment analysis
(GSEA) technique.
4. The system of claim 1, wherein the gene groups associated with
cancer malignancy comprise at least three genes from each of the
following groups: the tumor properties group: MKI67, ESCO2, CETN3,
CDK2, CCND1, CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2,
BUB1, PLK1, CCNB1, MCM2, MCM6, PIK3CA, PIK3CB, PIK3CG, PIK3CD,
AKT1, MTOR, PTEN, PRKCA, AKT2, AKT3, BRAF, FNTA, FNTB, MAP2K1,
MAP2K2, MKNK1, MKNK2, ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1,
FGFR1, FGFR2, FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, PDGFRB, NGF,
CSF3, CSF2, FGF7, IGF1, IGF2, IL7, FGF2, TP53, SIK1, PTEN, DCN,
MTAP, AIM2, RB1, ESRP1, CTSL, HOXA1, SMARCA4, SNAI2, TWIST1, NEDD9,
PAPPA, HPSE, KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1,
MITF, APC, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2, CDH1, CDKN2A,
CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS, IDH1, KRAS,
MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1, NPM1, NRAS, PBRM1, PIK3CA,
PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2, TAF1, TP53, and VHL.
5. The system of claim 1, wherein determining the MF portrait
comprises: determining the gene group expression level for the
tumor properties group using the gene expression level obtained
from the RNA sequence data for at least three genes in the tumor
properties group.
6. The system of claim 1, wherein the gene groups associated with
cancer microenvironment comprise at least three genes from each of
the following groups: the anti-tumor immune microenvironment group:
HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, HLA-DRA, HLA-DRB1, HLA-DOB,
HLA-DPB2, HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1,
HLA-DQA1, HLA-DRB5, HLA-DQA2, HLA-DQB2, HLA-DRB6, CD80, CD86, CD40,
CD83, TNFRSF4, ICOSLG, CD28, IFNG, GZMA, GZMB, PRF1, LCK, GZMK,
ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B, NKG7, CD160, CD244,
NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1,
KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, CXCL9, CXCL10, CXCR3, CX3CL1,
CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, CCL5, EOMES, TBX21, ITK,
CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, LCK, UBASH3A, TRAT1, CD19,
MS4A1, TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22,
CD79A, CD79B, BLK, NOS2, IL12A, IL12B, IL23A, TNF, IL1B, SOCS3,
IFNG, IL2, CD40LG, IL15, CD27, TBX21, LTA, IL21, HMGB1, TNF, IFNB1,
IFNA2, CCL3, TNFSF10, and FASLG; and the tumor-promoting immune
microenvironment group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA,
HAVCR2, VSIR, CXCL12, TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10,
TNFRSF1B, CCL17, CXCR4, CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13,
CCL28, IDO1, ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB,
CXCR4, CD33, CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5,
CSF1, CXCL8, CXCL8, CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5, CXCL5,
CCR3, CCL26, PRG2, EPX, RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8,
PRG3, CMA1, TPSAB1, MS4A2, CPA3, IL4, IL5, IL13, SIGLEC8, MPO,
ELANE, PRTN3, CTSG, IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1,
LRP1, ARG1, PTGS1, MSR1, CD163, CSF1R, IL4, IL5, IL13, IL10, IL25,
GATA3, IL10, TGFB1, TGFB2, TGFB3, IL22, MIF, CFD, CFI, CD55, CD46,
and CR1; the fibroblasts group: LGALS1, COL1A1, COL1A2, COL4A1,
COL5A1, TGFB1, TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248, COL6A1,
COL6A2, and COL6A3; and the angiogenesis group: VEGFA, VEGFB,
VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2,
TEK, VWF, CDH5, NOS3, KDR, VCAM1, MMRN1, LDHA, HIF1A, EPAS1, CA9,
SPP1, LOX, SLC2A1, and LAMP3.
7. The system of claim 6, wherein determining the MF portrait
comprises: determining the gene group expression level for the
anti-tumor immune microenvironment group using the gene expression
level obtained from the RNA sequence data for at least three genes
in the anti-tumor immune microenvironment group; determining the
gene group expression level for the tumor-promoting immune
microenvironment group using the gene expression level obtained
from the RNA sequence data for at least three genes in the
tumor-promoting immune microenvironment group; determining the gene
group expression level for the fibroblasts group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the fibroblasts group; and determining the gene
group expression level for the angiogenesis group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the angiogenesis group.
8. The system of claim 1, wherein obtaining the RNA expression data
is performed using whole transcriptome sequencing or mRNA
sequencing.
9. The system of claim 1, wherein each of the biological samples is
from a tumor or tissue known or suspected of having cancerous
cells.
10. The system of claim 1, wherein the WES data is used to quantify
tumor burden (purity), identify specific mutations, and/or to
calculate the number of neoantigens.
Description
RELATED APPLICATIONS
[0001] This application claims the benefit under 35 U.S.C. .sctn.
119(e) of the filing date of U.S. provisional patent application
Ser. No. 62/518,787, entitled "Systems and Methods for Identifying
Cancer Treatments from Sequence Data", filed Jun. 13, 2017 and U.S.
provisional patent application Ser. No. 62/598,440, entitled
"Systems and Methods Identifying Cancer Treatments from Sequence
Data," filed Dec. 13, 2017, the entire contents of which are
incorporated herein by reference.
[0002] This application is filed on the same day as International
Application No.: PCT/US18/37017, entitled "SYSTEMS AND METHODS FOR
GENERATING, VISUALIZING AND CLASSIFYING MOLECULAR FUNCTIONAL
PROFILES", bearing Attorney Docket No. B1462.70002W000;
International Application No.: PCT/US18/37018, entitled "SYSTEMS
AND METHODS FOR IDENTIFYING RESPONDERS AND NON-RESPONDERS TO IMMUNE
CHECKPOINT BLOCKADE THERAPY", bearing Attorney Docket No.
B1462.70003W000; and International Application No.: PCT/US18/37008,
entitled "SYSTEMS AND METHODS FOR IDENTIFYING CANCER TREATMENTS
FROM NORMALIZED BIOMARKER SCORES", bearing Attorney Docket No.
B1462.70004W000, the entire contents of each of which are
incorporated herein by reference.
FIELD
[0003] Aspects of the technology described herein relate to
generating, visualizing and classifying molecular-functional (MF)
profiles of cancer patients.
[0004] Some aspects of the technology described herein relate to
generating a graphical user interface (GUI) for visualizing a
molecular-functional profile of a cancer patient.
[0005] Some aspects of the technology described herein relate to
identifying the type of MF profile of a patient, and predicting
prognoses, identifying therapies, and/or otherwise aiding in the
personalized care of the patient using the identified type.
BACKGROUND
[0006] Correctly characterizing the type or types of cancer a
patient or subject has and, potentially, selecting one or more
effective therapies for the patient can be crucial for the survival
and overall wellbeing of that patient. Advances in characterizing
cancers, predicting prognoses, identifying effective therapies, and
otherwise aiding in personalized care of patients with cancer are
needed.
SUMMARY
[0007] Provided herein, inter alia, are systems and methods for
generating a molecular-functional (MF) profile for a subject and
identifying an existing MF profile cluster that is associated with
the generated MF profile. Such information, in some embodiments, is
output to a user in a graphical user interface (GUI).
[0008] Systems and methods for identifying a molecular-functional
(MF) profile cluster with which to associate a MF profile for a
subject comprises, in some embodiments, obtaining RNA expression
data and/or whole exome sequencing (WES) data for the subject;
determining a MF profile for the subject, in part, by determining a
gene group expression level for each gene group in a set of gene
groups using the RNA expression data and/or WES data, the set of
gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; and identifying a MF profile cluster with which
to associate the MF profile for the subject from among multiple MF
profile clusters that were generated by determining a plurality of
MF profiles for a respective plurality of subjects using RNA
expression data obtained from biological samples for the plurality
of subjects, each of the plurality of MF profiles containing a gene
group expression level for each gene group in the set of gene
groups, and clustering the plurality of MF profiles to obtain the
MF profile clusters. Provided herein, inter alia, are systems and
methods for generating MF profile clusters. Such information, in
some embodiments, is stored in one or more databases.
[0009] Systems and methods for generating MF profile clusters
comprises, in some embodiments, obtaining RNA expression data
and/or whole exome sequencing (WES) data for a plurality of
subjects having a cancer of a particular type; determining a
respective plurality of MF profiles for the plurality of subjects,
in part, by determining, for each subject, a respective gene group
expression level for each gene group in a set of gene groups using
the RNA expression data and/or WES data, the set of gene groups
comprising gene groups associated with cancer malignancy and
different gene groups associated with cancer microenvironment;
clustering the plurality of MF profiles to obtain MF profile
clusters comprising a first MF profile cluster, a second MF profile
cluster, a third MF profile cluster, and a fourth MF profile
cluster; and storing the plurality of MF profiles in association
with information identifying the particular cancer type.
[0010] Provided herein, inter alia, are systems and methods for
generating a molecular-functional (MF) profile for a subject using
at least four (e.g., at least five) gene group expression levels
and identifying an existing MF profile cluster that is associated
with the generated MF profile. Such information, in some
embodiments, is output to a user in a graphical user interface
(GUI).
[0011] Systems and methods for identifying a molecular-functional
(MF) profile cluster with which to associate a MF profile for a
subject comprises, in some embodiments, obtaining RNA expression
data and/or whole exome sequencing (WES) data for the subject;
determining a MF profile for the subject, in part, by determining a
gene group expression level for each gene group in a set of gene
groups using the RNA expression data and/or WES data, the set of
gene groups comprising gene groups associated with cancer
malignancy that consists of a tumor properties group and gene
groups associated with cancer microenvironment that consists of a
tumor-promoting immune microenvironment group, a an anti-tumor
immune microenvironment group, an angiogenesis group, and a
fibroblasts group; and identifying a MF profile cluster with which
to associate the MF profile for the subject from among multiple MF
profile clusters that were generated by determining a plurality of
MF profiles for a respective plurality of subjects using RNA
expression data obtained from biological samples for the plurality
of subjects, each of the plurality of MF profiles containing a gene
group expression level for each gene group in the set of gene
groups, and clustering the plurality of MF profiles to obtain the
MF profile clusters.
[0012] Provided herein, inter alia, are systems and methods for
generating molecular-functional (MF) profile clusters, generating
MF profiles for a subject, and associating the patient's MF profile
with the MF profile cluster. Such information, in some embodiments,
is output to a user in a graphical user interface (GUI).
[0013] Systems and methods for generating molecular-functional (MF)
profile clusters, generating MF profiles for a subject, and
associating the patient's MF profile with the MF profile cluster
comprises, in some embodiments, obtaining RNA expression data
and/or whole exome sequencing (WES) data for a plurality of
subjects; determining a respective plurality of MF profiles for the
plurality of subjects, in part, by determining, for each subject, a
respective gene group expression level for each gene group in a set
of gene groups using the RNA expression data and/or WES data, the
set of gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters comprising a first MF profile cluster, a second
MF profile cluster, a third MF profile cluster, and a fourth MF
profile cluster; obtaining second RNA expression data from a
subject, determining a MF profile for the subject, in part, by
determining a gene group expression level for each gene group in
the set of gene groups using the second RNA expression data; and
identifying a MF profile cluster with which to associate the MF
profile for the subject from among multiple MF profile
clusters.
[0014] Provided herein, inter alia, are systems and methods for
generating a MF profile and generating a MF portrait for
visualizing the MF profile in a graphical user interface (GUI).
[0015] Systems and methods for generating a MF profile and
generating a MF portrait for visualizing the MF profile in a
graphical user interface (GUI) comprises, in some embodiments,
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a subject; determining a MF profile for the subject, in
part, by determining a gene group expression level for each gene
group in a set of gene groups using the RNA expression data and/or
WES data, the set of gene groups comprising gene groups associated
with cancer malignancy and different gene groups associated with
cancer microenvironment; determining a first visual characteristic
for a first GUI element using the first gene group expression
level; determining a second visual characteristic for a second GUI
element using the second gene group expression level; generating a
personalized GUI personalized to the subject; and presenting the
generated personalized GUI to a user.
[0016] Provided herein, inter alia, are systems and methods for
generating a MF profile by determining expression levels for e.g.,
four or five gene groups and generating a MF portrait for
visualizing the MF profile in a graphical user interface (GUI).
[0017] Systems and methods for generating a MF profile by
determining expression levels for e.g., four or five gene groups
and generating a MF portrait for visualizing the MF profile in a
graphical user interface (GUI) comprises, in some embodiments,
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a subject; determining a MF profile for the subject, in
part, by determining a gene group expression level for each gene
group in a set of gene groups using the RNA expression data and/or
WES data, the set of gene groups comprising gene groups associated
with cancer malignancy that consists of X and gene groups
associated with cancer microenvironment that consist of a
tumor-promoting immune microenvironment group, an anti-tumor immune
microenvironment group, an angiogenesis group, and a fibroblasts
group; determining a first visual characteristic for a first GUI
element using the first gene group expression level; determining a
second visual characteristic for a second GUI element using the
second gene group expression level; generating a personalized GUI
personalized to the subject; and presenting the generated
personalized GUI to a user.
[0018] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups, the set of gene groups comprising
gene groups associated with cancer malignancy and different gene
groups associated with cancer microenvironment; and identifying,
from among multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using RNA expression data obtained from
biological samples from the plurality of subjects, each of the
plurality of MF profiles containing a gene group expression level
for each gene group in the set of gene groups; and clustering the
plurality of MF profiles to obtain the MF profile clusters.
[0019] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups, the
set of gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; and identifying, from among multiple MF profile
clusters, an MF profile cluster with which to associate the MF
profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using RNA expression data obtained from biological samples from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0020] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; and identifying, from
among multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using RNA expression data obtained from
biological samples from the plurality of subjects, each of the
plurality of MF profiles containing a gene group expression level
for each gene group in the set of gene groups; and clustering the
plurality of MF profiles to obtain the MF profile clusters.
[0021] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data from biological
samples from a plurality of subjects, at least some of the subjects
having a cancer of a particular type; determining a respective
plurality of molecular-functional (MF) profiles for the plurality
of subjects at least in part by, for each of the plurality of
subjects, determining, using the RNA expression data, a respective
gene group expression level for each group in a set of gene groups,
the set of gene groups comprising gene groups associated with
cancer malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters comprising: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological sample; and storing the
plurality of MF profiles in association with information
identifying the particular cancer type.
[0022] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data from biological samples from a plurality of subjects, at least
some of the subjects having a cancer of a particular type;
determining a respective plurality of molecular-functional (MF)
profiles for the plurality of subjects at least in part by, for
each of the plurality of subjects, determining, using the RNA
expression data, a respective gene group expression level for each
group in a set of gene groups, the set of gene groups comprising
gene groups associated with cancer malignancy and different gene
groups associated with cancer microenvironment; clustering the
plurality of MF profiles to obtain MF profile clusters comprising:
a first MF profile cluster associated with inflamed and
vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological sample; and storing the plurality of MF profiles in
association with information identifying the particular cancer
type.
[0023] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data from biological samples from a
plurality of subjects, at least some of the subjects having a
cancer of a particular type; determining a respective plurality of
molecular-functional (MF) profiles for the plurality of subjects at
least in part by, for each of the plurality of subjects,
determining, using the RNA expression data, a respective gene group
expression level for each group in a set of gene groups, the set of
gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters comprising: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological sample; and storing the
plurality of MF profiles in association with information
identifying the particular cancer type.
[0024] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups, the set of gene groups comprising a
first gene group associated with cancer malignancy and a second
gene group associated with cancer microenvironment, wherein the
first and second gene groups are different, the determining
comprising: determining a first gene group expression level for the
first gene group, and determining a second gene group expression
level for the second gene group; determining a first visual
characteristic for a first graphical user interface (GUI) element
using the first gene group expression level; determining a second
visual characteristic for a second GUI element using the second
gene group expression level; generating a personalized GUI
personalized to the subject, the GUI comprising: a first GUI
portion associated with cancer malignancy and containing the first
GUI element having the first visual characteristic, and a second
GUI portion associated with cancer microenvironment and containing
the second GUI element having the second visual characteristic; and
presenting the generated personalized GUI to a user.
[0025] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups, the
set of gene groups comprising a first gene group associated with
cancer malignancy and a second gene group associated with cancer
microenvironment, wherein the first and second gene groups are
different, the determining comprising: determining a first gene
group expression level for the first gene group, and determining a
second gene group expression level for the second gene group;
determining a first visual characteristic for a first graphical
user interface (GUI) element using the first gene group expression
level; determining a second visual characteristic for a second GUI
element using the second gene group expression level; generating a
personalized GUI personalized to the subject, the GUI comprising: a
first GUI portion associated with cancer malignancy and containing
the first GUI element having the first visual characteristic, and a
second GUI portion associated with cancer microenvironment and
containing the second GUI element having the second visual
characteristic; and presenting the generated personalized GUI to a
user.
[0026] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups, the set of gene groups comprising a first gene group
associated with cancer malignancy and a second gene group
associated with cancer microenvironment, wherein the first and
second gene groups are different, the determining comprising:
determining a first gene group expression level for the first gene
group, and determining a second gene group expression level for the
second gene group; determining a first visual characteristic for a
first graphical user interface (GUI) element using the first gene
group expression level; determining a second visual characteristic
for a second GUI element using the second gene group expression
level; generating a personalized GUI personalized to the subject,
the GUI comprising: a first GUI portion associated with cancer
malignancy and containing the first GUI element having the first
visual characteristic, and a second GUI portion associated with
cancer microenvironment and containing the second GUI element
having the second visual characteristic; and presenting the
generated personalized GUI to a user.
[0027] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the tumor properties group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the tumor-promoting immune
microenvironment group, the anti-tumor immune microenvironment
group, the angiogenesis group, and the fibroblasts group; and
accessing information specifying multiple MF profile clusters for
the particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological sample, wherein
the MF profile clusters were generated by: determining a plurality
of MF profiles for a respective plurality of subjects using the
reference RNA expression data and RNA expression data from
biological samples obtained from the plurality of subjects, each of
the plurality of MF profiles containing a gene group expression
level for each gene group in the set of gene groups; and clustering
the plurality of MF profiles to obtain the MF profile clusters.
[0028] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject having a particular
type of cancer; determining a molecular-functional (MF) profile for
the subject at least in part by: determining, using the RNA
expression data and reference RNA expression data, a gene group
expression level for each gene group in a first set of gene groups
associated with cancer malignancy and consisting of the tumor
properties group; and determining, using the RNA expression data
and the reference RNA expression data, a gene group expression
level for each gene group in a second set of gene groups associated
with cancer microenvironment and consisting of the tumor-promoting
immune microenvironment group, the anti-tumor immune
microenvironment group, the angiogenesis group, and the fibroblasts
group; and accessing information specifying multiple MF profile
clusters for the particular cancer type; identifying, from among
the multiple MF profile clusters, an MF profile cluster with which
to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological sample, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using the reference RNA expression data and
RNA expression data from biological samples obtained from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0029] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the tumor properties group; and determining, using
the RNA expression data and the reference RNA expression data, a
gene group expression level for each gene group in a second set of
gene groups associated with cancer microenvironment and consisting
of the tumor-promoting immune microenvironment group, the
anti-tumor immune microenvironment group, the angiogenesis group,
and the fibroblasts group; and accessing information specifying
multiple MF profile clusters for the particular cancer type;
identifying, from among the multiple MF profile clusters, an MF
profile cluster with which to associate the MF profile for the
subject, the MF profile clusters comprising: a first MF profile
cluster associated with inflamed and vascularized biological
samples and/or inflamed and fibroblast-enriched biological samples,
a second MF profile cluster associated with inflamed and
non-vascularized biological samples and/or inflamed and
non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological sample, wherein
the MF profile clusters were generated by: determining a plurality
of MF profiles for a respective plurality of subjects using the
reference RNA expression data and RNA expression data from
biological samples obtained from the plurality of subjects, each of
the plurality of MF profiles containing a gene group expression
level for each gene group in the set of gene groups; and clustering
the plurality of MF profiles to obtain the MF profile clusters.
[0030] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the proliferation rate group,
the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group,
the receptor tyrosine kinases expression group, the tumor
suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the antigen presentation group,
the cytotoxic T and NK cells group, the B cells group, the
anti-tumor microenvironment group, the checkpoint inhibition group,
the Treg group, the MDSC group, the granulocytes group, the cancer
associated fibroblasts group, the angiogenesis group, and the
tumor-promotive immune group; and accessing information specifying
multiple MF profile clusters for the particular cancer type;
identifying, from among the multiple MF profile clusters, an MF
profile cluster with which to associate the MF profile for the
subject, the MF profile clusters comprising: a first MF profile
cluster associated with inflamed and vascularized biological
samples and/or inflamed and fibroblast-enriched biological samples,
a second MF profile cluster associated with inflamed and
non-vascularized biological samples and/or inflamed and
non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0031] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining obtaining RNA expression data and/or whole exome
sequencing (WES) data for a biological sample from a subject having
a particular type of cancer; determining a molecular-functional
(MF) profile for the subject at least in part by: determining,
using the RNA expression data and reference RNA expression data, a
gene group expression level for each gene group in a first set of
gene groups associated with cancer malignancy and consisting of the
proliferation rate group, the PI3K/AKT/mTOR signaling group, the
RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group; and determining, using the RNA expression
data and the reference RNA expression data, a gene group expression
level for each gene group in a second set of gene groups associated
with cancer microenvironment and consisting of the antigen
presentation group, the cytotoxic T and NK cells group, the B cells
group, the anti-tumor microenvironment group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the cancer associated fibroblasts group, the angiogenesis
group, and the tumor-promotive immune group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0032] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and determining, using the RNA
expression data and the reference RNA expression data, a gene group
expression level for each gene group in a second set of gene groups
associated with cancer microenvironment and consisting of the
antigen presentation group, the cytotoxic T and NK cells group, the
B cells group, the anti-tumor microenvironment group, the
checkpoint inhibition group, the Treg group, the MDSC group, the
granulocytes group, the cancer associated fibroblasts group, the
angiogenesis group, and the tumor-promotive immune group; and
accessing information specifying multiple MF profile clusters for
the particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0033] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the proliferation rate group,
the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group,
the receptor tyrosine kinases expression group, the growth factors
group, the tumor suppressors group, the metastasis signature group,
the anti-metastatic factors group, and the mutation status group;
and determining, using the RNA expression data and the reference
RNA expression data, a gene group expression level for each gene
group in a second set of gene groups associated with cancer
microenvironment and consisting of the MHCI group, the MHCII group,
the coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0034] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject having a particular
type of cancer; determining a molecular-functional (MF) profile for
the subject at least in part by: determining, using the RNA
expression data and reference RNA expression data, a gene group
expression level for each gene group in a first set of gene groups
associated with cancer malignancy and consisting of the
proliferation rate group, the PI3K/AKT/mTOR signaling group, the
RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the growth factors group, the tumor suppressors
group, the metastasis signature group, the anti-metastatic factors
group, and the mutation status group; and determining, using the
RNA expression data and the reference RNA expression data, a gene
group expression level for each gene group in a second set of gene
groups associated with cancer microenvironment and consisting of
the MHCI group, the MHCII group, the coactivation molecules group,
the effector cells group, the NK cells group, the T cell traffic
group, the T cells group, the B cells group, the M1 signatures
group, the Th1 signature group, the antitumor cytokines group, the
checkpoint inhibition group, the Treg group, the MDSC group, the
granulocytes group, the M2 signature group, the Th2 signature
group, the protumor cytokines group, the cancer associated
fibroblasts group, the angiogenesis group, and the complement
inhibition group; and accessing information specifying multiple MF
profile clusters for the particular cancer type; identifying, from
among the multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using the reference RNA expression data and
RNA expression data from biological samples obtained from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0035] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the growth factors group, the
tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the MHCI group, the MHCII group,
the coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0036] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining first RNA
expression data and/or first whole exome sequencing (WES) data from
biological samples from a plurality of subjects; determining a
respective plurality of molecular-functional (MF) profiles for the
plurality of subjects at least in part by, for each of the
plurality of subjects, determining, using the first RNA expression
data, a respective gene group expression level for each group in a
set of gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; clustering the plurality
of MF profiles to obtain MF profile clusters including: a first MF
profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples;
obtaining second RNA expression data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the second RNA
expression data, a gene group expression level for each group in
the set of gene groups; and identifying, from among the MF profile
clusters, a particular MF profile cluster with which to associate
the MF profile for the subject.
[0037] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining first RNA expression data and/or first whole exome
sequencing (WES) data from biological samples from a plurality of
subjects; determining a respective plurality of
molecular-functional (MF) profiles for the plurality of subjects at
least in part by, for each of the plurality of subjects,
determining, using the first RNA expression data, a respective gene
group expression level for each group in a set of gene groups, the
set of gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters including: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological samples; obtaining second RNA
expression data for a biological sample from a subject; determining
a molecular-functional (MF) profile for the subject at least in
part by determining, using the second RNA expression data, a gene
group expression level for each group in the set of gene groups;
and identifying, from among the MF profile clusters, a particular
MF profile cluster with which to associate the MF profile for the
subject.
[0038] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining first RNA expression data
and/or first whole exome sequencing (WES) data from biological
samples from a plurality of subjects; determining a respective
plurality of molecular-functional (MF) profiles for the plurality
of subjects at least in part by, for each of the plurality of
subjects, determining, using the first RNA expression data, a
respective gene group expression level for each group in a set of
gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; clustering the plurality
of MF profiles to obtain MF profile clusters including: a first MF
profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples;
obtaining second RNA expression data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the second RNA
expression data, a gene group expression level for each group in
the set of gene groups; and identifying, from among the MF profile
clusters, a particular MF profile cluster with which to associate
the MF profile for the subject.
[0039] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the tumor
properties group; and second gene groups associated with cancer
microenvironment consisting of the tumor-promoting immune
microenvironment group, the anti-tumor immune microenvironment
group, the angiogenesis group, and the fibroblasts group,
determining a first set of visual characteristics for a first
plurality of graphical user interface (GUI) elements using the gene
group expression levels determined for the first gene groups;
determining a second set of visual characteristics for a second
plurality of GUI elements using the gene group expression levels
determined for the second gene groups; generating a personalized
GUI personalized to the subject, the generating comprising:
generating a first GUI portion associated with cancer malignancy
and containing the first plurality of GUI elements having the
determined first set of visual characteristics; and generating a
second GUI portion associated with cancer microenvironment and
containing the second plurality of GUI elements having the
determined second set of visual characteristics; and presenting the
generated personalized GUI to a user.
[0040] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the tumor properties group; and second gene groups
associated with cancer microenvironment consisting of the
tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group, determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0041] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the tumor properties group; and second
gene groups associated with cancer microenvironment consisting of
the tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group, determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0042] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the antigen presentation group, the cytotoxic T
and NK cells group, the B cells group, the anti-tumor
microenvironment group, the checkpoint inhibition group, the Treg
group, the MDSC group, the granulocytes group, and the
tumor-promotive immune group; determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0043] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and second gene groups associated with
cancer microenvironment consisting of the cancer associated
fibroblasts group, the angiogenesis group, the antigen presentation
group, the cytotoxic T and NK cells group, the B cells group, the
anti-tumor microenvironment group, the checkpoint inhibition group,
the Treg group, the MDSC group, the granulocytes group, and the
tumor-promotive immune group; determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0044] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the tumor suppressors
group, the metastasis signature group, the anti-metastatic factors
group, and the mutation status group; and second gene groups
associated with cancer microenvironment consisting of the cancer
associated fibroblasts group, the angiogenesis group, the antigen
presentation group, the cytotoxic T and NK cells group, the B cells
group, the anti-tumor microenvironment group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, and the tumor-promotive immune group; determining a first
set of visual characteristics for a first plurality of graphical
user interface (GUI) elements using the gene group expression
levels determined for the first gene groups; determining a second
set of visual characteristics for a second plurality of GUI
elements using the gene group expression levels determined for the
second gene groups; generating a personalized GUI personalized to
the subject, the generating comprising: generating a first GUI
portion associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0045] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the growth factors group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and second gene groups associated with
cancer microenvironment consisting of the cancer associated
fibroblasts group, the angiogenesis group, the MHCI group, the
MHCII group, the coactivation molecules group, the effector cells
group, the NK cells group, the T cell traffic group, the T cells
group, the B cells group, the M1 signatures group, the Th1
signature group, the antitumor cytokines group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the M2 signature group, the Th2 signature group, the
protumor cytokines group, and the complement inhibition group;
determining a first set of visual characteristics for a first
plurality of graphical user interface (GUI) elements using the gene
group expression levels determined for the first gene groups;
determining a second set of visual characteristics for a second
plurality of GUI elements using the gene group expression levels
determined for the second gene groups; generating a personalized
GUI personalized to the subject, the generating comprising:
generating a first GUI portion associated with cancer malignancy
and containing the first plurality of GUI elements having the
determined first set of visual characteristics; and generating a
second GUI portion associated with cancer microenvironment and
containing the second plurality of GUI elements having the
determined second set of visual characteristics; and presenting the
generated personalized GUI to a user.
[0046] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the growth factors group, the
tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the MHCI group, the MHCII group, the
coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, and the complement inhibition group; determining a first set
of visual characteristics for a first plurality of graphical user
interface (GUI) elements using the gene group expression levels
determined for the first gene groups; determining a second set of
visual characteristics for a second plurality of GUI elements using
the gene group expression levels determined for the second gene
groups; generating a personalized GUI personalized to the subject,
the generating comprising: generating a first GUI portion
associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0047] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the growth factors
group, the tumor suppressors group, the metastasis signature group,
the anti-metastatic factors group, and the mutation status group;
and second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the MHCI group, the MHCII group, the
coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, and the complement inhibition group; determining a first set
of visual characteristics for a first plurality of graphical user
interface (GUI) elements using the gene group expression levels
determined for the first gene groups; determining a second set of
visual characteristics for a second plurality of GUI elements using
the gene group expression levels determined for the second gene
groups; generating a personalized GUI personalized to the subject,
the generating comprising: generating a first GUI portion
associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
BRIEF DESCRIPTION OF THE DRAWINGS
[0048] Various aspects and embodiments will be described with
reference to the following figures. The figures are not necessarily
drawn to scale.
[0049] FIG. 1A is a graphical representation of an exemplary
bioinformatics pipeline for determining tumor functional properties
in a molecular functional profile (MF profile), in accordance with
some embodiments of the technology described herein.
[0050] FIG. 1B is a graphical representation of tumor functional
properties in a MF profile comprising 28 functional modules, in
accordance with some embodiments of the technology described
herein. The size of the modules correspond to their intensity rate.
Colors reflect the module pro- or anti-cancer activity. Solid
shades without cross-marking are assigned to the modules that
promote tumor growth, while shades of with cross-marking are
assigned to those having anticancer activity. The malignancy
modules are collected in the Tumor Burden sector, which are located
in the right top quarter of the graphical representation.
[0051] FIG. 1C shows an exemplary MF profile, in accordance with
some embodiments of the technology described herein.
[0052] FIG. 2A is a block diagram of an illustrative environment
200 in which some embodiments of the technology described herein
may be implemented.
[0053] FIG. 2B is a block diagram of an illustrative graphical user
interface 250 including patient data that may be presented to a
user (e.g., a doctor), in accordance with some embodiments of the
technology described herein.
[0054] FIG. 2C is an illustrative example of the graphical user
interface 250 of FIG. 2B, in accordance with some embodiments of
the technology described herein. FIG. 3 is a graphic illustrating
different types of screens that may be shown to a user of the
software program.
[0055] FIG. 4 is a screenshot of the user's account profile screen
presented to the user in response to the user logging into the
software program.
[0056] FIG. 5 is a screenshot presenting the selected patient's
information provided to the user in response to the user selecting
the patient.
[0057] FIG. 6 is a screenshot presenting that the patient's tumor
biopsy sequencing data was downloaded (as shown in the lower right
panel).
[0058] FIG. 7 is a screenshot presenting the selected patient's
report including information related to the patient's sequencing
data, the patient, and the patient's cancer.
[0059] FIG. 8 is a screenshot presenting information related to
anti-PD1 immunotherapy provided in response to selecting anti-PD1
immunotherapy (as shown by highlighting) in the immunotherapy
biomarkers portion of the screen (as shown in the left panel).
[0060] FIG. 9 is a screenshot presenting selection of mutational
burden biomarker by a user.
[0061] FIG. 10 is a screenshot presenting information relating to
the mutational burden biomarker (as shown in the middle panel)
provided in response to the user selecting the mutational burden
biomarker.
[0062] FIG. 11 is a screenshot presenting that the mutational
status gene group and neo-antigens load gene group in the MF
profile are highlighted in response to the user selecting the
mutational burden biomarker (as shown in highlighting).
[0063] FIG. 12 is a screenshot presenting that the T cells gene
group in the MF profile is highlighted in response to the user
selecting the CD8 T cell biomarker (as shown in highlighting).
[0064] FIG. 13 is a screenshot presenting that the checkpoint
inhibition gene group in the MF profile is highlighted in response
to the user selecting the PDL1 expression biomarker.
[0065] FIG. 14 is a screenshot presenting information related to
sunitinib therapy provided in response to selecting sunitinib (as
shown by highlighting) in the targeted therapy biomarkers portion
of the screen (as shown in the left panel).
[0066] FIG. 15 is a screenshot presenting clinical trial data
relating to anti-PD1 therapy effectivity in patients having stage
IV metastatic melanoma (as shown in the right panel) provided in
response to the user selecting anti-PD1 immunotherapy (as shown in
the left panel).
[0067] FIG. 16 is a screenshot presenting clinical trial data
relating to anti-CTLA4 therapy effectivity in patients having stage
IV metastatic melanoma (as shown in the right panel) provided in
response to the user selecting anti-CTLA4 immunotherapy (as shown
in the left panel).
[0068] FIG. 17 is a screenshot presenting clinical trial data
relating to the NCT01295827 clinical trial of anti-PD1 treatment
(as shown in the middle panel) provided in response to the user
selecting the NCT01295827 clinical trial (as shown in the right
panel).
[0069] FIG. 18 is a screenshot presenting the treatment regimen of
the selected clinical data provided in response to the user
minimizing the therapy class description and drug description
portions. The screen may also present information relating to
ongoing clinical trials (marked by the letter A).
[0070] FIG. 19 is a screenshot presenting a patient's MF profile
(as shown in the middle panel).
[0071] FIG. 20 is a screenshot presenting additional gene groups
associated with the tumor properties gene group provided to the
user in response to selecting the tumor properties gene group.
[0072] FIG. 21 is a screenshot presenting information relating to
the tumor proliferation rate (as shown in the right panel) provided
in response to the user selecting the tumor proliferation rate gene
group (as shown in highlighting) in the MF profile.
[0073] FIG. 22 is a screenshot presenting information relating to
the purity of the patient's tumor in the tumor purity portion (as
shown in the lower right panel) and information relating to the
clonal evolution of the patient's tumor in the tumor clones
evolution portion (as shown in the lower right panel).
[0074] FIG. 23 is a screenshot presenting information relating to
the anti-tumor immune environment (as shown in the left panel)
provided in response to the user selecting the anti-tumor immune
environment gene group and information relating to the pro-tumor
immune environment (as shown in the right panel) in response to the
user selecting the pro-tumor immune environment gene group.
[0075] FIG. 24 is a screenshot presenting information relating to
expression of genes that determine T cell activity within the tumor
in the anti-tumor microenvironment portion (as shown in the lower
left panel) provided in response to the user selecting the T cell
gene group in the MF profile (as shown by highlighting).
[0076] FIG. 25 is a screenshot presenting information relating to
expression of genes that determine cancer associated fibroblast
activity within the tumor in the pro-tumor microenvironment portion
(as shown in the lower right panel) provided in response to the
user selecting the cancer associated fibroblast gene group in the
MF profile (as shown by highlighting).
[0077] FIG. 26 is a screenshot presenting information relating to
the number of non-malignant cells in the patient's tumor (as shown
in the lower left panel) provided in response to the user selecting
tumor infiltrate in the anti-tumor immune environment portion (as
shown in the upper left panel).
[0078] FIG. 27 is a screenshot presenting information relating to
the TCR repertoire in the patient's tumor (as shown in the lower
right panel) provided in response to the user selecting tumor
infiltrate in the pro-tumor immune environment portion (as shown in
the upper right panel).
[0079] FIG. 28 is a screenshot showing a MF profile presenting
twenty-eight gene groups is shown in (as shown in the middle
panel).
[0080] FIG. 29 is a screenshot presenting the combo therapy portion
(as shown in the right panel) provided to the user in response to
selecting the combinational therapy portion (as shown in the middle
panel).
[0081] FIG. 30 is a screenshot presenting anti-PD1 therapy
incorporated into the combo therapy portion (as shown in the upper
right panel).
[0082] FIG. 31 is a screenshot presenting information related to
sunitinib treatment in the therapy biological influence portion (as
shown in the lower middle panel) in response to the user selecting
sunitinib in the targeted therapy biomarkers portion (as shown by
highlighting).
[0083] FIG. 32 is a screenshot presenting sunitinib incorporation
in the combo therapy portion in response to the user selecting
sunitinib.
[0084] FIG. 33 is a screenshot presenting potential vaccine
therapies such as a personalized neo-antigenic vaccine and an off
the shelf vaccine provided to the user in response to selecting
vaccine in the immunotherapy biomarkers portion (as shown in the
left panel).
[0085] FIG. 34 is a screenshot presenting information relating to
treatment with a personalized neo-antigenic vaccine (as shown in
the lower middle panel) provided to the user in response to
selecting a personalized neo-antigenic vaccine (as shown by
highlighting).
[0086] FIG. 35 is a screenshot presenting incorporation of a
personalized neo-antigenic vaccine in the combo therapy portion
provided to the user in response to the user selecting the
personalized neo-antigenic vaccine.
[0087] FIG. 36 is a screenshot presenting the personalized
neo-antigenic vaccine therapy, anti-PD1 therapy, and sunitinib
therapy in the combo therapy portion provided to the user in
response to the user incorporating each of these therapies into the
combo therapy portion.
[0088] FIG. 37 is a screenshot presenting an alert that
substitution of sunitinib therapy with vemurafenib therapy is
recognized by the software as an inappropriate combination for the
patient.
[0089] FIG. 38 is a block diagram of an illustrative computer
system that may be used in implementing some embodiments of the
technology described herein.
[0090] FIG. 39A is a flowchart of an illustrative process 3900 for
identifying an MF profile cluster with which to associate an MF
profile for a subject, in accordance with some embodiments of the
technology described herein.
[0091] FIG. 39B is a flowchart of an illustrative process 3920 for
generating MF profile clusters using RNA expression data obtained
from subjects having a particular type of cancer, in accordance
with some embodiments of the technology described herein.
[0092] FIG. 39C is a flowchart of an illustrative process 3940 for
identifying an MF profile cluster with which to associate an MF
profile determined for a subject at least in part by determining
the subject's expression levels for multiple gene groups, in
accordance with some embodiments of the technology described
herein.
[0093] FIG. 39D is a flowchart of an illustrative process 3960 for
generating MF profile clusters using RNA expression data obtained
from subjects having a particular type of cancer, and associating a
subject with one of the generated MF clusters based on the
subject's MF profile, in accordance with some embodiments of the
technology described herein.
[0094] FIG. 40A is a flowchart of an illustrative process 4000 for
generating an MF profile and generating an MF portrait for
visualizing the MF profile in a graphical user interface (GUI), in
accordance with some embodiments of the technology described
herein.
[0095] FIG. 40B is a flowchart of an illustrative process 4020 for
generating an MF profile by determining expression levels for
multiple gene groups and generating an MF portrait for visualizing
the MF profile in a graphical user interface (GUI), in accordance
with some embodiments of the technology described herein.
[0096] FIG. 41A shows a series of MF profiles of melanoma patients
(n=45) chosen randomly, in accordance with some embodiments of the
technology described herein.
[0097] FIG. 41B shows data from an unsupervised dense subgraph
network cluster analysis of tumor functional processes calculated
from RNA-Seq data of patient melanoma tumors (n=470 patients), in
accordance with some embodiments of the technology described
herein. The determined clusters were labeled Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively).
[0098] FIG. 41C is a graphical representation of a
correlation-based graph network of patients showing determined
clusters, in accordance with some embodiments of the technology
described herein. Each dot represents an individual melanoma
patient, who is connected to other patients with a weight
corresponding to its correlation value. The size of the dot
corresponds to the vertex degree.
[0099] FIG. 41D shows data from a k-means clustering analysis of
tumor functional processes calculated from RNA-Seq data of melanoma
tumors (n=470 patient tumors), in accordance with some embodiments
of the technology described herein. The determined clusters were
labeled Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively).
[0100] FIG. 41E shows data from a cell composition analysis of
melanoma tumors grouped into determined cluster Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively)using
MCP-counter and CIBERSORT, in accordance with some embodiments of
the technology described herein.
[0101] FIG. 41F shows data from a gene set enrichment analysis of
melanoma tumors grouped into determined cluster Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively), in
accordance with some embodiments of the technology described
herein.
[0102] FIG. 41G is a graphical representation of functional process
intensity associated with tumor growth (e.g., CAF, Angiogenesis, or
Proliferation rate) or intratumoral immune infiltrate (e.g.,
effector cells or regulatory T cells (Tregs)) layered on cancers of
determined cluster Types A-D (1.sup.st-4.sup.th MF profile
clusters, respectively), in accordance with some embodiments of the
technology described herein.
[0103] FIG. 41H shows data from a log(p-value) t-test difference in
process activity (enrichment score) between cancers of determined
cluster Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively), in accordance with some embodiments of the
technology described herein.
[0104] FIG. 41I shows Kaplan-Meier survival curves for melanoma
patients split into cohorts according to the their MF profile
determined cluster types (Types A-D; which are equivalent to the
1.sup.st-4.sup.th types of portraits described herein,
respectively) using unsupervised dense subgraph network clustering,
in accordance with some embodiments of the technology described
herein.
[0105] FIG. 41J shows Kaplan-Meier survival curves for melanoma
patients split into cohorts according to the their MF profile
determined cluster types (Types A-D; which are equivalent to the
1.sup.st-4.sup.th types of portraits described herein,
respectively) using k-means clustering, in accordance with some
embodiments of the technology described herein.
[0106] FIG. 41K shows data from a purity, mutational load and
mutational status analysis of melanoma tumors grouped according to
their determined cluster Types A-D (which are equivalent to the
1.sup.st-4.sup.th types of portraits described herein,
respectively), in accordance with some embodiments of the
technology described herein.
[0107] FIG. 42A shows a MF profile type A (first type) as
determined in accordance with some embodiments of the technology
described herein.
[0108] FIG. 42B shows a MF profile type B (second type), as
determined in accordance with some embodiments of the technology
described herein.
[0109] FIG. 42C shows a MF profile type C (third type), as
determined in accordance with some embodiments of the technology
described herein.
[0110] FIG. 42D shows a MF profile type D (fourth type), as
determined in accordance with some embodiments of the technology
described herein.
[0111] FIG. 43A shows data from a tSNE analysis over non-normalized
process enrichment scores, in accordance with some embodiments of
the technology described herein. Each data point corresponds to an
individual analyzed tumor sample. Different datasets (e.g., cancer
types) are indicated by various grayscale intensities.
[0112] FIG. 43B shows data from a tSNE analysis over process
enrichment scores normalized within specific cancer types, in
accordance with some embodiments of the technology described
herein. Each data point corresponds to an individual tumor sample
analyzed. Different datasets (e.g., cancer types) are indicated by
various grayscale intensities.
[0113] FIG. 43C shows data from an unsupervised dense subgraph
network cluster analysis of tumor functional processes calculated
from RNA-Seq data of different patient tumors. The following
cancers were analyzed using TCGA data (listed n values indicate the
numbers of individual patients): ACC--adrenocortical carcinoma
(n=80), BLCA--bladder urothelial carcinoma (n=412), BRCA--breast
invasive carcinoma (n=1100), CESC--cervical squamous cell carcinoma
and endocervical adenocarcinoma (n=308), COAD--colon adenocarcinoma
(n=461), ESCA--esophageal carcinoma (n=185), KIRC--kidney renal
clear cell carcinoma (n=536), KIRP--kidney renal papillary cell
carcinoma (n=291), LIHC--liver hepatocellular carcinoma (n=377),
LUAD--lung adenocarcinoma (n=521), LUSC--lung squamous cell
carcinoma (n=510), OV--ovarian serous cystadenocarcinoma (n=586),
PAAD--pancreatic adenocarcinoma (n=185), PRAD--prostate
adenocarcinoma (n=498), READ--rectal adenocarcinoma (n=172),
SKCM--skin cutaneous melanoma (n=470), STAD--stomach adenocarcinoma
(n=445), THCA--thyroid carcinoma (n=507), UCEC--uterine corpus
endometrial carcinoma (n=548), CHOL--Cholangiocarcinoma-(n=36).
[0114] FIG. 43D shows the frequency of determined cancer cluster
Types A-D (1.sup.st-4.sup.th MF profile clusters, respectively) in
patients having different malignant neoplasms, in accordance with
some embodiments of the technology described herein.
[0115] FIG. 43E shows data from an unsupervised dense subgraph
network cluster analysis of tumor functional processes calculated
from RNA-Seq data of patient having different malignant neoplasms,
in accordance with some embodiments of the technology described
herein. The determined clusters were labeled Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively).
