U.S. patent application number 17/402018 was filed with the patent office on 2022-03-03 for genetic abnormalities in plasma cell dyscrasias.
The applicant listed for this patent is Dana-Farber Cancer Institute, Inc.. Invention is credited to Irene Ghobrial, Salomon Manier, Yuji Mishima.
Application Number | 20220064738 17/402018 |
Document ID | / |
Family ID | |
Filed Date | 2022-03-03 |
United States Patent
Application |
20220064738 |
Kind Code |
A1 |
Ghobrial; Irene ; et
al. |
March 3, 2022 |
GENETIC ABNORMALITIES IN PLASMA CELL DYSCRASIAS
Abstract
Provided herein are non-invasive methods and biomarkers that
identify progression and clonal evolution of plasma cell
dyscrasias. Also provided are materials and methods for the
diagnosis, prognosis, staging, and monitoring of plasma cell
dyscrasias based on the presence of the biomarkers in a blood
biopsy, as well as methods for monitoring the progression of a
plasma cell dyscrasia, determining the efficacy of a therapeutic
agent, determining a targeted therapy related to a plasma cell
dyscrasia, and/or treating a plasma cell dyscrasia. The methods
provided herein provide several advantages over invasive
biopsies.
Inventors: |
Ghobrial; Irene; (Wellesley,
MA) ; Manier; Salomon; (Lille, FR) ; Mishima;
Yuji; (Tokyo, JP) |
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Applicant: |
Name |
City |
State |
Country |
Type |
Dana-Farber Cancer Institute, Inc. |
Boston |
MA |
US |
|
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Appl. No.: |
17/402018 |
Filed: |
August 13, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15742815 |
Jan 8, 2018 |
11124838 |
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PCT/US16/45815 |
Aug 5, 2016 |
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17402018 |
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62202314 |
Aug 7, 2015 |
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International
Class: |
C12Q 1/6886 20060101
C12Q001/6886; C12Q 1/6883 20060101 C12Q001/6883; A61P 35/02
20060101 A61P035/02; G01N 33/50 20060101 G01N033/50; G01N 33/574
20060101 G01N033/574 |
Goverment Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
[0002] This invention was made with government support under grant
numbers R01 CA181683 and R01 CA154648 awarded by The National
Institutes of Health. The government has certain rights in the
invention.
Claims
1. A method comprising: determining that circulating free DNA
(cfDNA), DNA from a circulating exosome (exoDNA), RNA from a
circulating exosome (exoRNA), or DNA from a circulating tumor cell
(CTC) from a blood biopsy from a human subject has one or more gene
abnormalities; wherein the one or more gene abnormalities
comprises: (i) a translocation selected from the group consisting
of t(4;14), t(6;14), t(11;14), t(14;16), and t(14;20); (ii) a copy
number variation (CNV) selected from the group consisting of a 1q21
amplification, a 1p32 deletion, a 13q deletion, a 16q deletion, and
a 17p deletion; and (iii) a single nucleotide variation (SNV) in a
gene selected from the group consisting of CR1, DPY19L2, TMPRSS13,
HBG1, KRAS, NRAS, BRAF, IRF4, MPEG1, RYR2, SLC24A1, FAT1, BCLAF1,
CDC27, HLA-B, NBPF1, and ZFHX3.
2. The method of claim 1, wherein the determining comprises
analysis of all or part of an exome.
3. (canceled)
4. (canceled)
5. The method of claim 1, wherein the one or more gene
abnormalities comprises a translocation selected from the group
consisting of t(4;14), t(6;14), t(11;14), t(14;16), and
t(14;20).
6. The method of claim 1, wherein the one or more gene
abnormalities comprises a CNV selected from the group consisting of
a 1q21 amplification, a 1p32 deletion, a 13q deletion, a 16q
deletion, and a 17p deletion.
7. The method of claim 1, wherein the one or more gene
abnormalities comprises a SNV in a gene selected from the group
consisting of CR1 DPY19L2, TMPRSS13, HBG1, KRAS, NRAS, BRAF, IRF4,
MPEG1, RYR2, SLC24A1, FAT1, BCLAF1, CDC27, HLA-B, NBPF1, and
ZFHX3.
8. The method of claim 7, wherein the SNV is selected from the
group consisting of CR1 (p.R2194*), CR1 (p.M2208T), DPY19L2
(p.I647V), TMPRSS13 (p.A77G), TMPRSS13 (p.Q78R), HBG1 (p.A137G),
KRAS (p.G12D), KRAS (p.Q61H), NRAS (p.G12D), BRAF (p.G469R), IRF4
(p.L116R), MPEG1 (p.G537E), RYR2 (p.I784V), SLC24A1 (p.R686G), FAT1
(p.V3464I), FAT (p.K2895R), BCLAF1 (p.N629S), CDC27 (p.A273G),
HLA-B (p.K210N), NBPF1 (p.D679E), NBPF1 (p.K41R), NBPF1 (p.L648V),
ZFHX3 (p.Q2007*), ZFHX3 (p.H2001N), and ZFHX3 (p.F1800L).
9.-25. (canceled)
26. A method comprising: detecting in circulating free DNA (cfDNA),
DNA from a circulating tumor cell (CTC), or DNA from a circulating
exosome (exoDNA) or RNA from a circulating exosome (exoRNA) from a
human subject one or more gene abnormalities; wherein the one or
more gene abnormalities comprises: (i) a translocation selected
from the group consisting of t(4;14), t(6;14), t(11;14), t(14;16),
and t(14;20); (ii) a copy number variation (CNV) selected from the
group consisting of a 1q21 amplification, a 1p32 deletion, a 13q
deletion, a 16q deletion, and a 17p deletion; and (iii) a single
nucleotide variation (SNV) in a gene selected from the group
consisting of CR1, DPY19L2, TMPRSS13, HBG1, KRAS, NRAS, BRAF, IRF4,
MPEG1, RYR2, SLC24A1, FAT1, BCLAF1, CDC27, HLA-B, NBPF1, and ZFHX3,
and treating the human subject with a therapeutic agent for
treatment of multiple myeloma.
27.-29. (canceled)
30. The method of claim 26, wherein the detecting comprises
performing whole-exome sequencing and/or targeted deep sequencing
of the cfDNA, the DNA from the CTC, the exoDNA, or the exoRNA.