[0116] FIG. 43F shows Kaplan-Meier survival curves for patients
having different malignant neoplasms split into cohorts according
to the their determined cancer cluster Types A-D (1.sup.st-4.sup.th
MF profile clusters, respectively), in accordance with some
embodiments of the technology described herein.
[0117] FIG. 44A shows data from a k-means clustering analysis of
tumor functional processes calculated from RNA-Seq data for each
cancer sample, in accordance with some embodiments of the
technology described herein. The determined clusters were labeled
Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively).
[0118] FIG. 44B shows data from a k-means clustering analysis of
tumor functional processes calculated from RNA-Seq data for merged
pan-cancer tumors, in accordance with some embodiments of the
technology described herein. The determined clusters were labeled
Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively).
[0119] FIG. 44C shows data from a log(p-value) t-test difference in
process activity enrichment scores between determined cancer
cluster Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively) for merged pan-cancer tumors, in accordance with some
embodiments of the technology described herein.
[0120] FIG. 44D shows a heatmap of correlation between melanoma
samples (n=470) and the 10,000 most expressed genes, in accordance
with some embodiments of the technology described herein. Pearson
correlation matrices were clustered using Euclidean distance
measured by the complete linkage method. Dense clusters are
highlighted in column bar.
[0121] FIG. 44E shows a heatmap of correlation between melanoma
samples (n=470) and to 298 genes constituting the functional
processes, in accordance with some embodiments of the technology
described herein.
[0122] FIG. 44F shows a heatmap of correlation between melanoma
samples (n=470) and to 28 functional process scores, in accordance
with some embodiments of the technology described herein.
[0123] FIG. 44G shows a heatmap of correlation between 20 different
carcinoma tumors, in accordance with some embodiments of the
technology described herein. Panel (1) shows correlation with the
10,000 most expressed genes; panel (2) shows correlation with 298
genes constituting the functional processes; and panel (3) shows
correlation with the 28 functional process scores. Pearson
correlation matrices were clustered using Euclidean distance
measured by the complete linkage method. Dense clusters are
highlighted in column bar.
[0124] FIG. 45A shows data from an unsupervised dense subgraph
network cluster analysis of tumor functional processes calculated
from RNA-Seq data of patient glioblastoma tumors (n=159) and glioma
tumors (n=516), in accordance with some embodiments of the
technology described herein. The determined clusters were labeled
Types A-D (1.sup.st-4.sup.th MF profile clusters,
respectively).
[0125] FIG. 45B shows data from a log(p-value) t-test difference in
process activity enrichment scores between brain tumors determined
to fall within cluster Types A-D (1.sup.st-4.sup.th MF profile
clusters, respectively), in accordance with some embodiments of the
technology described herein.
[0126] FIG. 45C shows data from an unsupervised dense subgraph
network cluster analysis of tumor functional processes calculated
from RNA-Seq data of patient sarcoma tumors (n=261), in accordance
with some embodiments of the technology described herein. The
determined clusters were labeled Types A-D (1.sup.st-4.sup.th MF
profile clusters, respectively).
[0127] FIG. 45D shows data from a log(p-value) t-test difference in
process activity enrichment scores between sarcoma tumors
determined to fall within cluster Types A-D (1.sup.st-4.sup.th MF
profile clusters, respectively), in accordance with some
embodiments of the technology described herein.
[0128] FIG. 46A shows a heatmap showing processes of tumor MF
profiles of melanoma patients treated with anti-CTLA4 therapy, in
accordance with some embodiments of the technology described
herein. Annotation of responders and non-responders, MF profile
classification of determined cluster Types A-D (1.sup.st-4.sup.th
MF profile clusters, respectively), and total number of mutations
is shown above the heatmap. The average MF profiles corresponding
to patients from the heatmap and percent responders (R) and
non-responders (N) for patients having the indicated tumor type are
shown under the heatmap.
[0129] FIG. 46B shows a heatmap showing processes of tumor MF
profiles of melanoma patients treated with anti-PD1 therapy, in
accordance with some embodiments of the technology described
herein.
[0130] FIG. 46C shows a heatmap showing processes of tumor MF
profiles of melanoma patients treated with MAGE-A3 vaccine, in
accordance with some embodiments of the technology described
herein.
[0131] FIG. 46D shows a heatmap showing processes of tumor MF
profiles of mCRC patients from GSE5851 and HNSCC patients from
GSE65021 treated with cetuximab, in accordance with some
embodiments of the technology described herein. EGFR expression
status is also indicated.
[0132] FIG. 46E shows a heatmap showing processes of tumor MF
profiles of ccRCC patients treated with sunitinib, in accordance
with some embodiments of the technology described herein.
[0133] FIG. 46F shows data of receiver operating characteristics
for therapy response prediction based on MF profile type and AUC
scores, in accordance with some embodiments of the technology
described herein.
[0134] FIG. 46G shows Kaplan-Meier survival curves for melanoma
patients treated with anti-CTLA4 therapy split into cohorts
according to the their determined MF profile type (Types A-D;
1.sup.st-4.sup.th MF profile clusters, respectively), in accordance
with some embodiments of the technology described herein.
[0135] FIG. 46H shows Kaplan-Meier survival curves for melanoma
patients treated with anti-PD1 therapy split into cohorts according
to the their determined MF profile type (Types A-D;
1.sup.st-4.sup.th MF profile clusters, respectively), in accordance
with some embodiments of the technology described herein.
[0136] FIG. 46I shows Kaplan-Meier survival curves for sunitinib
treated patients having tumors with a high proliferation rate or a
low proliferation rate, in accordance with some embodiments of the
technology described herein.
[0137] FIG. 47A shows a graphical representation of melanoma
patients (dots) on two-dimensional coordinates of T cells and
Cancer Associated Fibroblast process intensity from MF profile
(z-scores), in accordance with some embodiments of the technology
described herein. MF profile type (Types A-D; 1.sup.st-4.sup.th MF
profile clusters, respectively) is indicated for each patient.
Dynamic changes in tumor MF profiles of five patients are shown by
arrows. Larger dots indicate pre-treatment tumors.
[0138] FIG. 47B shows a heatmap showing processes of determined MF
profile type (Types A-D; 1.sup.st-4.sup.th MF profile clusters,
respectively) for melanoma patients before and after treatment with
anti-PD1 therapy, in accordance with some embodiments of the
technology described herein. Annotation of responders and
non-responders, MF profile classification and total number of
mutations is shown above the heatmap. Pre-treatment MF profiles for
each patient are shown under the heatmap.
[0139] FIG. 47C shows a graph of receiver operating characteristics
for therapy response prediction based on tumor classification
before treatment, in accordance with some embodiments of the
technology described herein.
[0140] FIG. 48A shows an exemplary MF profile useful for designing
a combination therapy, in accordance with some embodiments of the
technology described herein.
[0141] FIG. 48B shows an exemplary MF profile type B useful for
designing a combination therapy, in accordance with some
embodiments of the technology described herein.
[0142] FIG. 48C shows an exemplary MF profile type C useful for
designing a combination therapy, in accordance with some
embodiments of the technology described herein.
[0143] FIG. 48D shows an exemplary MF profile type D useful for
designing a combination therapy, in accordance with some
embodiments of the technology described herein.
[0144] FIG. 49A is a graphical representation of an exemplary MF
profile having 28 functional processes, in accordance with some
embodiments of the technology described herein.
[0145] FIG. 49B is a graphical representation showing a
visualization of a MF profile having 19 functional processes, in
accordance with some embodiments of the technology described
herein.
[0146] FIG. 49C is a graphical representation showing a
visualization of a MF profile having 5 functional processes, in
accordance with some embodiments of the technology described
herein.
[0147] FIG. 50A shows data from a Pearson correlation analysis of
functional modules which form the basis for the tumor MF profiles,
in accordance with some embodiments of the technology described
herein.
[0148] FIG. 50B shows data from a Pearson correlation analysis of
Effector cells functional activity module with NK cells, Checkpoint
inhibition, MHC class II and Metastasis modules, in accordance with
some embodiments of the technology described herein.
[0149] FIG. 50C shows a graph showing SKCM and pan-cancer graph
node connectivity percent (%) on different edge weight thresholds,
in accordance with some embodiments of the technology described
herein. The solid line shows 1% node connectivity.
DETAILED DESCRIPTION
[0150] Recent advances in personalized genomic sequencing and
cancer genomic sequencing technologies have made it possible to
obtain patient-specific information about cancer cells (e.g., tumor
cells) and cancer microenvironments from one or more biological
samples obtained from individual patients. This information can be
used to characterize the type or types of cancer a patient or
subject has and, potentially, select one or more effective
therapies for the patient. This information may also be used to
determine how a patient is responding over time to a treatment and,
if necessary, to select a new therapy or therapies for the patient
as necessary. This information may also be used to determine
whether a patient should be included or excluded from participating
in a clinical trial.
[0151] The inventors have recognized and appreciated that many
different types of cancer including, but not limited to melanoma,
sarcoma, and glioblastoma, may be characterized as or classified
into one of four molecular function (MF) profiles, herein
identified as first MF profile (1.sup.st MF profile), second MF
profile (2.sup.nd MF profile), third MF profile (3.sup.rd MF
profile), and fourth MF profile (4.sup.th MF profile).
[0152] First MF profile cancers may also be described as
"inflamed/vascularized" and/or "inflamed/fibroblast-enriched";
Second MF profile cancers may also be described as
"inflamed/non-vascularized" and/or
"inflamed/non-fibroblast-enriched"; Third MF profile cancers may
also be described as "non-inflamed/vascularized" and/or
"non-inflamed/fibroblast-enriched"; and Fourth MF profile cancers
may also be described as "non-inflamed/non-vascularized" and/or
"non-inflamed/non-fibroblast-enriched" and/or "immune desert." Such
characteristics of MF clusters may be calculated in a number of
ways.
[0153] As used herein, "inflamed" refers to the level of
compositions and processes related to inflammation in a cancer
(e.g., a tumor). In some embodiments, inflamed cancers (e.g.,
tumors) are highly infiltrated by immune cells, and are highly
active with regard to antigen presentation and T-cell activation.
In some embodiments, inflamed cancers (e.g., tumors) may have an NK
cell and/or a T cell z score of, for example, at least 0.60, at
least 0.65, at least 0.70, at least 0.75, at least 0.80, at least
0.85, at least 0.90, at least 0.91, at least 0.92, at least 0.93,
at least 0.94, at least 0.95, at least 0.96, at least 0.97, at
least 0.98, or at least 0.99. In some embodiments, inflamed cancers
(e.g., tumors) may have an NK cell and/or a T cell z score of, for
example, not less than 0.60, not less than 0.65, not less than
0.70, not less than 0.75, not less than 0.80, not less than 0.85,
not less than 0.90, not less than 0.91, not less than 0.92, not
less than 0.93, not less than 0.94, not less than 0.95, not less
than 0.96, not less than 0.97, not less than 0.98, or not less than
0.99. In some embodiments, non-inflamed tumors are poorly
infiltrated by immune cells, and have low activity with regard to
antigen presentation and T-cell activation. In some embodiments,
non-inflamed cancers (e.g., tumors) may have an NK cell and/or a T
cell z score of, for example, less than -0.20, less than -0.25,
less than -0.30, less than -0.35, less than -0.40, less than -0.45,
less than -0.50, less than -0.55, less than -0.60, less than -0.65,
less than -0.70, less than -0.75, less than -0.80, less than -0.85,
less than -0.90, less than -0.91, less than -0.92, less than -0.93,
less than -0.94, less than -0.95, less than -0.96, less than -0.97,
less than -0.98, or less than -0.99. In some embodiments,
non-inflamed cancers (e.g., tumors) may have an NK cell and/or a T
cell z score of, for example, not more than -0.20, not more than
-0.25, not more than -0.30, not more than -0.35, not more than
-0.40, not more than -0.45, not more than -0.50, not more than
-0.55, not more than -0.60, not more than -0.65, not more than
-0.70, not more than -0.75, not more than -0.80, not more than
-0.85, not more than -0.90, not more than -0.91, not more than
-0.92, not more than -0.93, not more than -0.94, not more than
-0.95, not more than -0.96, not more than -0.97, not more than
-0.98, or not more than -0.99.
[0154] As used herein, "vascularized" refers to the formation of
blood vessels in a cancer (e.g., a tumor). In some embodiments,
vascularized cancers (e.g., tumors) comprise high levels of
cellular compositions and process related to blood vessel
formation. In some embodiments, vascularized cancers (e.g., tumors)
may have an angiogenesis z score of, for example, at least 0.60, at
least 0.65, at least 0.70, at least 0.75, at least 0.80, at least
0.85, at least 0.90, at least 0.91, at least 0.92, at least 0.93,
at least 0.94, at least 0.95, at least 0.96, at least 0.97, at
least 0.98, or at least 0.99. In some embodiments, vascularized
cancers (e.g., tumors) may have an NK cell and/or a T cell z score
of, for example, not less than 0.60, not less than 0.65, not less
than 0.70, not less than 0.75, not less than 0.80, not less than
0.85, not less than 0.90, not less than 0.91, not less than 0.92,
not less than 0.93, not less than 0.94, not less than 0.95, not
less than 0.96, not less than 0.97, not less than 0.98, or not less
than 0.99. In some embodiments, non-vascularized cancers (e.g.,
tumors) comprise few or no compositions and processes related to
blood vessel formation. In some embodiments, non-vascularized
cancers (e.g., tumors) may have an angiogenesis z score of, for
example, less than -0.20, less than -0.25, less than -0.30, less
than -0.35, less than -0.40, less than -0.45, less than -0.50, less
than -0.55, less than -0.60, less than -0.65, less than -0.70, less
than -0.75, less than -0.80, less than -0.85, less than -0.90, less
than -0.91, less than -0.92, less than -0.93, less than -0.94, less
than -0.95, less than -0.96, less than -0.97, less than -0.98, or
less than -0.99. In some embodiments, non-vascularized cancers
(e.g., tumors) may have an angiogenesis z score of, for example,
not more than -0.20, not more than -0.25, not more than -0.30, not
more than -0.35, not more than -0.40, not more than -0.45, not more
than -0.50, not more than -0.55, not more than -0.60, not more than
-0.65, not more than -0.70, not more than -0.75, not more than
-0.80, not more than -0.85, not more than -0.90, not more than
-0.91, not more than -0.92, not more than -0.93, not more than
-0.94, not more than -0.95, not more than -0.96, not more than
-0.97, not more than -0.98, or not more than -0.99.
[0155] As used herein, "fibroblast enriched" refers to the level or
amount of fibroblasts in a cancer (e.g., a tumor). In some
embodiments, fibroblast enriched tumors comprise high levels of
fibroblast cells. In some embodiments, fibroblast enriched cancers
(e.g., tumors) may have a fibroblast (cancer associated fibroblast)
z score of, for example, at least 0.60, at least 0.65, at least
0.70, at least 0.75, at least 0.80, at least 0.85, at least 0.90,
at least 0.91, at least 0.92, at least 0.93, at least 0.94, at
least 0.95, at least 0.96, at least 0.97, at least 0.98, or at
least 0.99. In some embodiments, fibroblast enriched cancers (e.g.,
tumors) may have an NK cell and/or a T cell z score of, for
example, not less than 0.60, not less than 0.65, not less than
0.70, not less than 0.75, not less than 0.80, not less than 0.85,
not less than 0.90, not less than 0.91, not less than 0.92, not
less than 0.93, not less than 0.94, not less than 0.95, not less
than 0.96, not less than 0.97, not less than 0.98, or not less than
0.99. In some embodiments, non-fibroblast-enriched cancers (e.g.,
tumors) comprise few or no fibroblast cells. In some embodiments,
non-fibroblast-enriched cancers (e.g., tumors) may have a
fibroblast (cancer associated fibroblast) z score of, for example,
less than -0.20, less than -0.25, less than -0.30, less than -0.35,
less than -0.40, less than -0.45, less than -0.50, less than -0.55,
less than -0.60, less than -0.65, less than -0.70, less than -0.75,
less than -0.80, less than -0.85, less than -0.90, less than -0.91,
less than -0.92, less than -0.93, less than -0.94, less than -0.95,
less than -0.96, less than -0.97, less than -0.98, or less than
-0.99. In some embodiments, non-fibroblast-enriched cancers (e.g.,
tumors) may have a fibroblast (cancer associated fibroblast) z
score of, for example, not more than -0.20, not more than -0.25,
not more than -0.30, not more than -0.35, not more than -0.40, not
more than -0.45, not more than -0.50, not more than -0.55, not more
than -0.60, not more than -0.65, not more than -0.70, not more than
-0.75, not more than -0.80, not more than -0.85, not more than
-0.90, not more than -0.91, not more than -0.92, not more than
-0.93, not more than -0.94, not more than -0.95, not more than
-0.96, not more than -0.97, not more than -0.98, or not more than
-0.99.
[0156] Each subject biological sample may be assigned to one of
four predefined MF profile clusters using a k-nearest neighbors
classifier. The classifier may be trained on the data by which the
MF profile clusters are defined and on their corresponding labels.
Sample vectors for the k-nearest neighbors classifier may be found
in Table 1, below. The classifier may then predict the type of MF
profile (MF profile cluster) for the subject sample utilizing its
relative processes intensity values. Relative processes intensity
values may be calculated as Z-values (arguments of the standard
normal distribution over training set of samples) of ssGSEA
algorithm outputs inferred from the RNA sequence data from the
subject sample as described herein.
TABLE-US-00001 TABLE 1 Sample vectors for the k-nearest neighbors
classifier (z-scores). MF profile type First Second Third Fourth
Angiogenesis 0.727815 -0.5907 0.71314 -0.42704 Cancer Associated
Fibroblasts 0.596986 -0.4871 0.82218 -0.49264
Receptor_tyrosine_kinases 0.370197 -0.4366 0.75614 -0.33472
NK_cells 0.624648 0.75725 -0.3987 -0.89695 Checkpoint_inhibition
0.671491 0.74881 -0.3928 -0.92683 Effector_cells 0.652837 0.77783
-0.3953 -0.93822 T_cells 0.701067 0.74591 -0.3827 -0.9518
Proliferation_rate -0.44244 0.10307 -0.457 0.509505
[0157] The identification and classification of 1.sup.st-4.sup.th
MF profile cluster types as described herein were not known in the
art, and such classifications provide more precise diagnoses that
might not be seen by the use of any single marker or less complex
combination of elements. The methods, systems, and graphical user
interfaces (GUIs) based on such classifications described herein
are newly available and no previously described techniques or
methods existed to perform the elements of these techniques.
Further, the four molecular function (MF) profiles were not known
previously to exist and there could therefore be no motivation in
the art to define these cancer types. Additionally, the types of
analyses described herein would have been considered too involved,
costly, and/or time consuming to perform without understanding the
potential benefits that could be derived from such complex analyses
based on the multiplicity and mutability of the involved
factors.
[0158] The inventors have recognized and appreciated that several
of the elements described herein add something more than what is
well understood, routine, or conventional activity proposed by
others in the field. These meaningful non-routine steps result in
the improvements seen in the methods, systems, and GUIs described
herein and include, but are not limited to: the analysis of gene
expression levels and gene group expression levels for both cancer
malignancy and cancer microenvironment; the combination(s) of
specific genes used in the gene groups (or modules) provided
herein; the recognition that many different cancers can be
classified such that they are identifiable as one of
1.sup.st-4.sup.th MF profile cancer types; technical improvements
in analyses that allow for more precise identification of cancers
and resulting improvements in outcome for the patient; the creation
of improved graphical user interfaces to aid in the analysis of an
individual patient's cancer into cancer 1.sup.st-4.sup.th MF
profile cancer types; the specification of treatments for
individual patients based on the identified classification of one
or more cancers in the patient (i.e., 1.sup.st-4.sup.th MF profile
cancer types) and/or additional information about the patient or
the patient's cancer.
[0159] Therefore, aspects of the present disclosure relate to
methods and compositions for characterizing one or more cancers
(e.g., tumors) of or in a patient. In some embodiments,
characterizing a cancer (e.g., a tumor) comprises determining
differentially expressed genes in a sample from a subject (e.g., a
patient) having a cancer (e.g., a tumor). In some embodiments,
characterizing a cancer (e.g., a tumor) comprises determining
whether one or more genes are mutated in a sample from a subject
having a cancer (e.g., a tumor). In certain embodiments,
characterizing a cancer (e.g., a tumor) comprises identifying the
cancer (e.g., a tumor) as a specific subtype of cancer selected
from a 1.sup.st MF profile cancer type (inflamed/vascularized
and/or inflamed/fibroblast enriched); a 2.sup.nd MF profile cancer
type (inflamed/non-vascularized and/or inflamed/non-fibroblast
enriched); a 3.sup.rd MF profile cancer type
(non-inflamed/vascularized and/or non-inflamed/fibroblast
enriched); and a 4.sup.th MF profile cancer type
(non-inflamed/non-vascularized and/or non-inflamed/non-fibroblast
enriched; also identified herein as "immune desert").
[0160] Such methods and compositions may be useful for clinical
purposes including, for example, selecting a treatment, monitoring
cancer progression, assessing the efficacy of a treatment against a
cancer, evaluating suitability of a patient for participating in a
clinical trial, or determining a course of treatment for a subject
(e.g., a patient).
[0161] The methods and compositions described herein may also be
useful for non-clinical applications including (as a non-limiting
example) research purposes such as, e.g., studying the mechanism of
cancer development and/or biological pathways and/or biological
processes involved in cancer, and developing new therapies for
cancer based on such studies.
[0162] Further, systems which present this information in a
comprehensive and useable format will be needed to facilitate
treatment of patients with such conditions. Therefore, provided
herein are models and systems of cancer-immunity interrelationships
for a particular patient that result in a profile designed to
concisely and clearly describe important characteristics of
cancerous cells (e.g., tumor cells) of the patient (referred to
herein as, for example, "cancer malignancy"), as well as all the
key processes in the cancer (e.g., tumor) microenvironment
(discussed herein as, for example, "cancer microenvironment").
[0163] Such a model may take into consideration the full spectrum
of non-malignant components in the cancer microenvironment,
including fibroblasts and extracellular matrices, the network of
blood and lymphatic vessels, tissue macrophages, dendritic and mast
cells, different kinds of leukocytes/lymphocytes migrated to or
proliferating within tumor, as well as intrinsic properties of
malignant cells.
[0164] Certain aspects of the described model or system present the
cellular composition of the cancerous cells (e.g., the tumor),
while other aspects reflect the intensity of processes of the
cancerous (e.g., the tumor) cells of the biological sample and/or
patient. The presence and number of any cell type is an important
but insufficient parameter because it is also necessary to
understand how these cells function within the processes that make
up the cancer (e.g., the tumor). The size of particular functional
modules including, e.g., the intensity of processes ongoing in
these modules, actually comprises both concentration and functional
activity of the cell type. Therefore, a cancer (e.g., a tumor)
"profile" that comprises a set of functional modules with an
estimate of their intensity implicitly reflects the content of the
different cell types within the cancer (e.g., the tumor).
[0165] Therefore, in some embodiments the model described herein
enables the study of the structural-functional composition of a
particular patient's tumor and/or cancerous cells and also allows
the comparison of the same across different patients and groups of
patients. As a non-limiting example, the described model has been
used to compare human skin cutaneous melanoma (SKCM) tumors from
470 melanoma patients. Four general types of tumors were revealed
(described here as tumor types 1.sup.st MF profile type, 2.sup.nd
MF profile type, 3.sup.rd MF profile type, and 4.sup.th MF profile
type) pertaining to 22%, 28%, 24%, and 24% of melanoma patients,
respectively (representing 98% of total patients). Tumor types
1.sup.st MF profile type and 2.sup.nd MF profile type are
characterized by excessive infiltration with cells of the immune
system (so-called "inflamed" or "hot" tumors), and 3.sup.rd MF
profile type and 4.sup.th MF profile type are considered poorly
infiltrated (so-called "non-inflamed" or "cold" tumors), meaning
they have no obvious signs of inflammation or recruitment of immune
cells.
[0166] Generally, techniques described herein provide for
improvements over conventional computer-implemented techniques for
analysis of medical data such as evaluation of expression data
(e.g., RNA expression data) and determining whether one or more
therapies (e.g., targeted therapies and/or immunotherapies) will be
effective in treating the subject. Additionally, some embodiments
of the technology provided herein are directed to graphical user
interfaces that present oncological data in a new way which is
compact and highly informative. These graphical user interfaces not
only reduce the cognitive load on users working with them, but may
serve to reduce clinician errors and improve the functionality of a
computer by providing all needed information in a single
interactive interface. This eliminates the need for a clinician to
consult different sources of information (e.g., view multiple
different webpages, use multiple different application programs,
etc.), which would otherwise place an additional burden on the
processing, memory, and communications resources of the computer(s)
used by the clinician.
[0167] As described herein, some embodiments relate to a software
program for providing information related to a patient's cancer to
a user (e.g., an oncologist or other doctor, a healthcare provider,
a researcher, a patient, etc.). The software program may provide
information about the patient, e.g., the patient's age, overall
status, diagnosis, and treatment history.
[0168] In another aspect, the software program may provide
information about the patient's cancer, e.g., tumor histology,
tumor purity, tumor clone evolution, tumor cell composition, tumor
cell infiltrate, gene expression levels, gene mutations, the
results of medical examinations (e.g., MRI results) and sequencing
data (e.g., RNA sequencing data and/or whole exome sequencing (WES)
data).
[0169] In another aspect, the software program may provide
information about potential treatments (e.g., immunotherapies,
targeted therapies, etc.) and information related to potential
treatments, e.g., prognostic factors, therapeutic efficacy,
clinical trial efficacy, ongoing clinical trials, and relevant
publications.
[0170] In another aspect, the software program may provide
information about the patient's biomarkers (e.g., genetic
biomarkers, cellular biomarkers, and expression biomarkers) and
information related to the patient's biomarkers (e.g., a
description of the biomarker, how the biomarker value was
calculated, the patient's particular biomarker value compared to
other patients, and related publications).
[0171] In yet another aspect, the software program may also allow
the user to interactively design a panel of sequencing results
(e.g., results related to the sequences or levels of specified
biomarkers or genes) specific to the patient and/or a combination
therapy for the patient.
[0172] As used herein, the term "patient" means any mammal,
including mice, rabbits, and humans. In one embodiment, the patient
is a human or non-human primate. The terms "individual" or
"subject" may be used interchangeably with "patient."
Obtaining Expression Data
[0173] Expression data (e.g., RNA expression data and/or whole
exome sequencing (WES) data) as described herein may be obtained
from a variety of sources. In some embodiments, expression data may
be obtained by analyzing a biological sample from a patient. The
biological sample may be analyzed prior to performance of the
techniques described herein including the techniques for generating
MF clusters, associating a patient's MF profile with one of the MF
clusters, and generating an MF portrait from a patient's MF profile
to provide a visualization for the MF profile. In some such
embodiments, data obtained from the biological sample may be stored
(e.g., in a database) and accessed during performance of the
techniques described herein.
[0174] In some embodiments, expression data is obtained from a
database containing expression data for at least one patient.
Biological Samples
[0175] Any of the methods, systems, assays, or other claimed
elements may use or be used to analyze any biological sample from a
subject (i.e., a patient or individual). In some embodiments, the
biological sample may be any sample from a subject known or
suspected of having cancerous cells or pre-cancerous cells.
[0176] The biological sample may be from any source in the
subject's body including, but not limited to, any fluid [such as
blood (e.g., whole blood, blood serum, or blood plasma), saliva,
tears, synovial fluid, cerebrospinal fluid, pleural fluid,
pericardial fluid, ascitic fluid, and/or urine], hair, skin
(including portions of the epidermis, dermis, and/or hypodermis),
oropharynx, laryngopharynx, esophagus, stomach, bronchus, salivary
gland, tongue, oral cavity, nasal cavity, vaginal cavity, anal
cavity, bone, bone marrow, brain, thymus, spleen, small intestine,
appendix, colon, rectum, anus, liver, biliary tract, pancreas,
kidney, ureter, bladder, urethra, uterus, vagina, vulva, ovary,
cervix, scrotum, penis, prostate, testicle, seminal vesicles,
and/or any type of tissue (e.g., muscle tissue, epithelial tissue,
connective tissue, or nervous tissue).
[0177] The biological sample may be any type of sample including,
for example, a sample of a bodily fluid, one or more cells, a piece
of tissue, or some or all of an organ. In some embodiments, the
sample may be from a cancerous tissue or organ or a tissue or organ
suspected of having one or more cancerous cells. In some
embodiments, the sample may be from a healthy (e.g., non-cancerous)
tissue or organ. In some embodiments, a sample from a subject
(e.g., a biopsy from a subject) may include both healthy and
cancerous cells and/or tissue. In certain embodiments, one sample
will be taken from a subject for analysis. In some embodiments,
more than one (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, or more) samples may be taken from a
subject for analysis. In some embodiments, one sample from a
subject will be analyzed. In certain embodiments, more than one
(e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, or more) samples may be analyzed. If more than one sample
from a subject is analyzed, the samples may be procured at the same
time (e.g., more than one sample may be taken in the same
procedure), or the samples may be taken at different times (e.g.,
during a different procedure including a procedure 1, 2, 3, 4, 5,
6, 7, 8, 9, 10 days; 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 weeks; 1, 2, 3,
4, 5, 6, 7, 8, 9, 10 months, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 years,
or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 decades after a first procedure).
A second or subsequent sample may be taken or obtained from the
same region (e.g., from the same tumor or area of tissue) or a
different region (including, e.g., a different tumor). A second or
subsequent sample may be taken or obtained from the subject after
one or more treatments, and may be taken from the same region or a
different region. As a non-limiting example, the second or
subsequent sample may be useful in determining whether the cancer
in each sample has different characteristics (e.g., in the case of
samples taken from two physically separate tumors in a patient) or
whether the cancer has responded to one or more treatments (e.g.,
in the case of two or more samples from the same tumor prior to and
subsequent to a treatment).
[0178] Any of the biological samples described herein may be
obtained from the subject using any known technique. In some
embodiments, the biological sample may be obtained from a surgical
procedure (e.g., laparoscopic surgery, microscopically controlled
surgery, or endoscopy), bone marrow biopsy, punch biopsy,
endoscopic biopsy, or needle biopsy (e.g., a fine-needle
aspiration, core needle biopsy, vacuum-assisted biopsy, or
image-guided biopsy). In some embodiments, each of the at least one
biological samples is a bodily fluid sample, a cell sample, or a
tissue biopsy.
[0179] In some embodiments, one or more than one cell (i.e., a cell
sample) is obtained from a subject using a scrape or brush method.
The cell sample may be obtained from any area in or from the body
of a subject including, for example, from one or more of the
following areas: the cervix, esophagus, stomach, bronchus, or oral
cavity. In some embodiments, one or more than one piece of tissue
(e.g., a tissue biopsy) from a subject may be used. In certain
embodiments, the tissue biopsy may comprise one or more than one
(e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10) samples from
one or more tumors or tissues known or suspected of having
cancerous cells.
Sample Analysis
[0180] Methods and compositions described herein are based, at
least in part, on the identification and characterization of
certain biological processes and/or molecular and cellular
compositions that are present within and/or surrounding the cancer
(e.g., the tumor).
[0181] Biological processes within and/or surrounding cancer (e.g.,
a tumor) include, but are not limited to, angiogenesis, metastasis,
proliferation, cell activation (e.g., T cell activation), tumor
invasion, immune response, cell signaling (e.g., HER2 signaling),
and apoptosis.
[0182] Molecular and cellular compositions within and/or
surrounding cancer (e.g., a tumor) include, but are not limited to,
nucleic acids (e.g., DNA and/or RNA), molecules (e.g., hormones),
proteins (e.g., wild-type and/or mutant proteins), and cells (e.g.,
malignant and/or non-malignant cells).
[0183] The cancer microenvironment, as used herein, refers to the
molecular and cellular environment in which the cancer (e.g., a
tumor) exists including, but not limited to, blood vessels that
surround and/or are internal to a tumor, immune cells, fibroblasts,
bone marrow-derived inflammatory cells, lymphocytes, signaling
molecules, and the extracellular matrix (ECM).
[0184] The molecular and cellular composition and biological
processes present within and/or surrounding the tumor may be
directed toward promoting cancer (e.g., tumor) growth and survival
(e.g., pro-tumor) and/or inhibiting cancer (e.g., tumor) growth and
survival (e.g., anti-tumor).
[0185] The cancer (e.g., tumor) microenvironment may comprise
cellular compositions and biological processes directed toward
promoting cancer (e.g., tumor) growth and survival (e.g., pro-tumor
microenvironment) and/or inhibiting cancer (e.g., tumor) growth and
survival (e.g., anti-tumor microenvironment). In some embodiments,
the cancer (e.g., tumor) microenvironment comprises a pro-cancer
(e.g., tumor) microenvironment. In some embodiments, the cancer
(e.g., tumor) microenvironment comprises an anti-cancer (e.g.,
tumor) microenvironment. In some embodiments, the cancer (e.g.,
tumor) microenvironment comprises a pro-cancer (e.g., tumor)
microenvironment and an anti-cancer (e.g., tumor) microenvironment.
Any information relating to molecular and cellular compositions,
and biological processes that are present within and/or surrounding
cancer (e.g., a tumor) may be used in methods and compositions for
characterization of cancers (e.g., tumors) as described herein. In
some embodiments, cancer (e.g., a tumor) may be characterized based
on gene group expression level (e.g., on gene group RNA expression
level). In some embodiments, cancer (e.g., a tumor) is
characterized based on protein expression. In some embodiments,
cancer (e.g., a tumor) is characterized based on absence or
presence of at least one mutation (e.g., mutational load). In some
embodiments, the mutational load is estimated from whole exome
sequencing data (WES). In some embodiments, cancer (e.g., a tumor)
is characterized based on histology. In some embodiments, cancer
(e.g., a tumor) is characterized based on tumor purity. Tumor
purity may be determined using any means known in the art
including, but not limited to, cell sorting-based technology (e.g.,
Fluorescent-Activated Cell Sorting (FACS)). In some embodiments,
tumor purity is determined from whole exome sequencing (WES) data
of paired tumor and non-cancerous (e.g., normal) tissue. In some
embodiments, cancer (e.g., a tumor) is characterized based on the
number of neoantigens. The number of neoantigens may be determined
using any means known in the art including, but not limited to, the
use of whole exome sequencing (WES) data of paired cancer (e.g.,
tumor) and non-cancerous tissues.
[0186] Methods and compositions for characterization of cancers as
described herein may be applied to any cancer (e.g., any tumor).
Exemplary cancers include, but are not limited to, adrenocortical
carcinoma, bladder urothelial carcinoma, breast invasive carcinoma,
cervical squamous cell carcinoma, endocervical adenocarcinoma,
colon adenocarcinoma, esophageal carcinoma, kidney renal clear cell
carcinoma, kidney renal papillary cell carcinoma, liver
hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell
carcinoma, ovarian serous cystadenocarcinoma, pancreatic
adenocarcinoma, prostate adenocarcinoma, rectal adenocarcinoma,
skin cutaneous melanoma, stomach adenocarcinoma, thyroid carcinoma,
uterine corpus endometrial carcinoma, and cholangiocarcinoma.
[0187] In one embodiment, cancers of any type (including all the
types of cancer listed herein) may be classified as being 1.sup.st
MF profile type (inflamed/vascularized and/or inflamed/fibroblast
enriched), 2.sup.nd MF profile type (inflamed/non-vascularized
and/or inflamed/non-fibroblast enriched), 3.sup.rd MF profile type
(non-inflamed/vascularized and/or non-inflamed/fibroblast
enriched), or 4.sup.th MF profile type
(non-inflamed/non-vascularized and/or non-inflamed/non-fibroblast
enriched) cancers (e.g., tumors).
Expression Data
[0188] Expression data (e.g., indicating expression levels) for a
plurality of genes may be used for any of the methods or
compositions described herein. The number of genes which may be
examined may be up to and inclusive of all the genes of the
subject. In some embodiments, expression levels may be examined for
all of the genes of a subject. As a non-limiting example, four or
more, five or more, six or more, seven or more, eight or more, nine
or more, ten or more, eleven or more, twelve or more, 13 or more,
14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or
more, 20 or more, 21 or more, 22 or more, 23 or more, 24 or more,
25 or more, 26 or more, 27 or more, 28 or more, 29 or more, 30 or
more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more,
90 or more, 100 or more, 125 or more, 150 or more, 175 or more, 200
or more, 225 or more, 250 or more, 275 or more, or 300 or more
genes may be used for any evaluation described herein. As another
set of non-limiting examples, at least four, at least five, at
least six, at least seven, at least eight, at least nine, at least
ten, at least eleven, at least twelve, at least 13, at least 14, at
least 15, at least 16, at least 17, at least 18, at least 19, at
least 20, at least 21, at least 22, at least 23, at least 24, at
least 25, at least 26, at least 27, at least 28, at least 29, at
least 30, at least 40, at least 50, at least 60, at least 70, at
least 80, at least 90, at least 100, at least 125, at least 150, at
least 175, at least 200, at least 225, at least 250, at least 275,
or at least 300 genes may be used for any evaluation described
herein. In some embodiments, at least two, at least three, at least
four, at least five, at least six, at least seven, at least eight,
at least nine, at least ten, at least eleven, at least twelve, at
least 13, at least 14, at least 15, at least 16, at least 17, at
least 18, at least 19, at least 20, at least 21, at least 22, at
least 23, at least 24, at least 25, at least 26, at least 27, at
least 28, at least 29, at least 30, at least 40, at least 50, at
least 60, at least 70, at least 80, at least 90, at least 100, at
least 125, at least 150, at least 175, at least 200, at least 225,
at least 250, at least 275, or at least 300 genes may be examined
for each gene group or module evaluation described herein. In some
embodiments, up to 50 modules (e.g., up to two, up to three, up to
four, up to five, up to six, up to seven, up to eight, up to nine,
up to ten, up to eleven, up to twelve, up to 13, up to 14, up to
15, up to 16, up to 17, up to 18, up to 19, up to 20, up to 21, up
to 22, up to 23, up to 24, up to 25, up to 26, up to 27, up to 28,
up to 29, up to 30, up to 31, up to 32, up to 33, up to 34, up to
35, up to 36, up to 37, up to 38, up to 39, up to 40, up to 41, up
to 42, up to 43, up to 44, up to 45, up to 46, up to 47, up to 48,
up to 49, or up to 50) modules or gene groups may be used for any
evaluation described herein.
[0189] Any method may be used on a sample from a subject in order
to acquire expression data (e.g., indicating expression levels) for
the plurality of genes. As a set of non-limiting examples, the
expression data may be RNA expression data, DNA expression data, or
protein expression data.
[0190] DNA expression data, in some embodiments, refers to a level
of DNA in a sample from a subject. The level of DNA in a sample
from a subject having cancer may be elevated compared to the level
of DNA in a sample from a subject not having cancer, e.g., a gene
duplication in a cancer patient's sample. The level of DNA in a
sample from a subject having cancer may be reduced compared to the
level of DNA in a sample from a subject not having cancer, e.g., a
gene deletion in a cancer patient's sample.
[0191] DNA expression data, in some embodiments, refers to data for
DNA (or gene) expressed in a sample, for example, sequencing data
for a gene that is expressed in a patient's sample. Such data may
be useful, in some embodiments, to determine whether the patient
has one or more mutations associated with a particular cancer.
[0192] RNA expression data may be acquired using any method known
in the art including, but not limited to: whole transcriptome
sequencing, total RNA sequencing, mRNA sequencing, targeted RNA
sequencing, small RNA sequencing, ribosome profiling, RNA exome
capture sequencing, and/or deep RNA sequencing. DNA expression data
may be acquired using any method known in the art including any
known method of DNA sequencing. For example, DNA sequencing may be
used to identify one or more mutations in the DNA of a subject. Any
technique used in the art to sequence DNA may be used with the
methods and compositions described herein. As a set of non-limiting
examples, the DNA may be sequenced through single-molecule
real-time sequencing, ion torrent sequencing, pyrosequencing,
sequencing by synthesis, sequencing by ligation (SOLiD sequencing),
nanopore sequencing, or Sanger sequencing (chain termination
sequencing). Protein expression data may be acquired using any
method known in the art including, but not limited to: N-terminal
amino acid analysis, C-terminal amino acid analysis, Edman
degradation (including though use of a machine such as a protein
sequenator), or mass spectrometry.
[0193] In some embodiments, the expression data comprises whole
exome sequencing (WES) data. In some embodiments, the expression
data comprises whole genome sequencing (WGS) data. In some
embodiments, the expression data comprises next-generation
sequencing (NGS) data. In some embodiments, the expression data
comprises microarray data.
[0194] In some embodiments, expression data is used to determine
gene group expression levels. In some embodiments, the gene group
expression levels are calculated as a gene set enrichment analysis
(GSEA) score for the gene group. In some embodiments, GSEA
comprises calculating an enrichment score (ES), assessing ES
significance, adjusting ES for multiple hypothesis testing, and
weighting each gene. In some embodiments, each gene is weighted
equally. In some embodiments, each gene is weighted according to
their association with a phenotype.
[0195] In some embodiments, calculating an ES comprises ranking
genes by their expression difference, calculating cumulative sum
over ranked genes, and recording maximum deviation from zero as ES.
In some embodiments, calculating cumulative sum over ranked genes
comprises an increase in sum when a gene is present in a gene group
and a decrease in sum when a gene is absent from gene group. In
some embodiments, magnitude of increment depends on correlation of
a gene and a phenotype.
[0196] In some embodiments, assessing ES significance comprises
permutating phenotype labels. In some embodiments, assessing ES
significance comprises calculating ES for permutated data. In some
embodiments, assessing ES significance comprises comparing ES for
non-permutated data to ES for permutated data.
[0197] In some embodiments, adjusting ES for multiple hypothesis
testing comprises determining a normalized enrichment score (NES).
In some embodiments, adjusting ES for multiple hypothesis testing
determining a false discovery rate (FDR) for the NES. In some
embodiments, determining FDR comprises comparing tail of the
observed and null distributions for the NES. In some embodiments,
GSEA score is calculated at least once. In some embodiments, GSEA
score is calculated at least twice. In some embodiments, GSEA score
is calculated once for positively scoring gene groups and once for
negatively score gene groups.
Datasets
[0198] Any dataset containing expression data may be used to
generate MF profiles as described herein. In some embodiments,
expression data may be obtained from one or more databases and/or
any other suitable electronic repository of data. Examples of
databases include, but are not limited to, CGP (Cancer Genome
Project), CPTAC (Clinical Proteomic Tumor Analysis Consortium),
ICGC (International Cancer Genome Consortium), and TCGA (The Cancer
Genome Atlas). In some embodiments, expression data may be obtained
from data associated with a clinical trial. In some embodiments,
expression data may be predicted in association with a clinical
trial based on one or more similar drugs (e.g., drugs of a similar
class such as PD-1 inhibitors). In some embodiments, expression
data may be obtained from a hospital database. In some embodiments,
expression data may be obtained from a commercial sequencing
supplier. In some embodiments, expression data may be obtained from
a subject (e.g., a patient) and/or a subject's (e.g., a patient's)
relative, guardian, or caretaker.
Assays
[0199] Any of the biological samples described herein can be used
for obtaining expression data using conventional assays or those
described herein. Expression data, in some embodiments, includes
gene expression levels. Gene expression levels may be detected by
detecting a product of gene expression such as mRNA and/or
protein.
[0200] In some embodiments, gene expression levels are determined
by detecting a level of a protein in a sample and/or by detecting a
level of activity of a protein in a sample. As used herein, the
terms "determining" or "detecting" may include assessing the
presence, absence, quantity and/or amount (which can be an
effective amount) of a substance within a sample, including the
derivation of qualitative or quantitative concentration levels of
such substances, or otherwise evaluating the values and/or
categorization of such substances in a sample from a subject.
[0201] The level of a protein may be measured using an immunoassay.
Examples of immunoassays include any known assay (without
limitation), and may include any of the following: immunoblotting
assay (e.g., Western blot), immunohistochemical analysis, flow
cytometry assay, immunofluorescence assay (IF), enzyme linked
immunosorbent assays (ELIS As) (e.g., sandwich ELISAs),
radioimmunoas says, electrochemiluminescence-based detection
assays, magnetic immunoassays, lateral flow assays, and related
techniques.
[0202] Additional suitable immunoassays for detecting a level of a
protein provided herein will be apparent to those of skill in the
art.
[0203] Such immunoassays may involve the use of an agent (e.g., an
antibody) specific to the target protein. An agent such as an
antibody that "specifically binds" to a target protein is a term
well understood in the art, and methods to determine such specific
binding are also well known in the art. An antibody is said to
exhibit "specific binding" if it reacts or associates more
frequently, more rapidly, with greater duration and/or with greater
affinity with a particular target protein than it does with
alternative proteins. It is also understood by reading this
definition that, for example, an antibody that specifically binds
to a first target peptide may or may not specifically or
preferentially bind to a second target peptide. As such, "specific
binding" or "preferential binding" does not necessarily require
(although it can include) exclusive binding. Generally, but not
necessarily, reference to binding means preferential binding. In
some examples, an antibody that "specifically binds" to a target
peptide or an epitope thereof may not bind to other peptides or
other epitopes in the same antigen. In some embodiments, a sample
may be contacted, simultaneously or sequentially, with more than
one binding agent that binds different proteins (e.g., multiplexed
analysis).
[0204] As used herein, the term "antibody" refers to a protein that
includes at least one immunoglobulin variable domain or
immunoglobulin variable domain sequence. For example, an antibody
can include a heavy (H) chain variable region (abbreviated herein
as VH), and a light (L) chain variable region (abbreviated herein
as VL). In another example, an antibody includes two heavy (H)
chain variable regions and two light (L) chain variable regions.
The term "antibody" encompasses antigen-binding fragments of
antibodies (e.g., single chain antibodies, Fab and sFab fragments,
F(ab')2, Fd fragments, Fv fragments, scFv, and domain antibodies
(dAb) fragments (de Wildt et al., Eur J Immunol. 1996;
26(3):629-39.)) as well as complete antibodies. An antibody can
have the structural features of IgA, IgG, IgE, IgD, IgM (as well as
subtypes thereof). Antibodies may be from any source including, but
not limited to, primate (human and non-human primate) and
primatized (such as humanized) antibodies.
[0205] In some embodiments, the antibodies as described herein can
be conjugated to a detectable label and the binding of the
detection reagent to the peptide of interest can be determined
based on the intensity of the signal released from the detectable
label. Alternatively, a secondary antibody specific to the
detection reagent can be used. One or more antibodies may be
coupled to a detectable label. Any suitable label known in the art
can be used in the assay methods described herein. In some
embodiments, a detectable label comprises a fluorophore. As used
herein, the term "fluorophore" (also referred to as "fluorescent
label" or "fluorescent dye") refers to moieties that absorb light
energy at a defined excitation wavelength and emit light energy at
a different wavelength. In some embodiments, a detection moiety is
or comprises an enzyme. In some embodiments, an enzyme is one
(e.g., .beta.-galactosidase) that produces a colored product from a
colorless substrate.
[0206] It will be apparent to those of skill in the art that this
disclosure is not limited to immunoassays. Detection assays that
are not based on an antibody, such as mass spectrometry, are also
useful for the detection and/or quantification of a protein and/or
a level of protein as provided herein. Assays that rely on a
chromogenic substrate can also be useful for the detection and/or
quantification of a protein and/or a level of protein as provided
herein.
[0207] Alternatively, the level of nucleic acids encoding a gene in
a sample can be measured via a conventional method. In some
embodiments, measuring the expression level of nucleic acid
encoding the gene comprises measuring mRNA. In some embodiments,
the expression level of mRNA encoding a gene can be measured using
real-time reverse transcriptase (RT) Q-PCR or a nucleic acid
microarray. Methods to detect nucleic acid sequences include, but
are not limited to, polymerase chain reaction (PCR), reverse
transcriptase-PCR (RT-PCR), in situ PCR, quantitative PCR (Q-PCR),
real-time quantitative PCR (RT Q-PCR), in situ hybridization,
Southern blot, Northern blot, sequence analysis, microarray
analysis, detection of a reporter gene, or other DNA/RNA
hybridization platforms.
[0208] In some embodiments, the level of nucleic acids encoding a
gene in a sample can be measured via a hybridization assay. In some
embodiments, the hybridization assay comprises at least one binding
partner. In some embodiments, the hybridization assay comprises at
least one oligonucleotide binding partner. In some embodiments, the
hybridization assay comprises at least one labeled oligonucleotide
binding partner. In some embodiments, the hybridization assay
comprises at least one pair of oligonucleotide binding partners. In
some embodiments, the hybridization assay comprises at least one
pair of labeled oligonucleotide binding partners.
[0209] Any binding agent that specifically binds to a desired
nucleic acid or protein may be used in the methods and kits
described herein to measure an expression level in a sample. In
some embodiments, the binding agent is an antibody or an aptamer
that specifically binds to a desired protein. In other embodiments,
the binding agent may be one or more oligonucleotides complementary
to a nucleic acid or a portion thereof. In some embodiments, a
sample may be contacted, simultaneously or sequentially, with more
than one binding agent that binds different proteins or different
nucleic acids (e.g., multiplexed analysis).
[0210] To measure an expression level of a protein or nucleic acid,
a sample can be in contact with a binding agent under suitable
conditions. In general, the term "contact" refers to an exposure of
the binding agent with the sample or cells collected therefrom for
suitable period sufficient for the formation of complexes between
the binding agent and the target protein or target nucleic acid in
the sample, if any. In some embodiments, the contacting is
performed by capillary action in which a sample is moved across a
surface of the support membrane.
[0211] In some embodiments, an assay may be performed in a
low-throughput platform, including single assay format. In some
embodiments, an assay may be performed in a high-throughput
platform. Such high-throughput assays may comprise using a binding
agent immobilized to a solid support (e.g., one or more chips).
Methods for immobilizing a binding agent will depend on factors
such as the nature of the binding agent and the material of the
solid support and may require particular buffers. Such methods will
be evident to one of ordinary skill in the art.
Genes
[0212] The various genes recited herein are, in general, named
using human gene naming conventions. The various genes, in some
embodiments, are described in publically available resources such
as published journal articles. The gene names may be correlated
with additional information (including sequence information)
through use of, for example, the NCBI GenBank.RTM. databases
available at
www<dot>ncbi<dot>nlm<dot>nih<dot>gov; the
HUGO (Human Genome Organization) Gene Nomination Committee (HGNC)
databases available at www<dot>genenames<dot>org; the
DAVID Bioinformatics Resource available at
www<dot>david<dot>ncifcrf<dot>gov. The gene names
may also be correlated with additional information through printed
publications from the foregoing organizations, which are
incorporated by reference herein for this purpose. It should be
appreciated that a gene may encompass all variants of that gene.
For organisms or subjects other than human subjects, corresponding
specific-specific genes may be used. Synonyms, equivalents, and
closely related genes (including genes from other organisms) may be
identified using similar databases including the NCBI GenBank.RTM.
databases described above.
[0213] In some embodiments, gene MK167 may be identified as
GenBank.RTM. Accession number NM_002417.4 or NM_001145966.1; gene
ESCO2 may be identified as GenBank.RTM. Accession number
NM_001017420.2; gene CETN3 may be identified as GenBank.RTM.
Accession number NM_001297765.1, NM_004365.3 or NM_001297768.1;
gene CDK2 may be identified as GenBank.RTM. Accession number
NM_001798.4, NM_052827.3 or NM_001290230.1; gene CCND1 may be
identified as GenBank.RTM. Accession number NM_053056.2; gene CCNE1
may be identified as GenBank.RTM. Accession number NM_001238.3,
NM_001322259.1, NM_001322261.1 or NM_001322262.1; gene AURKA may be
identified as GenBank.RTM. Accession number NM_198433.2,
NM_003600.3, NM_198434.2, NM_198435.2, NM_198436.2, NM_198437.2,
NM_001323303.1, NM_001323304.1, or NM_001323305.1; gene AURKB may
be identified as GenBank.RTM. Accession number NM_004217.3,
NM_001256834.2, NM_001284526.1, NM_001313950.1, NM_001313951.1,
NM_001313952.1, NM_001313954.1, NM_001313953.2 or NM_001313955.1;
gene CDK4 may be identified as GenBank.RTM. Accession number
NM_000075.3; gene CDK6 may be identified as GenBank.RTM. Accession
number NM_001145306.1; gene PRC1 may be identified as GenBank.RTM.
Accession number NM_199413.2 or NM_003981.3. ; gene E2F1 may be
identified as GenBank.RTM. Accession number NM_005225.2; gene MYBL2
may be identified as GenBank.RTM. Accession number NM_002466.3 or
NM_001278610.1; gene BUB1 may be identified as GenBank.RTM.
Accession number NM_004336.4, NM_001278616.1, NM_001278617.1; gene
PLK1 may be identified as GenBank.RTM. Accession number
NM_005030.5; gene CCNB1 may be identified as GenBank.RTM. Accession
number NM_031966.3, NM_001354845.1, NM_001354844.1; gene MCM2 may
be identified as GenBank.RTM. Accession number NM_004526.3. ; gene
MCM6 may be identified as GenBank.RTM. Accession number
NM_005915.5; gene PIK3CA may be identified as GenBank.RTM.
Accession number NM_006218.3; gene PIK3CB may be identified as
GenBank.RTM. Accession number NM_006219.2 or NM_001256045.1; gene
PIK3CG may be identified as GenBank.RTM. Accession number
NM_002649.3, NM_001282427.1 or NM_001282426.1; gene PIK3CD may be
identified as GenBank.RTM. Accession number NM_005026.4,
NM_001350234.1, or NM_001350235.1; gene AKT1 may be identified as
GenBank.RTM. Accession number NM_005163.2, NM_001014431.1, or
NM_001014432.1; gene MTOR may be identified as GenBank.RTM.
Accession number NM_004958.3 ; gene PTEN may be identified as
GenBank.RTM. Accession number NM_001304717.2, NM_000314.6 or
NM_001304718.1; gene PRKCA may be identified as GenBank.RTM.
Accession number NM_002737.2; gene AKT2 may be identified as
GenBank.RTM. Accession number NM 001330511.1, NM_001243027.2,
NM_001243028.2, NM_001626.5; gene AKT3 may be identified as
GenBank.RTM. Accession number NM_005465.4, NM_181690.2 or
NM_001206729.1; gene BRAF may be identified as GenBank.RTM.
Accession number NM_001354609.1 or NM_004333.5; gene FNTA may be
identified as GenBank.RTM. Accession number NM_002027.2; gene FNTB
may be identified as GenBank.RTM. Accession number NM_002028.3;
gene MAP2K1 may be identified as GenBank.RTM. Accession number
NM_002755.3; gene MKNK1 may be identified as GenBank.RTM. Accession
number NM_003684.6, NM_198973.4 or NM_001135553.3; gene MKNK2 may
be identified as GenBank.RTM. Accession number NM 017572.3 or NM
199054.2.
MF Profiles
[0214] A "molecular functional tumor portrait (MF profile)," as
described herein, refers to a graphical depiction of a tumor with
regard to molecular and cellular composition, and biological
processes that are present within and/or surrounding the tumor.
Related compositions and processes present within and/or
surrounding a tumor are presented in functional modules (also
described herein as "gene groups") of a MF profile.
[0215] MF profiles may be constructed, in some embodiments, from
gene expression data (for example sequencing data, e.g., whole
exome sequencing data, RNA sequencing data, or other gene
expression data) of normal tissue and/or tumor tissue. FIG. 1A
shows an exemplary bioinformatics pipeline for constructing a tumor
portrait from sequencing data. MF profiles produced in accordance
with the bioinformatics pipeline in FIG. 1A may comprise functional
modules depicted as circles and arrange in an circular pattern as
shown in FIG. 1B. Each circle of the MF profile in FIG. 1B
represents a functional module, which are labeled using lines.
Related functional modules may be combined into a single functional
module. For example, FIG. 1B shows that the anti-metastatic factors
module, the metastatic factors module, and the tumor suppressors
module may be combined into the malignant cell properties
module.
[0216] FIG. 1C shows one embodiment of an MF profile as provided
herein. As shown in FIG. 1C, the MF profile 100 comprises 28
functional modules, three of which are labeled as 110, 120 and 130.
Module size indicates module intensity. For example, module 110 is
larger than module 120 indicating that module 110 has increased
module intensity as compared to module 120. The presence or absence
of cross-hatching of the module indicates whether the module is a
pro-tumor module or an anti-tumor module. Pro-tumor modules (e.g.,
module 120) are shown in solid shades without cross-marking
thereof, and anti-tumor modules (e.g., module 130) are shown with
cross-marking thereof. The depth of shading of the module indicates
module intensity. Modules relating to tumor malignancy 140 are
depicted in the top right quarter of the circle.
MF Profile Modules
[0217] A "functional module" or "gene group," as described herein,
refers to related compositions and processes present within and/or
surrounding a tumor.
[0218] For example, an immune response/inflammation module provides
information related to immune system composition and activity
within a tumor. Examples of immune system composition and activity
within a tumor presented in the immune response/inflammation module
include, but are not limited to, the number of unique tumor
antigens, MHC-restricted antigen presentation, expression of
co-stimulatory compounds that are involved in T cell activation,
intensities of activation and effector phases of adaptive and
innate immune responses, proportions of different lymphoid and
myeloid cell populations within a tumor, expression rates of
cancer-promoting and anti-cancer cytokines, and intensities of
immune response processes (e.g., activities of immunosuppressive
cells and expression of immune checkpoint inhibitory
molecules).
[0219] Exemplary modules in a MF profile may include, but are not
limited to, Major histocompatibility complex I (MHCI) module, Major
histocompatibility complex II (MHCII) module, Coactivation
molecules module, Effector cells module, Effector T cell module;
Natural killer cells (NK cells) module, T cell traffic module, T
cells module, B cells module, B cell traffic module, Benign B cells
module, Malignant B cell marker module, M1 signatures module, Th1
signature module, Antitumor cytokines module, Checkpoint inhibition
(or checkpoint molecules) module, Follicular dendritic cells
module, Follicular B helper T cells module, Protumor cytokines
module, Regulatory T cells (Treg) module, Treg traffic module,
Myeloid-derived suppressor cells (MDSCs) module, MDSC and TAM
traffic module, Granulocytes module, Granulocytes traffic module,
Eosinophil signature model, Neutrophil signature model, Mast cell
signature module, M2 signature module, Th2 signature module, Th17
signature module, Protumor cytokines module, Complement inhibition
module, Fibroblastic reticular cells module, Cancer associated
fibroblasts (CAFs) module, Matrix formation (or Matrix) module,
Angiogenesis module, Endothelium module, Hypoxia factors module,
Coagulation module, Blood endothelium module, Lymphatic endothelium
module, Proliferation rate (or Tumor proliferation rate) module,
Oncogenes module, PI3K/AKT/mTOR signaling module, RAS/RAF/MEK
signaling module, Receptor tyrosine kinases expression module,
Growth Factors module, Tumor suppressors module, Metastasis
signature module, Antimetastatic factors module, and Mutation
status module. In certain embodiments, the modules may be described
as "gene groups".
[0220] In some embodiments, the gene groups of the modules may
comprise at least two genes (e.g., at least two genes, at least
three genes, at least four genes, at least five genes, at least six
genes, at least seven genes, at least eight genes, at least nine
genes, at least ten genes, or more than ten genes as shown in the
following lists; in some embodiments all of the listed genes are
selected from each group; and in some embodiments the numbers of
genes in each selected group are not the same.
[0221] In some embodiments, the modules in a MF profile may
comprise or consist of: Major histocompatibility complex I (MHCI)
module, Major histocompatibility complex II (MHCII) module,
Coactivation molecules module, Effector cells (or Effector T cell)
module, Natural killer cells (NK cells) module, T cells module, B
cells module, M1 signatures module, Th1 signature module, Antitumor
cytokines module, Checkpoint inhibition (or checkpoint molecules)
module, Regulatory T cells (Treg) module, Myeloid-derived
suppressor cells (MDSCs) module, Neutrophil signature model, M2
signature module, Th2 signature module, Protumor cytokines module,
Complement inhibition module, Cancer associated fibroblasts (CAFs)
module, Angiogenesis module, Endothelium module, Proliferation rate
(or Tumor proliferation rate) module, PI3K/AKT/mTOR signaling
module, RAS/RAF/MEK signaling module, Receptor tyrosine kinases
expression module, Growth Factors module, Tumor suppressors module,
Metastasis signature module, and Antimetastatic factors module. The
MF profile may additionally include: T cell traffic module,
Antitumor cytokines module, Treg traffic module, MDSC and TAM
traffic module, Granulocytes or Granulocyte traffic module,
Eosinophil signature model, Mast cell signature module, Th17
signature module, Matrix formation (or Matrix) module, and Hypoxia
factors module. Such an MF profile could be useful for a subject
with a solid cancer (e.g., a melanoma).
[0222] In some embodiments, the modules in a MF profile may
comprise or consist of: Effector cells (or Effector T cell) module,
Natural killer cells (NK cells) module, T cells module, Malignant B
cell marker module, M1 signatures module, Th1 signature module,
Checkpoint inhibition (or checkpoint molecules) module, Follicular
dendritic cells module, Follicular B helper T cells module,
Protumor cytokines module, Regulatory T cells (Treg) module,
Neutrophil signature model, M2 signature module, Th2 signature
module, Complement inhibition module, Fibroblastic reticular cells
module, Angiogenesis module, Blood endothelium module,
Proliferation rate (or Tumor proliferation rate) module, Oncogenes
module, and Tumor suppressors module. The MF profile may
additionally include: Major histocompatibility complex I (MHCI)
module, Major histocompatibility complex II (MHCII) module,
Coactivation molecules module, B cell traffic module, Benign B
cells module, Antitumor cytokines module, Treg traffic module, Mast
cell signature module, Th17 signature module, Matrix formation (or
Matrix) module, Hypoxia factors module, Coagulation module, and
Lymphatic endothelium module. Such an MF profile could be useful
for a subject with follicular lymphoma.In some embodiments, the
gene groups of the modules may comprise at least two genes (e.g.,
at least two genes, at least three genes, at least four genes, at
least five genes, at least six genes, at least seven genes, at
least eight genes, at least nine genes, at least ten genes, or more
than ten genes as shown in the following lists; in some embodiments
all of the listed genes are selected from each group; and in some
embodiments the numbers of genes in each selected group are not the
same): Major histocompatibility complex I (MHCI) module: HLA-A,
HLA-B, HLA-C, B2M, TAP1, and TAP2; Major histocompatibility complex
II (MHCII) module: HLA-DRA, HLA-DRB1, HLA-DOB, HLA-DPB2, HLA-DMA,
HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DRB5,
HLA-DQA2, HLA-DQB2, and HLA-DRB6; Coactivation molecules module:
CD80, CD86, CD40, CD83, TNFRSF4, ICOSLG, CD28; Effector cells
module: IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70, GNLY, FASLG,
TBX21, EOMES, CD8A, and CD8B; Effector T cell module: IFNG, GZMA,
GZMB, PRF1, LCK, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, and
CD8B; Natural killer cells (NK cells) module: NKG7, CD160, CD244,
NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1,
KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, EOMES, CLIC3, FGFBP2, KLRF1,
and SH2D1B; T cell traffic module: CXCL9, CXCL10, CXCR3, CX3CL1,
CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, and CCL5; T cells module:
EOMES, TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, LCK,
UBASH3A, TRAT1, CD5, and CD28; B cells module: CD19, MS4A1,
TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A,
CD79B, BLK, FCRL5, PAX5, and STAP1; B cell traffic module: CXCL13
and CXCR5; Benign B cells module: CD19, MS4A1, TNFRSF13C, CD27,
CD24, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, and BLK;
Malignant B cell marker module: MME, CD70, CD20, CD22, and PAX5; M1
signatures module: NOS2, IL12A, IL12B, IL23A, TNF, IL1B, and SOCS3;
Th1 signature module: IFNG, IL2, CD4OLG, IL15, CD27, TBX21, LTA,
and IL21; Antitumor cytokines module: HMGB1, TNF, IFNB1, IFNA2,
CCL3, TNFSF10, and FASLG; Checkpoint inhibition (or checkpoint
molecules) module: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA,
HAVCR2, and VSIR; Follicular dendritic cells module: CR1, FCGR2A,
FCGR2B, FCGR2C, CR2, FCER2, CXCL13, MADCAM1, ICAM1, VCAM1, BST1,
LTBR, and TNFRSF1A; Follicular B helper T cells module: CXCR5,
B3GAT1, ICOS, CD4OLG, CD84, IL21, BCL6, MAF, and SAP; Protumor
cytokines module: IL10, TGFB1, TGFB2, TGFB3, IL22, MIF, TNFSF13B,
IL6, and IL7; Regulatory T cells (Treg) module: TGFB1, TGFB2,
TGFB3, FOXP3, CTLA4, IL10, TNFRSF18, TNFR2, and TNFRSF1B; Treg
traffic module: CCL17, CXCL12, CXCR4, CCR4, CCL22, CCL1, CCL2,
CCL5, CXCL13, and CCL28; Myeloid-derived suppressor cells (MDSCs)
module: IDO1, ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB,
CXCR4, and CD33; MDSC and TAM traffic module: CXCL1, CXCL5, CCL2,
CCL4, CCL8, CCR2, CCL3, CCL5, CSF1, and CXCL8; Granulocytes module:
CXCL8, CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5, CXCL5, CCR3, CCL26,
PRG2, EPX, RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8, PRG3, MPO, ELANE,
PRTN3, CTSG, FCGR3B, CXCR1, CXCR2, CD177, PI3, FFAR2, PGLYRP1,
CMA1, TPSAB1, MS4A2, CPA3, IL4, IL5, IL13, and SIGLEC8; Granulocyte
traffic module: CXCL8, CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5,
CXCL5, CCR3, and CCL26; Eosinophil signature model: PRG2, EPX,
RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8, and PRG3; Neutrophil
signature model: MPO, ELANE, PRTN3, CTSG, FCGR3B, CXCR1, CXCR2,
CD177, PI3, FFAR2, and PGLYRP1; Mast cell signature module: CMA1,
TPSAB1, MS4A2, CPA3, IL4, IL5, IL13, and SIGLEC8; M2 signature
module: IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1, LRP1, ARG1,
PTGS1, MSR1, CD163, and CSF1R; Th2 signature module: IL4, IL5,
IL13, IL10, IL25, and GATA3; Th17 signature module: IL17A, IL22,
IL26, IL17F, IL21, and RORC; Protumor cytokines module: IL10,
TGFB1, TGFB2, TGFB3, IL22, and MIF; Complement inhibition module:
CFD, CFI, CD55, CD46, CR1, and CD59; Fibroblastic reticular cells
module: DES, VIM, PDGFRA, PDPN, NT5E, THY1, ENG, ACTA2, LTBR,
TNFRSF1A, VCAM1, ICAM1, and BST1; Cancer associated fibroblasts
(CAFs) module: COL1A1, COL1A2, COL4A1, COL5A1, TGFB1, TGFB2, TGFB3,
ACTA2, FGF2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, FBLN1, LUM,
MFAP5, LGALS1, and PRELP; Matrix formation (or Matrix) module:
MMP9, FN1, COL1A1, COL1A2, COL3A1, COL4A1, CA9, VTN, LGALS7, TIMP1,
MMP2, MMP1, MMP3, MMP12, LGALS9, MMPI, and COL5A1; Angiogenesis
module: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF,
CXCL5, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5, NOS3, VCAM1, MMRN1,
LDHA, HIF1A, EPAS1, CA9, SPP1, LOX, SLC2A1, and LAMPS; Endothelium
module: VEGFA, NOS3, KDR, FLT1, VCAM1, VWF, CDH5, MMRN1, CLEC14A,
MMRN2, and ECSCR; Hypoxia factors module: LDHA, HIF1A, EPAS1, CA9,
SPP1, LOX, SLC2A1, and LAMP3; Coagulation module: HPSE, SERPINE1,
SERPINB2, F3, and ANXA2; Blood endothelium module: VEGFA, NOS3,
KDR, FLT1, VCAM1, VWF, CDH5, and MMRN1; Lymphatic endothelium
module: CCL21 and CXCL12; Proliferation rate (or Tumor
proliferation rate) module: MKI67, ESCO2, CETN3, CDK2, CCND1,
CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, PLK1, PRC1, CCNB1, MCM2,
MCM6, CDK4, and CDK6; Oncogenes module: MDM2, MYC, AKT1, BCL2, MME,
and SYK; PI3K/AKT/mTOR signaling module: PIK3CA, PIK3CB, PIK3CG,
PIK3CD, AKT1, MTOR, PTEN, PRKCA, AKT2, and AKT3; RAS/RAF/MEK
signaling module: BRAF, FNTA, FNTB, MAP2K1, MAP2K2, MKNK1, and
MKNK2; Receptor tyrosine kinases expression module: ALK, AXL, KIT,
EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2, FGFR3, ERBB4, ERBB3,
BCR-ABL, PDGFRA, PDGFRB, and ABL1; Growth Factors module: NGF,
CSF3, CSF2, FGF7, IGF1, IGF2, IL7, and FGF2; Tumor suppressors
module: TP53, MLL2, CREBBP, EP300, ARID1A, HIST1H1, EBF1, IRF4,
IKZF3, KLHL6, PRDM1, CDKN2A, RB1, EPHA7, TNFAIP3, TNFRSF14, FAS,
SHP1, SOCS1, SIK1, PTEN, DCN, MTAP, AIM2, and MITF; Metastasis
signature module: ESRP1, HOXA1, SMARCA4, TWIST1, NEDD9, PAPPA,
CTSL, SNAI2, and HPSE; Antimetastatic factors module: NCAM1, CDH1,
KISS1, BRMS1, ADGRG1, TCF21, PCDH10, and MITF; and Mutation status
module: APC, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2, CDH1, CDKN2A,
CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS, IDH1, KRAS,
MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1, NPM1,
[0223] NRAS, PBRM1, PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2,
TAF1, TP53, and VHL. In certain embodiments, two or more genes from
any combination of the listed modules may be included in an MF
portrait.
[0224] In some embodiments, the gene groups of the modules may
comprise at least two genes (e.g., at least two genes, at least
three genes, at least four genes, at least five genes, at least six
genes, at least seven genes, at least eight genes, at least nine
genes, at least ten genes, or more than ten genes as shown in the
following lists; in some embodiments all of the listed genes are
selected from each group; and in some embodiments the numbers of
genes in each selected group are not the same): Major
histocompatibility complex I (MHCI) module: HLA-A, HLA-B, HLA-C,
B2M, TAP1, and TAP2; Major histocompatibility complex II (MHCII)
module; HLA-DRA, HLA-DRB1, HLA-DOB, HLA-DPB2, HLA-DMA, HLA-DOA,
HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DRB5,
HLA-DQA2, HLA-DQB2, and HLA-DRB6; Coactivation molecules module:
CD80, CD86, CD40, CD83, TNFRSF4, ICOSLG, CD28; Effector cells (or
Effector T cell) module: IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70,
GNLY, FASLG, TBX21, EOMES, CD8A, and CD8B; Natural killer cells (NK
cells) module: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GNLY,
KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, EOMES, CLIC3,
FGFBP2, KLRF1, and SH2D1B; T cells module: TBX21, ITK, CD3D, CD3E,
CD3G, TRAC, TRBC1, TRBC2, LCK, UBASH3A, TRAT1, CD5, and CD28; B
cells module: CD19, MS4A1, TNFRSF13C, CD27, CD24, CR2, TNFRSF17,
TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, and STAP1; M1
signatures module: NOS2, IL12A, IL12B, IL23A, TNF, IL1B, and SOCS3;
Th1 signature module: IFNG, IL2, CD4OLG, IL15, CD27, TBX21, LTA,
and IL21; Checkpoint inhibition (or checkpoint molecules) module:
PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, and VSIR;
Regulatory T cells (Treg) module: TGFB1, TGFB2, TGFB3, FOXP3,
CTLA4, IL10, and TNFRSF1B; Myeloid-derived suppressor cells (MDSCs)
module: IDO1, ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB,
CXCR4, and CD33; Neutrophil signature model: MPO, ELANE, PRTN3,
CTSG, FCGR3B, CXCR1, CXCR2, CD177, PI3, FFAR2, and PGLYRP1; M2
signature module: IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1,
LRP1, ARG1, PTGS1, MSR1, CD163, and CSF1R; Th2 signature module:
IL4, ILS, IL13, IL10, IL25, and GATA3; Protumor cytokines module:
IL10, TGFB1, TGFB2, TGFB3, IL22, and MIF; Complement inhibition
module: CFD, CFI, CD55, CD46, and CR1; Cancer associated
fibroblasts (CAFs) module: COL1A1, COL1A2, COL4A1, COL5A1, TGFB1,
TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248, COL6A1, COL6A2,
COL6A3, FBLN1, LUM, MFAP5, and PRELP; Angiogenesis module: VEGFA,
VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1,
ANGPT2, TEK, VWF, CDH5, NOS3, VCAM1, and MMRN1; Endothelium module:
VEGFA, NOS3, KDR, FLT1, VCAM1, VWF, CDH5, MMRN1, CLEC14A, MMRN2,
and ECSCR; Proliferation rate (or Tumor proliferation rate) module:
MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2,
BUB1, PLK1, CCNB1, MCM2, MCM6, CDK4, and CDK6; PI3K/AKT/mTOR
signaling module: PIK3CA, PIK3CB, PIK3CG, PIK3CD, AKT1, MTOR, PTEN,
PRKCA, AKT2, and AKT3; RAS/RAF/MEK signaling module: BRAF, FNTA,
FNTB, MAP2K1, MAP2K2, MKNK1, and MKNK2; Receptor tyrosine kinases
expression module: ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1,
FGFR1, FGFR2, FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, PDGFRB, and
ABL1; Growth Factors module: NGF, CSF3, CSF2, FGF7, IGF1, IGF2,
IL7, and FGF2; Tumor suppressors module: TP53, SIK1, PTEN, DCN,
MTAP, AIM2, RB1, and MITF; Metastasis signature module: ESRP1,
HOXA1, SMARCA4, TWIST1, NEDD9, PAPPA, and HPSE; and Antimetastatic
factors module: NCAM1, CDH1, KISS1, and BRMS1. In some embodiments,
the gene groups of the modules may further comprise at least two
genes (e.g., at least two genes, at least three genes, at least
four genes, at least five genes, at least six genes, at least seven
genes, at least eight genes, at least nine genes, at least ten
genes, or more than ten genes as shown in the following lists; in
some embodiments all of the listed genes are selected from each
group; and in some embodiments the numbers of genes in each
selected group are not the same): T cell traffic module: CXCL9,
CXCL10, CXCR3, CX3CL1, CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, and
CCL5; Antitumor cytokines module: HMGB1, TNF, IFNB1, IFNA2, CCL3,
TNFSF10, and FASLG; Treg traffic module: CCL17, CXCL12, CXCR4,
CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13, and CCL28; MDSC and TAM
traffic module: CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5,
CSF1, and CXCL8; Granulocyte traffic module: CXCL8, CXCL2, CXCL1,
CCL11, CCL24, KITLG, CCL5, CXCL5, CCR3, and CCL26; Eosinophil
signature model: PRG2, EPX, RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8,
and PRG3; Mast cell signature module: CMA1, TPSAB1, MS4A2, CPA3,
IL4, ILS, IL13, and SIGLEC8; Th17 signature module: IL17A, IL22,
IL26, IL17F, IL21, and RORC; Matrix formation (or Matrix) module:
FN1, CA9, MMP1, MMP3, MMP12, LGALS9, MMPI, MMP9, COL1A1, COL1A2,
COL4A1, and COL5A1; and Hypoxia factors module: LDHA, HIF1A, EPAS1,
CA9, SPP1, LOX, SLC2A1, and LAMP3. In certain embodiments, two or
more genes from each of the listed modules are included. Any of the
foregoing sets of modules may be used in a MF portrait for a
subject with a solid cancer (e.g., melanoma).
[0225] In some embodiments, the gene groups of the modules may
comprise at least two genes (e.g., at least two genes, at least
three genes, at least four genes, at least five genes, at least six
genes, at least seven genes, at least eight genes, at least nine
genes, at least ten genes, or more than ten genes as shown in the
following lists; in some embodiments all of the listed genes are
selected from each group; and in some embodiments the numbers of
genes in each selected group are not the same): Effector T cell
module: IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70, GNLY, FASLG,
TBX21, EOMES, CD8A, and CD8B; Natural killer cells (NK cells)
module: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY,
IFNG, KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, and KIR2DS5; T
cells module: EOMES, TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1,
TRBC2, LCK, UBASH3A, and TRAT1; Benign B cells module: CD19, MS4A1,
TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A,
CD79B, and BLK; Malignant B cell marker module: MME, CD70, CD20,
CD22, and PAX5; M1 signatures module: NOS2, IL12A, IL12B, IL23A,
TNF, IL1B, and SOCS3; Th1 signature module: IFNG, IL2, CD4OLG,
IL15, CD27, TBX21, LTA, and IL21; Checkpoint inhibition (or
checkpoint molecules) module: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2,
BTLA, and HAVCR2; Follicular dendritic cells module: CR1, FCGR2A,
FCGR2B, FCGR2C, CR2, FCER2, CXCL13, MADCAM1, ICAM1, VCAM1, BST1,
LTBR, and TNFRSF1A; Follicular B helper T cells module: CXCR5,
B3GAT1, ICOS, CD4OLG, CD84, IL21, BCL6, MAF, and SAP; Protumor
cytokines module: IL10, TGFB1, TGFB2, TGFB3, IL22, MIF, TNFSF13B,
IL6, and IL7; Regulatory T cells (Treg) module: TGFB1, TGFB2,
TGFB3, FOXP3, CTLA4, IL10, TNFRSF18, and TNFR2; Neutrophil
signature model: MPO, ELANE, PRTN3, and CTSG; M2 signature module:
IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1, LRP1, ARG1, PTGS1,
MSR1, CD163, and CSF1R; Th2 signature module: IL4, ILS, IL13, IL10,
IL25, and GATA3; Complement inhibition module: CFD, CFI, CD55,
CD46, CR1, and CD59; Fibroblastic reticular cells module: DES, VIM,
PDGFRA, PDPN, NT5E, THY1, ENG, ACTA2, LTBR, TNFRSF1A, VCAM1, ICAM1,
and BST1; Angiogenesis module: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8,
CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2, TEK, VWF, and CDH5;
Blood endothelium module: VEGFA, NOS3, KDR, FLT1, VCAM1, VWF, CDH5,
and MMRN1; Proliferation rate (or Tumor proliferation rate) module:
MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2,
BUB1, PLK1, CCNB1, MCM2, and MCM6; Oncogenes module: MDM2, MYC,
AKT1, BCL2, MME, and SYK; and Tumor suppressors module: TP53, MLL2,
CREBBP, EP300, ARID1A, HIST1H1, EBF1, IRF4, IKZF3, KLHL6, PRDM1,
CDKN2A, RB1, EPHA7, TNFAIP3, TNFRSF14, FAS, SHP1, and SOCS1. In
some embodiments, the gene groups of the modules may further
comprise at least two genes (e.g., at least two genes, at least
three genes, at least four genes, at least five genes, at least six
genes, at least seven genes, at least eight genes, at least nine
genes, at least ten genes, or more than ten genes as shown in the
following lists; in some embodiments all of the listed genes are
selected from each group; and in some embodiments the numbers of
genes in each selected group are not the same): Coactivation
molecules module: TNFRSF4 and CD28; B cell traffic module: CXCL13
and CXCR5; Antitumor cytokines module: HMGB1, TNF, IFNB1, IFNA2,
CCL3, TNFSF10, FASLG; Treg traffic module: CCL17, CCR4, CCL22, and
CXCL13; Eosinophil signature model: PRG2, EPX, RNASE2, RNASE3,
IL5RA, GATA1, SIGLEC8, and PRG3; Mast cell signature module: CMA1,
TPSAB1, MS4A2, CPA3, IL4, ILS, IL13, and SIGLEC8; Th17 signature
module: IL17A, IL22, IL26, IL17F, IL21, and RORC; Matrix formation
(or Matrix) module: MMP9, FN1, COL1A1, COL1A2, COL3A1, COL4A1, CA9,
VTN, LGALS7, TIMP1, and MMP2; Hypoxia factors module: LDHA, HIF1A,
EPAS1, CA9, SPP1, LOX, SLC2A1, and LAMP3; Coagulation module: HPSE,
SERPINE1, SERPINB2, F3, and ANXA2; and Lymphatic endothelium
module: CCL21 and CXCL12. In certain embodiments, two or more genes
from each of the listed modules are included. Any of the foregoing
sets of modules may be used in a MF portrait for a subject with a
follicular lymphoma.
[0226] In some embodiments, the plurality of gene groups (or
modules) associated with cancer malignancy is the tumor properties
group. In some embodiments, the plurality of gene groups associated
with cancer microenvironment are the tumor-promoting immune
microenvironment group, the anti-tumor immune microenvironment
group, the angiogenesis group, and the fibroblasts group.
[0227] In certain embodiments, the plurality of gene groups
associated with cancer malignancy comprises at least three genes
from the following group (e.g., at least three genes, at least four
genes, at least five genes, at least six genes, at least seven
genes, at least eight genes, at least nine genes, at least ten
genes, or more than ten genes are selected from each group; in some
embodiments all of the listed genes are selected from each group):
the tumor properties group: MKI67, ESCO2, CETN3, CDK2, CCND1,
CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2, BUB1, PLK1,
CCNB1, MCM2, MCM6, PIK3CA, PIK3CB, PIK3CG, PIK3CD, AKT1, MTOR,
PTEN, PRKCA, AKT2, AKT3, BRAF, FNTA, FNTB, MAP2K1, MAP2K2, MKNK1,
MKNK2, ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2,
FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, PDGFRB, NGF, CSF3, CSF2,
FGF7, IGF1, IGF2, IL7, FGF2, TP53, SIK1, PTEN, DCN, MTAP, AIM2,
RB1, ESRP1, CTSL, HOXA1, SMARCA4, SNAI2, TWIST1, NEDD9, PAPPA,
HPSE, KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1, MITF, APC,
ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2, CDH1, CDKN2A, CTCF, CTNNB1,
DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS, IDH1, KRAS, MAP3K1, MTOR,
NAV3, NCOR1, NF1, NOTCH1, NPM1, NRAS, PBRM1, PIK3CA, PIK3R1, PTEN,
RB1, RUNX1, SETD2, STAG2, TAF1, TP53, and VHL. In certain
embodiments, the plurality of gene groups associated with cancer
microenvironment includes at least three genes from each of the
following groups (e.g., at least three genes, at least four genes,
at least five genes, at least six genes, at least seven genes, at
least eight genes, at least nine genes, at least ten genes, or more
than ten genes are selected from each group; in some embodiments
all of the listed genes are selected from each group): the
anti-tumor immune microenvironment group: HLA-A, HLA-B, HLA-C, B2M,
TAP1, TAP2, HLA-DRA, HLA-DRB1, HLA-DOB, HLA-DPB2, HLA-DMA, HLA-DOA,
HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DRB5,
HLA-DQA2, HLA-DQB2, HLA-DRB6, CD80, CD86, CD40, CD83, TNFRSF4,
ICOSLG, CD28, IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70, GNLY,
FASLG, TBX21, EOMES, CD8A, CD8B, NKG7, CD160, CD244, NCR1, KLRC2,
KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3,
KIR2DS4, KIR2DS5, CXCL9, CXCL10, CXCR3, CX3CL1, CCR7, CXCL11,
CCL21, CCL2, CCL3, CCL4, CCL5, EOMES, TBX21, ITK, CD3D, CD3E, CD3G,
TRAC, TRBC1, TRBC2, LCK, UBASH3A, TRAT1, CD19, MS4A1, TNFRSF13C,
CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK,
NOS2, IL12A, IL12B, IL23A, TNF, IL1B, SOCS3, IFNG, IL2, CD4OLG,
IL15, CD27, TBX21, LTA, IL21, HMGB1, TNF, IFNB1, IFNA2, CCL3,
TNFSF10, and FASLG; the tumor-promoting immune microenvironment
group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, VSIR,
CXCL12, TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10, TNFRSF1B, CCL17,
CXCR4, CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13, CCL28, IDOL ARG1,
IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB, CXCR4, CD33, CXCL1,
CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5, CSF1, CXCL8, CXCL8,
CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5, CXCL5, CCR3, CCL26, PRG2,
EPX, RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8, PRG3, CMA1, TPSAB1,
MS4A2, CPA3, IL4, IL5, IL13, SIGLEC8, MPO, ELANE, PRTN3, CTSG,
IL10, VEGFA, TGFB1, IDOL PTGES, MRC1, CSF1, LRP1, ARG1, PTGS1,
MSR1, CD163, CSF1R, IL4, IL5, IL13, IL10, IL25, GATA3, IL10, TGFB1,
TGFB2, TGFB3, IL22, MIF, CFD, CFI, CD55, CD46, and CR1; the
fibroblasts group: LGALS1, COL1A1, COL1A2, COL4A1, COL5A1, TGFB1,
TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248, COL6A1, COL6A2, and
COL6A3; and the angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC,
CXCL8, CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2, TEK, VWF,
CDH5, NOS3, KDR, VCAM1, MMRN1, LDHA, HIF1A, EPAS1, CA9, SPP1, LOX,
SLC2A1, and LAMPS. In some embodiments, an unequal number of genes
may be selected from each of the listed groups for use. In specific
embodiments, all or almost all of the listed genes are used.
[0228] In some embodiments, the plurality of gene groups associated
with cancer malignancy are: the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the tumor suppressors
group, the metastasis signature group, the anti-metastatic factors
group, and the mutation status group. In some embodiments, the
plurality of gene groups associated with cancer microenvironment
are: the cancer associated fibroblasts group, the angiogenesis
group, the antigen presentation group, the cytotoxic T and NK cells
group, the B cells group, the anti-tumor microenvironment group,
the checkpoint inhibition group, the Treg group, the MDSC group,
the granulocytes group, and the tumor-promotive immune group.
[0229] In some embodiments, the plurality of gene groups associated
with cancer malignancy comprises at least three genes from each of
the following groups (e.g., at least three genes, at least four
genes, at least five genes, at least six genes, at least seven
genes, at least eight genes, at least nine genes, at least ten
genes, or more than ten genes are selected from each group): the
proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1,
AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2, BUB1, PLK1, CCNB1,
MCM2, and MCM6; the PI3K/AKT/mTOR signaling group: PIK3CA, PIK3CB,
PIK3CG, PIK3CD, AKT1, MTOR, PTEN, PRKCA, AKT2, and AKT3; the
RAS/RAF/MEK signaling group: BRAF, FNTA, FNTB, MAP2K1, MAP2K2,
MKNK1, and MKNK2; the receptor tyrosine kinases expression group:
ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2, FGFR3,
ERBB4, ERBB3, BCR-ABL, PDGFRA, and PDGFRB; the tumor suppressors
group: TP53, SIK1, PTEN, DCN, MTAP, AIM2, and RB1; the metastasis
signature group: ESRP1, CTSL, HOXA1, SMARCA4, SNAI2, TWIST1, NEDD9,
PAPPA, and HPSE; the anti-metastatic factors group: KISS1, ADGRG1,
BRMS1, TCF21, CDH1, PCDH10, NCAM1, and MITF; and the mutation
status group: APC, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2, CDH1,
CDKN2A, CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS, IDH1,
KRAS, MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1, NPM1, NRAS, PBRM1,
PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2, TAF1, TP53, and
VHL.
[0230] In some embodiments, the plurality of gene groups associated
with cancer microenvironment comprises at least three genes from
each of the following groups (e.g., at least three genes, at least
four genes, at least five genes, at least six genes, at least seven
genes, at least eight genes, at least nine genes, at least ten
genes, or more than ten genes are selected from each group): the
cancer associated fibroblasts group: LGALS1, COL1A1, COL1A2,
COL4A1, COL5A1, TGFB1, TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248,
COL6A1, COL6A2, and COL6A3; the angiogenesis group: VEGFA, VEGFB,
VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2,
TEK, VWF, CDH5, NOS3, KDR, VCAM1, MMRN1, LDHA, HIF1A, EPAS1, CA9,
SPP1, LOX, SLC2A1, and LAMP3; the antigen presentation group:
HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, HLA-DRA, HLA-DRB1, HLA-DOB,
HLA-DPB2, HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1,
HLA-DQA1, HLA-DRB5, HLA-DQA2, HLA-DQB2, HLA-DRB6, CD80, CD86, CD40,
CD83, TNFRSF4, ICOSLG, and CD28; the cytotoxic T and NK cells
group: IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70, GNLY, FASLG,
TBX21, EOMES, CD8A, CD8B, NKG7, CD160, CD244, NCR1, KLRC2, KLRK1,
CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3,
KIR2DS4, KIR2DS5, CXCL9, CXCL10, CXCR3, CX3CL1, CCR7, CXCL11,
CCL21, CCL2, CCL3, CCL4, CCL5, EOMES, TBX21, ITK, CD3D, CD3E, CD3G,
TRAC, TRBC1, TRBC2, LCK, UBASH3A, and TRAT1; the B cells group:
CD19, MS4A1, TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22,
CD79A, CD79B, and BLK; the anti-tumor microenvironment group: NOS2,
IL12A, IL12B, IL23A, TNF, IL1B, SOCS3, IFNG, IL2, CD4OLG, IL15,
CD27, TBX21, LTA, IL21, HMGB1, TNF, IFNB1, IFNA2, CCL3, TNFSF10,
and FASLG; the checkpoint inhibition group: PDCD1, CD274, CTLA4,
LAGS, PDCD1LG2, BTLA, HAVCR2, and VSIR; the Treg group: CXCL12,
TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10, TNFRSF1B, CCL17, CXCR4,
CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13, and CCL28; the MDSC group:
IDOL ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB, CXCR4,
CD33, CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5, CSF1, and
CXCL8; the granulocytes group: CXCL8, CXCL2, CXCL1, CCL11, CCL24,
KITLG, CCL5, CXCL5, CCR3, CCL26, PRG2, EPX, RNASE2, RNASE3, IL5RA,
GATA1, SIGLEC8, PRG3, CMA1, TPSAB1, MS4A2, CPA3, IL4, ILS, IL13,
SIGLEC8, MPO, ELANE, PRTN3, and CTSG; the tumor-promotive immune
group: IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1, LRP1, ARG1,
PTGS1, MSR1, CD163, CSF1R, IL4, ILS, IL13, IL10, IL25, GATA3, IL10,
TGFB1, TGFB2, TGFB3, IL22, MIF, CFD, CFI, CD55, CD46, and CR1. In
some embodiments, an unequal number of genes may be selected from
each of the listed groups for use. In specific embodiments, all or
almost all of the listed genes are used.