31.-49. (canceled)
50. The method of claim 26, wherein the detecting comprises
analysis of all or part of an exome.
51. The method of claim 26, wherein the one or more gene
abnormalities comprises a translocation selected from the group
consisting of t(4;14), t(6;14), t(11;14), t(14;16), and
t(14;20).
52. The method of claim 26, wherein the one or more gene
abnormalities comprises a CNV selected from the group consisting of
a 1q21 amplification, a 1p32 deletion, a 13q deletion, a 16q
deletion, and a 17p deletion.
53. The method of claim 26, wherein the one or more gene
abnormalities comprises a SNV in a gene selected from the group
consisting of CR1, DPY19L2, TMPRSS13, HBG1, KRAS, NRAS, BRAF, IRF4,
MPEG1, RYR2, SLC24A1, FAT1, BCLAF1, CDC27, HLA-B, NBPF1, and
ZFHX3.
54. The method of claim 53, wherein the SNV is selected from the
group consisting of CR1 (p.R2194*), CR1 (p.M2208T), DPY19L2
(p.I647V), TMPRSS13 (p.A77G), TMPRSS13 (p.Q78R), HBG1 (p.A137G),
KRAS (p.G12D), KRAS (p.Q61H), NRAS (p.G12D), BRAF (p.G469R), IRF4
(p.L116R), MPEG1 (p.G537E), RYR2 (p.I784V), SLC24A1 (p.R686G), FAT1
(p.V3464I), FAT (p.K2895R), BCLAF1 (p.N629S), CDC27 (p.A273G),
HLA-B (p.K210N), NBPF1 (p.D679E), NBPF1 (p.K41R), NBPF1 (p.L648V),
ZFHX3 (p.Q2007*), ZFHX3 (p.H2001N), and ZFHX3 (p.F1800L).
55. The method of claim 26, wherein the method comprises detecting
in the cfDNA isolated from a blood biopsy from a human subject the
one or more gene abnormalities.
56. The method of claim 26, wherein the method comprises detecting
in the exoDNA isolated from a blood biopsy from a human subject the
one or more gene abnormalities.
57. The method of claim 26, wherein the method comprises detecting
in the exoRNA isolated from a blood biopsy from a human subject the
one or more gene abnormalities.
58. The method of claim 26, wherein the method comprises detecting
in the DNA from a CTC isolated from a blood biopsy from a human
subject the one or more gene abnormalities.
59. The method of claim 1, wherein the determining comprises
performing whole-exome sequencing and/or targeted deep sequencing
of the cfDNA, the DNA from the CTC, the exoDNA, or the exoRNA.
60. The method of claim 1, wherein the method comprises determining
that the cfDNA isolated from a blood biopsy from a human subject
has the one or more gene abnormalities.
61. The method of claim 1, wherein the method comprises determining
that the exoDNA isolated from a blood biopsy from a human subject
has the one or more gene abnormalities.
62. The method of claim 1, wherein the method comprises determining
that the exoRNA isolated from a blood biopsy from a human subject
has the one or more gene abnormalities.
63. The method of claim 1, wherein the method comprises determining
that the DNA from a CTC isolated from a blood biopsy from a human
subject has the one or more gene abnormalities.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of and claims priority to
U.S. application Ser. No. 15/742,815, issued as U.S. Pat. No.
11,124,838, having a 371 completion date of Jan. 8, 2018, which is
a U.S. National Stage application, and claims priority of
International Application No. PCT/US2016/045815, filed Aug. 5,
2016, which claims the benefit of the priority of U.S. Provisional
Appl. No. 62/202,314, filed Aug. 7, 2015, the contents of all of
which are incorporated by reference herein in its entirety.
TECHNICAL FIELD
[0003] This disclosure relates generally to non-invasive biopsies
for the diagnosis, prognosis, and treatment of patients having
plasma cell dyscrasias.
BACKGROUND
[0004] Plasma cell dyscrasias are disorders of plasma cells.
Multiple Myeloma (MM) is a plasma cell dyscrasia characterized by
patchy bone marrow infiltration leading to multiple bone lytic
lesions and cytopenias at the time of diagnosis. Bone marrow
biopsies are limited in that sampling allows assessment of only one
site where the tumor clones can be different from those present in
other areas of the bone marrow and may not be reflective of the
total disease heterogeneity. It is also a painful procedure for
patients and many patients with precursor state monoclonal
gammopathy of undetermined significance (MGUS) or smoldering
multiple myeloma (SMM) do not have bone marrow biopsies
performed.
SUMMARY
[0005] Provided herein is a non-invasive method (e.g., a blood
biopsy) to identify progression and clonal evolution of plasma cell
dyscrasias. Also provided are materials and methods for the
diagnosis, prognosis, staging, and monitoring of plasma cell
dyscrasias based on the presence of biomarkers in a blood biopsy,
as well as methods for monitoring the progression of a plasma cell
dyscrasia, determining the efficacy of a therapeutic agent,
determining a targeted therapy for a plasma cell dyscrasia, and/or
treating a plasma cell dyscrasia.
[0006] The methods described herein provide several advantages over
bone marrow biopsies. For example, a blood biopsy is a non-invasive
procedure for which multiple sequential samples can easily be
obtained. A blood biopsy allows one to determine a mutational
profile of the majority if not all clones present in the bone
marrow instead of sampling only one site of the bone marrow, and
also allows one to monitor changes in the mutational profile over
time which may be indicative of a change in the plasma cell
dyscrasia (e.g., a response to a therapeutic agent, a progression
of the plasma cell dyscrasia, etc.). A blood biopsy that gives
critical information for diagnosis and prognosis and replaces bone
marrow biopsies for patients with plasma cell dyscrasias represents
a major advance in the diagnosis, prognosis and potentially
treatment decision of patients having, or at risk of developing,
plasma cell dyscrasias. In one aspect, this disclosure provides a
method of determining whether a human subject has, or is at risk of
developing, a plasma cell dyscrasia. The method includes
determining whether circulating free DNA (cfDNA), DNA or RNA from a
circulating exosome, or DNA from a circulating tumor cell (CTC)
from a blood biopsy from the subject has one or more gene
abnormalities associated with a plasma cell dyscrasia. The method
can include analysis of all or part of an exome. The method can
include analysis of one or more genes of interest. The one or more
gene abnormalities can be selected from the group consisting of a
translocation (e.g., t(4;14), t(6;14), t(11;14), t(14;16), and/or
t(14;20)), a copy number variation (CNV; e.g., 1q21 amplification,
1p32 deletion, 13q deletion, 16q deletion, and/or 17p deletion), a
single nucleotide variation (SNV), and/or an epigenetic
abnormality. In some cases an SNV is in a gene selected from the
group consisting of KRAS, NRAS, BRAF, IRF4, MPEG1, RYR2, SLC24A1,
FAT1, BCLAF1, CDC27, HLA-B, NBPF1, and/or ZFHX3 (e.g., KRAS
(p.G12D), NRAS (p.G12D), KRAS (p.Q61H), BRAF (p.G469R), IRF4
(p.L116R), MPEG1 (p.G537E), RYR2 (p.I784V), SLC24A1 (p.R686G), FAT1
(p.V3464I), FAT (p.K2895R), BCLAF1 (p.N629S), CDC27 (p.A273G),
HLA-B (p.K210N), NBPF1 (p.D679E), NBPF1 (p.K41R), NBPF1 (p.L648V),
ZFHX3 (p.Q2007*), ZFHX3 (p.H2001N), and/or ZFHX3 (p.F1800L)). In
some cases, an SNV is in a gene selected from the group consisting
of CR1, DPY19L2, TMPRSS13 and/or HBG1 (e.g., CR1 (p.R2194*), CR1
(p.M2208T), DPY19L2 (p.I647V), TMPRSS13 (p.A77G), TMPRSS13
(p.Q78R), and/or HBG1 (p.A137G)). If the subject has one or more of
the gene abnormalities in the CTC, cfDNA, or exoDNA or RNA/miRNA
from the blood biopsy from the subject, the subject is determined
to have or be at risk of developing a plasma cell dyscrasia (e.g.,
MGUS, SMM, MM). In some embodiments, the detection of the genetic
abnormality or abnormalities in the cfDNA is performed by a method
comprising whole exome sequencing or targeted deep sequencing.
[0007] In one aspect, this disclosure provides a method of treating
a human subject having, or at risk of developing, a plasma cell
dyscrasia. The method includes administering to the human subject a
therapeutic agent targeted to a first gene or a gene product of the
first gene, the first gene determined to have a one or more gene
abnormalities in a CTC, cfDNA, or exoDNA or RNA/miRNA from a blood
biopsy from the human subject; or administering to the human
subject a therapeutic agent targeted to a second gene or a gene
product of the second gene, the second gene being associated with
the first gene. The one or more gene abnormalities can be selected
from the group consisting of a translocation (e.g., t(4;14),
t(6;14), t(11;14), t(14;16), and/or t(14;20)), a copy number
variation (CNV; e.g., 1q21 amplification, 1p32 deletion, 13q
deletion, 16q deletion, and/or 17p deletion), a single nucleotide
variation (SNV), and/or an epigenetic abnormality. In some cases an
SNV is in a gene selected from the group consisting of KRAS, NRAS,
BRAF, IRF4, MPEG1, RYR2, SLC24A1, FAT1, BCLAF1, CDC27, HLA-B,
NBPF1, and/or ZFHX3 (e.g., KRAS (p.G12D), KRAS (p.Q61H), NRAS
(p.G12D), BRAF (p.G469R), IRF4 (p.L116R), MPEG1 (p.G537E), RYR2
(p.I784V), SLC24A1 (p.R686G), FAT1 (p.V3464I), FAT (p.K2895R),
BCLAF1 (p.N629S), CDC27 (p.A273G), HLA-B (p.K210N), NBPF1
(p.D679E), NBPF1 (p.K41R), NBPF1 (p.L648V), ZFHX3 (p.Q2007*), ZFHX3
(p.H2001N), and/or ZFHX3 (p.F1800L)). In some cases, an SNV is in a
gene selected from the group consisting of CR1, DPY19L2, TMPRSS13
and/or HBG1 (e.g., CR1 (p.R2194*), CR1 (p.M2208T), DPY19L2
(p.I647V), TMPRSS13 (p.A77G), TMPRSS13 (p.Q78R), and/or HBG1
(p.A137G)).
[0008] In one aspect, this disclosure provides a method of
determining a prognosis of a human subject having multiple myeloma
(MM). The method includes detecting CTCs present in a blood biopsy
from the human subject. Detection of CTCs in the blood biopsy is
indicative of disease progression and absence of CTC detection is
indicative of progression-free survival. In some embodiments, the
CTCs are detected using multiparameter flow cytometry. In certain
instances, the CTCs are e.g., >0.001%, >0.002%, 0.003%,
>0.005%, >0.006%, >0.010%, >0.015%, >0.020%,
>0.05%, >0.1%, >0.2%, >0.5%, >1% relative to white
blood cells in a blood biopsy.
[0009] In one aspect, this disclosure provides a method of
determining treatment efficacy of a therapeutic agent in a human
subject having MM. The method includes measuring a percentage of
CTCs relative to white blood cells present in a first blood biopsy
from the human subject obtained prior to administration of the
therapeutic agent, and measuring a percentage of CTCs relative to
white blood cells present in a second blood biopsy from the human
subject obtained after administration of the therapeutic agent, and
comparing the percentage of CTCs in the first blood biopsy to the
percentage of CTCs in the second blood biopsy. A decrease in the
percentage of CTCs in the second blood biopsy relative to the
percentage of CTCs in the first blood biopsy indicates that the
therapeutic agent is effective treatment. No change in the
percentage of CTCs or an increase in the percentage of CTCs in the
second blood biopsy relative to the percentage of CTCs in the first
blood biopsy indicates that the therapeutic agent is ineffective.
In some embodiments, the CTCs are detected using multiparameter
flow cytometry.