[0231] In some embodiments, the plurality of gene groups associated
with cancer malignancy are: the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the growth factors
group, the tumor suppressors group, the metastasis signature group,
the anti-metastatic factors group, and the mutation status group.
In some embodiments, the plurality of gene groups associated with
cancer microenvironment are: the cancer associated fibroblasts
group, the angiogenesis group, the MHCI group, the MHCII group, the
coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, and the complement inhibition group.
[0232] In some embodiments, the plurality of gene groups associated
with cancer malignancy comprises at least three genes from each of
the following groups (e.g., at least three genes, at least four
genes, at least five genes, at least six genes, at least seven
genes, at least eight genes, at least nine genes, at least ten
genes, or more than ten genes are selected from each group): the
proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1,
AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2, BUB1, PLK1, CCNB1,
MCM2, and MCM6; the PI3K/AKT/mTOR signaling group: PIK3CA, PIK3CB,
PIK3CG, PIK3CD, AKT1, MTOR, PTEN, PRKCA, AKT2, and AKT3; the
RAS/RAF/MEK signaling group: BRAF, FNTA, FNTB, MAP2K1, MAP2K2,
MKNK1, and MKNK2; the receptor tyrosine kinases expression group:
ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2, FGFR3,
ERBB4, ERBB3, BCR-ABL, PDGFRA, and PDGFRB; the growth factors
group: NGF, CSF3, CSF2, FGF7, IGF1, IGF2, IL7, and FGF2; the tumor
suppressors group: TP53, SIK1, PTEN, DCN, MTAP, AIM2, and RB1; the
metastasis signature group: ESRP1, CTSL, HOXA1, SMARCA4, SNAI2,
TWIST1, NEDD9, PAPPA, and HPSE; the anti-metastatic factors group:
KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1, and MITF; and the
mutation status group: APC, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2,
CDH1, CDKN2A, CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS,
IDH1, KRAS, MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1, NPM1, NRAS,
PBRM1, PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2, TAF1, TP53,
and VHL. In some embodiments, the plurality of gene groups
associated with cancer microenvironment comprises at least three
genes from each of the following groups: the cancer associated
fibroblasts group: LGALS1, COL1A1, COL1A2, COL4A1, COL5A1, TGFB1,
TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248, COL6A1, COL6A2, and
COL6A3; the angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8,
CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5,
NOS3, KDR, VCAM1, MMRN1, LDHA, HIF1A, EPAS1, CA9, SPP1, LOX,
SLC2A1, and LAMP3; the MHCI group: HLA-A, HLA-B, HLA-C, B2M, TAP1,
and TAP2; the MHCII group: HLA-DRA, HLA-DRB1, HLA-DOB, HLA-DPB2,
HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1, HLA-DQA1,
HLA-DRB5, HLA-DQA2, HLA-DQB2, and HLA-DRB6; the coactivation
molecules group: CD80, CD86, CD40, CD83, TNFRSF4, ICOSLG, and CD28;
the effector cells group: IFNG, GZMA, GZMB, PRF1, LCK, GZMK, ZAP70,
GNLY, FASLG, TBX21, EOMES, CD8A, and CD8B; the NK cells group:
NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG,
KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, and KIR2DS5; the T
cell traffic group: CXCL9, CXCL10, CXCR3, CX3CL1, CCR7, CXCL11,
CCL21, CCL2, CCL3, CCL4, and CCL5; the T cells group: EOMES, TBX21,
ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, LCK, UBASH3A, and TRAT1;
the B cells group: CD19, MS4A1, TNFRSF13C, CD27, CD24, CR2,
TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, and BLK; the M1 signatures
group: NOS2, IL12A, IL12B, IL23A, TNF, IL1B, and SOCS3; the Th1
signature group: IFNG, IL2, CD4OLG, IL15, CD27, TBX21, LTA, and
IL21; the antitumor cytokines group: HMGB1, TNF, IFNB1, IFNA2,
CCL3, TNFSF10, and FASLG; the checkpoint inhibition group: PDCD1,
CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, and VSIR; the Treg
group: CXCL12, TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10, TNFRSF1B,
CCL17, CXCR4, CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13, and CCL28; the
MDSC group: IDOL ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB,
CXCR4, CD33, CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5,
CSF1, and CXCL8; the granulocytes group: CXCL8, CXCL2, CXCL1,
CCL11, CCL24, KITLG, CCL5, CXCL5, CCR3, CCL26, PRG2, EPX, RNASE2,
RNASE3, IL5RA, GATA1, SIGLEC8, PRG3, CMA1, TPSAB1, MS4A2, CPA3,
IL4, IL5, IL13, SIGLEC8, MPO, ELANE, PRTN3, and CTSG; the M2
signature group: IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1, LRP1,
ARG1, PTGS1, MSR1, CD163, and CSF1R; the Th2 signature group: IL4,
IL5, IL13, IL10, IL25, and GATA3; the protumor cytokines group:
IL10, TGFB1, TGFB2, TGFB3, IL22, and MIF; and the complement
inhibition group: CFD, CFI, CD55, CD46, and CR1. In some
embodiments, an unequal number of genes may be selected from each
of the listed groups for use. In specific embodiments, all or
almost all of the listed genes are used.
[0233] MF profiles may depict the intensity (e.g., amount) of a
module or gene group using a distinguishing feature (e.g., color,
shading or pattern, size, and/or shape). As used herein,
"intensity" refers to an amount of a gene group expression level
within a MF profile. For example, 2.sup.nd MF profile type cancers
have an intense proliferation rate module indicative of a high
proliferation rate of such cancers. Accordingly, in 2.sup.nd MF
profile type cancers, the proliferation rate module is depicted in
a larger size as an indication that this module is more abundant in
the tumor than other modules. In some embodiments, the MF profile
comprises modules of various sizes in which module size is
indicative of module intensity. In some embodiments, the MF profile
comprises modules of increasing sizes in which increasing module
size is indicative of increasing module intensity.
[0234] MF profiles may depict a module as a pro-tumor module or
anti-tumor module using a distinguishing feature (e.g., color,
shading or pattern, size, and/or shape). In some embodiments, the
MF profile comprises a pro-tumor module as one color or pattern and
an anti-tumor module as another color or pattern. In some
embodiments, the MF profile comprises a pro-tumor module as
burgundy or a shade thereof and an anti-tumor module as blue or a
shade thereof. In some embodiments, the MF profile comprises a
pro-tumor module as solid shades without cross-marking and an
anti-tumor module as shades with cross-marking.
[0235] MF profiles may comprise any number of functional modules.
In some embodiments, the MF profile comprises at least 2, at least
3, at least 4, at least 5, at least 6, at least 7, at least 8, at
least 9, at least 10, at least 11, at least 12, at least 13, at
least 14, at least 15, at least 16, at least 17, at least 18, at
least 19, at least 20, at least 21, at least 22, at least 23, at
least 24, at least 25, at least 26, at least 27, or at least 28
modules. In some embodiments, the MF profile comprises up to 2, up
to 3, up to 4, up to 5, up to 6, up to 7, up to 8, up to 9, up to
10, up to 11, up to 12, up to 13, up to 14, up to 15, up to 16, up
to 17, up to 18, up to 19, up to 20, up to 21, up to 22, up to 23,
up to 24, up to 25, up to 26, up to 27, or up to 28 modules.
MF Profile Types
[0236] The present disclosure is based, in part, on the finding
that various cancers (e.g., tumors) can be categorized into four
types (i.e., first MF profile type or "1.sup.st MF profile," second
MF profile type or "2.sup.nd MF profile," third MF profile type or
MF profile," and fourth MF profile type or "4.sup.th MF profile"
cancers) based on certain properties of the cancer or tumor (e.g.,
expression data).
[0237] As used herein, the term "cancer type," "tumor type," or "MF
profile type" refers to a cancer (e.g., a tumor) having certain
features including certain molecular and cellular compositions, and
biological processes.
[0238] MF profile type, in some embodiments, may provide
information relating to a level of immune cells within and/or
surrounding a tumor. For example, an "inflamed" or "hot" MF profile
type includes a cancer (e.g., a tumor) that is highly infiltrated
by immune cells, a "non-inflamed" or "cold" MF profile type
describes a cancer (e.g., a tumor) that is poorly infiltrated by
immune cells. In some embodiments, describing a cancer as a
1.sup.st MF profile type cancer indicates that the cancer (e.g., a
tumor) is inflamed. In some embodiments, describing a cancer as a
2.sup.nd MF profile type cancer indicates that the cancer (e.g., a
tumor) is inflamed. In some embodiments, describing a cancer as a
3.sup.rd MF profile type cancer indicates that the cancer (e.g., a
tumor) is non-inflamed. In some embodiments, describing a cancer as
a 4.sup.th MF profile type cancer indicates that the cancer (e.g.,
a tumor) is non-inflamed.
[0239] MF profile type, in some embodiments, provides information
relating to an average ratio of malignant to nonmalignant cells of
a tumor (e.g., tumor purity). In some embodiments, the average
ratio of malignant to nonmalignant cells increases with MF profile
type. For example, 4.sup.th MF profile>3.sup.rd MF
profile>2.sup.nd MF profile>1.sup.st MF profile with respect
to an average ratio of malignant to nonmalignant cells.
[0240] In some embodiments, describing a cancer as a 1.sup.st MF
profile type cancer indicates that the tumor has about 2 times
(twice) as many nonmalignant cells as malignant cells. In some
embodiments, describing a cancer as a 1.sup.st MF profile type
cancer indicates that the tumor has an average ratio of malignant
to nonmalignant cells of between 0.4 to 0.6. In some embodiments,
describing a cancer as a 1.sup.st MF profile type cancer indicates
that the cancer has an average ratio of malignant to nonmalignant
cells of about 0.5.
[0241] In some embodiments, describing a cancer as a 2.sup.nd MF
profile type cancer indicates that the cancer has about 1.5 times
as many nonmalignant cells as malignant cells. In some embodiments,
describing a cancer as a 2.sup.nd MF profile type cancer indicates
that the cancer has an average ratio of malignant to nonmalignant
cells between 0.6 to 0.7. In some embodiments, describing a cancer
as a 2.sup.nd MF profile type cancer indicates that the cancer has
an average ratio of malignant to nonmalignant cells of about
0.65.
[0242] In some embodiments, describing a cancer as a 3.sup.rd MF
profile type cancer indicates that the cancer has about 1.3 times
as many nonmalignant cells as malignant cells. In some embodiments,
describing a cancer as a 3.sup.rd MF profile type cancer indicates
that the cancer has an average ratio of malignant to nonmalignant
cells between 0.7 to 0.8. In some embodiments, describing a cancer
as a 3.sup.rd MF profile type cancer indicates that a tumor has an
average ratio of malignant to nonmalignant cells of about 0.8.
[0243] In some embodiments, describing a cancer as a 4.sup.th MF
profile type cancer indicates that the cancer has about 1.1 times
as many nonmalignant cells s malignant cells. In some embodiments,
describing a cancer as a 4.sup.th MF profile type cancer indicates
that the cancer has an average ratio of malignant to nonmalignant
cells between 0.8 to 0.9. In some embodiments, describing a cancer
as a 4.sup.th MF profile type cancer indicates that the cancer has
an average ratio of malignant to nonmalignant cells of about
0.85.
[0244] MF profile type, in some embodiments, provides information
relating to tumor vascularization. In some embodiments, describing
a cancer as a 1.sup.st MF profile type cancer indicates that the
cancer (e.g., the tumor) is vascularized. In some embodiments,
describing a cancer as a 2.sup.nd MF profile type cancer indicates
that the cancer (e.g., the tumor) is non-vascularized. In some
embodiments, describing a cancer as a 3.sup.rd MF profile type
cancer indicates that the cancer (e.g., the tumor) is vascularized.
In some embodiments, describing a cancer as a 4.sup.th MF profile
type cancer indicates that the cancer (e.g., the tumor) is
non-vascularized.
[0245] MF profile type, in some embodiments, provides information
relating to levels of cancer associated fibroblasts (CAFs) within
and/or surrounding a tumor. In some embodiments, describing a
cancer as a 1.sup.st MF profile type cancer indicates that the
cancer (e.g., the tumor) comprises CAFs. In some embodiments,
describing a cancer as a 2.sup.nd MF profile type cancer indicates
that the cancer (e.g., the tumor) is devoid of CAFs. In some
embodiments, describing a cancer as a 3.sup.rd MF profile type
cancer indicates that the cancer (e.g., the tumor) comprises CAFs.
In some embodiments, describing a cancer as a 4.sup.th MF profile
type cancer indicates that the cancer (e.g., the tumor) is devoid
of CAFs.
[0246] MF profile type, in some embodiments, provides information
relating to tumor proliferation rates. In some embodiments,
describing a cancer as a 1.sup.st MF profile type cancer indicates
that the cancer (e.g., the tumor) has an average proliferation
rate. In some embodiments, describing a cancer as a 2.sup.nd MF
profile type cancer indicates that the cancer (e.g., the tumor) has
a high proliferation rate. In some embodiments, describing a cancer
as a 3.sup.rd MF profile type cancer indicates that the cancer
(e.g., the tumor) has an average proliferation rate. In some
embodiments, describing a cancer as a 4.sup.th MF profile type
cancer indicates that the cancer (e.g., the tumor) has a high
proliferation rate.
[0247] MF profile type, in some embodiments, provides information
relating to patient survival rate. In some embodiments, the patient
survival rate increases with MF profile type. For example, 1.sup.st
MF profile>2.sup.nd MF profile>3.sup.rd MF
profile>4.sup.th MF profile with respect to patient survival
rate.
[0248] In some embodiments, describing a cancer as a 1.sup.st MF
profile type cancer indicates a good patient survival rate. In some
embodiments, describing a cancer as a 2.sup.nd MF profile type
cancer indicates an optimal patient survival rate. In some
embodiments, describing a cancer as a 3.sup.rd MF profile type
cancer indicates that a poor patient survival rate. In some
embodiments, describing a cancer as a 4.sup.th MF profile type
cancer indicates that a poor patient survival rate.
[0249] MF profile type, in some embodiments, provides information
relating to patient treatment. In some embodiments, the MF profile
type provides information relating to an expected treatment outcome
of a therapy. In some embodiments, the MF profile indicates that a
specific treatment option is recommended. In some embodiments, the
MF profile indicates that a specific treatment option is
non-curative. In some embodiments, the MF profile indicates that a
specific treatment option is dependent on a certain feature of a
tumor, for example, mutational status of the tumor.
[0250] In some embodiments, identifying a cancer as a 1.sup.st MF
profile type cancer indicates that a treatment selected from the
group consisting of an angiogenesis inhibitor, a CAFs inhibitor, an
immunosuppressive factor inhibitor, a MDSC inhibitor, a Treg
inhibitor, a metastatic activity inhibitor, and an immunotherapy
should be recommended or used. In some embodiments, identifying a
cancer as a 1.sup.st MF profile type cancer indicates that
treatment using a growth factor inhibitor dependent on a certain
feature of a tumor (e.g., mutational status) should be recommended
or used.
[0251] In some embodiments, identifying a cancer as a 2.sup.nd MF
profile type cancer indicates that a treatment selected from the
group consisting of an immunosuppressive factor inhibitor, a MDSC
inhibitor, a Treg inhibitor, a metastatic activity inhibitor, a
checkpoint inhibitor, and an immunotherapy should be recommended or
used. In some embodiments, identifying a cancer as a 2.sup.nd MF
profile type cancer indicates that treatment using a growth factor
inhibitor dependent on a certain feature of a tumor (e.g.,
mutational status) should be recommended or used.
[0252] In some embodiments, identifying a cancer as a 3.sup.rd MF
profile type indicates that a treatment selected from the group
consisting of an angiogenesis inhibitor, a CAFs inhibitor, an
immunosuppressive factor inhibitor, a M2 macrophage inhibitor, a
MDSC inhibitor, and a Treg inhibitor should be recommended or used.
In some embodiments, identifying a cancer as a 3.sup.rd MF profile
type indicates that a checkpoint inhibitor should be recommended or
used.
[0253] In some embodiments, identifying a cancer as a 4.sup.th MF
profile type cancer indicates that a treatment such as an
angiogenesis inhibitor and/or an immunotherapy should be
recommended or used. In some embodiments, identifying a cancer as a
4.sup.th MF profile type indicates that a non-curative treatment
option may be selected from the group consisting of a kinase
inhibitor, a radiotherapy, and a chemotherapy.
Visualization of MF Profiles
[0254] In some embodiments, a software program may provide a user
with a visual representation of a patient's MF profile and/or other
information related to a patient's cancer using an interactive
graphical user interface (GUI).
[0255] In response to being launched, the interactive GUI may
provide the user of the software program with initial information
related to a patient's cancer. Subsequently, the user may interact
with the GUI to obtain additional and/or alternative information
related to a patient's cancer. FIGS. 3-37 show illustrative
screenshots of the interactive graphical user interface and are
described below.
[0256] FIG. 3 is a graphic illustrating different types of screens
that may be shown to a user of the software program. Each of the
different screens illustrated in FIG. 3 may be used to present
different types of information to the user. A screenshot of a
control screen of the software program is shown in the middle of
FIG. 3. The control screen includes portions for presenting
information relating to treatment selection, tumor properties, and
clinical evidence of treatment efficacy and is described further
with respect to FIGS. 7-37.
[0257] A user may interact with the control screen to obtain
additional information about, for example, immunotherapy selection,
targeted therapy selection, combination therapy design, tumor
properties and tumor microenvironment, clinical evidence of
targeted therapy efficacy, and clinical evidence of immunotherapy
efficacy. The user may select a portion of the control screen
(e.g., the immunotherapy portion) to view one or more additional
screens presenting information relating to the selected portion. As
shown in FIG. 3, arrows point from a portion of the control screen
that may be selected toward the screens presenting additional
information related to the selected portion.
[0258] For example, the user may select the immunotherapy selection
portion of the control screen to view one or more screens
presenting information relating to various immunotherapies,
biomarkers associated with an immunotherapy (e.g., genetic
biomarkers, cellular biomarkers, and expression biomarkers), immune
cell properties of the patient's tumor, and clinical trials (e.g.,
information from and/or regarding published clinical trials and
ongoing clinical trials).
[0259] In another example, the user may select the targeted therapy
selection portion of the control screen to view one or more screens
presenting information relating to various targeted therapies,
biomarkers associated with targeted therapies (e.g., genetic
biomarkers, cellular biomarkers, and/or expression biomarkers),
properties of the patient's tumor associated with the targeted
therapy, and clinical trials (e.g., published clinical trials and
ongoing clinical trials).
[0260] In another example, the user may select the
molecular-functional portrait (MF profile) portion of the control
screen to view one or more screens presenting information relating
to the patient's tumor microenvironment. Such information may
include information about tumor properties (e.g., proliferation
rate), angiogenesis, metastasis, cellular composition, cancer
associated fibroblasts, pro-tumor immune environment, and
anti-tumor immune environment.
[0261] In yet another example, the user may select the clinical
evidence of treatment efficacy portion of the control screen to
view one or more screens presenting information relating to a
therapy (e.g., an immunotherapy or targeted therapy). Such
information may include description of the therapy, therapy
efficacy, potential adverse effects, related publications,
treatment regimen, and patient survival data.
[0262] A user of the software program may interact with the GUI to
log into the software program. FIG. 4 is a screenshot of the user's
account profile screen presented to the user in response to the
user logging into the software program. The user's account profile
screen may provide information for one or more patients, such as
patient identification and diagnosis (e.g., Hugo27, Melanoma,
Stage: IV) in a patient selection portion (as shown in the upper
left panel). The user's account profile screen may also provide
reports generated from the patient's information by the software
program in a report layout portion (as shown in the right panel).
The report layout portion may provide the user with portions for
viewing stored reports that were previously generated by the
software program or for creating a new report.
[0263] In response to selection by a user, a selected portion of
the GUI may be visually highlighted. As a set of non-limiting
examples, a "visually highlighted" element may be highlighted
through a difference in font (e.g., by italicizing, bolding, and/or
underlining), by surrounding the section with a visual object
(e.g., a box), by "popping" the element out (e.g., by increasing
the zoom for that element), by changing the color of an element, by
shading the element, by incorporation of movement into the element
(e.g., by causing the element to move), any combination of the
foregoing in a portion or the whole of the element, or in any other
suitable way.
[0264] If a user's account profile screen provides information
about one patient, the patient may be selected by the user to view
a screen presenting the patient's information. If a user's account
profile screen provides information about more than one patient,
any one of the patients may be selected by the user to view a
screen presenting the selected patient's information. The user may
select a stored report to view a screen presenting information
relating to the selected report. The user may select the create new
report portion to view a screen for creating a new report. For
example, the user may select the patient Hugo27, as shown in the
upper left panel.
[0265] FIG. 5 is a screenshot presenting the selected patient's
information provided to the user in response to the user selecting
the patient. An overview of the patient's information is presented
in the patient overview portion (as shown in the left panel)
including clinical characteristics of the patient's disease (e.g.,
histology report). Additional information about the patient or the
patient's cancer including overall status, disease characteristics
and general recommendations (as shown in the upper middle panel) is
provided. Information relating to the selected patient's sequencing
data is presented in the Data Files portion (as shown in the right
panel) including whole exome sequencing data (WES). The user may
use the Upload Data File portion of the screen to upload the
patient's tumor biopsy sequencing data.
[0266] FIG. 6 is a screenshot presenting that the patient's tumor
biopsy sequencing data was downloaded (as shown in the lower right
panel). The user may select start in the launch analysis portion of
the screen (as shown in the lower middle panel) to view a report
created from the patient's sequencing data and other information
relating to the patient or the patient's cancer.
[0267] FIG. 7 is a screenshot presenting the selected patient's
report including information related to the patient's sequencing
data, the patient, and the patient's cancer. The therapy biomarkers
portion (as shown in the left panel) presents information related
to available therapies (e.g., immunotherapies and targeted
therapies) and their predicted efficacy in the selected patient.
Additional predictions of the efficacy of a therapy in the patient
are provided in the machine predictor portion and additional
portion (as shown in the left panel). The MF profile portion
presents information relating to the molecular characteristics of a
tumor including tumor genetics, pro-tumor microenvironment factors,
and anti-tumor immune response factors (as shown in the middle
panel). The clinical trials portion provides information relating
to clinical trials (as shown in the right panel). The monotherapy
or combinational therapy portion (as shown in the middle panel) may
be selected by the user to interactively design a personalized
treatment for a patient.
[0268] A user may select various portions of the screen to view
additional information. For example, a user may select anti-PD1 in
the immunotherapy biomarkers portion of the screen (as shown in the
left panel) to view information relating to anti-PD1 treatment
including biomarkers associated with anti-PD1 and tumor cell
processes associated with anti-PD1 treatment.
[0269] FIG. 8 is a screenshot presenting information related to
anti-PD1 immunotherapy provided in response to selecting anti-PD1
immunotherapy (as shown by highlighting) in the immunotherapy
biomarkers portion of the screen (as shown in the left panel).
Information relating to biomarkers associated with anti-PD1
immunotherapy is provided in the biomarkers portion (as shown in
the right panel). The biomarkers portion presents genetic
biomarkers, cellular biomarkers, and expression biomarkers, as well
as patient specific information related to those biomarkers.
[0270] The user may select any one of the biomarkers presented in
the biomarkers markers portion to view additional information
relating to that biomarker including general information about the
selected biomarker, patient specific information relating to the
selected biomarker, information relating to tumor molecular
processes associated with the selected biomarker, and treatment
related information associated with the selected biomarker.
[0271] In response to selection by a user, the selected biomarker
may be highlighted. FIG. 9 is a screenshot presenting the
mutational burden biomarker (as shown by highlighting) was selected
by the user. The user may select another portion of the mutational
burden biomarker to view a screen presenting information relating
to the mutational burden biomarker such as relevant
publications.
[0272] FIG. 10 is a screenshot presenting information relating to
the mutational burden biomarker (as shown in the middle panel)
provided in response to the user selecting the mutational burden
biomarker. The information may include a description of the
biomarker, how the biomarker was calculated, the patient's
particular biomarker value compared to other patients (as shown in
a histogram), and information from publications relating to the
selected biomarker.
[0273] Biomarkers are indicative of the molecular processes that
take place in the tumor microenvironment. Accordingly, a patient's
biomarkers provide information specific to the patient's tumor
microenvironment. The system allows a user to interactively view
biomarker information as it relates to a molecular process in the
tumor. Gene groups relating to tumor molecular processes associated
with a particular biomarker are highlighted in response to
selecting that biomarker.
[0274] FIGS. 11-13 are screenshots demonstrating that tumor
molecular processes gene groups presented in the MF profile that
are associated with the selected biomarker are highlighted in
response to the user selecting that biomarker.
[0275] For example, the user may select the mutational burden
biomarker which is associated with the mutational status gene group
and the neo-antigens load gene group in the tumor microenvironment.
FIG. 11 is a screenshot presenting that the mutational status gene
group and neo-antigens load gene group in the MF profile are
highlighted in response to the user selecting the mutational burden
biomarker (as shown in highlighting).
[0276] In another example, the user may select the CD8 T cells
biomarker which is associated with the T cells gene group in the
tumor microenvironment. FIG. 12 is a screenshot presenting that the
T cells gene group in the MF profile is highlighted in response to
the user selecting the CD8 T cell biomarker (as shown in
highlighting).
[0277] In yet another example, the user may select the PDL1
expression biomarker which is associated with the checkpoint
inhibition gene group in the tumor microenvironment. FIG. 13 is a
screenshot presenting that the checkpoint inhibition gene group in
the MF profile is highlighted in response to the user selecting the
PDL1 expression biomarker.
[0278] The user may select a targeted therapy to view information
relating to treatment with the selected targeted therapy including
biomarkers associated with the selected therapy and tumor cell
processes associated with the selected therapy. For example, the
user may select the targeted therapy sunitinib.
[0279] FIG. 14 is a screenshot presenting information related to
sunitinib therapy provided in response to selecting sunitinib (as
shown by highlighting) in the targeted therapy biomarkers portion
of the screen (as shown in the left panel). Information relating to
biomarkers associated with sunitinib therapy is provided in the
biomarkers portion (as shown in the right panel). The biomarkers
portion presents genetic biomarkers, cellular biomarkers, and
expression biomarkers, as well as patient specific information
related to those biomarkers.
[0280] Biomarkers are predictive of the efficacy of a therapy.
Accordingly, a patient's biomarkers are predictive of the patient's
response to a therapy. The system allows a user to interactively
view biomarker information as it relates to a predicted response to
a therapy. Clinical evidence of treatment efficacy for a therapy
(e.g., an immunotherapy or a targeted therapy) may be interactively
viewed by the user. FIGS. 15-18 are screenshots demonstrating that
a user may select a therapy to view a screen presenting clinical
trial data relating to the selected therapy.
[0281] For example, the user may select treatment with anti-PD1
immunotherapy. FIG. 15 is a screenshot presenting clinical trial
data relating to anti-PD1 therapy effectivity in patients having
stage IV metastatic melanoma (as shown in the right panel) provided
in response to the user selecting anti-PD1 immunotherapy (as shown
in the left panel). In another example, the user may select
treatment with anti-CTLA4 immunotherapy.
[0282] FIG. 16 is a screenshot presenting clinical trial data
relating to anti-CTLA4 therapy effectivity in patients having stage
IV metastatic melanoma (as shown in the right panel) provided in
response to the user selecting anti-CTLA4 immunotherapy (as shown
in the left panel).
[0283] A particular clinical trial can be selected to view further
information relating to the clinical trial such as therapy
efficacy, adverse effects of the therapy, treatment regimen, and
published results. FIG. 17 is a screenshot presenting clinical
trial data relating to the NCT01295827 clinical trial of anti-PD1
treatment (as shown in the middle panel) provided in response to
the user selecting the NCT01295827 clinical trial (as shown in the
right panel).
[0284] A user can interactively view information relating to the
clinical trial. For example, the user can minimize various portions
of information to view information in other portions. FIG. 18 is a
screenshot presenting the treatment regimen of the selected
clinical data provided in response to the user minimizing the
therapy class description and drug description portions. The screen
may also present information relating to ongoing clinical trials
(marked by the letter A).
[0285] Information relating to a patient's tumor microenvironment
is based on expression of genes within the tumor microenvironment.
The MF profile is a visual representation of gene groups within the
tumor microenvironment that provide information about tumor
properties, tumor processes (e.g., angiogenesis), tumor immune
environment, and cellular composition (e.g., cancer associated
fibroblasts). FIGS. 19-37 are screenshots demonstrating that a user
may select portions of the MF profile to view screens presenting
information related to the tumor microenvironment.
[0286] FIG. 19 is a screenshot presenting a patient's MF profile
(as shown in the middle panel). The MF profile may present any
number of gene groups. As a non-limiting example, FIG. 19 presents
five gene groups including the tumor properties gene group,
angiogenesis gene group, cancer associated fibroblasts gene group
(the fibroblasts group), pro-tumor immune environment gene group
(tumor-promoting immune microenvironment group), and anti-tumor
immune environment gene group (anti-tumor immune microenvironment
group). Any one of these gene groups may be selected to view a
screen presenting additional gene groups associated with the
selected gene group and information relating to the selected gene
group. For example, a user may select the tumor properties gene
group of the MF profile to view additional gene groups associated
with the tumor properties gene group and information related to
particular tumor properties (e.g., tumor genetics and tumor cell
properties).
[0287] FIG. 20 is a screenshot presenting additional gene groups
associated with the tumor properties gene group provided to the
user in response to selecting the tumor properties gene group.
These gene groups include mutational status (mutation status) gene
group, anti-metastatic (antimetastatic) factors gene group,
metastatic factors (metastasis signature) gene group, tumor growth
factors (growth factors) gene group, tumor suppressors gene group,
oncogenes gene group (activated signaling pathways; including
PI3K/AKT/mTOR signaling, RAS/RAF/MEK signaling, and Receptor
tyrosine kinases expression), and proliferation rate gene group.
Information relating to tumor genetics (as shown in the left panel)
and tumor cell properties (as shown in the right panel) are
provided in response to the user selecting the tumor properties
gene group. Each of the additional gene groups may be selected to
view information relating to the selected gene group. For example,
a user may select the proliferation rate gene group in the MF
profile.
[0288] FIG. 21 is a screenshot presenting information relating to
the tumor proliferation rate (as shown in the right panel) provided
in response to the user selecting the tumor proliferation rate gene
group (as shown in highlighting) in the MF profile. The user may
also view additional information relating to properties of the
patient's tumor.
[0289] The user may view different screens presenting information
relating to different tumor properties such as a screen presenting
information related to tumor purity and tumor clone evolution. FIG.
22 is a screenshot presenting information relating to the purity of
the patient's tumor in the tumor purity portion (as shown in the
lower right panel) and information relating to the clonal evolution
of the patient's tumor in the tumor clones evolution portion (as
shown in the lower right panel).
[0290] The MF profile provides information relating to the
pro-tumor immune environment (tumor-promoting immune
microenvironment), and anti-tumor immune environment (anti-tumor
immune microenvironment). For example, the user may select the
anti-tumor immune environment (anti-tumor immune microenvironment)
gene group in the MF profile to view information relating to the
anti-tumor immune environment and the user may select the pro-tumor
immune environment (tumor-promoting immune microenvironment) gene
group in the MF profile to view information relating to the
pro-tumor immune environment (tumor-promoting immune
microenvironment).
[0291] FIG. 23 is a screenshot presenting information relating to
the anti-tumor immune environment (as shown in the left panel;
anti-tumor immune microenvironment) provided in response to the
user selecting the anti-tumor immune environment (anti-tumor immune
microenvironment) gene group and information relating to the
pro-tumor immune environment (as shown in the right panel;
tumor-promoting immune microenvironment) in response to the user
selecting the pro-tumor immune environment (tumor-promoting immune
microenvironment) gene group. Additional gene groups relating to
the tumor microenvironment are presented in the MF profile in
response to selecting the anti-tumor and pro-tumor immune
environment (anti-tumor immune microenvironment and tumor-promoting
immune microenvironment) gene groups in the MF profile (as shown in
the middle panel).
[0292] Any one of these additional gene groups in the MF profile
may be selected to view information relating to that gene group.
For example, the user may select the T cells gene group in the MF
profile. FIG. 24 is a screenshot presenting information relating to
expression of genes that determine T cell activity within the tumor
in the anti-tumor microenvironment portion (as shown in the lower
left panel) provided in response to the user selecting the T cell
gene group in the MF profile (as shown by highlighting).
[0293] FIG. 25 is a screenshot presenting information relating to
expression of genes that determine cancer associated fibroblast
activity within the tumor in the pro-tumor microenvironment
(anti-tumor immune microenvironment) portion (as shown in the lower
right panel) provided in response to the user selecting the cancer
associated fibroblast (fibroblasts) gene group in the MF profile
(as shown by highlighting).
[0294] The user may select portions in the anti-tumor immune
environment portion (as shown in the left panel; anti-tumor immune
microenvironment) and the pro-tumor immune environment portion (as
shown in the right panel; tumor-promoting immune microenvironment)
to view additional information relating to anti-tumor cells and
pro-tumor (or tumor promoting) cells within the tumor
microenvironment (anti-tumor immune microenvironment and
tumor-promoting immune microenvironment).
[0295] FIG. 26 is a screenshot presenting information relating to
the number of non-malignant cells in the patient's tumor (as shown
in the lower left panel) provided in response to the user selecting
tumor infiltrate in the anti-tumor immune environment portion (as
shown in the upper left panel).
[0296] FIG. 27 is a screenshot presenting information relating to
the TCR repertoire in the patient's tumor (as shown in the lower
right panel) provided in response to the user selecting tumor
infiltrate in the pro-tumor immune environment portion (as shown in
the upper right panel; tumor-promotive immune infiltrate).
[0297] As disclosed herein, the MF profile may present five gene
groups including the tumor properties gene group, angiogenesis gene
group, cancer associated fibroblasts gene group (the fibroblasts
group), pro-tumor immune environment gene group (tumor-promoting
immune microenvironment group), and anti-tumor immune environment
gene group (anti-tumor immune microenvironment group). Each of
these gene groups may be selected by the user to view associated
gene groups. When each of these gene groups is selected, the MF
profile may present twenty-eight gene groups. A screen presenting a
MF profile presenting twenty-eight gene groups (also described
elsewhere herein) is shown in FIG. 28 (as shown in the middle
panel).
[0298] The "combo therapy" (or "combination therapy") portion can
be used to design a combination therapy based on one or more
therapies. Combination therapies can be designed to target cancer
(e.g., tumor) properties presented in the MF profile. For example,
a combination therapy including a treatment to suppress pro-tumor
process may be designed for a patient in which the MF profile
showed active pro-tumor processes.
[0299] The combo therapy portion may present information to the
user relating to the selected therapy including a description of
the selected therapy, gene groups targeted by the selected therapy,
clinical data related to the selected therapy, and predictions of
the patient's response to the selected therapy based on information
relating to the patient and the patient's cancer. FIGS. 29-37 are
screenshots demonstrating that a user may interactively design a
combination therapy using the combo therapy portion.
[0300] FIG. 29 is a screenshot presenting the combo therapy portion
(as shown in the right panel) provided to the user in response to
selecting the combinational therapy portion (as shown in the middle
panel).
[0301] FIG. 30 is a screenshot presenting anti-PD1 therapy
incorporated into the combo therapy portion (as shown in the upper
right panel). Gene groups targeted by anti-PD1 therapy in the MF
profile are marked with arrows. Information relating to the
biological influence of anti-PD1 therapy is presented in the
therapy biological influence portion (as shown in the lower middle
panel).
[0302] FIG. 31 is a screenshot presenting information related to
sunitinib treatment in the therapy biological influence portion (as
shown in the lower middle panel) in response to the user selecting
sunitinib in the targeted therapy biomarkers portion (as shown by
highlighting). The user may determine whether the selected
treatment should be incorporated into the combination therapy based
on this information.
[0303] FIG. 32 is a screenshot presenting sunitinib incorporation
in the combo therapy portion in response to the user selecting
sunitinib. Gene groups targeted by the anti-PD1 and sunitinib
combination therapy are marked with arrows in the MF profile.
Information relating to the combination of anti-PD1 and sunitinib
therapy is presented in the proposed effectivity portion (as shown
in the right panel) and in the potential adverse effects portion
(as shown in the right panel). Information relating to published
and ongoing clinical trials matching the selected combination
therapy are presented in the ongoing and finished combo trials
portion (as shown in the right panel).
[0304] The combination therapy may include more than two therapies.
For example, a user may add a vaccine therapy to the anti-PD1 and
sunitinib combination therapy designed by the user.
[0305] FIG. 33 is a screenshot presenting potential vaccine
therapies such as a personalized neo-antigenic vaccine and an off
the shelf vaccine provided to the user in response to selecting
vaccine in the immunotherapy biomarkers portion (as shown in the
left panel).
[0306] FIG. 34 is a screenshot presenting information relating to
treatment with a personalized neo-antigenic vaccine (as shown in
the lower middle panel) provided to the user in response to
selecting a personalized neo-antigenic vaccine (as shown by
highlighting).
[0307] FIG. 35 is a screenshot presenting incorporation of a
personalized neo-antigenic vaccine in the combo therapy portion
provided to the user in response to the user selecting the
personalized neo-antigenic vaccine.
[0308] FIG. 36 is a screenshot presenting the personalized
neo-antigenic vaccine therapy, anti-PD1 therapy, and sunitinib
therapy in the combo therapy portion provided to the user in
response to the user incorporating each of these therapies into the
combo therapy portion.
[0309] Any one of the therapies in the combination therapy may be
substituted for a different therapy. However, a particular
combination therapy may be inappropriate for a patient. In response
to the user's design of an inappropriate combination therapy, the
software will provide an alert to the user indicating that the
designed combo therapy is or may be inappropriate for the patient.
The user may also receive an alert if the designed combination of
therapies has a low effectivity score.
[0310] FIG. 37 is a screenshot presenting an alert that
substitution of sunitinib therapy with vemurafenib therapy is
recognized by the software as an inappropriate combination for the
patient.
Computer Implemented Methods For Generating, Visualizing and
Classifying MF Profiles
[0311] Aspects of the technology described herein provide computer
implemented methods for generating, visualizing and classifying
molecular-functional (MF) profiles of cancer patients.
[0312] In some embodiments, a software program may provide a user
with a visual representation of a patient's MF profile and/or other
information related to a patient's cancer using an interactive
graphical user interface (GUI). Such a software program may execute
in any suitable computing environment including, but not limited
to, a cloud-computing environment, a device co-located with a user
(e.g., the user's laptop, desktop, smartphone, etc.), one or more
devices remote from the user (e.g., one or more servers), etc.
[0313] For example, in some embodiments, the techniques described
herein may be implemented in the illustrative environment 200 shown
in FIG. 2A. As shown in FIG. 2A, within illustrative environment
200, one or more biological samples of a patient 202 may be
provided to a laboratory 204. Laboratory 204 may process the
biological sample(s) to obtain expression data (e.g., DNA, RNA,
and/or protein expression data) and provide it, via network 208, to
at least one database 206 that stores information about patient
202.
[0314] Network 208 may be a wide area network (e.g., the Internet),
a local area network (e.g., a corporate Intranet), and/or any other
suitable type of network. Any of the devices shown in FIG. 2A may
connect to the network 208 using one or more wired links, one or
more wireless links, and/or any suitable combination thereof.
[0315] In the illustrated embodiment of FIG. 2A, the at least one
database 206 may store expression data for the patient, medical
history data for the patient, test result data for the patient,
and/or any other suitable information about the patient 202.
Examples of stored test result data for the patient include biopsy
test results, imaging test results (e.g., MRI results), and blood
test results. The information stored in at least one database 206
may be stored in any suitable format and/or using any suitable data
structure(s), as aspects of the technology described herein are not
limited in this respect. The at least one database 206 may store
data in any suitable way (e.g., one or more databases, one or more
files). The at least one database 206 may be a single database or
multiple databases.
[0316] As shown in FIG. 2A, illustrative environment 200 includes
one or more external databases 216, which may store information for
patients other than patient 202. For example, external databases
216 may store expression data (of any suitable type) for one or
more patients, medical history data for one or more patients, test
result data (e.g., imaging results, biopsy results, blood test
results) for one or more patients, demographic and/or biographic
information for one or more patients, and/or any other suitable
type of information. In some embodiments, external database(s) 216
may store information available in one or more publically
accessible databases such as TCGA (The Cancer Genome Atlas), one or
more databases of clinical trial information, and/or one or more
databases maintained by commercial sequencing suppliers. The
external database(s) 216 may store such information in any suitable
way using any suitable hardware, as aspects of the technology
described herein are not limited in this respect.
[0317] In some embodiments, the at least one database 206 and the
external database(s) 216 may be the same database, may be part of
the same database system, or may be physically co-located, as
aspects of the technology described herein are not limited in this
respect.
[0318] In some embodiments, information stored in patient
information database 206 and/or in external database(s) 216 may be
used to perform any of the techniques described herein related to
determining whether a subject is likely to respond positively or
not likely to respond positively to an immune checkpoint blockade
therapy. For example, the information stored in the database(s) 206
and/or 216 may be accessed, via network 208, by software executing
on server(s) 210 to perform any one or more of the techniques
described herein including with reference to FIGS. 39A, 39B, 39C,
39D, 40A and 40B.
[0319] For example, in some embodiments, server(s) 210 may access
information stored in database(s) 206 and/or 216 and use this
information to perform process 3900, described with reference to
FIG. 39A, for identifying a MF profile cluster with which to
associate an MF profile for a subject.
[0320] As another example, in some embodiments, server(s) 210 may
access information stored in database(s) 206 and/or 216 and use
this information to perform process 3920, described with reference
to FIG. 39B, for generating MF profile clusters using RNA
expression data obtained from subjects having a particular type of
cancer.
[0321] As another example, in some embodiments, server(s) 210 may
access information stored in database(s) 206 and/or 216 and use
this information to perform process 3940, described with reference
to FIG. 39C, for identifying an MF profile cluster with which to
associate an MF profile determined for a subject at least in part
by determining the subject's expression levels for multiple gene
groups.
[0322] As another example, in some embodiments, server(s) 210 may
access information stored in database(s) 206 and/or 216 and use
this information to perform process 3960, described with reference
to FIG. 39D, for generating MF profile clusters using RNA
expression data obtained from subjects having a particular type of
cancer, and associating a subject with one of the generated MF
clusters based on the subject's MF profile.
[0323] As another example, in some embodiments, server(s) 210 may
access information stored in database(s) 206 and/or 216 and use
this information to perform process 4000, described with reference
to FIG. 40A, for generating an MF profile for a subject and
generating an MF portrait for visualizing the MF profile in a
graphical user interface.
[0324] As another example, in some embodiments, server(s) 210 may
access information stored in database(s) 206 and/or 216 and use
this information to perform process 4020, described with reference
to FIG. 40B, for presenting a generated personalized graphical user
interface (GUI) to a user.
[0325] In some embodiments, server(s) 210 may include one or
multiple computing devices. When server(s) 210 include multiple
computing devices, the device(s) may be physically co-located
(e.g., in a single room) or distributed across multi-physical
locations. In some embodiments, server(s) 210 may be part of a
cloud computing infrastructure. In some embodiments, one or more
server(s) 210 may be co-located in a facility operated by an entity
(e.g., a hospital, research institution) with which doctor 214 is
affiliated. In such embodiments, it may be easier to allow
server(s) 210 to access private medical data for the patient
202.
[0326] As shown in FIG. 2A, in some embodiments, the results of the
analysis performed by server(s) 210 may be provided to doctor 214
through a computing device 214 (which may be a portable computing
device, such as a laptop or smartphone, or a fixed computing device
such as a desktop computer). The results may be provided in a
written report, an e-mail, a graphical user interface, and/or any
other suitable way. It should be appreciated that although in the
embodiment of FIG. 2A, the results are provided to a doctor, in
other embodiments, the results of the analysis may be provided to
patient 202 or a caretaker of patient 202, a healthcare provider
such as a nurse, or a person involved with a clinical trial.
[0327] In some embodiments, the results may be part of a graphical
user interface (GUI) presented to the doctor 214 via the computing
device 212. In some embodiments, the GUI may be presented to the
user as part of a webpage displayed by a web browser executing on
the computing device 212. In some embodiments, the GUI may be
presented to the user using an application program (different from
a web-browser) executing on the computing device 212. For example,
in some embodiments, the computing device 212 may be a mobile
device (e.g., a smartphone) and the GUI may be presented to the
user via an application program (e.g., "an app") executing on the
mobile device.
[0328] The GUI presented on computing device 212 provides a wide
range of oncological data relating to both the patient and the
patient's cancer in a new way that is compact and highly
informative. Previously, oncological data was obtained from
multiple sources of data and at multiple times making the process
of obtaining such information costly from both a time and financial
perspective. Using the techniques and graphical user interfaces
illustrated herein, a user can access the same amount of
information at once with less demand on the user and with less
demand on the computing resources needed to provide such
information. Low demand on the user serves to reduce clinician
errors associated with searching various sources of information.
Low demand on the computing resources serves to reduce processor
power, network bandwidth, and memory needed to provide a wide range
of oncological data, which is an improvement in computing
technology.
[0329] FIG. 2B shows a block diagram of an illustrative GUI 250
containing information about patient 202. GUI 250 may include
separate portions providing different types of information about
patient 202. Illustrative GUI 150 includes the following portions:
Patient Information Portion 252, Molecular-Functional (MF) Portrait
Portion 260, Clinical Trial Information Portion 262, Immunotherapy
Portion 254, Efficacy Predictor Portion 256, and Targeted Therapy
Selection Portion 258.
[0330] Patient Information Portion 252 may provide general
information about the patient and the patient's cancer. General
information about the patient may include such information as the
patient's name and date of birth, the patient's insurance provider,
and contact information for the patient such as address and phone
number. General information about the patient's cancer may include
the patient's diagnosis, the patient's history of relapse and/or
remission, and information relating to stage of the patient's
cancer. Patient Information Portion 252 may also provide
information relating to potential treatment options for the patient
and/or previously administered treatments.
[0331] Molecular-Functional (MF) Portrait Portion 260 may include a
molecular functional tumor portrait (MF profile) which refers to a
graphical depiction of a tumor with regard to its molecular and
cellular composition, and biological processes that are present
within and/or surrounding the tumor. Further aspects relating to a
patient's MF profile are provided herein.
[0332] Clinical Trial Information Portion 262 may include
information relating to a clinical trial for a therapy that may be
and/or will be administered to the patient. Clinical Trial
Information Portion 262 may provide information about an ongoing
clinical trial or a completed clinical trial. Information that may
be provided in Clinical Trial Information Portion 262 may include
information related to a therapy used in the clinical trial such as
dosage and dosage regimen, number and diagnosis of patients
participating in the clinical trial, and patient outcomes.
[0333] Immunotherapy Portion 254 may include patient specific
information as it relates to an immunotherapy. Immunotherapy
Portion 254 may provide such information for different
immunotherapies, for example, immune checkpoint blockade therapies,
anti-cancer vaccine therapies, and T cell therapies. Patient
specific information relating to an immunotherapy may include
information about the patient such as the patient's biomarkers
associated with an immunotherapy and/or information about the
patient's cancer such as composition of immune cells in the
patient's tumor.
[0334] Efficacy Predictor Portion 256 may include information
indicative of the patient's predicted response to an immunotherapy
based on patient specific information presented in Immunotherapy
Portion 254. Efficacy Predictor Portion 256 may provide predicted
efficacy of an immunotherapy determined, in some embodiments, using
a patient's biomarkers as described in International patent
application number PCT/US18/37008, entitled "Systems and Methods
for Identifying Cancer Treatments from Normalized Biomarker
Scores," filed Jun. 12, 2018, the entire contents of which are
incorporated herein by reference. Additionally or alternatively,
Efficacy Predictor Portion 256 may provide predicted efficacy of an
immune checkpoint blockade therapy determined using patient
specific information such as gene expression data as described in
International patent application number PCT/US18/37018, entitled
"Systems and Methods for Identifying Responders and Non-Responders
to Immune Checkpoint Blockade Therapy," filed Jun. 12, 2018, the
entire contents of which are incorporated herein by reference.
Targeted Therapy Selection Portion 258 may include patient specific
information as it relates to a targeted therapy. Targeted Therapy
Selection Portion 258 may provide such information for different
targeted therapies, for example, a kinase inhibitor therapy, a
chemotherapy, and anti-cancer antibody therapy. Patient specific
information relating to an a targeted therapy may include
information about the patient such as the patient's biomarkers
associated with a targeted therapy and/or information about the
patient's cancer such as whether a mutation is present in the
patient's tumor.
[0335] An illustrative example of the graphical user interface 250
of FIG. 2B is shown as graphical user interface 270 of FIG. 2C. As
shown in FIG. 2C, Patient Information Portion 272 may provide
different information in different panels, for example, Overall
Status panel, Disease Characteristics panel, and General
Recommendations panel. Overall Status panel, in some embodiments,
may provide general information about the patient such as patient
name and patient age. Disease Characteristics panel, in some
embodiments, may provide information about the patient's cancer
such as type of cancer and stage of cancer. General Recommendations
panel, in some embodiments, may provide previous treatments and
possible treatment options for the patient.
[0336] Clinical Trial Information Portion 282a provides information
relating to a clinical trial for anti-PD1 therapy. Clinical Trial
Information Portion 282a (as shown in the upper portion) shows a
graph providing patient overall response rate (ORR) for anti-PD1
therapy and other therapies such as vaccine or IFNa therapies. A
user may select portions of the Clinical Trial Information Portion
282a to access information related to patient progression-free
survival (PFS) and/or patient overall survival (OS). Clinical Trial
Information Portion 282a (as shown in the lower portion) provides
information relating to different clinical trials that may be
presented to a user including a brief description of the clinical
trial.
[0337] Clinical Trial Information Portion 282b provides information
relating to a clinical trial for different targeted therapies.
Clinical Trial Information Portion 282b (as shown in the upper
portion) shows a graph providing patient overall response rate
(ORR) for different targeted therapies including sunitinib (SU),
imatinib (IM), vemurafenib (VER) and dabrafenib (DAB). A user may
select portions of the Clinical Trial Information Portion 282b to
access information related to patient progression-free survival
(PFS) and/or patient overall survival (OS). Clinical Trial
Information Portion 282b (as shown in the lower portion) provides
information relating to different clinical trials that may be
presented to a user including a brief description of the clinical
trial.
[0338] Immunotherapy Portion 274 provides patient specific
information associated with an immunotherapy and information
indicative of the patient's predicted response to that
immunotherapy. Immunotherapy Portion 274 provides such information
for anti-PD1 therapy, a therapeutic cancer vaccine, IFNa therapy,
IL2 therapy, anti-CTLA4 therapy, and anti-angiogenic therapy.
Patient specific information shown in Immunotherapy Portion 274
includes the patient's biomarker information relating to various
immunotherapies and the patient's therapy scores calculated from
their biomarkers.
[0339] Efficacy Predictor Portion 276a provides information
indicative of the patient's predicted response to anti-PD1 therapy
based on patient specific information presented in Immunotherapy
Portion 274. Efficacy Predictor Portion 276b provides information
indicative of the patient's predicted response to anti-CTLA4
therapy based on patient specific information presented in
Immunotherapy Portion 274.
[0340] Targeted Therapy Selection Portion 278 provides patient
specific information associated with a targeted therapy and
information indicative of the patient's predicted response to the
targeted therapy. Targeted Therapy Selection Portion 278 provides
such information for sunitinib (SU), imatinib (IM), vemurafenib
(VER), dabrafenib (DAB), trametinib, and pazopanib. Patient
specific information shown in Targeted Therapy Selection Portion
278 includes a patient's biomarker information relating to various
targeted therapies and the patient's therapy scores calculated from
their biomarkers.
[0341] An illustrative implementation of a computer system 3800
that may be used in connection with any of the embodiments of the
technology described herein is shown in FIG. 38. The computer
system 600 may include one or more computer hardware processors
3800 and one or more articles of manufacture that comprise
non-transitory computer-readable storage media (e.g., memory 3820
and one or more non-volatile storage devices 3830). The
processor(s) 3810 may control writing data to and reading data from
the memory 3820 and the non-volatile storage device(s) 3830 in any
suitable manner. To perform any of the functionality described
herein, the processor(s) 3810 may execute one or more
processor-executable instructions stored in one or more
non-transitory computer-readable storage media (e.g., the memory
3820), which may serve as non-transitory computer-readable storage
media storing processor-executable instructions for execution by
the processor(s) 3810.
[0342] Systems and methods described herein provide for calculating
an MF profile of a subject and associating the MF profile with an
existing MF profile cluster. For example, computer-implemented
processes for calculating a MF profile of a subject and associating
the calculated MF profile with an existing MF profile cluster are
described with reference to FIGS. 39A and 39C.
[0343] FIG. 39A is a flowchart of an illustrative
computer-implemented process 3900 for identifying a MF profile
cluster with which to associate an MF profile for a subject (e.g.,
a cancer patient), in accordance with some embodiments of the
technology described herein. Process 3900 may be performed by any
suitable computing device(s). For example, may be performed by a
laptop computer, a desktop computer, one or more servers, in a
cloud computing environment, or in any other suitable way.
[0344] Process 3900 begins at act 3902, where RNA expression data
and/or whole exome sequencing (WES) data for a subject is obtained.
RNA expression data may be acquired using any method known in the
art, e.g., whole transcriptome sequencing, total RNA sequencing,
and mRNA sequencing. In some embodiments, obtaining RNA expression
data and/or whole exome sequencing (WES) data comprises obtaining
expression data from a biological sample from a patient and/or from
a database storing such expression data. Further aspects relating
to obtaining expression data are provided in section titled
"Obtaining Expression Data".
[0345] Next, process 3900 proceeds to act 3904, where the MF
profile for the subject is determined by determining a set of
expression levels for a respective set of gene groups that includes
gene groups associated with cancer malignancy and cancer
microenvironment. The MF profile may be determined for a subject
having any type of cancer, including any of the types described
herein. The MF profile may be determined using any number of gene
groups that relate to compositions and processes present within
and/or surrounding the subject's tumor. Gene group expression
levels, in some embodiments, may be calculated as a gene set
enrichment (GSEA) score for the gene group. Further aspects
relating to determining MF profiles are provided in section titled
"MF Profiles".
[0346] Next, process 3900 proceeds to act 3906, where a MF profile
cluster with which to associate the MF profile of the subject is
identified. The MF profile of the subject may be associated with
any of the types of MF profile clusters types described herein. A
subject's MF profile may be associated with one or multiple of the
MF profile clusters in any suitable way. For example, an MF profile
may be associated with one of the MF profile clusters using a
similarity metric (e.g., by associating the MF profile with the MF
profile cluster whose centroid is closest to the MF profile
according to the similarity metric). As another example, a
statistical classifier (e.g., k-means classifier or any other
suitable type of statistical classifier) may be trained to classify
the MF profile as belonging to one or multiple of the MF clusters.
Further aspects relating to determining MF profiles are provided in
section "MF Profiles".
[0347] Optionally, process 3900 proceeds to act 3908, where a
therapy for the subject is identified based on the identified MF
profile cluster. The identified therapy may be any type of
anti-cancer therapy depending on the patient's cancer and their
identified MF profile cluster. A single anti-cancer therapy or a
combination of anti-cancer therapies may be identified in act 3908.
Identifying a therapy based on the MF profile cluster includes
excluding those therapies that may be ineffective or harmful to the
subject in order to identify a suitable therapy for the subject.
Further aspects related to using a patient's identified MF profile
cluster for clinical purposes are provided in section
"Applications".
[0348] The MF profile of the subject may be output to a user, in
some embodiments, by displaying the MF profile to the user in a
graphical user interface (GUI), including the information about the
MF profile in a report, sending an email to the user, and/or in any
other suitable way. For example, the MF profile of the subject and
other patient related information may be provided to a user in a
GUI as shown in FIGS. 3-37.
[0349] In this way, a patient's MF profile can be identified and
used for various clinical purposes including assessing the efficacy
of a treatment for cancer and/or evaluating suitability of a
patient for participating in a clinical trial.
[0350] FIG. 39C is a flowchart of an illustrative
computer-implemented process 3940 for identifying an existing MF
profile cluster with which to associate a MF profile for a subject
(e.g., a cancer patient), in accordance with some embodiments of
the technology described herein.
[0351] Process 3940 may be performed by any suitable computing
device(s). For example, may be performed by a laptop computer, a
desktop computer, one or more servers, in a cloud computing
environment, or in any other suitable way.
[0352] Process 3940 begins at act 3942, where RNA expression data
and/or whole exome sequencing (WES) data for a subject having a
particular type of cancer is obtained. RNA expression data may be
acquired using any method known in the art, e.g., whole
transcriptome sequencing, total RNA sequencing, and mRNA
sequencing. In some embodiments, obtaining RNA expression data
and/or whole exome sequencing (WES) data comprises obtaining
expression data from a biological sample from a patient and/or from
a database storing such expression data. Further aspects relating
to obtaining expression data are provided in section "Obtaining
Expression Data".
[0353] Next, process 3940 proceeds to act 3944, where the MF
profile for the subject is determined by determining a set of
expression levels for a respective set of gene groups that includes
at least one gene group associated with cancer malignancy and at
least four gene groups associated with cancer microenvironment. The
at least one gene group associated with cancer malignancy, in some
embodiments, consists of a tumor properties gene group. The at
least four gene groups associated with cancer microenvironment, in
some embodiments, consists of tumor-promoting immune
microenvironment group, anti-tumor immune microenvironment group,
angiogenesis group, and fibroblasts group.
[0354] It should be appreciated that act 3944 may be performed
using any number of gene groups associated with cancer malignancy
and cancer microenvironment. For example, MF profiles may be
determined using set of gene groups that includes 19 gene groups
where the gene groups associated with cancer malignancy consists of
the proliferation rate group, the PI3K/AKT/mTOR signaling group,
the RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group, and the gene groups associated with cancer
microenvironment consists of the antigen presentation group, the
cytotoxic T and NK cells group, the B cells group, the anti-tumor
microenvironment group, the checkpoint inhibition group, the Treg
group, the MDSC group, the granulocytes group, the cancer
associated fibroblasts group, the angiogenesis group, and the
tumor-promotive immune group.
[0355] In another example, MF profiles may be determined using set
of gene groups that includes 30 gene groups where the gene groups
associated with cancer malignancy consists of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the growth factors group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group, and the gene groups associated with
cancer microenvironment consists of the MHCI group, the MHCII
group, the coactivation molecules group, the effector cells group,
the NK cells group, the T cell traffic group, the T cells group,
the B cells group, the M1 signatures group, the Th1 signature
group, the antitumor cytokines group, the checkpoint inhibition
group, the Treg group, the MDSC group, the granulocytes group, the
M2 signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group.
[0356] The MF profile may be determined using any number of gene
groups (or functional modules) that relate to compositions and
processes present within and/or surrounding the subject's tumor.
Gene groups may comprise any number of genes and may be related to
any composition and process. Further aspects relating to the gene
groups are provided in section "MF Profile Modules". Gene group
expression levels, in some embodiments, may be calculated as a gene
set enrichment (GSEA) score for the gene group. Further aspects
relating to determining MF profiles are provided in section "MF
Profiles".
[0357] Next, process 3940 proceeds to act 3946, where information
specifying MF profile clusters for the particular cancer type are
accessed. Different MF profile clusters are accessed for different
cancers. For example, MF profile clusters associated with lung
cancer are accessed when process 3940 is performed for a patient
having lung cancer and MF profile clusters associated with melanoma
are accessed when process 3940 is performed for a patient having
melanoma. Any number of MF profile clusters for the particular
cancer may be accessed including at least two, at least 5, at least
10 or at least 20. The number of accessed MF profiles, in some
embodiments, may be between 2-20, between 2-10, or between 15-20.
The number of accessed MF profile clusters may vary depending on
the particular cancer with which the MF profile clusters are
associated. For example, 5 MF profile clusters may be accessed when
the particular cancer type is lung cancer and 12 MF profile
clusters may be accessed when the particular cancer is melanoma.
Accessing information specifying MF profile clusters for the
particular cancer may include accessing information from a variety
of sources and/or a variety of databases.
[0358] Next, process 3940 proceeds to act 3948, where a MF profile
cluster with which to associate the MF profile of the subject is
identified. The MF profile of the subject may be associated with
any of the types of MF profile clusters types described herein. A
subject's MF profile may be associated with one or multiple of the
MF profile clusters in any suitable way. For example, an MF profile
may be associated with one of the MF profile clusters using a
similarity metric (e.g., by associating the MF profile with the MF
profile cluster whose centroid is closest to the MF profile
according to the similarity metric). As another example, a
statistical classifier (e.g., k-means classifier or any other
suitable type of statistical classifier) may be trained to classify
the MF profile as belonging to one or multiple of the MF clusters.
Further aspects relating to determining MF profiles are provided in
section "MF Profiles".
[0359] The MF profile of the subject may be output to a user, in
some embodiments, by displaying the MF profile to the user in a
graphical user interface (GUI), including the information about the
MF profile in a report, sending an email to the user, and/or in any
other suitable way. For example, the MF profile of the subject and
other patient related information may be provided to a user in a
GUI as shown in FIGS. 3-37.
[0360] In this way, a patient's MF profile can be identified and
used for various clinical purposes including assessing the efficacy
of a treatment for cancer and/or evaluating suitability of a
patient for participating in a clinical trial.
[0361] Systems and methods described herein provide for generating
MF profile clusters and for generating a MF profile for a patient
and associating that MF profile to a generated MF cluster. For
example, a computer-implemented process 3920 for generating MF
profile clusters using RNA expression data obtained from subjects
having a particular type of cancer is described with reference to
FIG. 39B. As another example, a computer-implemented process 3960
for generating MF profile clusters using RNA expression data
obtained from subjects having a particular type of cancer, and
associating a subject with one of the generated MF clusters based
on the subject's MF profile is described with reference to FIG.
39D.
[0362] FIG. 39B is a flowchart of an illustrative
computer-implemented process 3920 for generating MF profile
clusters using expression data obtained from subjects having a
particular type of cancer, in accordance with some embodiments of
the technology described herein. MF profile clusters may be
generated for any cancer using expression data obtained from
patients having that type of cancer. For example MF profile
clusters associated with melanoma may be generated using expression
data from melanoma patients. In another example MF profile clusters
associated with lung cancer may be generated using expression data
from lung cancer patients.
[0363] Process 3920 begins at act 3922, where RNA expression data
and/or whole exome sequencing (WES) data for a plurality of
subjects having a particular cancer are obtained. The plurality of
subjects for which expression data is obtained may comprise any
number of patients having a particular cancer. For example,
expression data may be obtained for a plurality of melanoma
patients, for example, 100 melanoma patients, 1000 melanoma
patients, or any number of melanoma patients as the technology is
not so limited. RNA expression data may be acquired using any
method known in the art, e.g., whole transcriptome sequencing,
total RNA sequencing, and mRNA sequencing. Further aspects relating
to obtaining expression data are provided in section "Obtaining
Expression Data".
[0364] Next, process 3920 proceeds to act 3924, where the MF
profile for each subject in the plurality of subject is determined
by determining a set of expression levels for a respective set of
gene groups that includes gene groups associated with cancer
malignancy and cancer microenvironment. MF profiles may be
determined using any number of gene groups that relate to
compositions and processes present within and/or surrounding the
subject's tumor. Gene group expression levels, in some embodiments,
may be calculated as a gene set enrichment (GSEA) score for the
gene group. Further aspects relating to determining MF profiles are
provided in section titled "MF Profiles".
[0365] Next, process 3920 proceeds to act 3926, where the plurality
of MF profiles are clustered to obtain MF profile clusters. MF
profiles may be clustered using any of the techniques described
herein including, for example, community detection clustering,
dense clustering, k-means clustering, or hierarchical clustering.
MF profiles may be clustered for any type of cancer using MF
profiles generated for patients having that type of cancer. MF
profile clusters, in some embodiments, comprises a 1.sup.st MF
profile cluster, a 2.sup.nd MF profile cluster, a 3.sup.rd MF
profile, and a 4.sup.th MF profile. The relative sizes of
1.sup.st-4.sup.th MF clusters may vary among cancer types. For
example, the size of the 3.sup.rd MF profile cluster (shown as C)
was larger for ACC (adrenocortical carcinoma) than that of BLCA
(bladder urothelial carcinoma. MF profiles were clustered for
different cancers as shown in Example 4. Further aspects relating
to MF profile clusters are provided in section titled "MF
profiles".
[0366] Next, process 3920 proceeds to act 3928, where the plurality
of MF profiles in association with information identifying the
particular cancer type are stored. MF profiles may be stored in a
database in any suitable format and/or using any suitable data
structure(s), as aspects of the technology described herein are not
limited in this respect. The database may store data in any
suitable way, for example, one or more databases and/or one or more
files. The database may be a single database or multiple
databases.
[0367] In this way, MF profile clusters can be stored and used as
existing MF profile clusters with which a patient's MF profile can
be associated. Existing MF profiles clusters, in some embodiments,
may be associated with a patient's MF profile generated using five
gene groups, 19 gene groups, or 30 gene groups as described with
respect to FIG. 39C.
[0368] FIG. 39D is a flowchart of an illustrative
computer-implemented process 3960 for generating MF profile
clusters using expression data obtained from subjects having a
particular type of cancer, and associating a subject with one of
the generated MF clusters based on the subject's MF profile, in
accordance with some embodiments of the technology described
herein. Process 3960 may be performed by any suitable computing
device(s). For example, may be performed by a laptop computer, a
desktop computer, one or more servers, in a cloud computing
environment, or in any other suitable way.
[0369] Process 3960 begins at act 3962, where RNA expression data
and/or whole exome sequencing (WES) data for each subject in a
plurality of subjects having a particular type of cancer is
obtained. RNA expression data may be acquired using any method
known in the art, e.g., whole transcriptome sequencing, total RNA
sequencing, and mRNA sequencing. In some embodiments, obtaining RNA
expression data and/or whole exome sequencing (WES) data comprises
obtaining expression data from a biological sample from a patient
and/or from a database storing such expression data. Further
aspects relating to obtaining expression data are provided in
section "Obtaining Expression Data".
[0370] Next, process 3960 proceeds to act 3964, where the MF
profile for each subject in the plurality of subjects is determined
by determining a set of expression levels for a respective set of
gene groups that includes at least one gene group associated with
cancer malignancy and at least four gene groups associated with
cancer microenvironment. The MF profile may be determined using any
number of gene groups (or functional modules) that relate to
compositions and processes present within and/or surrounding the
subject's tumor. Gene groups may comprise any number of genes and
may be related to any composition and process. Further aspects
relating to the gene groups are provided in section "MF Profile
Modules". Gene group expression levels, in some embodiments, may be
calculated as a gene set enrichment (GSEA) score for the gene
group. Further aspects relating to determining MF profiles are
provided in section "MF Profiles".
[0371] Next, process 3960 proceeds to act 3966, where the plurality
of MF profiles are clustered to obtain MF profile clusters. MF
profiles may be clustered using any of the techniques described
herein including, for example, community detection clustering,
dense clustering, k-means clustering, or hierarchical clustering.
MF profiles may be clustered for any type of cancer using MF
profiles generated for patients having that type of cancer. MF
profile clusters, in some embodiments, comprises a 1.sup.st MF
profile cluster, a 2.sup.nd MF profile cluster, a 3.sup.rd MF
profile, and a 4.sup.th MF profile. The relative sizes of
1.sup.st-4.sup.th MF clusters may vary among cancer types. For
example, the size of the 3.sup.rd MF profile cluster (shown as C)
was larger for ACC (adrenocortical carcinoma) than that of BLCA
(bladder urothelial carcinoma. MF profiles were clustered for
different cancers as shown in Example 4. Further aspects relating
to MF profile clusters are provided in section titled "MF
profiles".
[0372] Next, process 3960 proceeds to act 3968, where RNA
expression data and/or whole exome sequencing (WES) data for an
additional subject is obtained. Expression data for an additional
subject may be obtained by any suitable means as described in
further detail in section "Obtaining Expression Data". Expression
data for the additional subject may be obtained in the same manner
used for obtaining expression data of the plurality of subjects.
Alternatively or in addition to, expression data for the additional
subject may be obtained in a manner different from that used to
obtain expression data of the plurality of subjects. Further
aspects relating to obtaining expression data are provided in
section "Obtaining Expression Data".
[0373] Next, process 3960 proceeds to act 3970, where MF profiles
for the additional subject are determined using the additional
subject's expression data. The MF profile for the additional
subject is determined by determining a set of expression levels for
a respective set of gene groups that includes at least one gene
group associated with cancer malignancy and at least four gene
groups associated with cancer microenvironment. The MF profile may
be determined using any number of gene groups (or functional
modules) that relate to compositions and processes present within
and/or surrounding the subject's tumor. Gene groups may comprise
any number of genes and may be related to any composition and
process. Further aspects relating to the gene groups are provided
in section "MF Profile Modules". Gene group expression levels, in
some embodiments, may be calculated as a gene set enrichment (GSEA)
score for the gene group.
[0374] Further aspects relating to determining MF profiles are
provided in section "MF Profiles".
[0375] Next, process 3960 proceeds to act 3972, where a MF profile
cluster with which to associate the MF profile of the subject is
identified. The MF profile of the subject may be associated with
any of the types of MF profile clusters determined in act 3966. A
subject's MF profile may be associated with one or multiple of the
MF profile clusters in any suitable way. For example, an MF profile
may be associated with one of the MF profile clusters using a
similarity metric (e.g., by associating the MF profile with the MF
profile cluster whose centroid is closest to the MF profile
according to the similarity metric). As another example, a
statistical classifier (e.g., k-means classifier or any other
suitable type of statistical classifier) may be trained to classify
the MF profile as belonging to one or multiple of the MF clusters.
Further aspects relating to determining MF profiles are provided in
section "MF Profiles".
[0376] Optionally, process 3960 proceeds to act 3974, where a
therapy for the subject is identified based on the identified MF
profile cluster. The identified therapy may be any type of
anti-cancer therapy depending on the patient's cancer and their
identified MF profile cluster. A single anti-cancer therapy or a
combination of anti-cancer therapies may be identified in act 3974.
Identifying a therapy based on the MF profile cluster includes
excluding those therapies that may be ineffective or harmful to the
subject in order to identify a suitable therapy for the subject.
Further aspects related to using a patient's identified MF profile
cluster for clinical purposes are provided in section
"Applications".
[0377] The MF profile of the subject may be output to a user, in
some embodiments, by displaying the MF profile to the user in a
graphical user interface (GUI), including the information about the
MF profile in a report, sending an email to the user, and/or in any
other suitable way. For example, the MF profile of the subject and
other patient related information may be provided to a user in a
GUI as shown in FIGS. 3-37.
[0378] In this way, a patient's MF profile can be identified and
used for various clinical purposes including assessing the efficacy
of a treatment for cancer and/or evaluating suitability of a
patient for participating in a clinical trial.
[0379] Systems and methods described herein provide for generating
a MF profile for a patient and generating a visualization of the
generated MF profile as a MF portrait. For example, a
computer-implemented process for generating a MF profile and an
associated MF portrait is shown in FIG. 40A, and a
computer-implemented process for generating a MF profile using five
gene groups and an associated MF portrait is shown in FIG. 40B.
[0380] FIG. 40A is a flowchart of an illustrative
computer-implemented process 4000 for generating a MF profile and
an associated MF portrait, in accordance with some embodiments of
the technology described herein. Process 4000 may be performed by
any suitable computing device(s). For example, may be performed by
a laptop computer, a desktop computer, one or more servers, in a
cloud computing environment, or in any other suitable way.
[0381] Process 4000 begins at act 4002, where RNA expression data
and/or whole exome sequencing (WES) data for a subject having a
particular type of cancer is obtained. RNA expression data may be
acquired using any method known in the art, e.g., whole
transcriptome sequencing, total RNA sequencing, and mRNA
sequencing. In some embodiments, obtaining RNA expression data
and/or whole exome sequencing (WES) data comprises obtaining
expression data from a biological sample from a patient and/or from
a database storing such expression data. Further aspects relating
to obtaining expression data are provided in section "Obtaining
Expression Data".
[0382] Next, process 4000 proceeds to act 4004, where the MF
profile for the subject is determined by determining a set of
expression levels for a respective set of gene groups that includes
gene groups associated with cancer malignancy and gene groups
associated with cancer microenvironment. The MF profile may be
determined for a subject having any type of cancer, including any
of the types described herein. The MF profile may be determined
using any number of gene groups (or functional modules) that relate
to compositions and processes present within and/or surrounding the
subject's tumor. Gene group expression levels, in some embodiments,
are calculated as a gene set enrichment (GSEA) score for the gene
group. Further aspects relating to determining MF profiles are
provided in section "MF Profiles".
[0383] Next, process 4000 proceeds to act 4006, where a first set
of visual characteristics for a first plurality of GUI elements
using the first gene group expression levels are determined.
Examples of visual characteristics for a GUI element include color,
shading or pattern, size, and/or shape. A set of visual
characteristics may contain any number of visual characteristics.
GUI elements, for example, include genes, gene groups, biomarkers,
and biomarker information. A plurality of GUI elements may contain
any number of GUI elements. Further aspects of visual
characteristics and GUI elements are shown in and/or described with
reference to FIGS. 3-37.
[0384] Next, process 4000 proceeds to act 4008, where a second set
of visual characteristics for a second plurality of GUI elements
using the second gene group expression levels are determined.
Examples of visual characteristics for a GUI element include color,
shading or pattern, size, and/or shape. A set of visual
characteristics may contain any number of visual characteristics.
GUI elements, for example, include genes, gene groups, biomarkers,
and biomarker information. A plurality of GUI elements may contain
any number of GUI elements. Further aspects of visual
characteristics and GUI elements are shown in and/or described with
reference to FIGS. 3-37.
[0385] Next, process 4000 proceeds to act 4010, where a GUI
containing a first portion including the first GUI element and a
second portion including the second GUI element is generated. For
example, the MF profile of the subject and other patient related
information may be provided to a user in a GUI as shown in FIGS.
3-37. Further aspects relating to the GUI as shown in FIGS. 3-37
are provided in section "Visualization of MF Profiles".
[0386] Next, process 4000 proceeds to act 4012, where the generated
personalized GUI is presented to a user. In some embodiments, the
GUI may be presented to the user as part of a webpage displayed by
a web browser. In some embodiments, the GUI may be presented to the
user using an application program (different from a web-browser).
For example, in some embodiments, the GUI may be presented to the
user via an application program (e.g., "an app") executing on a
mobile device.
[0387] FIG. 40B is a flowchart of an illustrative
computer-implemented process 4020 for generating a MF profile using
at least one gene group associated with cancer malignancy and at
least four gene groups associated with cancer microenvironment, and
an associated MF portrait, in accordance with some embodiments of
the technology described herein. Process 4020 may be performed by
any suitable computing device(s). For example, may be performed by
a laptop computer, a desktop computer, one or more servers, in a
cloud computing environment, or in any other suitable way.
[0388] Process 4020 begins at act 4022, where RNA expression data
and/or whole exome sequencing (WES) data for a subject having a
particular type of cancer is obtained. RNA expression data may be
acquired using any method known in the art, e.g., whole
transcriptome sequencing, total RNA sequencing, and mRNA
sequencing. In some embodiments, obtaining RNA expression data
and/or whole exome sequencing (WES) data comprises obtaining
expression data from a biological sample from a patient and/or from
a database storing such expression data. Further aspects relating
to obtaining expression data are provided in section "Obtaining
Expression Data".
[0389] Next, process 4020 proceeds to act 4024, where the MF
profile for the subject is determined by determining a set of
expression levels for a respective set of gene groups that includes
at least one gene group associated with cancer malignancy and at
least four gene groups associated with cancer microenvironment. The
at least one gene group associated with cancer malignancy, in some
embodiments, consists of a tumor properties gene group. The at
least four gene groups associated with cancer microenvironment, in
some embodiments, consists of tumor-promoting immune
microenvironment group, anti-tumor immune microenvironment group,
angiogenesis group, and fibroblasts group.
[0390] It should be appreciated that act 4024 may be performed
using any number of gene groups associated with cancer malignancy
and cancer microenvironment. For example, MF profiles may be
determined using set of gene groups that includes 19 gene groups
where the gene groups associated with cancer malignancy consists of
the proliferation rate group, the PI3K/AKT/mTOR signaling group,
the RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group, and the gene groups associated with cancer
microenvironment consists of the antigen presentation group, the
cytotoxic T and NK cells group, the B cells group, the anti-tumor
microenvironment group, the checkpoint inhibition group, the Treg
group, the MDSC group, the granulocytes group, the cancer
associated fibroblasts group, the angiogenesis group, and the
tumor-promotive immune group.
[0391] In another example, MF profiles may be determined using set
of gene groups that includes 30 gene groups where the gene groups
associated with cancer malignancy consists of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the growth factors group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group, and the gene groups associated with
cancer microenvironment consists of the MHCI group, the MHCII
group, the coactivation molecules group, the effector cells group,
the NK cells group, the T cell traffic group, the T cells group,
the B cells group, the Ml signatures group, the Th1 signature
group, the antitumor cytokines group, the checkpoint inhibition
group, the Treg group, the MDSC group, the granulocytes group, the
M2 signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group.
[0392] The MF profile may be determined using any number of gene
groups (or functional modules) that relate to compositions and
processes present within and/or surrounding the subject's tumor.
Gene groups may comprise any number of genes and may be related to
any composition and process. Further aspects relating to the gene
groups are provided in section "MF Profile Modules". Gene group
expression levels, in some embodiments, may be calculated as a gene
set enrichment (GSEA) score for the gene group. Further aspects
relating to determining MF profiles are provided in section "MF
Profiles".
[0393] Next, process 4020 proceeds to act 4026, where a first set
of visual characteristics for a first plurality of GUI elements
using the first gene group expression levels are determined.
Examples of visual characteristics for a GUI element include color,
shading or pattern, size, and/or shape. A set of visual
characteristics may contain any number of visual characteristics.
GUI elements, for example, include genes, gene groups, biomarkers,
and biomarker information. A plurality of GUI elements may contain
any number of GUI elements. Further aspects of visual
characteristics and GUI elements are shown in and/or described with
reference to FIGS. 3-37.
[0394] Next, process 4020 proceeds to act 4028, where a second set
of visual characteristics for a second plurality of GUI elements
using the second gene group expression levels are determined.
Examples of visual characteristics for a GUI element include color,
shading or pattern, size, and/or shape. A set of visual
characteristics may contain any number of visual characteristics.
GUI elements, for example, include genes, gene groups, biomarkers,
and biomarker information. A plurality of GUI elements may contain
any number of GUI elements.
[0395] Further aspects of visual characteristics and GUI elements
are shown in and/or described with reference to FIGS. 3-37.
[0396] Next, process 4020 proceeds to act 4030, where a GUI
containing a first portion including the first GUI element and a
second portion including the second GUI element is generated. For
example, the MF profile of the subject and other patient related
information may be provided to a user in a GUI as shown in FIGS.
3-37. Further aspects relating to the GUI as shown in FIGS. 3-37
are provided in section "Visualization of MF Profiles".
[0397] Next, process 4020 proceeds to act 4032, where the generated
personalized GUI is presented to a user. In some embodiments, the
GUI may be presented to the user as part of a webpage displayed by
a web browser. In some embodiments, the GUI may be presented to the
user using an application program (different from a web-browser).
For example, in some embodiments, the GUI may be presented to the
user via an application program (e.g., "an app") executing on a
mobile device.
[0398] Such MF portraits provided in the GUI can used for various
clinical purposes described herein including assessing the efficacy
of a treatment for cancer and/or evaluating suitability of a
patient for participating in a clinical trial.
Applications
[0399] Methods and compositions for tumor type characterization as
described herein may be used for various clinical purposes
including, but not limited to, monitoring the progress of cancer in
a subject, assessing the efficacy of a treatment for cancer,
identifying patients suitable for a particular treatment,
evaluating suitability of a patient for participating in a clinical
trial and/or predicting relapse in a subject. Accordingly,
described herein are diagnostic and prognostic methods for cancer
treatment based on tumor type described herein.
[0400] Methods and compositions described herein can be used to
evaluate the efficacy of a cancer treatment, such as those
described herein, given the correlation between cancer type (e.g.,
tumor types) and cancer prognosis. For example, multiple biological
samples, such as those described herein, can be collected from a
subject to whom a treatment is performed either before and after
the treatment or during the course of the treatment. The cancer
type (e.g., the tumor type) in the biological sample from the
subject can be determined using any of the methods described
herein. For example, if the cancer type indicates that the subject
has a poor prognosis and the cancer type changes to a cancer type
indicative of a favorable prognosis after the treatment or over the
course of treatment (e.g., 1.sup.st MF profile cancer type in a
later collected sample when compared to 4.sup.th MF profile cancer
type in an earlier collected sample), it indicates that the
treatment is effective.
[0401] If the subject is identified as not responsive to the
treatment based on cancer type (e.g., no change in cancer type is
identified in response to treatment), a higher dose and/or greater
frequency of dosage of the anti-cancer therapeutic agent may be
administered to the identified subject. Alternatively, an
alternative treatment can be administered to a subject who is found
to not be responsive to a first or subsequent treatment. In some
embodiments, the dosage or frequency of dosage of the therapeutic
agent is maintained, lowered, or ceased in a subject identified as
responsive to the treatment or not in need of further treatment. In
certain embodiments, the dosage or frequency of dosage of the
therapeutic agent is increased in a subject identified as
non-responsive to the treatment. In some embodiments, a first
therapeutic agent is halted and a new (second) therapeutic is used
to treat the subject; or (alternatively) an additional (second)
therapeutic is added in a subject identified as non-responsive to
the first therapeutic agent.
[0402] In some embodiments, cancer types can also be used to
identify a cancer that may be treatable using a specific
anti-cancer therapeutic agent (e.g., a chemotherapy). To practice
this method, the cancer type in a sample (e.g., a tumor biopsy)
collected from a subject having cancer can be determined using
methods described herein. If the cancer type is identified as being
susceptible to treatment with an anti-cancer therapeutic agent, the
method may further comprise administering to the subject having the
cancer an effective amount of the anti-cancer therapeutic
agent.
[0403] In some embodiments, the methods and compositions for cancer
type characterization as described herein may be relied on in the
development of new therapeutics for cancer. In some embodiments,
the cancer type may indicate or predict the efficacy of a new
therapeutic or the progression of cancer in a subject prior to,
during, or after the administration of the new therapy.
[0404] In some embodiments, methods and compositions for cancer
type characterization as described herein may be used to evaluate
suitability of a patient for participating in a clinicial trial. In
some embodiments, the cancer type may be used to include patients
in a clinical trial. In some embodiments, patients having a
specified cancer type (e.g., type A, or 1.sup.st MF profile) are
included in a clinical trial. Herein, cancer types A-D correspond
to the 1.sup.st-4.sup.th MF profile types, respectively. In some
embodiments, patients having any one of two specified cancer types
(e.g., 1.sup.st MF profile or 4.sup.th MF profile) are included in
a clinical trial. In some embodiments, patients having any one of
three specified cancer types (e.g., patients having a 1.sup.st MF
profile, a 2.sup.nd MF profile, or a 3.sup.rd MF profile) are
included in a clinical trial. In some embodiments, patients having
any one of four specified cancer types (e.g., patients having a
1.sup.st MF profile, a 2.sup.nd MF profile, a 3.sup.rd MF profile,
or a 4.sup.th MF profile) are included in a clinical trial.
[0405] In some embodiments, the cancer type may be used to exclude
patients in a clinical trial. In some embodiments, patients having
a specified cancer type (e.g., 1.sup.st MF profile) are excluded
from a clinical trial. In some embodiments, patients having any one
of two specified cancer types (e.g., 1.sup.st MF profile or
4.sup.th MF profile) are excluded from a clinical trial. In some
embodiments, patients having any one of three specified cancer
types (e.g., patients having a 1.sup.st MF profile, a 2.sup.nd MF
profile, or a 3.sup.rd MF profile) are excluded from a clinical
trial. In some embodiments, patients having any one of four
specified cancer types (e.g., patients having a 1.sup.st MF
profile, a 2.sup.nd MF profile, a 3.sup.rd MF profile, or a
4.sup.th MF profile) are excluded from a clinical trial.
[0406] Further, methods and compositions for tumor type
characterization as described herein may be applied for
non-clinical uses including, for example, for research purposes. In
some embodiments, the methods described herein may be used to study
cancer cell function. For example, the methods described herein may
be used to evaluate a tumor process (e.g., tumor metastasis), which
can be used for various purposes including identifying targets that
specifically effect the tumor process being evaluated.
Methods of Treatment
[0407] In certain methods described herein, an effective amount of
anti-cancer therapy described herein may be administered or
recommended for administration to a subject (e.g., a human) in need
of the treatment via a suitable route (e.g., intravenous
administration).
[0408] The subject to be treated by the methods described herein
may be a human patient having, suspected of having, or at risk for
a cancer. Examples of a cancer include, but are not limited to,
melanoma, lung cancer, brain cancer, breast cancer, colorectal
cancer, pancreatic cancer, liver cancer, prostate cancer, skin
cancer, kidney cancer, bladder cancer, or prostate cancer. The
subject to be treated by the methods described herein may be a
mammal (e.g., may be a human). Mammals include, but are not limited
to: farm animals (e.g., livestock), sport animals, laboratory
animals, pets, primates, horses, dogs, cats, mice, and rats.
[0409] A subject having a cancer may be identified by routine
medical examination, e.g., laboratory tests, biopsy, PET scans, CT
scans, or ultrasounds. A subject suspected of having a cancer might
show one or more symptoms of the disorder, e.g., unexplained weight
loss, fever, fatigue, cough, pain, skin changes, unusual bleeding
or discharge, and/or thickening or lumps in parts of the body. A
subject at risk for a cancer may be a subject having one or more of
the risk factors for that disorder. For example, risk factors
associated with cancer include, but are not limited to, (a) viral
infection (e.g., herpes virus infection), (b) age, (c) family
history, (d) heavy alcohol consumption, (e) obesity, and (f)
tobacco use.
[0410] "An effective amount" as used herein refers to the amount of
each active agent required to confer therapeutic effect on the
subject, either alone or in combination with one or more other
active agents. Effective amounts vary, as recognized by those
skilled in the art, depending on the particular condition being
treated, the severity of the condition, the individual patient
parameters including age, physical condition, size, gender and
weight, the duration of the treatment, the nature of concurrent
therapy (if any), the specific route of administration and like
factors within the knowledge and expertise of the health
practitioner. These factors are well known to those of ordinary
skill in the art and can be addressed with no more than routine
experimentation. It is generally preferred that a maximum dose of
the individual components or combinations thereof be used, that is,
the highest safe dose according to sound medical judgment. It will
be understood by those of ordinary skill in the art, however, that
a patient may insist upon a lower dose or tolerable dose for
medical reasons, psychological reasons, or for virtually any other
reasons.
[0411] Empirical considerations, such as the half-life of a
therapeutic compound, generally contribute to the determination of
the dosage. For example, antibodies that are compatible with the
human immune system, such as humanized antibodies or fully human
antibodies, may be used to prolong half-life of the antibody and to
prevent the antibody being attacked by the host's immune system.
Frequency of administration may be determined and adjusted over the
course of therapy, and is generally (but not necessarily) based on
treatment, and/or suppression, and/or amelioration, and/or delay of
a cancer. Alternatively, sustained continuous release formulations
of an anti-cancer therapeutic agent may be appropriate. Various
formulations and devices for achieving sustained release are known
in the art.
[0412] In some embodiments, dosages for an anti-cancer therapeutic
agent as described herein may be determined empirically in
individuals who have been administered one or more doses of the
anti-cancer therapeutic agent. Individuals may be administered
incremental dosages of the anti-cancer therapeutic agent. To assess
efficacy of an administered anti-cancer therapeutic agent, one or
more aspects of a cancer (e.g., tumor formation, tumor growth, or
cancer or tumor Type A-D) may be analyzed.
[0413] Generally, for administration of any of the anti-cancer
antibodies described herein, an initial candidate dosage may be
about 2 mg/kg. For the purpose of the present disclosure, a typical
daily dosage might range from about any of 0.1 .mu.g/kg to 3
.mu.g/kg to 30 .mu.g/kg to 300 .mu.g/kg to 3 mg/kg, to 30 mg/kg to
100 mg/kg or more, depending on the factors mentioned above. For
repeated administrations over several days or longer, depending on
the condition, the treatment is sustained until a desired
suppression or amelioration of symptoms occurs or until sufficient
therapeutic levels are achieved to alleviate a cancer, or one or
more symptoms thereof.
[0414] An exemplary dosing regimen comprises administering an
initial dose of about 2 mg/kg, followed by a weekly maintenance
dose of about 1 mg/kg of the antibody, or followed by a maintenance
dose of about 1 mg/kg every other week. However, other dosage
regimens may be useful, depending on the pattern of pharmacokinetic
decay that the practitioner (e.g., a medical doctor) wishes to
achieve. For example, dosing from one-four times a week is
contemplated. In some embodiments, dosing ranging from about 3
.mu.g/mg to about 2 mg/kg (such as about 3 .mu.g/mg, about 10
.mu.g/mg, about 30 .mu.g/mg, about 100 .mu.g/mg, about 300
.mu.g/mg, about 1 mg/kg, and about 2 mg/kg) may be used. In some
embodiments, dosing frequency is once every week, every 2 weeks,
every 4 weeks, every 5 weeks, every 6 weeks, every 7 weeks, every 8
weeks, every 9 weeks, or every 10 weeks; or once every month, every
2 months, or every 3 months, or longer. The progress of this
therapy may be monitored by conventional techniques and assays
and/or by monitoring cancer Types A-D (; 1.sup.st-4.sup.th MF
profile clusters, respectively) as described herein. The dosing
regimen (including the therapeutic used) may vary over time.