[0010] In one aspect, this disclosure provides a method of
diagnosing whether a human subject has, or is at risk of
developing, MM. In one embodiment, the method includes detecting in
cfDNA, DNA from a CTC, or exoDNA or RNA from the human subject at
least one genetic abnormality selected from the group consisting of
a translocation involving chromosome 14, a copy number variation
(CNV) involving chromosome 1, a CNV involving chromosome 13, and a
CNV involving chromosome 17. Detection of the at least one genetic
abnormality indicates that the human subject has, or is at risk of
developing, MM. In another embodiment, the method includes
detecting in cfDNA, DNA from a CTC, or exoDNA from the human
subject at least one genetic abnormality in a gene associated with
MM. Detection of the at least one genetic abnormality indicates
that the human subject has, or is at risk of developing, MM. In any
embodiment, the method can include treating the human subject with
a therapeutic agent for treatment of MM. In some embodiments, the
detection of the genetic abnormality or abnormalities in the cfDNA
is performed by a method comprising whole exome sequencing or
targeted deep sequencing.
[0011] In one aspect, this disclosure provides a method of
monitoring a plasma cell dyscrasia in a human subject. The method
includes detecting in cfDNA, DNA from a CTC, or exoDNA at least one
MM biomarker in the DNA. The detecting can be done both before and
at one or more time points after the subject is administered a
therapy to treat the plasma cell dyscrasia (e.g., MGUS, SMM, MM).
In certain instances the detection is performed using a blood
biopsy. In certain instances peripheral blood samples are taken
from the subject, e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 2
months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months,
9 months, 10 months, 11 months, 1 year, 2 years, or 3 years after
commencement of the therapy to treat the plasma cell dyscrasia.
Detection of the at least one MM biomarker indicates progression of
the plasma cell dyscrasia. In some embodiments, the detection of
the MM biomarker in the cfDNA is performed by a method comprising
whole exome sequencing or targeted deep sequencing.
[0012] In one aspect, this disclosure provides a method that
includes detecting in cfDNA, DNA from a CTC, or exoDNA from a human
subject at least one genetic abnormality in a gene associated with
MM. Detection of the at least one genetic abnormality in a gene
associated with MM indicates that the human subject has MM or is at
risk of developing MM. Detection of the at least one genetic
abnormality in a gene associated with MM indicates that the human
subject is a candidate for a therapeutic agent targeted to the gene
associated with MM. In some embodiments, the detection of the
genetic abnormality or abnormalities in the cfDNA is performed by a
method comprising whole exome sequencing or targeted deep
sequencing.
[0013] In one aspect, this disclosure features a method for
determining the prognosis of a human subject having, or suspected
of having, a plasma cell dyscrasia (e.g., MGUS, SMM, or multiple
myeloma). In certain instances, the method involves determining the
expression level of RNA including a miRNA from exosomes isolated
from the human subject, wherein a lower expression level of the
miRNA identifies the subject as having a poorer prognosis than a
subject with a higher expression level of the miRNA. In certain
instances, the method involves determining that the expression
level of a miRNA from exosomes isolated from the human subject is
lower than the expression level of that same miRNA from a subject
who is known to not have a plasma cell dyscrasia (e.g., MGUS, SMM,
or multiple myeloma). The lower expression level of the miRNA is
indicative of a better outcome than a higher expression level of
the miRNA. In certain embodiments, the miRNA is one or more of
let-7b, let-7e, miR-106a, miR-106b, miR-16, miR-17, miR-181a,
miR-18a, miR-20a, miR-21, miR-25 and miR-744. In certain
embodiments, the miRNA is one or more of let-7e, miR-106a,
miR-106b, miR-16, miR-17, miR-18a, miR-20a, and miR-25. In other
embodiments, the miRNA is one or more of let-7b, let-7e, and
miR-16. In certain embodiments, the expression level of at least
let-7b, let-7e, and miR-16 is assessed. In other embodiments, the
expression level of at least let-7e, miR-106a, miR-106b, miR-16,
miR-17, miR-18a, miR-20a, and miR-25 is determined. The expression
levels of an miRNA can be determined by, e.g., quantitative RT-PCR.
In some instances, the method further comprises performing the
International Staging System (based on albumin and beta-2
microglobulin levels in peripheral blood at the time, or at
substantially the same time as, the exosomes are isolated from the
subject) and/or analysis of chromosomal abnormalities (e.g.,
t(4:14), 17p deletion, 1q21 amplification). In certain instances,
the outcome is progression free survival. In other instances, the
outcome is improved survival.
[0014] In one aspect, the disclosure relates to a method that
involves isolating circulating exosomes from a human subject having
or suspected of having a plasma cell dyscrasia (e.g., MGUS, SMM,
multiple myeloma); extracting RNA from the exosomes; measuring the
expression level of an miRNA using the RNA from the exosomes; and
determining that the expression level of the miRNA is lower than
the level of that miRNA in a subject not having or not suspected of
having the plasma cell dyscrasia (e.g., MGUS, SMM, multiple
myeloma). The lower expression level is indicative of a worse
prognosis for the subject than a higher expression level. In
certain embodiments, the miRNA is one or more of let-7b, let-7e,
miR-106a, miR-106b, miR-16, miR-17, miR-181a, miR-18a, miR-20a,
miR-21, miR-25 and miR-744. In certain embodiments, the miRNA is
one or more of let-7e, miR-106a, miR-106b, miR-16, miR-17, miR-18a,
miR-20a, and miR-25. In other embodiments, the miRNA is one or more
of let-7b, let-7e, and miR-16. In certain embodiments, the
expression level of at least let-7b, let-7e, and miR-16 is
assessed. In other embodiments, the expression level of at least
let-7e, miR-106a, miR-106b, miR-16, miR-17, miR-18a, miR-20a, and
miR-25 is determined. In certain embodiments, the method further
comprises administering a therapy for the plasma cell dyscrasia
(MGUS, SMM, multiple myeloma). Such therapies are known in the art.
The expression levels of an miRNA can be determined by, e.g.,
quantitative RT-PCR. In some instances, the method further
comprises performing the International Staging System (based on
albumin and beta-2 microglobulin levels in peripheral blood at the
time, or at substantially the same time as, the exosomes are
isolated from the subject) and/or analysis of chromosomal
abnormalities (e.g., t(4:14), 17p deletion, 1q21 amplification). In
certain instances, the outcome is progression free survival. In
other instances, the outcome is improved survival.