[0415] When the anti-cancer therapeutic agent is not an antibody,
it may be administered at the rate of about 0.1 to 300 mg/kg of the
weight of the patient divided into one to three doses, or as
disclosed herein. In some embodiments, for an adult patient of
normal weight, doses ranging from about 0.3 to 5.00 mg/kg may be
administered. The particular dosage regimen, e.g.., dose, timing,
and/or repetition, will depend on the particular subject and that
individual's medical history, as well as the properties of the
individual agents (such as the half-life of the agent, and other
considerations well known in the art).
[0416] For the purpose of the present disclosure, the appropriate
dosage of an anti-cancer therapeutic agent will depend on the
specific anti-cancer therapeutic agent(s) (or compositions thereof)
employed, the type and severity of cancer, whether the anti-cancer
therapeutic agent is administered for preventive or therapeutic
purposes, previous therapy, the patient's clinical history and
response to the anti-cancer therapeutic agent, and the discretion
of the attending physician. Typically the clinician will administer
an anti-cancer therapeutic agent, such as an antibody, until a
dosage is reached that achieves the desired result.
[0417] Administration of an anti-cancer therapeutic agent can be
continuous or intermittent, depending, for example, upon the
recipient's physiological condition, whether the purpose of the
administration is therapeutic or prophylactic, and other factors
known to skilled practitioners. The administration of an
anti-cancer therapeutic agent (e.g., an anti-cancer antibody) may
be essentially continuous over a preselected period of time or may
be in a series of spaced dose, e.g., either before, during, or
after developing cancer.
[0418] As used herein, the term "treating" refers to the
application or administration of a composition including one or
more active agents to a subject, who has a cancer, a symptom of a
cancer, or a predisposition toward a cancer, with the purpose to
cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve,
or affect the cancer or one or more symptoms of the cancer, or the
predisposition toward a cancer.
[0419] Alleviating a cancer includes delaying the development or
progression of the disease, or reducing disease severity.
Alleviating the disease does not necessarily require curative
results. As used therein, "delaying" the development of a disease
(e.g., a cancer) means to defer, hinder, slow, retard, stabilize,
and/or postpone progression of the disease. This delay can be of
varying lengths of time, depending on the history of the disease
and/or individuals being treated. A method that "delays" or
alleviates the development of a disease, or delays the onset of the
disease, is a method that reduces probability of developing one or
more symptoms of the disease in a given time frame and/or reduces
extent of the symptoms in a given time frame, when compared to not
using the method. Such comparisons are typically based on clinical
studies, using a number of subjects sufficient to give a
statistically significant result.
[0420] "Development" or "progression" of a disease means initial
manifestations and/or ensuing progression of the disease.
Development of the disease can be detected and assessed using
clinical techniques known in the art. Alternatively or in addition
to the clinical techniques known in the art, development of the
disease may be detectable and assessed based on the cancer types
(1.sup.st-4.sup.th MF profile types) described herein. However,
development also refers to progression that may be undetectable.
For purpose of this disclosure, development or progression refers
to the biological course of the symptoms. "Development" includes
occurrence, recurrence, and onset. As used herein "onset" or
"occurrence" of a cancer includes initial onset and/or
recurrence.
[0421] In some embodiments, the anti-cancer therapeutic agent
(e.g., an antibody) described herein is administered to a subject
in need of the treatment at an amount sufficient to reduce cancer
(e.g., tumor) growth by at least 10% (e.g., 20%, 30%, 40%, 50%,
60%, 70%, 80%, 90% or greater). In some embodiments, the
anti-cancer therapeutic agent (e.g., an antibody) described herein
is administered to a subject in need of the treatment at an amount
sufficient to reduce cancer cell number or tumor size by at least
10% (e.g., 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more). In
other embodiments, the anti-cancer therapeutic agent is
administered in an amount effective in altering cancer type (e.g.,
from cancer Type D to cancer Type A). Alternatively, the
anti-cancer therapeutic agent is administered in an amount
effective in reducing tumor formation or metastasis.
[0422] Conventional methods, known to those of ordinary skill in
the art of medicine, may be used to administer the anti-cancer
therapeutic agent to the subject, depending upon the type of
disease to be treated or the site of the disease. The anti-cancer
therapeutic agent can also be administered via other conventional
routes, e.g., administered orally, parenterally, by inhalation
spray, topically, rectally, nasally, buccally, vaginally or via an
implanted reservoir. The term "parenteral" as used herein includes
subcutaneous, intracutaneous, intravenous, intramuscular,
intraarticular, intraarterial, intrasynovial, intrasternal,
intrathecal, intralesional, and intracranial injection or infusion
techniques. In addition, an anti-cancer therapeutic agent may be
administered to the subject via injectable depot routes of
administration such as using 1-, 3-, or 6-month depot injectable or
biodegradable materials and methods.
[0423] Injectable compositions may contain various carriers such as
vegetable oils, dimethylactamide, dimethyformamide, ethyl lactate,
ethyl carbonate, isopropyl myristate, ethanol, and polyols (e.g.,
glycerol, propylene glycol, liquid polyethylene glycol, and the
like). For intravenous injection, water soluble anti-cancer
therapeutic agents can be administered by the drip method, whereby
a pharmaceutical formulation containing the antibody and a
physiologically acceptable excipients is infused. Physiologically
acceptable excipients may include, for example, 5% dextrose, 0.9%
saline, Ringer's solution, and/or other suitable excipients.
Intramuscular preparations, e.g., a sterile formulation of a
suitable soluble salt form of the anti-cancer therapeutic agent,
can be dissolved and administered in a pharmaceutical excipient
such as Water-for-Injection, 0.9% saline, and/or 5% glucose
solution.
[0424] In one embodiment, an anti-cancer therapeutic agent is
administered via site-specific or targeted local delivery
techniques. Examples of site-specific or targeted local delivery
techniques include various implantable depot sources of the agent
or local delivery catheters, such as infusion catheters, an
indwelling catheter, or a needle catheter, synthetic grafts,
adventitial wraps, shunts and stents or other implantable devices,
site specific carriers, direct injection, or direct application.
See, e.g., PCT Publication No. WO 00/53211 and U.S. Pat. No.
5,981,568, the contents of each of which are incorporated by
reference herein for this purpose.
[0425] Targeted delivery of therapeutic compositions containing an
antisense polynucleotide, expression vector, or subgenomic
polynucleotides can also be used. Receptor-mediated DNA delivery
techniques are described in, for example, Findeis et al., Trends
Biotechnol. (1993) 11:202; Chiou et al., Gene Therapeutics: Methods
And Applications Of Direct Gene Transfer (J. A. Wolff, ed.) (1994);
Wu et al., J. Biol. Chem. (1988) 263:621; Wu et al., J. Biol. Chem.
(1994) 269:542; Zenke et al., Proc. Natl. Acad. Sci. USA (1990)
87:3655; Wu et al., J. Biol. Chem. (1991) 266:338. The contents of
each of the foregoing are incorporated by reference herein for this
purpose.
[0426] Therapeutic compositions containing a polynucleotide may be
administered in a range of about 100 ng to about 200 mg of DNA for
local administration in a gene therapy protocol. In some
embodiments, concentration ranges of about 500 ng to about 50 mg,
about 1 .mu.g to about 2 mg, about 5 .mu.g to about 500 .mu.g, and
about 20 .mu.g to about 100 .mu.g of DNA or more can also be used
during a gene therapy protocol.
[0427] Therapeutic polynucleotides and polypeptides can be
delivered using gene delivery vehicles. The gene delivery vehicle
can be of viral or non-viral origin (e.g., Jolly, Cancer Gene
Therapy (1994) 1:51; Kimura, Human Gene Therapy (1994) 5:845;
Connelly, Human Gene Therapy (1995) 1:185; and Kaplitt, Nature
Genetics (1994) 6:148). The contents of each of the foregoing are
incorporated by reference herein for this purpose. Expression of
such coding sequences can be induced using endogenous mammalian or
heterologous promoters and/or enhancers. Expression of the coding
sequence can be either constitutive or regulated.
[0428] Viral-based vectors for delivery of a desired polynucleotide
and expression in a desired cell are well known in the art.
Exemplary viral-based vehicles include, but are not limited to,
recombinant retroviruses (see, e.g., PCT Publication Nos. WO
90/07936; WO 94/03622; WO 93/25698; WO 93/25234; WO 93/11230; WO
93/10218; WO 91/02805; U.S. Pat. Nos. 5,219,740 and 4,777,127; GB
Patent No. 2,200,651; and EP Patent No. 0 345 242),
alphavirus-based vectors (e.g., Sindbis virus vectors, Semliki
forest virus (ATCC VR-67; ATCC VR-1247), Ross River virus (ATCC
VR-373; ATCC VR-1246) and Venezuelan equine encephalitis virus
(ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532)), and
adeno-associated virus (AAV) vectors (see, e.g., PCT Publication
Nos. WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO
95/11984 and WO 95/00655). Administration of DNA linked to killed
adenovirus as described in Curiel, Hum. Gene Ther. (1992) 3:147 can
also be employed. The contents of each of the foregoing are
incorporated by reference herein for this purpose.
[0429] Non-viral delivery vehicles and methods can also be
employed, including, but not limited to, polycationic condensed DNA
linked or unlinked to killed adenovirus alone (see, e.g., Curiel,
Hum. Gene Ther. (1992) 3:147); ligand-linked DNA (see, e.g., Wu, J.
Biol. Chem. (1989) 264:16985); eukaryotic cell delivery vehicles
cells (see, e.g., U.S. Pat. No. 5,814,482; PCT Publication Nos. WO
95/07994; WO 96/17072; WO 95/30763; and WO 97/42338) and nucleic
charge neutralization or fusion with cell membranes. Naked DNA can
also be employed. Exemplary naked DNA introduction methods are
described in PCT Publication No. WO 90/11092 and U.S. Pat. No.
5,580,859. Liposomes that can act as gene delivery vehicles are
described in U.S. Pat. No. 5,422,120; PCT Publication Nos. WO
95/13796; WO 94/23697; WO 91/14445; and EP Patent No. 0524968.
Additional approaches are described in Philip, Mol. Cell. Biol.
(1994) 14:2411, and in Woffendin, Proc. Natl. Acad. Sci. (1994)
91:1581. The contents of each of the foregoing are incorporated by
reference herein for this purpose. It is also apparent that an
expression vector can be used to direct expression of any of the
protein-based anti-cancer therapeutic agents (e.g., anti-cancer
antibody). For example, peptide inhibitors that are capable of
blocking (from partial to complete blocking) a cancer causing
biological activity are known in the art.
[0430] In some embodiments, more than one anti-cancer therapeutic
agent, such as an antibody and a small molecule inhibitory
compound, may be administered to a subject in need of the
treatment. The agents may be of the same type or different types
from each other. At least one, at least two, at least three, at
least four, or at least five different agents may be
co-administered. Generally anti-cancer agents for administration
have complementary activities that do not adversely affect each
other. Anti-cancer therapeutic agents may also be used in
conjunction with other agents that serve to enhance and/or
complement the effectiveness of the agents. Treatment efficacy can
be assessed by methods well-known in the art, e.g., monitoring
tumor growth or formation in a patient subjected to the treatment.
Alternatively or in addition to, treatment efficacy can be assessed
by monitoring tumor type over the course of treatment (e.g.,
before, during, and after treatment). See, e.g., Example 5
below.
Combination Therapy
[0431] Compared to monotherapies, combinations of treatment
approaches showed higher efficacy in many studies, but the choice
of remedies to be combined and designing the combination therapy
regimen remain speculative. Given that the number of possible
combinations is now extremely high, there is great need for a tool
that would help to select drugs and combinations of remedies based
on objective information about a particular patient. Use of cancer
MF profiles for designing or electing a specific combination
therapy establishes a scientific basis for choosing the optimal
combination of preparations.
[0432] When using MF profiles for designing a combination therapy
one can define a rational level of portrait detail. It is advisable
to create a portrait of the modules with known therapeutic
effectors, while modules that currently can't be influenced using
medical approaches could be excluded. At the same time, there may
be modules that are important to the outcome of the disease, having
no effectors embodied in drugs or other therapies (e.g., radiation,
cell therapy, oncolytic viruses, etc.). Such modules may have
scientific value and their preservation is reasonable in portraits
intended for research work.
[0433] As noted above, also provided herein are methods of treating
a cancer or recommending treating a cancer using any combination of
anti-cancer therapeutic agents or one or more anti-cancer
therapeutic agents and one or more additional therapies (e.g.,
surgery and/or radiotherapy). The term combination therapy, as used
herein, embraces administration of more than one treatment (e.g.,
an antibody and a small molecule or an antibody and radiotherapy)
in a sequential manner, that is, wherein each therapeutic agent is
administered at a different time, as well as administration of
these therapeutic agents, or at least two of the agents or
therapies, in a substantially simultaneous manner.
[0434] Sequential or substantially simultaneous administration of
each agent or therapy can be affected by any appropriate route
including, but not limited to, oral routes, intravenous routes,
intramuscular, subcutaneous routes, and direct absorption through
mucous membrane tissues. The agents or therapies can be
administered by the same route or by different routes. For example,
a first agent (e.g., a small molecule) can be administered orally,
and a second agent (e.g., an antibody) can be administered
intravenously.
[0435] As used herein, the term "sequential" means, unless
otherwise specified, characterized by a regular sequence or order,
e.g., if a dosage regimen includes the administration of an
antibody and a small molecule, a sequential dosage regimen could
include administration of the antibody before, simultaneously,
substantially simultaneously, or after administration of the small
molecule, but both agents will be administered in a regular
sequence or order. The term "separate" means, unless otherwise
specified, to keep apart one from the other. The term
"simultaneously" means, unless otherwise specified, happening or
done at the same time, i.e., the agents of the invention are
administered at the same time. The term "substantially
simultaneously" means that the agents are administered within
minutes of each other (e.g., within 10 minutes of each other) and
intends to embrace joint administration as well as consecutive
administration, but if the administration is consecutive it is
separated in time for only a short period (e.g., the time it would
take a medical practitioner to administer two agents separately).
As used herein, concurrent administration and substantially
simultaneous administration are used interchangeably. Sequential
administration refers to temporally separated administration of the
agents or therapies described herein.
[0436] Combination therapy can also embrace the administration of
the anti-cancer therapeutic agent (e.g., an antibody) in further
combination with other biologically active ingredients (e.g., a
vitamin) and non-drug therapies (e.g., surgery or
radiotherapy).
[0437] It should be appreciated that any combination of anti-cancer
therapeutic agents may be used in any sequence for treating a
cancer. The combinations described herein may be selected on the
basis of a number of factors, which include but are not limited to
the effectiveness of altering identified tumor type (e.g., Type
A-D), reducing tumor formation or tumor growth, and/or alleviating
at least one symptom associated with the cancer, or the
effectiveness for mitigating the side effects of another agent of
the combination. For example, a combined therapy as provided herein
may reduce any of the side effects associated with each individual
members of the combination, for example, a side effect associated
with an administered anti-cancer agent.
[0438] In some embodiments, an anti-cancer therapeutic agent is an
antibody, an immunotherapy, a radiation therapy, a surgical
therapy, and/or a chemotherapy.
[0439] Examples of the antibody anti-cancer agents include, but are
not limited to, alemtuzumab (Campath), trastuzumab (Herceptin),
Ibritumomab tiuxetan (Zevalin), Brentuximab vedotin (Adcetris),
Ado-trastuzumab emtansine (Kadcyla), blinatumomab (Blincyto),
Bevacizumab (Avastin), Cetuximab (Erbitux), ipilimumab (Yervoy),
nivolumab (Opdivo), pembrolizumab (Keytruda), atezolizumab
(Tecentriq), avelumab (Bavencio), durvalumab (Imfinzi), and
panitumumab (Vectibix).
[0440] Examples of an immunotherapy include, but are not limited
to, a PD-1 inhibitor or a PD-L1 inhibitor, a CTLA-4 inhibitor,
adoptive cell transfer, therapeutic cancer vaccines, oncolytic
virus therapy, T-cell therapy, and immune checkpoint
inhibitors.
[0441] Examples of radiation therapy include, but are not limited
to, ionizing radiation, gamma-radiation, neutron beam radiotherapy,
electron beam radiotherapy, proton therapy, brachytherapy, systemic
radioactive isotopes, and radiosensitizers.
[0442] Examples of a surgical therapy include, but are not limited
to, a curative surgery (e.g., tumor removal surgery), a preventive
surgery, a laparoscopic surgery, and a laser surgery.
[0443] Examples of the chemotherapeutic agents include, but are not
limited to, Carboplatin or Cisplatin, Docetaxel, Gemcitabine,
Nab-Paclitaxel, Paclitaxel, Pemetrexed, and Vinorelbine.
[0444] Additional examples of chemotherapy include, but are not
limited to, Platinating agents, such as Carboplatin, Oxaliplatin,
Cisplatin, Nedaplatin, Satraplatin, Lobaplatin, Triplatin,
Tetranitrate, Picoplatin, Prolindac, Aroplatin and other
derivatives; Topoisomerase I inhibitors, such as Camptothecin,
Topotecan, irinotecan/SN38, rubitecan, Belotecan, and other
derivatives; Topoisomerase II inhibitors, such as Etoposide
(VP-16), Daunorubicin, a doxorubicin agent (e.g., doxorubicin,
doxorubicin hydrochloride, doxorubicin analogs, or doxorubicin and
salts or analogs thereof in liposomes), Mitoxantrone, Aclarubicin,
Epirubicin, Idarubicin, Amrubicin, Amsacrine, Pirarubicin,
Valrubicin, Zorubicin, Teniposide and other derivatives;
Antimetabolites, such as Folic family (Methotrexate, Pemetrexed,
Raltitrexed, Aminopterin, and relatives or derivatives thereof);
Purine antagonists (Thioguanine, Fludarabine, Cladribine,
6-Mercaptopurine, Pentostatin, clofarabine, and relatives or
derivatives thereof) and Pyrimidine antagonists (Cytarabine,
Floxuridine, Azacitidine, Tegafur, Carmofur, Capacitabine,
Gemcitabine, hydroxyurea, 5-Fluorouracil (5FU), and relatives or
derivatives thereof); Alkylating agents, such as Nitrogen mustards
(e.g., Cyclophosphamide, Melphalan, Chlorambucil, mechlorethamine,
Ifosfamide, mechlorethamine, Trofosfamide, Prednimustine,
Bendamustine, Uramustine, Estramustine, and relatives or
derivatives thereof); nitrosoureas (e.g., Carmustine, Lomustine,
Semustine, Fotemustine, Nimustine, Ranimustine, Streptozocin, and
relatives or derivatives thereof); Triazenes (e.g., Dacarbazine,
Altretamine, Temozolomide, and relatives or derivatives thereof);
Alkyl sulphonates (e.g., Busulfan, Mannosulfan, Treosulfan, and
relatives or derivatives thereof); Procarbazine; Mitobronitol, and
Aziridines (e.g., Carboquone, Triaziquone, ThioTEPA,
triethylenemalamine, and relatives or derivatives thereof);
Antibiotics, such as Hydroxyurea, Anthracyclines (e.g., doxorubicin
agent, daunorubicin, epirubicin and relatives or derivatives
thereof); Anthracenediones (e.g., Mitoxantrone and relatives or
derivatives thereof); Streptomyces family antibiotics (e.g.,
Bleomycin, Mitomycin C, Actinomycin, and Plicamycin); and
ultraviolet light.
EXAMPLES
[0445] In order that the invention described herein may be more
fully understood, the following examples are set forth. The
examples described in this application are offered to illustrate
the methods, compositions, and systems provided herein and are not
to be construed in any way as limiting their scope.
Example 1
Methods
Molecular and Clinical Data
[0446] Genomic, transcriptomic and clinical data for 23 solid
tumors from The Cancer Genome Atlas (TCGA) were downloaded via the
TCGA data portal (https://tcga-data.nci.nih.gov). Mutations were
obtained out of corresponding TCGA MAF files. RNA-sequencing data
were downloaded and processed in FPKM units. Tumor samples were
used.
Creating Biologically Relevant Gene Sets to Evaluate Processes in a
Tumor Microenvironment
[0447] To visualize the composition of a patient's tumor
microenvironment and the immune system processes occurring within
the tumor, an approach based on analysis of signature gene lists
was used. The analysis required associating target gene expression
with biological processes and/or cell functions. The signatures
used in the analysis comprised a diverse set of adaptive and innate
immune cell types, as well as tumor tissue functioning and growth
associated processes. The latter included tumor-supporting
components of microenvironment: cancer-associated fibroblasts,
tumor vasculature abundance and angiogenesis-inducing processes.
Tumor purity (cellularity) indicating percentage of malignant cells
in a tumor was also included in the visualization of the patient's
cancer-immune portrait to represent size of the malignant
compartment. The immune-related gene expression signatures
comprised 327 genes. Genes highly specific to the functional
process they describe were selected.
[0448] The list of gene set annotations is shown in Table 2. The
created gene sets were compared to The Molecular Signatures
Database (MSigDB), a publicly available collection of annotated
gene sets. The similarity between proposed gene sets and the MSigDB
collection was calculated using a hypergeometric test
(FDR<0.05). Each gene was scientifically validated to represent
its true influence on the process for which it was designated. Gene
annotations were confirmed using scientific publications.
TABLE-US-00002 TABLE 2 List of Gene Set Annotations. Level 1 Level
2 Level 3 GMT Anti-tumor Antigen MHCI HLA-A HLA-C TAP1 immune
infiltrate presentation HLA-B B2M TAP2 MHCII HLA-DRA HLA-DOA
HLA-DQA1 HLA-DRB1 HLA-DPA1 HLA-DRB5 HLA-DOB HLA-DPB1 HLA-DQA2
HLA-DPB2 HLA-DMB HLA-DQB2 HLA-DMA HLA-DQB1 HLA-DRB6 Coactivation
CD80 TNFRSF4 CD83 molecules CD40 CD86 COSLG CD28 Cytotoxic T and
Effector cells IFNG LCK FASLG NK cells PRF1 GNLY TBX21 ZAP70 GZMB
CD8A GZMA GZMK CD8B EOMES NK cells NKG7 KIR2DS1 GNLY KLRK1 CD244
KIR2DS3 KIR2DL4 GZMH KLRC2 CD160 KIR2DS2 IFNG CD226 NCR1 KIR2DS4
KIR2DS5 T cell traffic CXCL9 CCR7 CCL3 CXCL10 CXCL11 CCL4 CXCR3
CCL21 CCL5 CX3CL1 CCL2 T cells EOMES CD3G UBASH3A CD3E LCK CD3D
TRBC2 ITK TRBC1 TBX21 TRAC TRAT1 B cells B cells CD19 CR2 CD79B
CD24 CD79A CD27 CD22 TNFRSF13C NFRSF13B MS4A1 TNFRSF17 BLK
Anti-tumor M1 signatures NOS2 TNF IL23A microenvironment IL12B
IL12A IL1B SOCS3 Th1 signature IFNG CD27 IL15 CD40LG IL2 TBX21 LTA
Antitumor cytokines HMGB1 TNF NFSF10 IFNB1 IFNA2 FASLG CCL3
Tumor-promoting Checkpoint Checkpoint PDCD1 CD274 HAVCR2 immune
infiltrate inhibition inhibition CTLA4 LAG3 VSIR PDCD1LG2 BTLA
CXCL12 IL10 Treg Treg TGFB1 TNFRSF1B CCL1 TGFB2 CCL17 CCL2 TGFB3
CXCR4 CCL5 FOXP3 CCR4 CXCL13 MDSC MDSC CTLA4 CCL22 CCL28 IDO1 NOS2
CCL4 ARG1 CYBB CCL8 IL4R CXCR4 CCR2 IL10 CD33 CCL3 TGFB1 CXCL1 CCL5
TGFB2 CXCL5 CSF1 TGFB3 CCL2 CXCL8 Granulocytes Granulocytes CXCL8
PRG2 MS4A2 CXCL2 EPX CPA3 CXCL1 RNASE2 IL4 CCL11 RNASE3 IL5 CCL24
IL5RA IL13 KITLG GATA1 SIGLEC8 CCL5 SIGLEC8 MPO CXCL5 PRG3 ELANE
CCR3 CMA1 PRTN3 CCL26 TPSAB1 CTSG Tumor- M2 signature IL10 MRC1
MSR1 promoting VEGFA CSF1 CD163 immune infiltrate TGFB1 LRP1 CSF1R
IDO1 ARG1 PTGS1 PTGES Th2 signature IL4 IL13 IL25 IL5 IL10 GATA3
Protumor cytokines IL10 TGFB2 IL22 TGFB1 TGFB3 MIF Complement CFD
CD55 CR1 inhibition CFI CD46 Fibroblasts CAF CAF LGALS1 TGFB1 FAP
COL1A1 TGFB2 LRP1 COL1A2 TGFB3 CD248 COL4A1 ACTA2 COL6A1 COL5A1
FGF2 COL6A2 COL6A3 Angiogenesis Angiogenesis Angiogenesis VEGFA KDR
MMRN1 VEGFB ANGPT1 LDHA VEGFC ANGPT2 HIF1A PDGFC TEK EPAS1 CXCL8
VWF CA9 CXCR2 CDH5 SPP1 FLT1 NOS3 LOX PIGF KDR SLC2A1 CXCL5 VCAM1
LAMP3 Tumor Properties Proliferation rate Proliferation rate MKI67
AURKA MYBL2 ESCO2 AURKB BUB1 CETN3 CDK4 PLK1 CDK2 CDK6 CCNB1 CCND1
PRC1 MCM2 CCNE1 E2F1 MCM6 Activated PI3K/AKT/mTOR PIK3CA AKT1 PRKCA
signaling signaling PIK3CB MTOR AKT2 pathways PIK3CG PTEN AKT3
PIK3CD RAS/RAF/MEK BRAF MAP2K1 MKNK1 signaling FNTA MAP2K2 MKNK2
FNTB Receptor tyrosine ALK MET ERBB4 kinases expression AXL NTRK1
ERBB3 KIT FGFR1 BCR-ABL EGFR FGFR2 PDGFRA ERBB2 FGFR3 PDGFRB FLT3
Growth Factors NGF FGF7 IL7 CSF3 IGF1 FGF2 CSF2 IGF2 Tumor Tumor
suppressors TP53 DCN AIM2 suppressors SIK1 MTAP RB1 PTEN Metastasis
Metastasis signature ESRP1 SMARCA4 NEDD9 signature CTSL SNAI2 PAPPA
HOXA1 TWIST1 HPSE Antimetastatic Antimetastatic KISS1 TCF21 NCAM1
factors factors ADGRG1 CDH1 MITF BRMS1 PCDH10 Mutation status
Mutation status Major Recurrent Mutations Additional modules Purity
Malignant cells Non-malignant 1-Purity microenvironment
Quantification of Process Intensity
[0449] ssGSEA enrichment scores (ES) were calculated using the GSVA
R package with default parameters (gsea method with type="ssgsea";
normalized=True). ES were then transformed into z-scores and
clipped to the range [-4, 4] for each functional process in each
dataset.
[0450] For tumor purity estimation, CPE metric values obtained from
Aran et al. Systematic pan-cancer analysis of tumour purity. Nat
Commun. Nature Publishing Group; 2015;6:8971 were used. Tumor
infiltration cell number (nonmalignant cell number) was calculated
as 1-tumor purity.
[0451] Mutation data including presence of driver mutations and
total number of nonsynonymous mutations for the "Mutation status"
node was obtained from TCGA MAF files.
Quantification of Tumor Microenvironment with Deconvolution
Methods
[0452] Cell type deconvolution was performed using CIBERSORT with
LM22 matrix and MCP-counter, capable of estimating the abundance of
tissue-infiltrating immune and stromal cell populations according
to gene expression. In addition, single-sample GSEA (ssGSEA), an
extension of Gene Set Enrichment Analysis (GSEA), was performed on
widely used gene signatures of immune infiltrate.
Hierarchical Organization of Processes
[0453] Biological properties describing the tumor microenvironment
and tumor processes were hierarchically organized according to
their associated biology. A clustered graph structure was created
from descriptions from the highest to the lowest granularity
including genes, biological processes including high-level and
low-level processes, and biological categories. The high-level
processes were chosen as follows: tumor (as tumor burden or tumor
purity), tumor nonmalignant microenvironment comprised of the
angiogenesis module, cancer-associated fibroblasts,
tumor-promoting, and anti-tumor immune infiltrates. As a
non-limiting example, CD80 genes were made part of a "co-activation
molecules" process, which was a part of an "antigen presentation"
process, which in turn was part of an "anti-tumor immune
infiltration" module. Gene annotations for each high- or low-level
process are presented in Table 2. Using the determined hierarchical
organization of the tumor processes, a cancer-immune portrait was
visualized at different levels of detail.
Visualization of the Cancer-Immune Portrait
[0454] Portraits were visualized as a graph based structure using
Mathematica 11 standard packages (Wolfram Research, USA). A node
size that described an intensity of a process in a particular
patient was taken according to a normalized score calculated for
process intensity. A distribution of ssGSEA enrichment scores for
each process was mapped to the range of (0,1), by a cumulative
distribution function (CDF) within the corresponding TCGA cohort.
Driver mutations influencing therapeutic and prognostic outcomes
were depicted in the tumor properties group as the "Mutation
status" node representing a total number of nonsynonymous mutations
found in the patient tumor, while the upper genes arising from this
node demonstrated recurrent mutations. The "mutation status" node
size was also transformed to the range of (0,1) by CDF from the
corresponding cohort distribution.
[0455] All the processes were labeled either anti-tumor or
pro-tumor. Anti-tumor processes were colored in a blue gradient,
pro-tumor processes were colored in a burgundy gradient. The
intensity (i.e., intensity of the shade or darkness/lightness)
represented process intensity. Gene nodes were accorded a fixed
size and color using the same method as the processes. The size of
the "Malignant cells", as well as the "Non-malignant
microenvironment" nodes were visualized based on the tumor purity.
The same visualization principles were applied to the molecular
functional portraits with different levels of detail.
Survival Analysis
[0456] Survival curves were calculated according to the
Kaplan-Meier method, and differences between curves were assessed
using the log-rank test.
Dense Clustering
[0457] Edges that represent<40% samples correlation were removed
to get connected graphs with<1% node connectivity (.about.0.6%
for pan-cancer and SKCM). Node connectivity was calculated using
the NetworkX python package. All edges with weight>50 were
removed, leading to graph connectivity break.
[0458] The similarity of tumor samples was measured using the
Pearson correlation [-1, 1] between process intensities (ssGSEA
enrichment scores). Similarities in the space of 28 processes were
calculated using python pandas and SciPy. Distance matrix was
converted into a NetworkX graph as follows: each sample formed a
node; two nodes formed an edge with weight equal to their Pearson
correlation. Later edges with weight<0.4 were removed. The
Louvain community detection algorithm was applied to calculate
graph partitioning into clusters using python-louvain with default
parameters. Final partitions were labeled as Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively).
[0459] Dense clusters were visualized in Cytoscape (v3.4.0). Nodes
were organized using "Perfuse force directed layout" (default
spring coefficient=le-5, number of iterations=100). Node size
represents the number of its neighbors (adjacent edges). Node color
corresponds to tumor subtype (A-D) unless otherwise specified.
K-Means Clustering
[0460] 28 functional processes were organized into four clusters
using GENE-E k-means algorithm with 20,000 iterations using the
Pearson correlation as a distance metric.
Comparison of Clusters by the Process Values
[0461] Comparison of each process activity between cluster pairs
was performed by t-test. Per-cluster prevalence and deficiency of
mutations in the driver genes were analyzed by the Fisher exact
test.
Heatmaps
[0462] Python-matplotlib (v1.5.1) or python-seaborn (v0.7.1) or
GENE-E were used to create heatmaps. The Pearson correlation was
used as the default similarity metric (unless otherwise mentioned)
for correlation matrixes. Hierarchical clustering was performed
using complete linkage and euclidean distance for correlation
matrixes clustering.
tSNE
[0463] tSNE analysis was performed by Rtsne (v0.13) package in R
and visualized by R plot function.
Validating Prevalent (Dominant) Molecular-Functional Types of
Cancers
[0464] In order to validate the proposed molecular-functional types
of cancer organization, additional analysis was performed. The
additional analysis showed the dominant clusters of MF profiles in
20 epithelial cancers. The additional analysis further showed that
the quantified melanoma microenvironment activity by functional
process scores formed explicit clusters, but that the underlying
expressions of the 10,000 most expressed genes did not, due to the
increased noise generated from the addition of multiple unnecessary
and unrelated genes. In that sense, expression profiles of 298
genes composing functional processes showed a fuzzier structure
with less distinct clusters than expression profiles of functional
process scores. Pan-cancer patient correlation analysis also
confirmed the formation of distinct types of cancer
molecular-functional portraits.
Prevalent Types Analysis
[0465] MCP-counter, CIBERSORT, and cell deconvolution algorithms
were applied to the RNA-Seq data of 470 melanoma patients. This
analysis demonstrated that Type A, B, C and D clusters
(1.sup.st-4.sup.th MF profile clusters, respectively) were
segregated using the MCP-counter but not with CIBERSORT. Notably,
the MCP-counter revealed the main types of leukocytes and
lymphocytes, tumor-associated fibroblasts, and endothelial
cells.
[0466] CIBERSORT with LM22 matrix provided a composition of
leukocyte/lymphocyte infiltrate, but did not take into account
endothelial cells and CAFs. However, Types A and B (first and
second MF profile clusters, respectively) melanomas displaying
dominant CD8 T cells were segregated from Types C and D (third and
fourth MF profile clusters, respectively) displaying dominant
tumor-associated macrophages (e.g., M2 macrophages) using
CIBERSORT/LM22.
[0467] Deconvolution methods based on gene sets proposed by
Senbabaoglu et al. were analyzed. See Senbabaoglu et al. Tumor
immune microenvironment characterization in clear cell renal cell
carcinoma identifies prognostic and immunotherapeutically relevant
messenger RNA signatures; Genome Biology (2016) 17:231, which is
herein incorporated by reference for this purpose. However, this
analysis was unable to differentiate between the four tumor cell
clusters corresponding to Types A-D (1.sup.st-4.sup.th MF profile
clusters, respectively). Driver mutations are thought to be key
factors of tumorigenesis. In order to analyze whether driver
mutations are associated with any of the prevalent four types of
melanomas, the abundance of such mutations in each cluster along
with their enrichment or deficiency in the cluster was computed.
Fisher's exact test was used to evaluate the cluster's enrichment
with samples containing mutations in any given gene. However, after
correction for multiple testing, no driver genes showed significant
(FDR<0.05) enrichment. The APC gene (FDR=0.084) had almost
reached a significant cutoff as being overrepresented (incidence
ratio 2.38) in Type D melanomas.
[0468] Results for 38 driver mutations found in different melanoma
types are provided in Table 3. Values that were statistically
significant in single tests (p-value<0.05) are marked.
Mutation-rich melanoma types (underlined) had a relative abundance
over 1.0, and mutation-deficient melanoma types (bold) had a
relative abundance under 1.0.
TABLE-US-00003 TABLE 3 Percent of patients with indicated mutations
and relative abundance of these mutations in the melanoma cohort
(470 patients). Patients with indicated mutation Relative abundance
of mutation compared in the given melanoma type to the whole
melanoma cohort A B C D A B C D APC 5.1% 8.6% 2.9% 17.7% 0.68 1.16
0.39 2.38 ARID1A 2.2% 5.2% 5.8% 3.8% 0.51 1.22 1.37 0.89 ATM 3.6%
5.2% 5.8% 3.8% 0.78 1.11 1.24 0.81 ATRX 4.3% 6.0% 7.2% 2.5% 0.82
1.14 1.37 0.48 BAP1 0.7% 2.6% 0.7% 2.5% 0.49 1.74 0.49 1.70 BRAF
50.7% 50.0% 57.2% 32.9% 1.03 1.01 1.16 0.67 BRCA2 5.1% 4.3% 8.0%
7.6% 0.82 0.70 1.29 1.23 CDH1 0.0% 1.7% 2.2% 2.5% 0.00 1.16 1.46
1.70 CDKN2A 6.5% 12.1% 7.2% 11.4% 0.73 1.35 0.81 1.28 CTCF 0.0%
0.0% 1.4% 1.3% 0.00 0.00 2.28 1.99 CTNNB1 4.3% 5.2% 4.3% 5.1% 0.93
1.11 0.93 1.08 DNMT3 2.2% 3.4% 1.4% 3.8% 0.85 1.35 0.57 1.49 EGFR
7.2% 1.7% 3.6% 13.9% 1.22 0.29 0.61 2.34 FBXW7 1.4% 1.7% 4.3% 5.1%
0.49 0.58 1.46 1.70 FLT3 4.3% 12.9% 8.0% 11.4% 0.50 1.49 0.92 1.31
GATA3 1.4% 2.6% 0.0% 6.3% 0.68 1.22 0.00 2.98 HRAS 0.7% 1.7% 1.4%
0.0% 0.68 1.62 1.37 0.00 IDH1 3.6% 6.9% 2.2% 6.3% 0.81 1.55 0.49
1.42 KRAS 1.4% 2.6% 2.2% 2.5% 0.68 1.22 1.02 1.19 MAP3K1 1.4% 0.9%
0.7% 0.0% 1.71 1.02 0.85 0.00 MTOR 3.6% 6.9% 5.1% 7.6% 0.66 1.25
0.92 1.38 NAV3 5.1% 12.9% 12.3% 11.4% 0.50 1.27 1.21 1.12 NCOR1
0.7% 4.3% 7.2% 12.7% 0.13 0.78 1.31 2.29 NF1 7.2% 13.8% 8.7% 20.3%
0.63 1.20 0.76 1.77 NOTCH1 2.2% 2.6% 2.2% 5.1% 0.79 0.94 0.79 1.83
NPM1 0.0% 0.9% 1.4% 1.3% 0.00 1.02 1.71 1.49 NRAS 18.1% 30.2% 23.9%
41.8% 0.68 1.13 0.89 1.56 PBRM1 3.6% 4.3% 4.3% 6.3% 0.81 0.97 0.98
1.42 PIK3CA 2.2% 1.7% 2.2% 2.5% 1.02 0.81 1.02 1.19 PIK3R1 2.2%
0.9% 1.4% 0.0% 1.71 0.68 1.14 0.00 PTEN 2.9% 6.9% 8.7% 1.3% 0.55
1.30 1.64 0.24 RB1 2.9% 2.6% 1.4% 1.3% 1.37 1.22 0.68 0.60 RUNX1
1.4% 0.0% 0.0% 0.0% 3.41 0.00 0.00 0.00 SETD2 1.4% 9.5% 3.6% 7.6%
0.28 1.86 0.71 1.49 STAG2 0.7% 3.4% 2.2% 0.0% 0.43 2.03 1.28 0.00
TAF1 0.7% 6.0% 2.2% 3.8% 0.24 2.03 0.73 1.28 TP53 10.1% 14.7% 7.2%
17.7% 0.87 1.26 0.62 1.52 VHL 0.0% 0.0% 0.7% 1.3% 0.00 0.00 1.71
2.98
[0469] Prevalent melanoma types appeared to be enriched or
deficient in distinct sets of driver mutations. It appeared that
key MAPK pathway genes varied according to the mutation rate among
four melanoma types. In addition, no single factor explicitly
defined a melanoma type to a specific mutation. Taken together,
these results suggested that mutations are associated with but do
not determine the molecular-functional types of these cancers
(i.e., cancer Types A-D; 1.sup.st-4.sup.th MF profile clusters,
respectively).
Classification of Tumor Organization into Four Prevalent Types
[0470] The following procedure was used for preprocessing data from
TCGA: [0471] 1) Calculated TCGA X cancer cohort processes values
using ssGSEA. Calculated mean and standard of each process.
Obtained Z-score TCGA X cancer cohort.
[0471] ZscoredSampleProcess x = SampleProcess x - mean (
TCGACohortProcess x ) std ( TCGACohortProcess x ) ##EQU00001##
[0472] 2) Calculated patient's processes values using ssGSEA.
Obtained Z-score patients processes values using mean and standard
from previous step cancer cohort.
[0472] ZscoredPatentProcess x = PatentsProcess x - mean (
TCGACohortProcess x ) std ( TCGACohortProcess x ) ##EQU00002##
[0473] 3) Patient's sample was classified according to MF profile
type with the closest (smallest) distance from patient's processes
z-scored vector to MFP cancer cohort centroids. [0474] 4) Distance
was calculated as Euclidean distance in z-scored processes space or
(1-pearson/spearman correlation). [0475] 5) 1-distance to the each
of MF profile types was treated as a similarity measure in the case
of intermediate cases (if, for example, a patient's sample was very
close to 2 prevalent types resulting in mixed features from both
types).
[0476] The following procedure was used for preprocessing other
data types (e.g., data from DNA microarrays, other references,
outlying patient data from TCGA X cancer cohort PCA projection into
2-dimm space): [0477] 1) Calculated TCGA X cancer cohort processes
values using ssGSEA, Z-score TCGA X cancer cohort. [0478] 2)
Obtained a cohortA of patients with X cancer, processed them
similarly as the patient (>40 samples). Calculated cohortA
processes values using ssGSEA. [0479] 3) Calculated patient's
processes values using ssGSEA. Obtained Z-score for combined
cohortA and the patient. [0480] 4) If z-scored TCGA X cancer cohort
and z-scored cohortA admixed on combined PCA 2-dimm projection, the
procedure continued with step 3 described herein.
Example 2
Creating a Molecular Functional (MF) Portrait of a Tumor
[0481] A bioinformatics pipeline was constructed to determine tumor
properties (e.g., malignant properties, non-malignant properties),
and depict the tumor properties in a Molecular Functional Portrait
(MF profile). The MF profile was designed to depict tumor cell
composition and functional activities, and to facilitate the
practical use of such information in cancer therapy. An exemplary
bioinformatics pipeline for constructing a tumor portrait is shown
in FIG. 1A. An exemplary MF profile is shown in FIG. 1B.
[0482] In brief, the bioinformatics pipeline was used to (i)
evaluate the intrinsic properties of tumor cells such as oncogenic
pathways, proliferation rate, epithelial-mesenchymal transition
(EMT), and metastatic capacities; (ii) reconstruct the
comprehensive immune, stromal and vascular networks of the tumor
microenvironment; (iii) quantify the functional activities of
different tumor associated cell types; and (iv) determine the
intensity of processes that collectively either stimulated or
inhibited progressive tumor growth.
[0483] Tumor cell composition was reconstructed from RNA-Seq and
Exome-Seq data of tumor and normal tissue using in silico methods
for inferring tumor purity and through deconvolution of the
expression profiles for assessing functional subsets of both
infiltrating hematopoietic cells and stromal cells. RNA-Seq data
also provided a measure of certain cellular processes based on the
expression of specific gene signatures associated with defined
biological functions distributed among different cell types, such
as antigen presentation, metastasis and inflammation.
[0484] A comprehensive cancer model was formulated by analysis of
more than 373 publications, and yielded 28 functional modules
listed in Table 2. The intensity of the "Mutation status" module
was evaluated through quantitating mutations in 38 driver genes.
The intensities of the remaining 27 modules were evaluated by gene
set enrichment analysis (ssGSEA) on custom built signatures, which
enabled estimation of the activity of different intratumoral
processes. Taken together, these modules inherently reflected the
relative content of the main cell types in a tumor tissue.
[0485] The qualitative and quantitative functional properties as
the intensities of processes in 28 functional modules were
graphically depicted in FIG. 1B. Module size corresponds to its
ssGSEA enrichment score (or mutation counts) normalized within the
same TCGA cohort. Colors reflect the module pro- or anti-cancer
activity. Solid shades without cross-marking were assigned to the
modules that promote tumor growth, while shades shades with
cross-marking were assigned to those having anti-cancer activity.
The coloration of the modules was also dependent on the ssGSEA
score.
Example 3
Prevalent Types of Melanoma According to their
Structural-Functional Organization Revealed via an MF Profile
[0486] The visualization method described herein enables a user to
study the structural and functional composition of a particular
patient's tumor, as well as to compare tumors from different
patients. MF profiles for 470 patient human skin cutaneous melanoma
(SKCM) tumors were constructed using data available from TCGA. The
MF profile of each particular patient tumor was unique, yet the
model clearly revealed a similarity of tumor MF profiles among
different patients (FIG. 41A).
[0487] The prevalent types of melanoma tumors were further revealed
using unsupervised dense clustering analysis based on detection of
the tightly connected networks of similar patients within the
patients' correlation graph (FIG. 41B). This analysis revealed that
the graph contained four distinct dense subpopulations (FIG. 41C).
These four tumor types were labeled as Types A, B, C and D
(1.sup.st-4.sup.th MF profile clusters, respectively). Analysis of
tumor type abundance demonstrated that Type A, B, C, and D tumors
were present in 22%, 28%, 24%, and 24% of melanoma patients,
respectively. In other words, 98% of melanoma patients could be
determined to have one of the four prevalent tumor types.
[0488] As an alternative approach, k-means clustering was applied,
which gave rise to nearly the same clusters of patients as the
unsupervised dense clustering approach (FIGS. 41D). These clusters
were also supported by tumor dissection using MCP-counter cell
(FIG. 41E), CIBERSORT deconvolution algorithm (FIG. 41E), and by
dissection based on phenotype-specific gene signatures (FIG.
41F).
[0489] These four types of MF profiles are significantly different
according to the activity of 28 functional modules. Inter-cluster
analysis revealed that the differences between the clusters resides
in the activity of their underlying processes (FIG. 41G). Process
activity between the cluster pairs were compared using the t-test.
Each pair of clusters differed by the activity of at least six
processes with a p-value<10.sup.-7 (FIG. 41H).
[0490] The four tumor types were characterized in terms of patient
prognosis and abundance of driver mutations. Patients having Types
A and B (first and second MF profile clusters, respectively)
melanomas had significantly longer survival time as compared to
patients with Types C and D melanomas (third and fourth MF profile
clusters, respectively) (FIGS. 41I and 41J). The four prevalent
melanoma types appeared to be enriched or deficient in distinct
sets of driver mutations, yet it was revealed that mutations are
associated but do not determine molecular-functional types of
melanoma tumors (FIG. 41K).
[0491] Detailed MF profiles representative for Types A-D melanomas
(1.sup.st-4.sup.th MF profile clusters, respectively) are shown in
FIGS. 42A-42D. Types A and B (first and second MF profile clusters,
respectively) were characterized as "inflamed" tumors, and types C
and D (third and fourth MF profile clusters, respectively)were
characterized as "noninflamed" tumors. "Inflamed" tumors are
characterized by excessive infiltration with immune cells.
"Noninflamed" tumors are poorly infiltrated by hematopoietic
cells.
[0492] Human skin cutaneous melanomas characterized as MF profile
type A were characterized by abundant infiltration of immune cells
and the presence of factors necessary for antigen presentation to T
cells and their activation (e.g., MHC class I and II, CD80, CD86,
CD40, etc.). An average ratio of malignant to nonmalignant cells
(tumor purity) in this type of melanoma was 0.57. Type A cancers
have pronounced signs of tumor infiltration by immune cells known
to possess anticancer effector activity (e.g., cytotoxic T, NK
cells, Th1 and M1 cells). Balanced against anti-cancer (e.g.,
anti-tumor) processes, Type A tumors also demonstrated active
expression of checkpoint inhibitor molecules and recruitment of
suppressor cells (e.g., MDSC and Treg), as well as other types of
cells that support tumor growth (e.g., M2 and Th2). Type A tumors
had a highly developed network of blood vessels and an increased
concentration of cancer-associated fibroblasts, which promote
epithelial-mesenchymal transition and malignant cell metastatic
spread. Taken together, the analysis revealed that Type A tumors
are characterized by high intensities of both anticancer and
pro-cancer immune processes.
[0493] Type B melanoma tumors had similar features to Type A
melanoma tumors except that Type B tumors demonstrated a lower
intensity of tumor immune/inflammatory infiltration and lacked
extensive angiogenesis and CAF networks. Type B melanoma tumors had
0.64 tumor purity on average.
[0494] Type C melanoma tumors and Type D melanoma tumors were
demonstrated to have poor or no leukocyte/lymphocyte infiltration.
Type C melanoma tumors had extensive vascularization and increased
levels of CAFs. By contrast, excessive angiogenesis and CAF
networks were not found in Type D melanoma tumors. Average tumor
purities for Type C melanoma tumors and Type D melanoma tumors were
0.81 and 0.85, respectively, reflecting the predominance of
malignant cells.
[0495] Type B melanoma tumors and Type D melanoma tumors were
characterized by high tumor proliferation rates, and a lack of
intensive angiogenesis and CAF networks.
[0496] In sum, highly prevalent MF profiles revealed in a large
cohort (n=470) of melanoma patients suggested that melanoma tumors
comprised a restricted number of principal variants in terms of
their functional organization, which includes a pro-tumor
microenvironment in dynamic equilibrium with an anti-tumor immune
microenvironment.
[0497] Characteristics of melanoma tumor Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively) were
correlated with patient survival, intensity of cell infiltration
(e.g., immune cells, stromal cells, and inflammatory cells), and
tumor vascularization to provide a brief description of the four
melanoma MF profiles. The brief description of the identified MF
profiles in terms of a treatment perspective (e.g., good, optimal,
poor) and cellular infiltrate (e.g., immune, vascular, fibrotic)
were: [0498] A--good (immune, vascular, fibrotic); [0499]
B--optimal (immune); [0500] C--poor (immunosuppressive, vascular,
fibrotic); and [0501] D--poor (immune "desert").
Example 4
Four General Types of MF Profiles were Revealed Throughout
Different Cancers
[0502] To determine whether the MF profile classification method
displayed tissue-specificity, t-distributed stochastic neighbor
embedding (tSNE) analysis was performed on 20 epithelial cancers
(n=7920, TCGA) over process activity values (ES scores). This
analysis showed that process activity values formed distinct tissue
of origin specific sample subsets (FIG. 43A). A common cluster for
colon (COAD) and rectal (READ) cancers was coherent with the
current view that they have similar molecular and cellular origins.
In order to minimize cancer specificity, process activity values
were normalized by Z-score transformation within each cancer type.
Following such normalization the MF profiles formed a uniform
single set in tSNE analysis (FIG. 43B).
[0503] Methods of building tumor MF profiles as described herein
were applied to carcinomas of different tissue origins. Using NGS
data of cancer patients available from TCGA, unsupervised dense
subgraph clustering analysis was performed and tumor MF profiles
for 7920 patients with 20 different epithelial cancers were
reconstructed. Among the different carcinoma patients studied, four
prevalent types of molecular-functional organization were
identified that were strikingly similar to the organization of MF
profiles for melanoma. The relative sizes of A, B, C and D clusters
varied among cancer types (FIG. 43C). The four MF profile types
were also clearly evident in the analysis of the combined dataset
of 20 cancer types (FIG. 43E). Similar results were obtained by the
k-means pan-cancer clustering algorithm (FIGS. 44A-44G).
[0504] MF profile types for the different cancers and patient
survival were evaluated. The Type C (e.g., immunosuppression,
vascular, fibrotic) cluster of carcinoma patients was linked with
the poorest overall survival, while the Type B (e.g., immune)
cluster had the best prognosis (FIG. 43F). These results were
similar to what was seen in the melanoma cohort.
[0505] The molecular-functional organization of non-epithelial
neoplasms including sarcoma, glioblastoma and glioma were analyzed.
This analysis revealed that glioblastoma and glioma (FIGS.
45A-45B), and sarcoma (FIGS. 45C-45D) types can be classified in a
manner that is similar to carcinomas. However, Types A-D
(1.sup.st-4.sup.th MF profile clusters, respectively) of the
analyzed non-epithelial cancers demonstrated a set of distinct
molecular processes discriminating one type from another (FIGS. 45B
and 45D).
Example 5
Tumor Type as a Basis for Response to Immune and Targeted
Therapies
[0506] An MF profile was created to be a personalized picture of
patient's tumor microenvironment. Therefore, it could be used as a
basis to understand the influence of microenvironment on the
efficacy of different therapies.
[0507] To examine whether the four prevalent types of tumor
organization are indicative of a patient's response to certain
therapies, the link between a patient's MF profile and response to
therapy was analyzed.
[0508] Efficacy of immune checkpoint blockage therapy (e.g.,
anti-CTLA-4 and anti-PD-1) is dependent on the amount of active
immune infiltrate in the tumor microenvironment and tumor
antigenicity. The expression levels of immune checkpoint inhibitor
molecules cannot predict the efficacy of check point blockade
therapy on their own. On the concatenated datasets of patients
treated with anti-CTLA-4 (Nathanson et al., 2016; Van Allen et al.,
2015) it was determined that patients with tumor MF-types A and B
(first and second MF profile clusters, respectively) having high
intratumoral immune content and high mutational burden were more
likely to respond to therapy (FIG. 46A). However, patients with
immune suppressive fibrotic MF-type C tumors (the third MF profile
cluster) appeared to be completely non-responsive, regardless of
mutation load in their tumors. See Nathanson T et al. Somatic
Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4
Blockade. Cancer Immunol Res. 2017 January; 5(1):84-91. See also
Van Allen E M et al. Genomic correlates of response to CTLA-4
blockade in metastatic melanoma. Science. 2015 Oct. 9;
350(6257):207-211. Each of the foregoing references are
incorporated herein by reference in their entirety.
[0509] Analysis of the cohort of patients treated by anti-PD1 (Hugo
et al.) yielded similar results. See Hugo W et al. Genomic and
Transcriptomic Features of Response to Anti-PD-1 Therapy in
Metastatic Melanoma. Cell. 2016 Mar. 24; 165(1):35-44, which is
hereby incorporated by reference in its entirety. Patients having
tumor type C did not respond to therapy (FIG. 46B). MF profile B
patients responded to immunotherapy independently of their tumor
mutation status (FIG. 46B), which is consistent with the
characterization of Type B tumors as having low levels of pro-tumor
angiogenic and fibrotic activities. However, the analysis revealed
that type A tumors which have increased levels of both immune and
fibrotic processes need to possess high mutational burden to
increase the probability of response. It is determined that tumors
with high immune content (e.g., type A) may also contain many
highly suppressive cancer-associated fibroblasts that suppress T
cell activation independently of T-cell checkpoint inhibition
mechanisms.
[0510] Application of MF profiles to datasets of patients treated
with anti-CTLA-4 and anti-PD-1 therapies resulted in 0.72 and 0.76
AUC scores for response prediction respectively (FIG. 46F). With
regard to response to treatment, patients with type B tumors
displayed the most favorable survival rate, and patients with type
C tumors displayed unfavorable survival rates (FIGS. 46G-46H).
[0511] The efficacy of therapeutic MAGEA3-vaccine use depended on
the tumor MF-type (FIG. 46F; AUC score of 0.72). As similarly
determined for checkpoint inhibitor therapies, type B tumors are
associated with increased response to vaccination (FIG. 46C).
Non-responders had "immune desert" type D tumors, which have no
immune infiltration to drive anti-tumor immune response (FIG.
46C).
[0512] MF profiles were also associated with a targeted therapy
outcome. An individual patient's mutational status seemed to be the
most important characteristic when choosing appropriate targeted
therapy, but some targeted therapies also affected the tumor
microenvironment and thus response to them was found to strongly
depend on the tumor organization.
[0513] Patients treated with cetuximab (EGFR inhibitor) from two
independent cohorts (GSE5851, GSE65021) were arranged by tumor type
from the most immune to the least immune (B, A, D, C) and
stratified by EGFR expression status. Patients with tumor types A
and B (first and second MF profile clusters, respectively) were
unlikely to benefit from anti-EGFR therapy (FIG. 46D). On the
contrary, among patients with tumor types C and D (third and fourth
MF profile clusters, respectively) the number of responders was
higher (FIG. 46D). These tumor types seemed to be strongly
dependent on the activity of growth factors which act via EGFR. In
fact, the combination of the tumor MF-type classification (types D
and C) with EGFR-expression status increased response prediction up
to 80% of patients and had an overall AUC score of 0.8 (FIGS. 46D
and 46F).
[0514] The above examples show that additional personalization of
the patient tumor MF profile by combining the tumor type with
traits like mutational burden or EGFR expression status lead to the
possibility of using portraits in different cancers and for
prediction of response to various therapies.
[0515] Alternatively, just one of the processes comprised in the
tumor MF profile could serve a key predictor of certain therapy
effectiveness. For instance, treatment efficacy of sunitinib, a
pan-tyrosine kinase inhibitor, was dependent only on tumor
proliferation rate (AUC score 0.91) which constitutes a single
process of MF profile (FIGS. 46E-46F and FIG. 461).
Example 6
Dynamic Evolution of Tumor MF Profile Predicts Response to Immune
Checkpoint Inhibitors
[0516] A dataset of 3 non-responder and 2 responder melanoma
patients treated with anti-PD1 therapy whose tumors were measured
before and after treatment was obtained. The dynamics of each
patient's tumor were plotted on a map created using 470 melanoma
patients (TCGA).
[0517] Pre-treatment tumors for three non-responding patients were
classified according to their MF profiles as type C (Pt3, Pt4) and
type A (Pt5) tumors. These tumor types were associated with low
mutation burden, which, according to the analysis of Hugo et al.
dataset, was associated with the absence of response. Evolution of
non-responder tumors can be clearly seen on the map of melanoma
patients plotted on the PCA and colored according to MF profile
types (FIG. 47A). The non-responding patients (Pt3, Pt4, Pt5) move
deeply into the type C tumors that constitute a "bad" zone of
non-responders according to the analysis of the Hugo et al. dataset
(FIGS. 47A-47B).
[0518] Alternatively, responder tumors were classified as immune
enriched type B (Pt2) and immune desert type D (Ptl) with high and
mid number of mutations before treatment. After the treatment
responder tumors moved even further to the zone of "best
responders" of tumor types B (Pt1) and A (Pt2) (FIG. 47A). In a
type D patient (Pt1) the number of immune cells were increased, and
the patient's tumor became type B (FIG. 47B). Receiver operating
characteristics for therapy response prediction based on tumor
classification before treatment with AUC scores was determined
(FIG. 47C).
Example 7
Application of Tumor MF Profiles for Personalized Combination
Therapy Design
[0519] Tumor molecular-functional portraits (MF profiles) can
facilitate development of combination therapies. For example, if
there is no visible tumor infiltration with MDSC, there is no
reason to use remedies directed against MDSC. Conversely, when
there are clear signs in the tumor of an overexpressed vascular
network this indicates a reasonable demand for anti-angiogenic
agents to be applied during treatment. In addition, if a functional
module is substantial, then a therapy directed at regulating that
functional module may be selected. In another example, if a tumor
module is absent, then a therapy can be selected to induce the
appearance of the module, should an appropriate inducer exist.
[0520] To facilitate development of specific combination therapies,
the MF profile was complemented with a list of known pharmaceutical
compounds directed to particular functional modules (FIGS.
48A-48D). The MF profile enabled the user to specify which
functional module to target. Ultimately, it is the clinician's
decision whether or not to use a particular option, and if so, how
to use it. The schematic shown in FIGS. 48A-48D is a representation
of the interface created in order to allow a user to objectively
evaluate a patient's tumor for the presence or absence of primary
molecular and cellular targets for the existing modes of
therapeutic intervention. Importantly, the schematic readily
discards those remedies that would be irrelevant to this particular
patient because of the absence of functional modules to which these
remedies are directed.
[0521] Prevalent MF profiles for Types A-D (1.sup.st-4.sup.th MF
profile clusters, respectively) tumors form the basis for designing
therapeutic protocols relevant to each of these four tumor types.
Described herein are pre-compiled combination therapy designs for
tumors having MF profiles of types A, B, C and D (1.sup.st-4.sup.th
MF profile clusters, respectively), starting with the latter as
having the simplest molecular-functional organization.
[0522] Type D tumors (the fourth MF profile cluster) represent the
simplest MF profile that are nearly devoid of any modules but have
an increased expression of cancer signaling pathways and a high
proliferative activity of malignant cells (FIG. 42D). For patients
with Type D tumors, one can apply a chemotherapeutic regimen,
radiotherapy, targeted tyrosine kinase, or cyclin-dependent kinase
inhibitors to block cell divisions, but most probably none of these
standard care therapies will be curative and tumors will likely
recur. In such patients, there is a need to evoke the immune system
as a way of destroying the tumor cell variants that could escape
conventional therapies. Treatment options that would effectively
attract cytotoxic T cells, Th1, and NK cells into the tumor could
be useful for such "non-inflamed" cancers.
[0523] Type C tumors were also identified to be "uninflamed" or
"non-inflamed" (FIG. 42C). At the same time, they have increased
expression of cancer signaling pathways and/or metastatic
capabilities. Type C tumors are also characterized by the
prominence of tumor-promoting CAFs, an extensively developed
network of tumor vasculature, and increased expression of
tumor-promoting cytokines. In addition, myeloid lineage
compartments (MDSC, granulocytes, M2 macrophages) that greatly
promote tumor progression are pronounced in Type C tumors.
Accordingly, when designing a combination therapy for Type C tumor
patients (FIG. 48B), therapies interfering with the refined
cancer-signaling pathways, as well as inhibitors of angiogenesis,
CAFs and/or immunosuppressive factors (e.g., TGF.beta.) that are
produced by these cells would likely be used. In addition, remedies
that are capable of M2 macrophages and MDSC reprogramming would
likely be useful in combination therapies for patients having Type
C tumors.
[0524] Treatment strategies for "inflamed" tumors are more
multifarious. For patients with Type B tumors (FIG. 48C) checkpoint
inhibitors in combination with blockaders of Treg, MDSC and
immunosuppressive (e.g., TGF.beta., IDO-1) factors could be used.
Compared to Type B (second type) tumors, Type A (first type) tumors
(FIG. 42A) require the addition of angiogenesis and CAF inhibitors.
As the infiltrating T cell compartments are well expressed in Types
A and B (first and second type tumors, respectively) tumors, they
could be fully exploited by the application of either personalized
vaccines or vaccines based on the shared tumor-specific antigens,
or both. In addition, for the treatment of Types A and B tumors
(first and second type, respectively), a combination of the
referenced therapies with therapies that inhibit metastatic or
growth-signaling activities of malignant cells, or therapies that
block the action of tumor growth factors if they are prominently
expressed in the particular patient's MF profile could be used.
[0525] Therapeutic combinations compiled for Types A, B, C and D
tumors (first-fourth type tumors, respectively) can be adapted for
a particular patient. The identified and described cancer MF
profiles provide an objective basis for choosing a functionally
relevant combination of therapeutic components. Specific
combinations of therapies for Types A-D (1.sup.st-4.sup.th type,
respectively) tumors ("treatment standards") can be pre-designed
and tuned by adding or excluding certain remedies based on the
unique characteristics of a patient's tumor.
[0526] Given the efficiency and wide application of targeted
inhibitors, the MF profiles were further expanded to include a
mutation status module that represented the most important
recurrent and therapy relevant mutations in oncogenes. The presence
of these mutations may be used as a biomarker for selecting
targeted inhibitors. In another example, a MF profile was modified
to design a combination therapy that included targeted inhibitors,
relevant to the driver mutation (KIT) found in the tumor of a
melanoma patient (FIG. 48D). Identified mutations could also
provide useful information for designing of personalized neoantigen
vaccine.
Example 8
MF Profile Complexity
[0527] The degree of detail of MF profiles was decreased from 28
modules (FIG. 49A) down to 19 modules (FIG. 49B) or 5 modules (FIG.
49C) by collapsing related functional processes. A reduction of
model complexity was achieved by merging inherently related
modules. For example, the T cell, T cell traffic and Cytotoxic T
cell modules were be merged with NK cell module in the combined
Effector T and NK cell module. Similarly, Th2 cells, M2 macrophages
and Pro-tumor cytokines were joined within the Tumor-promoting
immune infiltrate module.
[0528] The level of detail can be selected depending on the task.
For example, the most simplified MF profile can serve to classify a
tumor principal type, e.g., "non-inflamed" or "inflamed," or having
extensive angiogenesis, or containing an excess of
cancer-associated fibroblasts, or exhibiting hypertrophy of
suppressor cells. A more sophisticated MF profile can be employed
for the refined analysis of a tumor functional organization,
specifically to identify the composition of infiltrating immune
cells, intensity of anticancer cytotoxic mechanisms, types of
immunosuppressive cells and molecules, the number, differentiation
phase and activity of CAFs, and finally, malignancy details of
cancerous cells.
Example 9
Analysis of Relationships Between Functional Modules
[0529] The MF profiles of Types A-D tumors (1.sup.st-4.sup.th type
tumors, respectively) differ by the intensity of processes assigned
to 28 functional modules. These processes reflect the presence and
functional activity of certain cell types--malignant, endothelial,
fibroblasts, as well as leukocytes/lymphocytes of various
differentiation lineages. The presence and functional status of
each cell type influences the presence and function of other cell
types in the tumor microenvironment, which in turn influences the
presence and function of the former cell type.
[0530] Three principal variants of mutual interaction among cell
types occur, and thus influences interaction between functional
modules. The first variant is a synergistic action of two
particular cell types or two functional modules, which means that
activation of one module promotes activation of the other. The
second variant is an antagonism of two particular cell types or two
functional modules, when activation of one module suppresses the
other module. The third variant is the absence of any mutual
influence of two modules on each other.
[0531] In the case of a positive relationship, functionally
connected modules could be either co-activated or co-extinguished
(e.g., not activated). The intensity of antagonistic functional
modules should be the opposite--one active, the other not. In the
absence of mutual influence, modules should randomly vary from
portrait to portrait with no signs of connection.
[0532] Pearson correlation analysis of relationships between any
two of the 28 functional modules revealed two groups of modules
bound by positive correlations (FIGS. 50A-50C). Modules in the
first group having a positive relationship included T cell
signatures, T cell trafficking, Th1 cells, Effector T cells, NK
cells, MHC class II expression as well as the Checkpoint inhibition
and Treg modules. With lower positive correlation coefficients, MHC
Class I, Co-activation molecules, Anti-tumor cytokines and B cells
modules were adjacent to this group of modules. Modules of this
first group were generally related to effective anti-tumor
responses. Remarkably, these modules had negative correlation with
the tumor malignancy modules such as the Tumor proliferation rate
and Cancer signaling (RAS/RAF/MEK) modules. In other words, the
worse the malignancy of the tumor, the less developed the immune
responses were within the tumor. Conversely, if the tumor had no
prominent malignancy signs, an intensive immune response was
observed.
[0533] Modules in the second group having an antagonistic
relationship included CAFs, Angiogenesis and the Tumor-promoting
growth factors, as well as Pro-tumor cytokines, M2 macrophages,
Granulocytes and MDSC modules. This second group of modules
functions to promote tumor growth, survival and metastasis while
suppressing immune responses that control tumor outgrowth. In
addition, this second group of modules were negatively correlated
with cancer signaling (RAS/RAF/MEK) and proliferation modules.
[0534] Taken together, the relationship between modules suggested
that tumors comprising driver mutations and/or high proliferation
rates were devoid of tumor immune defenses and tumor-promoting
modules (e.g., CAFs, angiogenesis, M2, MDSC). Thus, the malignancy
of certain cells forms a basis for the development of
"non-inflamed" tumors, wherein the activity of the microenvironment
is reduced to a minimum.
EXAMPLE EMBODIMENTS
[0535] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups, the set of gene groups comprising
gene groups associated with cancer malignancy and different gene
groups associated with cancer microenvironment; and identifying,
from among multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using RNA expression data obtained from
biological samples from the plurality of subjects, each of the
plurality of MF profiles containing a gene group expression level
for each gene group in the set of gene groups; and clustering the
plurality of MF profiles to obtain the MF profile clusters.
[0536] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups, the
set of gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; and identifying, from among multiple MF profile
clusters, an MF profile cluster with which to associate the MF
profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using RNA expression data obtained from biological samples from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0537] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; and identifying, from
among multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using RNA expression data obtained from
biological samples from the plurality of subjects, each of the
plurality of MF profiles containing a gene group expression level
for each gene group in the set of gene groups; and clustering the
plurality of MF profiles to obtain the MF profile clusters.
[0538] In some embodiments, the gene groups associated with cancer
malignancy is the tumor properties group; and the MF profile for
the subject comprises determining a gene group expression level for
the tumor properties group. In some embodiments, the gene groups
associated with cancer microenvironment are the tumor-promoting
immune microenvironment group, the anti-tumor immune
microenvironment group, the angiogenesis group, and the fibroblasts
group; and determining the MF profile for the subject comprises
determining a gene group expression level for each of the
tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group. In some embodiments, the gene groups associated
with cancer malignancy comprise at least three genes from the
following group: the tumor properties group: MKI67, ESCO2, CETN3,
CDK2, CCND1, CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2,
BUB1, PLK1, CCNB1, MCM2, MCM6, PIK3CA, PIK3CB, PIK3CG, PIK3CD,
AKT1, MTOR, PTEN, PRKCA, AKT2, AKT3, BRAF, FNTA, FNTB, MAP2K1,
MAP2K2, MKNK1, MKNK2, ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1,
FGFR1, FGFR2, FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, PDGFRB, NGF,
CSF3, CSF2, FGF7, IGF1, IGF2, IL7, FGF2, TP53, SIK1, PTEN, DCN,
MTAP, AIM2, RB1, ESRP1, CTSL, HOXA1, SMARCA4, SNAI2, TWIST1, NEDD9,
PAPPA, HPSE, KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1,
MITF, APC, ARID1A, ATM, ATRX, BAP1, BRAF, BRCA2, CDH1, CDKN2A,
CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3, GATA3, HRAS, IDH1, KRAS,
MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1, NPM1, NRAS, PBRM1, PIK3CA,
PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2, TAF1, TP53, and VHL.
[0539] In some embodiments, determining the MF portrait comprises:
determining the gene group expression level for the tumor
properties group using the gene expression level obtained from the
RNA sequence data for at least three genes in the tumor properties
group. In certain embodiments, the gene groups associated with
cancer microenvironment comprise at least three genes from each of
the following groups: the anti-tumor immune microenvironment group:
HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, HLA-DRA, HLA-DRB1, HLA-DOB,
HLA-DPB2, HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DPB1, HLA-DMB, HLA-DQB1,
HLA-DQA1, HLA-DRB5, HLA-DQA2, HLA-DQB2, HLA-DRB6, CD80, CD86, CD40,
CD83, TNFRSF4, ICOSLG, CD28, IFNG, GZMA, GZMB, PRF1, LCK, GZMK,
ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B, NKG7, CD160, CD244,
NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1,
KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, CXCL9, CXCL10, CXCR3, CX3CL1,
CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, CCL5, EOMES, TBX21, ITK,
CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, LCK, UBASH3A, TRAT1, CD19,
MS4A1, TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22,
CD79A, CD79B, BLK, NOS2, IL12A, IL12B, IL23A, TNF, IL1B, SOCS3,
IFNG, IL2, CD4OLG, IL15, CD27, TBX21, LTA, IL21, HMGB1, TNF, IFNB1,
IFNA2, CCL3, TNFSF10, and FASLG; the tumor-promoting immune
microenvironment group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA,
HAVCR2, VSIR, CXCL12, TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10,
TNFRSF1B, CCL17, CXCR4, CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13,
CCL28, IDOL ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB,
CXCR4, CD33, CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2, CCL3, CCL5,
CSF1, CXCL8, CXCL8, CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5, CXCL5,
CCR3, CCL26, PRG2, EPX, RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8,
PRG3, CMA1, TPSAB1, MS4A2, CPA3, IL4, ILS, IL13, SIGLEC8, MPO,
ELANE, PRTN3, CTSG, IL10, VEGFA, TGFB1, IDO1, PTGES, MRC1, CSF1,
LRP1, ARG1, PTGS1, MSR1, CD163, CSF1R, IL4, ILS, IL13, IL10, IL25,
GATA3, IL10, TGFB1, TGFB2, TGFB3, IL22, MIF, CFD, CFI, CD55, CD46,
and CR1; the fibroblasts group: LGALS1, COL1A1, COL1A2, COL4A1,
COL5A1, TGFB1, TGFB2, TGFB3, ACTA2, FGF2, FAP, LRP1, CD248, COL6A1,
COL6A2, and COL6A3; and the angiogenesis group: VEGFA, VEGFB,
VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF, CXCL5, KDR, ANGPT1, ANGPT2,
TEK, VWF, CDH5, NOS3, KDR, VCAM1, MMRN1, LDHA, HIF1A, EPAS1, CA9,
SPP1, LOX, SLC2A1, and LAMPS. In some embodiments, determining the
MF portrait comprises: determining the gene group expression level
for the anti-tumor immune microenvironment group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the anti-tumor immune microenvironment group;
determining the gene group expression level for the tumor-promoting
immune microenvironment group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
tumor-promoting immune microenvironment group; determining the gene
group expression level for the fibroblasts group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the fibroblasts group; and determining the gene
group expression level for the angiogenesis group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the angiogenesis group. In certain embodiments, the
gene groups associated with cancer malignancy are: the
proliferation rate group, the PI3K/AKT/mTOR signaling group, the
RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group; and determining the MF profile for the
subject comprises determining a gene group expression level for
each of the proliferation rate group, the PI3K/AKT/mTOR signaling
group, the RAS/RAF/MEK signaling group, the receptor tyrosine
kinases expression group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group. In some embodiments, the gene groups
associated with cancer microenvironment are: the antigen
presentation group, the cytotoxic T and NK cells group, the B cells
group, the anti-tumor microenvironment group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the cancer associated fibroblasts group, the angiogenesis
group, and the tumor-promotive immune group; and determining the MF
profile for the subject comprises determining a gene group
expression level for each of the antigen presentation group, the
cytotoxic T and NK cells group, the B cells group, the anti-tumor
microenvironment group, the checkpoint inhibition group, the Treg
group, the MDSC group, the granulocytes group, the cancer
associated fibroblasts group, the angiogenesis group, and the
tumor-promotive immune group.
[0540] In certain embodiments, the gene groups associated with
cancer malignancy comprise at least three genes from each of the
following groups: the proliferation rate group: MKI67, ESCO2,
CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1,
MYBL2, BUB1, PLK1, CCNB1, MCM2, and MCM6; the PI3K/AKT/mTOR
signaling group: PIK3CA, PIK3CB, PIK3CG, PIK3CD, AKT1, MTOR, PTEN,
PRKCA, AKT2, and AKT3; the RAS/RAF/MEK signaling group: BRAF, FNTA,
FNTB, MAP2K1, MAP2K2, MKNK1, and MKNK2; the receptor tyrosine
kinases expression group: ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET,
NTRK1, FGFR1, FGFR2, FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, and
PDGFRB; the tumor suppressors group: TP53, SIK1, PTEN, DCN, MTAP,
AIM2, and RB1; the metastasis signature group: ESRP1, CTSL, HOXA1,
SMARCA4, SNAI2, TWIST1, NEDD9, PAPPA, and HPSE; the anti-metastatic
factors group: KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1,
and MITF; and the mutation status group: APC, ARID1A, ATM, ATRX,
BAP1, BRAF, BRCA2, CDH1, CDKN2A, CTCF, CTNNB1, DNMT3A, EGFR, FBXW7,
FLT3, GATA3, HRAS, IDH1, KRAS, MAP3K1, MTOR, NAV3, NCOR1, NF1,
NOTCH1, NPM1, NRAS, PBRM1, PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2,
STAG2, TAF1, TP53, and VHL. In certain embodiments, determining the
MF portrait comprises: determining the gene group expression level
for the proliferation rate group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
proliferation rate group; determining the gene group expression
level for the PI3K/AKT/mTOR signaling group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the PI3K/AKT/mTOR signaling group; determining the
gene group expression level for the RAS/RAF/MEK signaling group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the RAS/RAF/MEK signaling group;
determining the gene group expression level for the receptor
tyrosine kinases expression group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
receptor tyrosine kinases expression group; determining the gene
group expression level for the tumor suppressors group using the
gene expression level obtained from the RNA sequence data for at
least three genes in the tumor suppressors group; determining the
gene group expression level for the metastasis signature group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the metastasis signature group;
determining the gene group expression level for the anti-metastatic
factors group using the gene expression level obtained from the RNA
sequence data for at least three genes in the anti-metastatic
factors group; and determining the gene group expression level for
the mutation status group using the gene expression level obtained
from the RNA sequence data for at least three genes in the mutation
status group. In certain embodiments, the gene groups associated
with cancer microenvironment comprise at least three genes from
each of the following groups: the cancer associated fibroblasts
group: LGALS1, COL1A1, COL1A2, COL4A1, COL5A1, TGFB1, TGFB2, TGFB3,
ACTA2, FGF2, FAP, LRP1, CD248, COL6A1, COL6A2, and COL6A3; the
angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1,
PIGF, CXCL5, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5, NOS3, KDR, VCAM1,
MMRN1, LDHA, HIF1A, EPAS1, CA9, SPP1, LOX, SLC2A1, and LAMP3; the
antigen presentation group: HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2,
HLA-DRA, HLA-DRB1, HLA-DOB, HLA-DPB2, HLA-DMA, HLA-DOA, HLA-DPA1,
HLA-DPB1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DRB5, HLA-DQA2,
HLA-DQB2, HLA-DRB6, CD80, CD86, CD40, CD83, TNFRSF4, ICOSLG, and
CD28; the cytotoxic T and NK cells group: IFNG, GZMA, GZMB, PRF1,
LCK, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B, NKG7,
CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4,
KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, CXCL9, CXCL10, CXCR3,
CX3CL1, CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, CCL5, EOMES, TBX21,
ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, LCK, UBASH3A, and TRAT1;
the B cells group: CD19, MS4A1, TNFRSF13C, CD27, CD24, CR2,
TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, and BLK; the anti-tumor
microenvironment group: NOS2, IL12A, IL12B, IL23A, TNF, IL1B,
SOCS3, IFNG, IL2, CD4OLG, IL15, CD27, TBX21, LTA, IL21, HMGB1, TNF,
IFNB1, IFNA2, CCL3, TNFSF10, and FASLG; the checkpoint inhibition
group: PDCD1, CD274, CTLA4, LAGS, PDCD1LG2, BTLA, HAVCR2, and VSIR;
the Treg group: CXCL12, TGFB1, TGFB2, TGFB3, FOXP3, CTLA4, IL10,
TNFRSF1B, CCL17, CXCR4, CCR4, CCL22, CCL1, CCL2, CCL5, CXCL13, and
CCL28; the MDSC group: IDO1, ARG1, IL4R, IL10, TGFB1, TGFB2, TGFB3,
NOS2, CYBB, CXCR4, CD33, CXCL1, CXCL5, CCL2, CCL4, CCL8, CCR2,
CCL3, CCL5, CSF1, and CXCL8; the granulocytes group: CXCL8, CXCL2,
CXCL1, CCL11, CCL24, KITLG, CCL5, CXCL5, CCR3, CCL26, PRG2, EPX,
RNASE2, RNASE3, IL5RA, GATA1, SIGLEC8, PRG3, CMA1, TPSAB1, MS4A2,
CPA3, IL4, IL5, IL13, SIGLEC8, MPO, ELANE, PRTN3, and CTSG; the
tumor-promotive immune group: IL10, VEGFA, TGFB1, IDO1, PTGES,
MRC1, CSF1, LRP1, ARG1, PTGS1, MSR1, CD163, CSF1R, IL4, IL5, IL13,
IL10, IL25, GATA3, IL10, TGFB1, TGFB2, TGFB3, IL22, MIF, CFD, CFI,
CD55, CD46, and CR1. In certain embodiments, determining the MF
portrait comprises: determining the gene group expression level for
the cancer associated fibroblasts group using the gene expression
level obtained from the RNA sequence data for at least three genes
in the cancer associated fibroblasts group; determining the gene
group expression level for the angiogenesis group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the angiogenesis group; determining the gene group
expression level for the antigen presentation group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the antigen presentation group; determining the gene
group expression level for the cytotoxic T and NK cells group using
the gene expression level obtained from the RNA sequence data for
at least three genes in the cytotoxic T and NK cells group;
determining the gene group expression level for the B cells group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the B cells group; determining the gene
group expression level for the anti-tumor microenvironment group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the anti-tumor microenvironment group;
determining the gene group expression level for the checkpoint
inhibition group using the gene expression level obtained from the
RNA sequence data for at least three genes in the checkpoint
inhibition group; determining the gene group expression level for
the Treg group using the gene expression level obtained from the
RNA sequence data for at least three genes in the Treg group;
determining the gene group expression level for the MDSC group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the MDSC group; determining the gene
group expression level for the granulocytes group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the granulocytes group; and determining the gene
group expression level for the tumor-promotive immune group using
the gene expression level obtained from the RNA sequence data for
at least three genes in the tumor-promotive immune group.
[0541] In some embodiments, the gene groups associated with cancer
malignancy are: the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the growth factors group, the
tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
determining the MF profile for the subject comprises determining a
gene group expression level for each of the proliferation rate
group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling
group, the receptor tyrosine kinases expression group, the growth
factors group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group. In certain embodiments, the gene groups
associated with cancer microenvironment are: the cancer associated
fibroblasts group, the angiogenesis group, the MHCI group, the
MHCII group, the coactivation molecules group, the effector cells
group, the NK cells group, the T cell traffic group, the T cells
group, the B cells group, the M1 signatures group, the Th1
signature group, the antitumor cytokines group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the M2 signature group, the Th2 signature group, the
protumor cytokines group, and the complement inhibition group; and
determining the MF profile for the subject comprises determining a
gene group expression level for each of the cancer associated
fibroblasts group, the angiogenesis group, the MHCI group, the
MHCII group, the coactivation molecules group, the effector cells
group, the NK cells group, the T cell traffic group, the T cells
group, the B cells group, the M1 signatures group, the Th1
signature group, the antitumor cytokines group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the M2 signature group, the Th2 signature group, the
protumor cytokines group, and the complement inhibition group. In
certain embodiments, the gene groups associated with cancer
malignancy comprise at least three genes from each of the following
groups: the proliferation rate group: MKI67, ESCO2, CETN3, CDK2,
CCND1, CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2, BUB1,
PLK1, CCNB1, MCM2, and MCM6; the PI3K/AKT/mTOR signaling group:
PIK3CA, PIK3CB, PIK3CG, PIK3CD, AKT1, MTOR, PTEN, PRKCA, AKT2, and
AKT3; the RAS/RAF/MEK signaling group: BRAF, FNTA, FNTB, MAP2K1,
MAP2K2, MKNK1, and MKNK2; the receptor tyrosine kinases expression
group: ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2,
FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, and PDGFRB; the growth
factors group: NGF, CSF3, CSF2, FGF7, IGF1, IGF2, IL7, and FGF2;
the tumor suppressors group: TP53, SIK1, PTEN, DCN, MTAP, AIM2, and
RB1; the metastasis signature group: ESRP1, CTSL, HOXA1, SMARCA4,
SNAI2, TWIST1, NEDD9, PAPPA, and HPSE; the anti-metastatic factors
group: KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1, and MITF;
and the mutation status group: APC, ARID1A, ATM, ATRX, BAP1, BRAF,
BRCA2, CDH1, CDKN2A, CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3,
GATA3, HRAS, IDH1, KRAS, MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1,
NPM1, NRAS, PBRM1, PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2,
TAF1, TP53, and VHL. In certain embodiments, determining the MF
portrait comprises: determining the gene group expression level for
the proliferation rate group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
proliferation rate group; determining the gene group expression
level for the PI3K/AKT/mTOR signaling group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the PI3K/AKT/mTOR signaling group; determining the
gene group expression level for the RAS/RAF/MEK signaling group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the RAS/RAF/MEK signaling group;
determining the gene group expression level for the receptor
tyrosine kinases expression group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
receptor tyrosine kinases expression group; determining the gene
group expression level for the growth factors group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the growth factors group; determining the gene group
expression level for the tumor suppressors group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the tumor suppressors group; determining the gene
group expression level for the metastasis signature group using the
gene expression level obtained from the RNA sequence data for at
least three genes in the metastasis signature group; determining
the gene group expression level for the anti-metastatic factors
group using the gene expression level obtained from the RNA
sequence data for at least three genes in the anti-metastatic
factors group; and determining the gene group expression level for
the mutation status group using the gene expression level obtained
from the RNA sequence data for at least three genes in the mutation
status group.
[0542] In some embodiments, the gene groups associated with cancer
microenvironment comprise at least three genes from each of the
following groups: the cancer associated fibroblasts group: LGALS1,
COL1A1, COL1A2, COL4A1, COL5A1, TGFB1, TGFB2, TGFB3, ACTA2, FGF2,
FAP, LRP1, CD248, COL6A1, COL6A2, and COL6A3; the angiogenesis
group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PIGF, CXCL5,
KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5, NOS3, KDR, VCAM1, MMRN1, LDHA,
HIF1A, EPAS1, CA9, SPP1, LOX, SLC2A1, and LAMPS; the MHCI group:
HLA-A, HLA-B, HLA-C, B2M, TAP1, and TAP2; the MHCII group: HLA-DRA,
HLA-DRB1, HLA-DOB, HLA-DPB2, HLA-DMA, HLA-DOA, HLA-DPA1, HLA-DPB1,
HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DRB5, HLA-DQA2, HLA-DQB2, and
HLA-DRB6; the coactivation molecules group: CD80, CD86, CD40, CD83,
TNFRSF4, ICOSLG, and CD28; the effector cells group: IFNG, GZMA,
GZMB, PRF1, LCK, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, and
CD8B; the NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1,
CD226, GZMH, GNLY, IFNG, KIR2DL4, KIR2DS1, KIR2DS2, KIR2DS3,
KIR2DS4, and KIR2DS5; the T cell traffic group: CXCL9, CXCL10,
CXCR3, CX3CL1, CCR7, CXCL11, CCL21, CCL2, CCL3, CCL4, and CCL5; the
T cells group: EOMES, TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1,
TRBC2, LCK, UBASH3A, and TRAT1; the B cells group: CD19, MS4A1,
TNFRSF13C, CD27, CD24, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A,
CD79B, and BLK; the M1 signatures group: NOS2, IL12A, IL12B, IL23A,
TNF, IL1B, and SOCS3; the Th1 signature group: IFNG, IL2, CD4OLG,
IL15, CD27, TBX21, LTA, and IL21; the antitumor cytokines group:
HMGB1, TNF, IFNB1, IFNA2, CCL3, TNFSF10, and FASLG; the checkpoint
inhibition group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA,
HAVCR2, and VSIR; the Treg group: CXCL12, TGFB1, TGFB2, TGFB3,
FOXP3, CTLA4, IL10, TNFRSF1B, CCL17, CXCR4, CCR4, CCL22, CCL1,
CCL2, CCL5, CXCL13, and CCL28; the MDSC group: IDO1, ARG1, IL4R,
IL10, TGFB1, TGFB2, TGFB3, NOS2, CYBB, CXCR4, CD33, CXCL1, CXCL5,
CCL2, CCL4, CCL8, CCR2, CCL3, CCL5, CSF1, and CXCL8; the
granulocytes group: CXCL8, CXCL2, CXCL1, CCL11, CCL24, KITLG, CCL5,
CXCL5, CCR3, CCL26, PRG2, EPX, RNASE2, RNASE3, IL5RA, GATA1,
SIGLEC8, PRG3, CMA1, TPSAB1, MS4A2, CPA3, IL4, IL5, IL13, SIGLEC8,
MPO, ELANE, PRTN3, and CTSG; the M2 signature group: IL10, VEGFA,
TGFB1, IDO1, PTGES, MRC1, CSF1, LRP1, ARG1, PTGS1, MSR1, CD163, and
CSF1R; the Th2 signature group: IL4, IL5, IL13, IL10, IL25, and
GATA3; the protumor cytokines group: IL10, TGFB1, TGFB2, TGFB3,
IL22, and MIF; and the complement inhibition group: CFD, CFI, CD55,
CD46, and CR1. In certain embodiments, determining the MF portrait
comprises: determining the gene group expression level for the
cancer associated fibroblasts group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
cancer associated fibroblasts group; determining the gene group
expression level for the angiogenesis group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the angiogenesis group; determining the gene group
expression level for the MHCI group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
MHCI group; determining the gene group expression level for the
MHCII group using the gene expression level obtained from the RNA
sequence data for at least three genes in the MHCII group;
determining the gene group expression level for the coactivation
molecules group using the gene expression level obtained from the
RNA sequence data for at least three genes in the coactivation
molecules group; determining the gene group expression level for
the effector cells group using the gene expression level obtained
from the RNA sequence data for at least three genes in the effector
cells group; determining the gene group expression level for the NK
cells group using the gene expression level obtained from the RNA
sequence data for at least three genes in the NK cells group;
determining the gene group expression level for the T cell traffic
group using the gene expression level obtained from the RNA
sequence data for at least three genes in the T cell traffic group;
determining the gene group expression level for the T cells group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the T cells group; determining the gene
group expression level for the B cells group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the B cells group; determining the gene group
expression level for the M1 signatures group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the M1 signatures group; determining the gene group
expression level for the Th1 signature group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the Th1 signature group; determining the gene group
expression level for the antitumor cytokines group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the antitumor cytokines group; determining the gene
group expression level for the checkpoint inhibition group using
the gene expression level obtained from the RNA sequence data for
at least three genes in the checkpoint inhibition group;
determining the gene group expression level for the Treg group
using the gene expression level obtained from the RNA sequence data
for at least three genes in the Treg group; determining the gene
group expression level for the MDSC group using the gene expression
level obtained from the RNA sequence data for at least three genes
in the MDSC group; determining the gene group expression level for
the granulocytes group using the gene expression level obtained
from the RNA sequence data for at least three genes in the
granulocytes group; determining the gene group expression level for
the M2 signature group using the gene expression level obtained
from the RNA sequence data for at least three genes in the M2
signature group; determining the gene group expression level for
the Th2 signature group using the gene expression level obtained
from the RNA sequence data for at least three genes in the Th2
signature group; determining the gene group expression level for
the protumor cytokines group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
protumor cytokines group; and determining the gene group expression
level for the complement inhibition group using the gene expression
level obtained from the RNA sequence data for at least three genes
in the complement inhibition group.