[0015] In another aspect, the disclosure provides a method of
determining the effectiveness of a therapy administered to a human
subject with a plasma cell dyscrasia (e.g., MGUS, SMM, or MM). The
method involves determining the expression level of at least one
miRNA from exosomes isolated from the subject. The exosomes may be
obtained from a biological sample (e.g., blood or serum sample)
before and at one or more time points after commencement of the
therapy. In some embodiments, the at least one miRNA is selected
from the group consisting of let-7b, let-7e, miR-106a, miR-106b,
miR-16, miR-17, miR-181a, miR-18a, miR-20a, miR-21, miR-25, and
miR-744. In other embodiments, the at least one miRNA is selected
from the group consisting of let-7e, miR-106a, miR-106b, miR-16,
miR-17, miR-18a, miR-20a, and miR-25. In yet other embodiments, the
at least one miRNA is selected from the group consisting of let-7b,
let-7e, and miR-16. In certain embodiments, the expression level of
at least let-7b, let-7e, and miR-16 is assessed. In other
embodiments, the expression level of at least let-7e, miR-106a,
miR-106b, miR-16, miR-17, miR-18a, miR-20a, and miR-25 is
determined. Under this method, a low expression of the at least one
miRNA (relative to the expression level of the miRNA/miRNAs prior
to the administration of the therapy) identifies the subject as not
benefitting from the therapy. A high expression of the at least one
miRNA (relative to the expression level of the miRNA/miRNAs prior
to the administration of the therapy) identifies the subject as
benefitting from the therapy. The expression levels of an miRNA can
be determined by, e.g., quantitative RT-PCR. In some instances, the
method further comprises performing the International Staging
System (based on albumin and beta-2 microglobulin levels in
peripheral blood at the time, or at substantially the same time as,
the exosomes are isolated from the subject) and/or analysis of
chromosomal abnormalities (e.g., t(4:14), 17p deletion, 1q21
amplification).
[0016] In another aspect, the disclosure features a method for
predicting the progression free survival in a human subject having
or suspected of having a plasma cell dyscrasia (e.g., MGUS, SMM,
MM). The method involves determining the expression level of at
least one miRNA obtained from the exosomes of the subject. In
certain embodiments, the at least one miRNA is selected from the
group consisting of let-7b, let-7e, miR-106a, miR-106b, miR-16,
miR-17, miR-181a, miR-18a, miR-20a, miR-21, miR-25, and miR-744. In
other embodiments, the at least one miRNA is selected from the
group consisting of let-7e, miR-106a, miR-106b, miR-16, miR-17,
miR-18a, miR-20a, and miR-25. In yet other embodiments, the at
least one miRNA is selected from the group consisting of let-7b,
let-7e, and miR-16. In certain embodiments, the expression level of
at least let-7b, let-7e, and miR-16 is assessed. In other
embodiments, the expression level of at least let-7e, miR-106a,
miR-106b, miR-16, miR-17, miR-18a, miR-20a, and miR-25 is
determined. The expression level of the miRNA/miRNAs can be
determined, e.g., by quantitative RT-PCR. The subject is determined
to have a worse PFS if the expression level of the at least one
miRNA is lower than a control level (e.g., the expression level of
the at least one miRNA in a human subject not having MGUS, SMM,
MM). The subject is determined to have a better PFS if the
expression level of the at least one miRNA is higher than a control
level (e.g., the expression level of the at least one miRNA in a
human subject not having MGUS, SMM, MM).
[0017] In one aspect, the disclosure provides a blood biopsy. The
biopsy involves obtaining a biological (e.g., blood) sample from a
human subject being tested for a plasma cell dyscrasia (e.g., MGUS,
SMM, MM). The sample can be tested using circulating free DNA
(cfDNA), DNA or RNA (e.g., miRNA) from a circulating exosome, or
DNA from a circulating tumor cell (CTC) for one or more gene
abnormalities associated with a plasma cell dyscrasia described
herein. The results from the biopsy can be used to determine
appropriate treatments for the human subject.
[0018] A subject "suspected of having a plasma cell dyscrasia" is
one having one or more symptoms of the plasma cell dyscrasia. As
used herein, a subject "at risk of developing a hematological
malignancy" is a subject that has a biomarker for the plasma cell
dyscrasia regardless of whether or not the subject has one or more
symptoms of the plasma cell dyscrasia.
[0019] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this disclosure belongs. Methods
and materials are described herein for use in the present
disclosure; other, suitable methods and materials known in the art
can also be used. The materials, methods, and examples are
illustrative only and not intended to be limiting. All
publications, patent applications, patents, sequences, database
entries, and other references mentioned herein are incorporated by
reference in their entirety. In case of conflict, the present
specification, including definitions, will control.
[0020] The details of one or more embodiments of the invention are
set forth in the accompanying drawings and the description below.
Other features and advantages of the disclosure will be apparent
from the following detailed description and figures, and from the
claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0021] FIG. 1A-FIG. 1E are a series of graphical depictions of data
showing the prognostic value of circulating tumor cell (CTC)
monitoring in multiple myeloma (MM). FIG. 1A is a boxplot showing
the distributions of CTC at different stages of MM, as indicted.
Wilcoxon rank-sum test was used to compare the distribution of CTC
between two groups. FIG. 1B is a scatter-plot showing the
correlation between CTC and M-spike in MM. linear regression
p-value and adjusted R-squared are shown. FIG. 1C is a line graph
showing the clinical impact of CTC detection in newly diagnosed MM
patients. Patients were classified into two groups based on
presence of CTC (>0.001%). A log-rank test was used to estimate
the statistical significance of differences observed between
curves. FIG. 1D is histogram showing the distribution of CTC trend
in a sequential cohort. CTC trend was modeled using linear
regression and denoted by the resulting slope. Given the skewed
distribution of slopes, the median absolute deviation (MAD) was
calculated to represent a robust measure of the variability. A
cutoff was defined as Median+MAD=0.048; slopes that were greater
than this cutoff were defined as CTC UP group. FIG. 1E is a line
graph showing the clinical impact of CTC trend in MM patients.
Patients were classified as described in FIG. 1D, and differences
between survival curves were tested by log-rank test.