[0543] In some embodiments, the system, method, or
computer-readable storage medium further comprises identifying at
least one first therapy for the subject based on the identified MF
profile cluster. In some embodiments, identifying at least one
first therapy consists of identifying a single therapy. In some
embodiments, identifying at least one first therapy consists of
identifying two or more therapies. In some embodiments, identifying
the at least one therapy comprises identifying at least one therapy
selected from the group consisting of: chemotherapy, antibody drug
conjugates, hormonal therapy, viral therapy, genetic therapy,
non-immune protein therapy, antiangiogenic agents, anti-cancer
vaccines, radiotherapy, soluble receptor therapy, cell based
therapies, immunotherapy, and targeted therapy. In certain
embodiments, identifying the at least one therapy comprises
identifying at least one therapy selected from the group consisting
of: HGFR inhibitors, EGFR inhibitors, VEGF inhibitors, PDGF
inhibitors, CXR2 inhibitors, CXCR4 inhibitors, DPP-4 inhibitors,
galectin inhibitors, antifibrotic agents, LPR1 inhibitors, TGF-beta
inhibitors, IL5 inhibitors, IL4 inhibitors, IL13 inhibitors, IL22
inhibitors, CSF1R inhibitors, IDO inhibitors, LPR1 inhibitors, CD25
inhibitors, GITR inhibitors, PD1 inhibitors, CTLA1 inhibitors, PDL1
inhibitors, LAG3 inhibitors, TIM3 inhibitors, vaccines, PRIMA-1
analogues, CD40 agonists, ICOS agonists, OX40 agonists, Bc1-2
inhibitors, AKT inhibitors, MYC-targeting siRNA, pan-tyrosine
kinase inhibitors, CDK4/6 inhibitors, Aurora A inhibitors,
vaccines, LAG3 inhibitors, and any antibody-drug conjugate. In
certain embodiments, identifying the at least one therapy comprises
identifying at least one therapy selected from the group consisting
of: HGFR inhibitors, EGFR inhibitors, VEGF inhibitors, PDGF
inhibitors, CXR2 inhibitors, galectin inhibitors, antifibrotic
agents, LPR1 inhibitors, TGF-beta inhibitors, IL5 inhibitors, IL4
inhibitors, IL13 inhibitors, IL22 inhibitors, CSF1R inhibitors, IDO
inhibitors, CXCR4 inhibitors, CD25 inhibitors, GITR inhibitors, PD1
inhibitors, CTLA1 inhibitors, PDL1 inhibitors, LAG3 inhibitors,
TIM3 inhibitors, and vaccines. In certain embodiments, identifying
the at least one therapy comprises identifying at least one therapy
selected from the group consisting of: HGFR inhibitors, EGFR
inhibitors, PRIMA-1 analogues, TGF-beta inhibitors, IL22
inhibitors, CSF1R inhibitors, IDO inhibitors, LPR1 inhibitors,
CXCR4 inhibitors, CD25 inhibitors, GITR inhibitors, CD40 agonists,
ICOS agonists, OX40 agonists, and vaccines. In some embodiments,
identifying the at least one therapy comprises identifying at least
one therapy selected from the group consisting of: Bcl-2
inhibitors, AKT inhibitors, MYC-targeting siRNA, PRIMA-1 analogues,
VEGF inhibitors, PDGF inhibitors, CXR2 inhibitors, galectin
inhibitors, antifibrotic agents, LPR1 inhibitors, TGF-beta
inhibitors, IL5 inhibitors, IL4 inhibitors, IL13 inhibitors, CSF1R
inhibitors, IDO inhibitors, CXCR4 inhibitors, and vaccines.
[0544] In some embodiments, identifying the at least one therapy
comprises identifying at least one therapy selected from the group
consisting of: antibody-drug conjugates, HGFR inhibitors, EGFR
inhibitors, VEGF inhibitors, PDGF inhibitors, CXCR2 inhibitors,
galectin inhibitors, antifibrotic agents, LPR1 inhibitors, TGF-beta
inhibitors, IL22 inhibitors, and CXCL10 disrupting inhibitors. In
certain embodiments, identifying the at least one therapy comprises
identifying at least one therapy selected from the group consisting
of: Bc1-2 inhibitors, AKT inhibitors, MYC-targeting siRNA,
chemotherapy, pan-tyrosine kinase inhibitors, CDK4/6 inhibitors,
Aurora A inhibitors, and DPP-4 inhibitors.
[0545] In some embodiments, obtaining the RNA expression data is
performed using whole transcriptome sequencing or mRNA sequencing.
In certain embodiments, each of the biological samples is from a
tumor or tissue known or suspected of having cancerous cells.
[0546] In some embodiments, the system, method, or
computer-readable storage medium further comprises generating the
MF profile clusters, the generating comprising: obtaining RNA
expression data from biological samples obtained from a plurality
of subjects; determining a respective plurality of MF profiles for
the plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters. In certain embodiments, clustering
the plurality of MF profiles is performed by using a k-means
clustering technique.
[0547] In some embodiments, the system, method, or
computer-readable storage medium further comprises: determining at
least one visual characteristic of a first graphical user interface
(GUI) element using a first gene group expression level for at
least one gene group associated with cancer malignancy and at least
one visual characteristic of a second GUI element using a second
gene group expression level for at least one gene group associated
with cancer microenvironment; generating a personalized GUI
personalized to the subject, the GUI comprising: a first portion
associated with cancer malignancy and containing the first GUI
element; and a second portion associated with cancer
microenvironment and containing the second GUI element, wherein the
second portion is different from the first portion; and presenting
the generated personalized GUI to a user. In some embodiments,
determining the at least one visual characteristic of the first GUI
element comprises determining size of the first GUI element using
the first gene group expression level. In certain embodiments,
determining the at least one visual characteristic of the first GUI
element comprises determining color of the first GUI element using
the first gene group expression level. In certain embodiments, the
first portion comprises a first plurality of GUI elements
representing a respective plurality of gene groups associated with
cancer malignancy. In certain embodiments, the second portion
comprises a second plurality of GUI elements representing a
respective plurality of gene groups associated with cancer
microenvironment.
[0548] In some embodiments, the system, method, or
computer-readable storage medium further comprises: obtaining RNA
expression data for at least one additional biological sample
obtained from the subject subsequent to administration of at least
one first therapy; determining, using the RNA expression data for
at least one additional biological sample obtained from the subject
subsequent to administration of at least one therapy, a second MF
profile for the subject, wherein the second MF profile is
determined at least in part by determining, using the RNA
expression data for at least one additional biological sample
obtained from the subject subsequent to administration of at least
one therapy, a gene group expression level for each gene group in a
set of gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; and identifying, from
among the MF profile clusters, an MF profile cluster with which to
associate the MF profile for the subject.
[0549] In certain embodiments, the system, method, or
computer-readable storage medium further comprises determining that
the at least one first therapy is effectively treating the subject.
In some embodiments, the system, method, or computer-readable
storage medium further comprises: determining that the at least one
first therapy is not effectively treating the subject; and
identifying at least one second therapy for the subject based on
the second MF profile cluster. In certain embodiments, determining
the MF profile for the subject comprises: determining a first gene
group expression level for a first gene group of the gene groups
associated with cancer malignancy using a gene set enrichment
analysis (GSEA) technique; and determining a second gene group
expression level for a second gene group of the gene groups
associated with cancer microenvironment using the gene set
enrichment analysis (GSEA) technique.
[0550] In some embodiments, determining the MF profile for the
subject comprises: determining a first gene group expression level
for a first gene group of the gene groups associated with cancer
malignancy using a mutation count technique; and determining a
second gene group expression level for a second gene group of the
gene groups associated with cancer microenvironment using the
mutation count technique. In some embodiments, the WES data is used
to quantify tumor burden (purity), identify specific mutations,
and/or to calculate the number of neoantigens.
[0551] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data from biological
samples from a plurality of subjects, at least some of the subjects
having a cancer of a particular type; determining a respective
plurality of molecular-functional (MF) profiles for the plurality
of subjects at least in part by, for each of the plurality of
subjects, determining, using the RNA expression data, a respective
gene group expression level for each group in a set of gene groups,
the set of gene groups comprising gene groups associated with
cancer malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters comprising: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological sample; and storing the
plurality of MF profiles in association with information
identifying the particular cancer type.
[0552] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data from biological samples from a plurality of subjects, at least
some of the subjects having a cancer of a particular type;
determining a respective plurality of molecular-functional (MF)
profiles for the plurality of subjects at least in part by, for
each of the plurality of subjects, determining, using the RNA
expression data, a respective gene group expression level for each
group in a set of gene groups, the set of gene groups comprising
gene groups associated with cancer malignancy and different gene
groups associated with cancer microenvironment; clustering the
plurality of MF profiles to obtain MF profile clusters comprising:
a first MF profile cluster associated with inflamed and
vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological sample; and storing the plurality of MF profiles in
association with information identifying the particular cancer
type.
[0553] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data from biological samples from a
plurality of subjects, at least some of the subjects having a
cancer of a particular type; determining a respective plurality of
molecular-functional (MF) profiles for the plurality of subjects at
least in part by, for each of the plurality of subjects,
determining, using the RNA expression data, a respective gene group
expression level for each group in a set of gene groups, the set of
gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters comprising: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological sample; and storing the
plurality of MF profiles in association with information
identifying the particular cancer type.
[0554] In some embodiments, the system, method, or
computer-readable storage medium further comprises: obtaining RNA
expression data for at least one biological sample obtained from an
additional subject; determining, using the RNA expression data for
the at least one additional biological sample obtained from the
additional subject, an MF profile for the additional subject,
wherein the MF profile for the additional subject is determined at
least in part by determining, using the RNA expression data for the
at least one additional biological sample obtained from the
additional subject, a gene group expression level for each gene
group in a set of gene groups, the set of gene groups comprising
gene groups associated with cancer malignancy and different gene
groups associated with cancer microenvironment; and identifying,
from among the MF profile clusters, an MF profile cluster with
which to associate the MF profile for the additional subject.
[0555] In some embodiments, the system, method, or
computer-readable storage medium further comprises: determining at
least one visual characteristic of a first graphical user interface
(GUI) element using a first gene group expression level for at
least one gene group associated with cancer malignancy and at least
one visual characteristic of a second GUI element using a second
gene group expression level for at least one gene group associated
with cancer microenvironment; generating a personalized GUI
personalized to the additional subject, the GUI comprising: a first
portion associated with cancer malignancy and containing the first
GUI element; and a second portion associated with cancer
microenvironment and containing the second GUI element, wherein the
second portion is different from the first portion; and presenting
the generated personalized GUI to a user.
[0556] In certain embodiments, the first portion comprises a first
plurality of GUI elements representing a respective plurality of
gene groups associated with cancer malignancy. In certain
embodiments, the second portion comprises a second plurality of GUI
elements representing a respective plurality of gene groups
associated with cancer microenvironment. In some embodiments,
determining the respective gene group expression level for each
group in the set of gene groups is performed using a gene set
enrichment analysis (GSEA) technique. In some embodiments,
determining the respective gene group expression level for each
group in the set of gene groups is performed using a mutation count
technique. In certain embodiments, the clustering is performed
using a community detection clustering technique. In certain
embodiments, the clustering is performed using a k-means clustering
technique.
[0557] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups, the set of gene groups comprising a
first gene group associated with cancer malignancy and a second
gene group associated with cancer microenvironment, wherein the
first and second gene groups are different, the determining
comprising: determining a first gene group expression level for the
first gene group, and determining a second gene group expression
level for the second gene group; determining a first visual
characteristic for a first graphical user interface (GUI) element
using the first gene group expression level; determining a second
visual characteristic for a second GUI element using the second
gene group expression level; generating a personalized GUI
personalized to the subject, the GUI comprising: a first GUI
portion associated with cancer malignancy and containing the first
GUI element having the first visual characteristic, and a second
GUI portion associated with cancer microenvironment and containing
the second GUI element having the second visual characteristic; and
presenting the generated personalized GUI to a user.
[0558] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups, the
set of gene groups comprising a first gene group associated with
cancer malignancy and a second gene group associated with cancer
microenvironment, wherein the first and second gene groups are
different, the determining comprising: determining a first gene
group expression level for the first gene group, and determining a
second gene group expression level for the second gene group;
determining a first visual characteristic for a first graphical
user interface (GUI) element using the first gene group expression
level; determining a second visual characteristic for a second GUI
element using the second gene group expression level; generating a
personalized GUI personalized to the subject, the GUI comprising: a
first GUI portion associated with cancer malignancy and containing
the first GUI element having the first visual characteristic, and a
second GUI portion associated with cancer microenvironment and
containing the second GUI element having the second visual
characteristic; and presenting the generated personalized GUI to a
user.
[0559] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups, the set of gene groups comprising a first gene group
associated with cancer malignancy and a second gene group
associated with cancer microenvironment, wherein the first and
second gene groups are different, the determining comprising:
determining a first gene group expression level for the first gene
group, and determining a second gene group expression level for the
second gene group; determining a first visual characteristic for a
first graphical user interface (GUI) element using the first gene
group expression level; determining a second visual characteristic
for a second GUI element using the second gene group expression
level; generating a personalized GUI personalized to the subject,
the GUI comprising: a first GUI portion associated with cancer
malignancy and containing the first GUI element having the first
visual characteristic, and a second GUI portion associated with
cancer microenvironment and containing the second GUI element
having the second visual characteristic; and presenting the
generated personalized GUI to a user.
[0560] In some embodiments, determining the first visual
characteristic for the first GUI element comprises determining size
of the first GUI element using the first gene group expression
level; and determining the second visual characteristic for the
second GUI element comprises determining size of the second GUI
element using the second gene group expression level. In some
embodiments, determining the first visual characteristic for the
first GUI element comprises determining color and/or pattern of the
first GUI element using the first gene group expression level; and
determining the second visual characteristic for the second GUI
element comprises determining color and/or pattern of the second
GUI element using the second gene group expression level. In some
embodiments, determining the first visual characteristic for the
first GUI element comprises determining shape of the first GUI
element using the first gene group expression level; and
determining the second visual characteristic for the second GUI
element comprises determining shape of the second GUI element using
the second gene group expression level. In certain embodiments, in
response to a user selection of the first GUI element, the GUI is
configured to present information about at least one additional
gene group associated with cancer malignancy. In certain
embodiments, in response to a user selection of the second GUI
element, the GUI is configured to present information about at
least one additional gene group associated with cancer
microenvironment.
[0561] In some embodiments, generating the personalized GUI
comprises generating the GUI comprising: a first portion associated
with cancer malignancy and containing the first GUI element; and a
second portion associated with cancer microenvironment and
containing the second GUI element, wherein the second portion is
different from the first portion.
[0562] In some embodiments, the first portion comprises a first
plurality of GUI elements including a GUI element for each of the
gene groups associated with cancer malignancy, wherein the first
plurality of GUI elements comprises the first GUI element; and the
second portion comprises a second plurality of GUI elements
including a GUI element for each of the gene groups associated with
cancer microenvironment, wherein the second plurality of GUI
elements comprises the second GUI element.
[0563] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the tumor properties group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the tumor-promoting immune
microenvironment group, the anti-tumor immune microenvironment
group, the angiogenesis group, and the fibroblasts group; and
accessing information specifying multiple MF profile clusters for
the particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological sample, wherein
the MF profile clusters were generated by: determining a plurality
of MF profiles for a respective plurality of subjects using the
reference RNA expression data and RNA expression data from
biological samples obtained from the plurality of subjects, each of
the plurality of MF profiles containing a gene group expression
level for each gene group in the set of gene groups; and clustering
the plurality of MF profiles to obtain the MF profile clusters.
[0564] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject having a particular
type of cancer; determining a molecular-functional (MF) profile for
the subject at least in part by: determining, using the RNA
expression data and reference RNA expression data, a gene group
expression level for each gene group in a first set of gene groups
associated with cancer malignancy and consisting of the tumor
properties group; and determining, using the RNA expression data
and the reference RNA expression data, a gene group expression
level for each gene group in a second set of gene groups associated
with cancer microenvironment and consisting of the tumor-promoting
immune microenvironment group, the anti-tumor immune
microenvironment group, the angiogenesis group, and the fibroblasts
group; and accessing information specifying multiple MF profile
clusters for the particular cancer type; identifying, from among
the multiple MF profile clusters, an MF profile cluster with which
to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological sample, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using the reference RNA expression data and
RNA expression data from biological samples obtained from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0565] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the tumor properties group; and determining, using
the RNA expression data and the reference RNA expression data, a
gene group expression level for each gene group in a second set of
gene groups associated with cancer microenvironment and consisting
of the tumor-promoting immune microenvironment group, the
anti-tumor immune microenvironment group, the angiogenesis group,
and the fibroblasts group; and accessing information specifying
multiple MF profile clusters for the particular cancer type;
identifying, from among the multiple MF profile clusters, an MF
profile cluster with which to associate the MF profile for the
subject, the MF profile clusters comprising: a first MF profile
cluster associated with inflamed and vascularized biological
samples and/or inflamed and fibroblast-enriched biological samples,
a second MF profile cluster associated with inflamed and
non-vascularized biological samples and/or inflamed and
non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological sample, wherein
the MF profile clusters were generated by: determining a plurality
of MF profiles for a respective plurality of subjects using the
reference RNA expression data and RNA expression data from
biological samples obtained from the plurality of subjects, each of
the plurality of MF profiles containing a gene group expression
level for each gene group in the set of gene groups; and clustering
the plurality of MF profiles to obtain the MF profile clusters.
[0566] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the proliferation rate group,
the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group,
the receptor tyrosine kinases expression group, the tumor
suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the antigen presentation group,
the cytotoxic T and NK cells group, the B cells group, the
anti-tumor microenvironment group, the checkpoint inhibition group,
the Treg group, the MDSC group, the granulocytes group, the cancer
associated fibroblasts group, the angiogenesis group, and the
tumor-promotive immune group; and accessing information specifying
multiple MF profile clusters for the particular cancer type;
identifying, from among the multiple MF profile clusters, an MF
profile cluster with which to associate the MF profile for the
subject, the MF profile clusters comprising: a first MF profile
cluster associated with inflamed and vascularized biological
samples and/or inflamed and fibroblast-enriched biological samples,
a second MF profile cluster associated with inflamed and
non-vascularized biological samples and/or inflamed and
non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0567] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining obtaining RNA expression data and/or whole exome
sequencing (WES) data for a biological sample from a subject having
a particular type of cancer; determining a molecular-functional
(MF) profile for the subject at least in part by: determining,
using the RNA expression data and reference RNA expression data, a
gene group expression level for each gene group in a first set of
gene groups associated with cancer malignancy and consisting of the
proliferation rate group, the PI3K/AKT/mTOR signaling group, the
RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the tumor suppressors group, the metastasis
signature group, the anti-metastatic factors group, and the
mutation status group; and determining, using the RNA expression
data and the reference RNA expression data, a gene group expression
level for each gene group in a second set of gene groups associated
with cancer microenvironment and consisting of the antigen
presentation group, the cytotoxic T and NK cells group, the B cells
group, the anti-tumor microenvironment group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the cancer associated fibroblasts group, the angiogenesis
group, and the tumor-promotive immune group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0568] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and determining, using the RNA
expression data and the reference RNA expression data, a gene group
expression level for each gene group in a second set of gene groups
associated with cancer microenvironment and consisting of the
antigen presentation group, the cytotoxic T and NK cells group, the
B cells group, the anti-tumor microenvironment group, the
checkpoint inhibition group, the Treg group, the MDSC group, the
granulocytes group, the cancer associated fibroblasts group, the
angiogenesis group, and the tumor-promotive immune group; and
accessing information specifying multiple MF profile clusters for
the particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0569] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject having a particular type of cancer;
determining a molecular-functional (MF) profile for the subject at
least in part by: determining, using the RNA expression data and
reference RNA expression data, a gene group expression level for
each gene group in a first set of gene groups associated with
cancer malignancy and consisting of the proliferation rate group,
the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group,
the receptor tyrosine kinases expression group, the growth factors
group, the tumor suppressors group, the metastasis signature group,
the anti-metastatic factors group, and the mutation status group;
and determining, using the RNA expression data and the reference
RNA expression data, a gene group expression level for each gene
group in a second set of gene groups associated with cancer
microenvironment and consisting of the MHCI group, the MHCII group,
the coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0570] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject having a particular
type of cancer; determining a molecular-functional (MF) profile for
the subject at least in part by: determining, using the RNA
expression data and reference RNA expression data, a gene group
expression level for each gene group in a first set of gene groups
associated with cancer malignancy and consisting of the
proliferation rate group, the PI3K/AKT/mTOR signaling group, the
RAS/RAF/MEK signaling group, the receptor tyrosine kinases
expression group, the growth factors group, the tumor suppressors
group, the metastasis signature group, the anti-metastatic factors
group, and the mutation status group; and determining, using the
RNA expression data and the reference RNA expression data, a gene
group expression level for each gene group in a second set of gene
groups associated with cancer microenvironment and consisting of
the MHCI group, the MHCII group, the coactivation molecules group,
the effector cells group, the NK cells group, the T cell traffic
group, the T cells group, the B cells group, the M1 signatures
group, the Th1 signature group, the antitumor cytokines group, the
checkpoint inhibition group, the Treg group, the MDSC group, the
granulocytes group, the M2 signature group, the Th2 signature
group, the protumor cytokines group, the cancer associated
fibroblasts group, the angiogenesis group, and the complement
inhibition group; and accessing information specifying multiple MF
profile clusters for the particular cancer type; identifying, from
among the multiple MF profile clusters, an MF profile cluster with
which to associate the MF profile for the subject, the MF profile
clusters comprising: a first MF profile cluster associated with
inflamed and vascularized biological samples and/or inflamed and
fibroblast-enriched biological samples, a second MF profile cluster
associated with inflamed and non-vascularized biological samples
and/or inflamed and non-fibroblast-enriched biological samples, a
third MF profile cluster associated with non-inflamed and
vascularized biological samples and/or non-inflamed and
fibroblast-enriched biological samples, and a fourth MF profile
cluster associated with non-inflamed and non-vascularized
biological samples and/or non-inflamed and non-fibroblast-enriched
biological samples, wherein the MF profile clusters were generated
by: determining a plurality of MF profiles for a respective
plurality of subjects using the reference RNA expression data and
RNA expression data from biological samples obtained from the
plurality of subjects, each of the plurality of MF profiles
containing a gene group expression level for each gene group in the
set of gene groups; and clustering the plurality of MF profiles to
obtain the MF profile clusters.
[0571] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject having a particular type of cancer; determining a
molecular-functional (MF) profile for the subject at least in part
by: determining, using the RNA expression data and reference RNA
expression data, a gene group expression level for each gene group
in a first set of gene groups associated with cancer malignancy and
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the growth factors group, the
tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
determining, using the RNA expression data and the reference RNA
expression data, a gene group expression level for each gene group
in a second set of gene groups associated with cancer
microenvironment and consisting of the MHCI group, the MHCII group,
the coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, the cancer associated fibroblasts group, the angiogenesis
group, and the complement inhibition group; and accessing
information specifying multiple MF profile clusters for the
particular cancer type; identifying, from among the multiple MF
profile clusters, an MF profile cluster with which to associate the
MF profile for the subject, the MF profile clusters comprising: a
first MF profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples,
wherein the MF profile clusters were generated by: determining a
plurality of MF profiles for a respective plurality of subjects
using the reference RNA expression data and RNA expression data
from biological samples obtained from the plurality of subjects,
each of the plurality of MF profiles containing a gene group
expression level for each gene group in the set of gene groups; and
clustering the plurality of MF profiles to obtain the MF profile
clusters.
[0572] In some embodiments, the gene groups associated with cancer
malignancy comprise at least three genes from each of the following
groups: the proliferation rate group: MKI67, ESCO2, CETN3, CDK2,
CCND1, CCNE1, AURKA, AURKB, CDK4, CDK6, PRC1, E2F1, MYBL2, BUB1,
PLK1, CCNB1, MCM2, and MCM6; the PI3K/AKT/mTOR signaling group:
PIK3CA, PIK3CB, PIK3CG, PIK3CD, AKT1, MTOR, PTEN, PRKCA, AKT2, and
AKT3; the RAS/RAF/MEK signaling group: BRAF, FNTA, FNTB, MAP2K1,
MAP2K2, MKNK1, and MKNK2; the receptor tyrosine kinases expression
group: ALK, AXL, KIT, EGFR, ERBB2, FLT3, MET, NTRK1, FGFR1, FGFR2,
FGFR3, ERBB4, ERBB3, BCR-ABL, PDGFRA, and PDGFRB; the growth
factors group: NGF, CSF3, CSF2, FGF7, IGF1, IGF2, IL7, and FGF2;
the tumor suppressors group: TP53, SIK1, PTEN, DCN, MTAP, AIM2, and
RB1; the metastasis signature group: ESRP1, CTSL, HOXA1, SMARCA4,
SNAI2, TWIST1, NEDD9, PAPPA, and HPSE; the anti-metastatic factors
group: KISS1, ADGRG1, BRMS1, TCF21, CDH1, PCDH10, NCAM1, and MITF;
and the mutation status group: APC, ARID1A, ATM, ATRX, BAP1, BRAF,
BRCA2, CDH1, CDKN2A, CTCF, CTNNB1, DNMT3A, EGFR, FBXW7, FLT3,
GATA3, HRAS, IDH1, KRAS, MAP3K1, MTOR, NAV3, NCOR1, NF1, NOTCH1,
NPM1, NRAS, PBRM1, PIK3CA, PIK3R1, PTEN, RB1, RUNX1, SETD2, STAG2,
TAF1, TP53, and VHL.
[0573] In some embodiments, determining the MF portrait comprises:
determining the gene group expression level for the proliferation
rate group using the gene expression level obtained from the RNA
sequence data for at least three genes in the proliferation rate
group; determining the gene group expression level for the
PI3K/AKT/mTOR signaling group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
PI3K/AKT/mTOR signaling group; determining the gene group
expression level for the RAS/RAF/MEK signaling group using the gene
expression level obtained from the RNA sequence data for at least
three genes in the RAS/RAF/MEK signaling group; determining the
gene group expression level for the receptor tyrosine kinases
expression group using the gene expression level obtained from the
RNA sequence data for at least three genes in the receptor tyrosine
kinases expression group; determining the gene group expression
level for the growth factors group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
growth factors group; determining the gene group expression level
for the tumor suppressors group using the gene expression level
obtained from the RNA sequence data for at least three genes in the
tumor suppressors group; determining the gene group expression
level for the metastasis signature group using the gene expression
level obtained from the RNA sequence data for at least three genes
in the metastasis signature group; determining the gene group
expression level for the anti-metastatic factors group using the
gene expression level obtained from the RNA sequence data for at
least three genes in the anti-metastatic factors group; and
determining the gene group expression level for the mutation status
group using the gene expression level obtained from the RNA
sequence data for at least three genes in the mutation status
group.
[0574] In some embodiments, determining the MF profile for the
subject comprises: determining a first gene group expression level
for a first gene group of the first set of gene groups associated
with cancer malignancy using a gene set enrichment analysis (GSEA)
technique; and determining a second gene group expression level for
a second gene group of the second set of gene groups associated
with cancer microenvironment using the gene set enrichment analysis
(GSEA) technique.
[0575] In some embodiments, determining the MF profile for the
subject comprises: determining a first gene group expression level
for a first gene group of the first set of gene groups associated
with cancer malignancy using a mutation count technique; and
determining a second gene group expression level for a second gene
group of the second set of gene groups associated with cancer
microenvironment using the mutation count technique.
[0576] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining first RNA
expression data and/or first whole exome sequencing (WES) data from
biological samples from a plurality of subjects; determining a
respective plurality of molecular-functional (MF) profiles for the
plurality of subjects at least in part by, for each of the
plurality of subjects, determining, using the first RNA expression
data, a respective gene group expression level for each group in a
set of gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; clustering the plurality
of MF profiles to obtain MF profile clusters including: a first MF
profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples;
obtaining second RNA expression data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the second RNA
expression data, a gene group expression level for each group in
the set of gene groups; and identifying, from among the MF profile
clusters, a particular MF profile cluster with which to associate
the MF profile for the subject.
[0577] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining first RNA expression data and/or first whole exome
sequencing (WES) data from biological samples from a plurality of
subjects; determining a respective plurality of
molecular-functional (MF) profiles for the plurality of subjects at
least in part by, for each of the plurality of subjects,
determining, using the first RNA expression data, a respective gene
group expression level for each group in a set of gene groups, the
set of gene groups comprising gene groups associated with cancer
malignancy and different gene groups associated with cancer
microenvironment; clustering the plurality of MF profiles to obtain
MF profile clusters including: a first MF profile cluster
associated with inflamed and vascularized biological samples and/or
inflamed and fibroblast-enriched biological samples, a second MF
profile cluster associated with inflamed and non-vascularized
biological samples and/or inflamed and non-fibroblast-enriched
biological samples, a third MF profile cluster associated with
non-inflamed and vascularized biological samples and/or
non-inflamed and fibroblast-enriched biological samples, and a
fourth MF profile cluster associated with non-inflamed and
non-vascularized biological samples and/or non-inflamed and
non-fibroblast-enriched biological samples; obtaining second RNA
expression data for a biological sample from a subject; determining
a molecular-functional (MF) profile for the subject at least in
part by determining, using the second RNA expression data, a gene
group expression level for each group in the set of gene groups;
and identifying, from among the MF profile clusters, a particular
MF profile cluster with which to associate the MF profile for the
subject.
[0578] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining first RNA expression data
and/or first whole exome sequencing (WES) data from biological
samples from a plurality of subjects; determining a respective
plurality of molecular-functional (MF) profiles for the plurality
of subjects at least in part by, for each of the plurality of
subjects, determining, using the first RNA expression data, a
respective gene group expression level for each group in a set of
gene groups, the set of gene groups comprising gene groups
associated with cancer malignancy and different gene groups
associated with cancer microenvironment; clustering the plurality
of MF profiles to obtain MF profile clusters including: a first MF
profile cluster associated with inflamed and vascularized
biological samples and/or inflamed and fibroblast-enriched
biological samples, a second MF profile cluster associated with
inflamed and non-vascularized biological samples and/or inflamed
and non-fibroblast-enriched biological samples, a third MF profile
cluster associated with non-inflamed and vascularized biological
samples and/or non-inflamed and fibroblast-enriched biological
samples, and a fourth MF profile cluster associated with
non-inflamed and non-vascularized biological samples and/or
non-inflamed and non-fibroblast-enriched biological samples;
obtaining second RNA expression data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the second RNA
expression data, a gene group expression level for each group in
the set of gene groups; and identifying, from among the MF profile
clusters, a particular MF profile cluster with which to associate
the MF profile for the subject.
[0579] In some embodiments, the first portion comprises a first
plurality of GUI elements representing a respective plurality of
gene groups associated with cancer malignancy; and the second
portion comprises a second plurality of GUI elements representing a
respective plurality of gene groups associated with cancer
microenvironment.
[0580] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the tumor
properties group; and second gene groups associated with cancer
microenvironment consisting of the tumor-promoting immune
microenvironment group, the anti-tumor immune microenvironment
group, the angiogenesis group, and the fibroblasts group,
determining a first set of visual characteristics for a first
plurality of graphical user interface (GUI) elements using the gene
group expression levels determined for the first gene groups;
determining a second set of visual characteristics for a second
plurality of GUI elements using the gene group expression levels
determined for the second gene groups; generating a personalized
GUI personalized to the subject, the generating comprising:
generating a first GUI portion associated with cancer malignancy
and containing the first plurality of GUI elements having the
determined first set of visual characteristics; and generating a
second GUI portion associated with cancer microenvironment and
containing the second plurality of GUI elements having the
determined second set of visual characteristics; and presenting the
generated personalized GUI to a user.
[0581] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the tumor properties group; and second gene groups
associated with cancer microenvironment consisting of the
tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group, determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0582] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the tumor properties group; and second
gene groups associated with cancer microenvironment consisting of
the tumor-promoting immune microenvironment group, the anti-tumor
immune microenvironment group, the angiogenesis group, and the
fibroblasts group, determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0583] In some embodiments, determining the first set of visual
characteristics for the first plurality of GUI elements determining
sizes for each of the first plurality of GUI elements using the
gene expression levels determined for the first gene groups; and
determining the second set of visual characteristics for the first
plurality of GUI elements determining sizes for each of the second
plurality of GUI elements using the gene expression levels
determined for the second gene groups.
[0584] In some embodiments, determining the MF profile for the
subject comprises determining the gene expression levels for each
of the first gene groups using a gene set enrichment analysis
(GSEA) technique; and determining the MF profile for the subject
comprises determining the gene expression levels for each of the
second gene groups using the gene set enrichment analysis (GSEA)
technique.
[0585] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the antigen presentation group, the cytotoxic T
and NK cells group, the B cells group, the anti-tumor
microenvironment group, the checkpoint inhibition group, the Treg
group, the MDSC group, the granulocytes group, and the
tumor-promotive immune group; determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0586] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and second gene groups associated with
cancer microenvironment consisting of the cancer associated
fibroblasts group, the angiogenesis group, the antigen presentation
group, the cytotoxic T and NK cells group, the B cells group, the
anti-tumor microenvironment group, the checkpoint inhibition group,
the Treg group, the MDSC group, the granulocytes group, and the
tumor-promotive immune group; determining a first set of visual
characteristics for a first plurality of graphical user interface
(GUI) elements using the gene group expression levels determined
for the first gene groups; determining a second set of visual
characteristics for a second plurality of GUI elements using the
gene group expression levels determined for the second gene groups;
generating a personalized GUI personalized to the subject, the
generating comprising: generating a first GUI portion associated
with cancer malignancy and containing the first plurality of GUI
elements having the determined first set of visual characteristics;
and generating a second GUI portion associated with cancer
microenvironment and containing the second plurality of GUI
elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0587] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the tumor suppressors
group, the metastasis signature group, the anti-metastatic factors
group, and the mutation status group; and second gene groups
associated with cancer microenvironment consisting of the cancer
associated fibroblasts group, the angiogenesis group, the antigen
presentation group, the cytotoxic T and NK cells group, the B cells
group, the anti-tumor microenvironment group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, and the tumor-promotive immune group; determining a first
set of visual characteristics for a first plurality of graphical
user interface (GUI) elements using the gene group expression
levels determined for the first gene groups; determining a second
set of visual characteristics for a second plurality of GUI
elements using the gene group expression levels determined for the
second gene groups; generating a personalized GUI personalized to
the subject, the generating comprising: generating a first GUI
portion associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0588] In one aspect, provided herein is a system, comprising: at
least one computer hardware processor; and at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by the at
least one computer hardware processor, cause the at least one
computer hardware processor to perform: obtaining RNA expression
data and/or whole exome sequencing (WES) data for a biological
sample from a subject; determining a molecular-functional (MF)
profile for the subject at least in part by determining, using the
RNA expression data, a gene group expression level for each gene
group in a set of gene groups comprising: first gene groups
associated with cancer malignancy consisting of the proliferation
rate group, the PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK
signaling group, the receptor tyrosine kinases expression group,
the growth factors group, the tumor suppressors group, the
metastasis signature group, the anti-metastatic factors group, and
the mutation status group; and second gene groups associated with
cancer microenvironment consisting of the cancer associated
fibroblasts group, the angiogenesis group, the MHCI group, the
MHCII group, the coactivation molecules group, the effector cells
group, the NK cells group, the T cell traffic group, the T cells
group, the B cells group, the M1 signatures group, the Th1
signature group, the antitumor cytokines group, the checkpoint
inhibition group, the Treg group, the MDSC group, the granulocytes
group, the M2 signature group, the Th2 signature group, the
protumor cytokines group, and the complement inhibition group;
determining a first set of visual characteristics for a first
plurality of graphical user interface (GUI) elements using the gene
group expression levels determined for the first gene groups;
determining a second set of visual characteristics for a second
plurality of GUI elements using the gene group expression levels
determined for the second gene groups; generating a personalized
GUI personalized to the subject, the generating comprising:
generating a first GUI portion associated with cancer malignancy
and containing the first plurality of GUI elements having the
determined first set of visual characteristics; and generating a
second GUI portion associated with cancer microenvironment and
containing the second plurality of GUI elements having the
determined second set of visual characteristics; and presenting the
generated personalized GUI to a user.
[0589] In one aspect, provided herein is a method, comprising:
using at least one computer hardware processor to perform:
obtaining RNA expression data and/or whole exome sequencing (WES)
data for a biological sample from a subject; determining a
molecular-functional (MF) profile for the subject at least in part
by determining, using the RNA expression data, a gene group
expression level for each gene group in a set of gene groups
comprising: first gene groups associated with cancer malignancy
consisting of the proliferation rate group, the PI3K/AKT/mTOR
signaling group, the RAS/RAF/MEK signaling group, the receptor
tyrosine kinases expression group, the growth factors group, the
tumor suppressors group, the metastasis signature group, the
anti-metastatic factors group, and the mutation status group; and
second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the MHCI group, the MHCII group, the
coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the M1 signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, and the complement inhibition group; determining a first set
of visual characteristics for a first plurality of graphical user
interface (GUI) elements using the gene group expression levels
determined for the first gene groups; determining a second set of
visual characteristics for a second plurality of GUI elements using
the gene group expression levels determined for the second gene
groups; generating a personalized GUI personalized to the subject,
the generating comprising: generating a first GUI portion
associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
[0590] In one aspect, provided herein is at least one
non-transitory computer-readable storage medium storing
processor-executable instructions that, when executed by at least
one computer hardware processor, cause the at least one computer
hardware processor to perform: obtaining RNA expression data and/or
whole exome sequencing (WES) data for a biological sample from a
subject; determining a molecular-functional (MF) profile for the
subject at least in part by determining, using the RNA expression
data, a gene group expression level for each gene group in a set of
gene groups comprising: first gene groups associated with cancer
malignancy consisting of the proliferation rate group, the
PI3K/AKT/mTOR signaling group, the RAS/RAF/MEK signaling group, the
receptor tyrosine kinases expression group, the growth factors
group, the tumor suppressors group, the metastasis signature group,
the anti-metastatic factors group, and the mutation status group;
and second gene groups associated with cancer microenvironment
consisting of the cancer associated fibroblasts group, the
angiogenesis group, the MHCI group, the MHCII group, the
coactivation molecules group, the effector cells group, the NK
cells group, the T cell traffic group, the T cells group, the B
cells group, the Ml signatures group, the Th1 signature group, the
antitumor cytokines group, the checkpoint inhibition group, the
Treg group, the MDSC group, the granulocytes group, the M2
signature group, the Th2 signature group, the protumor cytokines
group, and the complement inhibition group; determining a first set
of visual characteristics for a first plurality of graphical user
interface (GUI) elements using the gene group expression levels
determined for the first gene groups; determining a second set of
visual characteristics for a second plurality of GUI elements using
the gene group expression levels determined for the second gene
groups; generating a personalized GUI personalized to the subject,
the generating comprising: generating a first GUI portion
associated with cancer malignancy and containing the first
plurality of GUI elements having the determined first set of visual
characteristics; and generating a second GUI portion associated
with cancer microenvironment and containing the second plurality of
GUI elements having the determined second set of visual
characteristics; and presenting the generated personalized GUI to a
user.
Equivalents and Scope
[0591] The terms "program" or "software" are used herein in a
generic sense to refer to any type of computer code or set of
processor-executable instructions that can be employed to program a
computer or other processor (physical or virtual) to implement
various aspects of embodiments as discussed above. Additionally,
according to one aspect, one or more computer programs that when
executed perform methods of the technology described herein need
not reside on a single computer or processor, but may be
distributed in a modular fashion among different computers or
processors to implement various aspects of the technology described
herein.
[0592] Processor-executable instructions may be in many forms, such
as program modules, executed by one or more computers or other
devices. Generally, program modules include routines, programs,
objects, components, data structures, etc. that perform particular
tasks or implement particular abstract data types. Typically, the
functionality of the program modules may be combined or
distributed.
[0593] Also, data structures may be stored in one or more
non-transitory computer-readable storage media in any suitable
form. For simplicity of illustration, data structures may be shown
to have fields that are related through location in the data
structure. Such relationships may likewise be achieved by assigning
storage for the fields with locations in a non-transitory
computer-readable medium that convey relationship between the
fields. However, any suitable mechanism may be used to establish
relationships among information in fields of a data structure,
including through the use of pointers, tags or other mechanisms
that establish relationships among data elements.
[0594] Various inventive concepts may be embodied as one or more
processes, of which examples have been provided. The acts performed
as part of each process may be ordered in any suitable way. Thus,
embodiments may be constructed in which acts are performed in an
order different than illustrated, which may include performing some
acts simultaneously, even though shown as sequential acts in
illustrative embodiments.
[0595] As used herein in the specification and in the claims, the
phrase "at least one," in reference to a list of one or more
elements, should be understood to mean at least one element
selected from any one or more of the elements in the list of
elements, but not necessarily including at least one of each and
every element specifically listed within the list of elements and
not excluding any combinations of elements in the list of elements.
This definition also allows that elements may optionally be present
other than the elements specifically identified within the list of
elements to which the phrase "at least one" refers, whether related
or unrelated to those elements specifically identified. Thus, for
example, "at least one of A and B" (or, equivalently, "at least one
of A or B," or, equivalently "at least one of A and/or B") can
refer, in one embodiment, to at least one, optionally including
more than one, A, with no B present (and optionally including
elements other than B); in another embodiment, to at least one,
optionally including more than one, B, with no A present (and
optionally including elements other than A); in yet another
embodiment, to at least one, optionally including more than one, A,
and at least one, optionally including more than one, B (and
optionally including other elements);etc.
[0596] The phrase "and/or," as used herein in the specification and
in the claims, should be understood to mean "either or both" of the
elements so conjoined, i.e., elements that are conjunctively
present in some cases and disjunctively present in other cases.
Multiple elements listed with "and/or" should be construed in the
same fashion, i.e., "one or more" of the elements so conjoined.
Other elements may optionally be present other than the elements
specifically identified by the "and/or" clause, whether related or
unrelated to those elements specifically identified. Thus, as an
example, a reference to "A and/or B", when used in conjunction with
open-ended language such as "comprising" can refer, in one
embodiment, to A only (optionally including elements other than B);
in another embodiment, to B only (optionally including elements
other than A); in yet another embodiment, to both A and B
(optionally including other elements); etc.
[0597] In the claims articles such as "a," "an," and "the" may mean
one or more than one unless indicated to the contrary or otherwise
evident from the context. Claims or descriptions that include "or"
between one or more members of a group are considered satisfied if
one, more than one, or all of the group members are present in,
employed in, or otherwise relevant to a given product or process
unless indicated to the contrary or otherwise evident from the
context. The disclosure includes embodiments in which exactly one
member of the group is present in, employed in, or otherwise
relevant to a given product or process. The disclosure includes
embodiments in which more than one, or all of the group members are
present in, employed in, or otherwise relevant to a given product
or process.
[0598] Furthermore, the described methods and systems encompass all
variations, combinations, and permutations in which one or more
limitations, elements, clauses, and descriptive terms from one or
more of the listed claims is introduced into another claim. For
example, any claim that is dependent on another claim can be
modified to include one or more limitations found in any other
claim that is dependent on the same base claim. Where elements are
presented as lists, e.g., in Markush group format, each subgroup of
the elements is also disclosed, and any element(s) can be removed
from the group. It should it be understood that, in general, where
the systems and methods described herein (or aspects thereof) are
referred to as comprising particular elements and/or features,
certain embodiments of the systems and methods or aspects of the
same consist, or consist essentially of, such elements and/or
features. For purposes of simplicity, those embodiments have not
been specifically set forth in haec verba herein.
[0599] It is also noted that the terms "including," "comprising,"
"having," "containing", "involving", are intended to be open and
permits the inclusion of additional elements or steps. Where ranges
are given, endpoints are included. Furthermore, unless otherwise
indicated or otherwise evident from the context and understanding
of one of ordinary skill in the art, values that are expressed as
ranges can assume any specific value or sub-range within the stated
ranges in different embodiments of the described systems and
methods, to the tenth of the unit of the lower limit of the range,
unless the context clearly dictates otherwise.
[0600] Use of ordinal terms such as "first," "second," "third,"
etc., in the claims to modify a claim element does not by itself
connote any priority, precedence, or order of one claim element
over another or the temporal order in which acts of a method are
performed. Such terms are used merely as labels to distinguish one
claim element having a certain name from another element having a
same name (but for use of the ordinal term).
[0601] Additionally, as used herein the terms "patient" and
"subject" may be used interchangeably. Such terms may include, but
are not limited to, human subjects or patients. Such terms may also
include non-human primates or other animals.
[0602] This application refers to various issued patents, published
patent applications, journal articles, and other publications, all
of which are incorporated herein by reference. If there is a
conflict between any of the incorporated references and the instant
specification, the specification shall control. In addition, any
particular embodiment of the present disclosure that fall within
the prior art may be explicitly excluded from any one or more of
the claims. Because such embodiments are deemed to be known to one
of ordinary skill in the art, they may be excluded even if the
exclusion is not set forth explicitly herein. Any particular
embodiment of the systems and methods described herein can be
excluded from any claim, for any reason, whether or not related to
the existence of prior art.
[0603] Those skilled in the art will recognize or be able to
ascertain using no more than routine experimentation many
equivalents to the specific embodiments described herein. The scope
of the present embodiments described herein is not intended to be
limited to the above Description, but rather is as set forth in the
appended claims. Those of ordinary skill in the art will appreciate
that various changes and modifications to this description may be
made without departing from the spirit or scope of the present
disclosure, as defined in the following claims.
* * * * *
References