[0022] FIG. 2 is a boxplot showing the coverage distribution of
targeted regions. The DepthOfCoverage function from Genome Analysis
Toolkit (GATK) was used to calculate the mean coverage of each
targeted region. The distribution of mean coverage in each sample
is represented by boxplot. Bone marrow (BM), CTC and germline (GL)
from the same patient were plotted. Reads of two WGA libraries from
the sample were merged.
[0023] FIG. 3A-FIG. 3F are a series of graphical depictions of data
showing sequencing metrics of the study on matched BM clonal plasma
cells (PCs) and CTCs from 8 newly diagnosed MM patients. FIG. 3A is
a stacked bar chart showing the breakdown of single nucleotide
variations (SNVs). The numbers of SNVs identified in patient-paired
BM clonal PCs and CTCs were 223 (interquartile ranges (IQR),
169-320) and 118 (IQR, 100-171), respectively. FIG. 3B is a stacked
bar chart showing the percentage contribution of each mutation. The
percentages of each type in BM myeloma PCs and CTCs were similar in
all but one patient (MM413). FIG. 3C is a stacked bar chart showing
the breakdown of SNVs by nucleotide change. FIG. 3D is a stacked
bar chart showing the percentage contribution of each group of
nucleotide change. FIG. 3E is a series of histograms showing the
distributions of allele fraction of all SNVs. FIG. 3F is a series
of scatter plots showing the linear regression of allele fraction
of shared SNVs. Regression line and slope are shown for each
patient.
[0024] FIG. 4 is a series of histograms showing coverage patterns
in the immunoglobulin heavy (IGH) region of MM patients. Each
plasma cell clone has a unique rearrangement in the IGH locus
(chr14:106032614-107288051) and therefore the coverage pattern in
the IGH region facilitates the determination of whether BM and CTC
samples have similar cell populations. Effective coverage was
calculated by GATK. BM, CTC and GL from the same patient were
plotted in descending order.
[0025] FIG. 5A-FIG. 5D show concordance of somatic variants found
in matched BM clonal PCs and CTCs. FIG. 5A is a bar graph showing
percentages of shared SNVs. FIG. 5B is a Venn diagram showing
numbers of shared and unique SNVs between BM clonal PCs and CTCs
across all patients in this study. FIG. 5C is a series of dot plots
showing instances of SNVs that occurred in curated MM driver genes,
potential MM driver genes, and pan cancer genes. The full list can
be found in Table 5. For each mutation, observed allele fraction
was plotted with circle and a 95% confidence interval was
calculated, represented as bars. Mutations from matched BM clonal
PCs and CTCs were linked by solid lines. Three SNVs only found in
one of the WGA libraries were also included and marked by
asterisks. FIG. 5D is a series of histograms showing CNVs
identified in case MM453 BM and CTC.
[0026] FIG. 6 is a chart showing mutations in MM or Pan cancer
driver genes. MM driver genes, including potential driver genes,
and pan cancer driver genes were curated as described in the
methods section. Three mutations (highlighted with white borders)
were identified in only one of the WGA libraries. We also examined
mutations in an additional 5 CTC samples. Mutations were found in
the same genes but at different locations, as indicated by changes
defined in the far right boxes. Patient MM413 had 2 different SNVs
in FAT1.
[0027] FIG. 7 is a chart showing unique SNVs identified in CTC.
Unique SNVs were identified by comparing BM and CTC samples from
each patient.
[0028] FIG. 8 is a chart showing unique SNVs identified in BM.
Unique SNVs were identified by comparing BM and CTC samples from
each patient.
[0029] FIG. 9 includes a bar graph and a pie chart showing genes in
a targeted multiple myeloma (MM) panel. The panel was designed
based on common mutations identified in MM in bone marrow
cells.
[0030] FIG. 10A is a distribution of mappable small RNAs by next
generation sequencing in circulating exosomes from 10 MM patients
and 5 healthy donors.
[0031] FIG. 10B is a volcano plot for MM against healthy donors
(HD) exosomal miRNA expression level from miRNA sequencing, showing
the adjusted p value (-log 10) vs. fold change (log 2).
[0032] FIG. 10C is a heat map of differentially expressed exosomal
miRNAs in MM vs. HD.
[0033] FIG. 10D shows the results of quantitative RT-PCR of
circulating exosomal miRNAs in 11 MM patients and 5 healthy donors.
Box plots represent the median and standard deviation of the
normalized expression level of 22 miRNAs. miRNA (microRNA), Mt_rRNA
and Mt_tRNA (ribosomal and transfer RNA located in mitochondrial
genome), snoRNA and snRNA (small nucleolar and nuclear RNA), rRNA
(ribosomal RNA), lincRNA (long intergenic non-coding RNA), misc_RNA
(miscellaneous other RNA), mRNA (messenger RNA).
[0034] FIG. 11A is a forest plot of progression-free survival (PFS)
in patients with Multiple Myeloma (MM), according to the univariate
analysis of circulating exosomal miRNA.
[0035] FIG. 11B is a Kaplan-Meier survival curve of PFS in patients
with MM according to the univariate analysis of circulating
exosomal miRNA.
[0036] FIG. 11C is a forest plot of the Cox PH model using each
miRNA individually together with ISS and cytogenetics.
[0037] FIG. 12A is a forest plot of the Cox PH model using the
Principal Component together with ISS and cytogenetics.
[0038] FIG. 12B shows Kaplan-Meier survival curves of PFS according
to the PC1 miRNA signature in patients with Multiple Myeloma
(MM).
[0039] FIG. 13 shows the alteration status of significantly mutated
genes in whole exome sequencing (WES) of tumor biopsy (BM),
cell-free DNA (cfDNA), and circulating tumor cell (CTC) obtained
from 10 patients with Multiple Myeloma (MM) that was predicted by
MutSig2CV. Most somatic single nucleotide variants (SSNVs) detected
in the tumor or cfDNA/CTC were confirmed to be present in cfDNA/CTC
or tumor, respectively.
[0040] FIG. 14 is a representation of genome-wide copy number from
whole exome sequencing (WES) of tumor biopsy (BM), cell-free DNA
(cfDNA), and circulating tumor cell (CTC) from a patient with
Multiple Myeloma. Somatic Copy Number Alteration (SCNA) for tumor,
cfDNA, and CTC WES were identified using Allelic CapSeg. SCNAs were
consistent among tumor DNA, cfDNA and CTC samples.
[0041] FIG. 15 is a summary of the alteration status of
significantly mutated genes in deep targeted sequencing of tumor
biopsy (BM) and cell-free DNA (cfDNA) from 8 patients with Multiple
Myeloma (MM) that was predicted by MutSig2CV. Most somatic single
nucleotide variants (SSNVs) detected in the tumor or cfDNA were
confirmed to be present in cfDNA or tumor, respectively.
DETAILED DESCRIPTION
[0042] This disclosure describes a novel method and biomarkers to
identify progression and clonal evolution of plasma cell
dyscrasias.
[0043] More specifically, the present disclosure provides materials
and methods for the diagnosis, prognosis, staging, and monitoring
of plasma cell dyscrasias based on the presence of the biomarkers
in a blood biopsy. This disclosure also provides methods for
monitoring the progression of a plasma cell dyscrasia, determining
the efficacy of a therapeutic agent, and/or determining a targeted
therapy related to a plasma cell dyscrasia. This disclosure also
provides methods for treating a human subject having, or at risk of
developing, a plasma cell dyscrasia based on the presence of the
biomarkers in a blood biopsy.
Plasma Cell Dyscrasias
[0044] Plasma cell dyscrasias are disorders of plasma cells that
generally arise as a result of abnormal proliferation of a
monoclonal population of plasma cells that may or may not secrete
detectable levels of a monoclonal immunoglobulin or immunoglobulin
fragment (paraprotein or M protein). Plasma cell dyscrasias
include, for example, multiple myeloma, solitary plasmacytoma of
bone, extramedullary plasmacytoma, Waldenstrom's macroglobulinemia
(WM), primary amyloidosis, light chain deposition disease,
paraproteinemia, and heavy-chain disease.
[0045] In some embodiments, the plasma cell dyscrasia is multiple
myeloma (also known as plasma cell myeloma, myelomatosis, or
Kahler's disease). MM is a cancer of plasma cells, a type of white
blood cell normally responsible for producing antibodies. In MM,
collections of abnormal plasma cells accumulate in the bone marrow,
where they interfere with the production of normal blood cells.
[0046] As used herein, unless otherwise indicated, multiple myeloma
(MM) refers to any stage of MM. Recent studies have shown that MM
is consistently preceded by a precursor state such as monoclonal
gammopathy of undetermined significance (MGUS) or smoldering
multiple myeloma (SMM) (Landgren et al., 2009 Blood 113:5412-5417;
Weiss et al., 2009 Blood 113:5418-5422). Thus, stages of MM include
MGUS and SMM, as well as symptomatic MM and plasma cell leukemia
(PCL; the most aggressive plasma cell disorder). MGUS is
characterized by blood M protein <30 g/L, bone marrow plasma
cells <10%, and no myeloma-related organ or tissue impairment.
MGUS is observed for progression, but is typically not treated. SMM
is characterized by blood M protein >30 g/L, Bone marrow plasma
cells >10%, and myeloma-related organ or tissue impairment. SMM
is typically observed and treated. MM is characterized by M protein
in blood and/or urine, and the presence of plasma cells >10% in
bone marrow or in any quantity in other tissues (plasmacytoma). MM
is typically treated immediately. PCL can evolve from an existing
case of multiple myeloma as part of the terminal phase of the
disease and characterized by plasma cells accounting for more than
20% of cells in the peripheral blood with an absolute plasma cell
count of more than 2.times.10.sup.9/L. Treatments for MM include,
for example, a proteasome inhibitor (e.g., Velcade.RTM.
(bortezomib) or Kyprolis.TM. (carfilzomib)), an oral agent (e.g.,
Thalomid.RTM. (thalidomide) or Revlimid.RTM. (lenalidomide)), a
chemotherapy agent (e.g., Doxil.RTM. (doxorubicin)), steroids
(e.g., corticosteroids, dexamethasone, or prednisone),
bisphosphonates (for individuals with osteolytic lesions,
osteoporosis, or osteopenia), and any combination thereof. In
addition, any treatment may be used alone or in combination with
other therapies.
[0047] Some patients rapidly progress from SMM to overt MM
(progressors) with a rate of progression of 70% over 5 years, while
others remain indolent with minimal progression (non-progressors)
over the same time period (Landgren, 2013 Hematology: ASH Education
Book 1:478-487). Biological factors that distinguish progressors
and non-progressors in MGUS/SMM are not well known (Ghobrial et al,
2014 Blood 124:3380-8). The current prognostic factors used to
assess progression are based on tumor burden markers including the
level of monoclonal spike, free light chains, and/or percent of
plasma cells in the bone marrow.
[0048] Given that MM is always preceded by a well-defined precursor
state, and given the ease of access to primary patient samples
(peripheral blood and bone marrow samples), MM can represent one of
the best models of cancer to determine biomarkers of tumor
progression in early premalignant conditions. This disclosure
provides molecular biomarkers of MM biomarkers useful for
diagnosis, prognosis, and/or staging of plasma cell dyscrasias that
will significantly impact the clinical care of patients having, or
at risk of developing, a plasma cell dyscrasia.
Liquid Biopsies
[0049] The development of non-invasive liquid biopsies opens new
opportunities for prognosis and monitoring of clonal heterogeneity
of plasma cell dyscrasias. Bodily fluids for which non-invasive
collection methods are available include, without limitation,
blood, lymph, cerebrospinal fluid, breast milk, urine, saliva, and
sputum. In some cases the liquid biopsy is a blood biopsy. A "blood
biopsy" is a sample of peripheral blood which can be used to detect
biomarkers that are usually observed in the bone marrow biopsies. A
blood biopsy provides a number of advantages over a bone marrow
(BM) biopsy.
[0050] A BM biopsy is a painful procedure for patients. As a
result, only a single BM biopsy is typically obtained from a
patient, and many patients with precursor state plasma cell
dyscrasias (e.g., MGUS or SMM) do not have BM biopsies performed at
all. A blood biopsy is a non-invasive method with minimal patient
discomfort and the ability to obtain multiple sequential
biopsies.
[0051] A blood biopsy can significantly change our understanding of
clonal evolution in MM. Disease complexity can be determined
through serial samples of peripheral blood during disease
progression and clonal evolution. A BM biopsy is limited in
sampling only a single BM site. MM is characterized by patchy BM
infiltration and genomic complexity which was recently corroborated
by massive parallel-sequencing studies displaying an average of 35
amino acid changing point mutations per sample and the lack of a
universal driving mutation (Lohr et al., 2014 Cancer Cell
25:91-101; Bolli et al., 2014 Nature Communications 5:2997; Chapman
et al., 2011 Nature 471:467-472). BM biopsies at a single site in
the BM vary significantly from clones located in distant BM sites;
thus, a BM biopsy may not be reflective of the total disease
heterogeneity. A blood biopsy allows a sample of multiple, and
potentially all, clones present in the bone marrow instead of
sampling only one site of the bone marrow thus providing a more
complete profile of MM clonal diversity. In addition, multiple
sequential blood biopsies can easily be obtained enabling one to
monitor changes in the mutational profile over time.
Biomarkers
[0052] Biomarkers described herein are detectable using a blood
biopsy. A biological marker, or "biomarker," as used herein refers
to a measurable genetic abnormality that is an indicator of some
biological state or condition. Provided herein are biomarkers
useful for diagnosis, prognosis, staging, monitoring, and/or
personalization or therapy related to plasma cell dyscrasias.
Biomarkers useful for the diagnosis, prognosis, staging,
monitoring, and/or personalization or therapy related to MM are
also referred to as MM biomarkers. Biomarkers are detectable in a
blood biopsy from a subject having, or at risk of developing, a
plasma cell dyscrasia, but are not detectable in a healthy (e.g.,
not having a plasma cell dyscrasia) subject.
[0053] In some cases a biomarker is a genetic abnormality. As used
herein a genetic abnormality is any mutation to a gene associated
with a plasma cell dyscrasia or associated with susceptibility to a
plasma cell dyscrasia. For example, a MM biomarker can be a genetic
abnormality in any gene associated with MM or associated with
susceptibility to MM. Many types of genetic abnormalities are known
in the art and may include mutations to a chromosome and/or
mutations to the genetic sequence. Genetic abnormalities are shown
herein using standard mutation nomenclature (den Dunnen and
Antonarakis, 2000 Human Mutation 15:7-12). For example, the
nomenclature of t(A;B) indicates a translocation which joins
chromosomes shown in the parentheses. For example, a p. indicates a
substitution in the protein with the wild type amino acid appearing
before the residue number and the mutated amino acid following the
residue number. An asterisk (*) in place of the second amino acid
indicates a stop codon has been introduced.
[0054] In some cases a biomarker is a genetic abnormality. As used
herein a genetic abnormality is any mutation to a gene associated
with a plasma cell dyscrasia or associated with susceptibility to a
plasma cell dyscrasia. For example, a MM biomarker can be a genetic
abnormality in any gene associated with MM or associated with
susceptibility to MM. Many types of genetic abnormalities are known
in the art and may include mutations to a chromosome and/or
mutations to the genetic sequence. Genetic abnormalities are shown
herein using standard mutation nomenclature (den Dunnen and
Anonarakis, 2000 Human Mutation 15:7-12). For example, the
nomenclature of t(A;B) indicates a translocation which joins
chromosomes shown in the parentheses. For example, a p. indicates a
substitution in the protein with the wild type amino acid appearing
before the residue number and the mutated amino acid following the
residue number. An asterisk (*) in place of the second amino acid
indicates a stop codon has been introduced.
[0055] Many types of chromosomal abnormalities are known in the art
and may include a structural abnormality (e.g., translocations,
inversions, or insertions) or an atypical number of chromosomes
(e.g., copy number variations such as deletions or duplications).
In some embodiments, a chromosomal abnormality is a translocation.
Exemplary translocations associated with plasma cell dyscrasias are
shown in Table 1. In some cases, the translocation is selected from
the group consisting of t(4;14), t(6;14), t(11;14), t(14;16), and
t(14;20). In some embodiments, a chromosomal anomaly MM biomarker
is a copy number variation (CNV). Exemplary CNVs are shown in, for
example, Table 6. In some cases, the CNV is a 1q21 amplification, a
1p32 deletion, a 13q deletion, a 16q deletion, or a 17p
deletion.
[0056] Many types of genetic abnormalities are known in the art and
may include one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 12 15,
20, 25, 30, 35, 40, 50, 75, 100 or more) single nucleotide
variations (SNVs; e.g., single nucleotide deletions, additions, or
substitutions), copy number variations (CNVs; e.g., insertions or
deletions), or frameshift mutations. The genetic abnormalities can
also be multiple (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 12 15, 20, 25,
30, 35, 40, 50, 75, 100, 150, 200, 400, 600, 800, 1,000, 1500,
2,000, 4,000, 5,000, 10,000 or more) contiguous or non-contiguous
nucleotide deletions, additions, or substitutions. In some cases, a
genetic abnormality may be in a gene associated with a plasma cell
dyscrasia. Mutations in genes can be synonymous or silent mutations
(i.e., having no effect on the function of the gene product) or
mutations can be non-synonymous (i.e., preventing the gene from
functioning properly and/or altering the function of the gene
product). Abnormalities described herein can be non-synonymous
mutations. In some cases, a genetic abnormality is non-synonymous
single nucleotide variations (NS-SNVs).
[0057] In some cases a biomarker is a genetic abnormality in a gene
associated with cancer or associated with susceptibility to cancer
(e.g., a gene whose mutation contributes to general cancer
formation and/or progression). Genes associated with general
susceptibility to multiple forms of cancer are referred to as
pan-cancer driver genes. For example, a genetic abnormality
detectable in a blood biopsy from a subject having, or at risk of
developing, a plasma cell dyscrasia can be in one or more of the
following pan-cancer driver genes: FAT1, BCLAF1, CDC27, HLA-B,
NBPF1, and ZFHX3. In some cases a genetic abnormality is one or
more of FAT1 (p.V3464I or p.K2895R), BCLAF1 (p.N629S), CDC27
(p.A273G), HLA-B (p.K210N), NBPF1 (p.D679E, p.K41R, or p.L648V),
and ZFHX3 (p.Q2007*, p.H2001N, or p.F1800L).
[0058] In some cases a biomarker is a genetic abnormality in a gene
associated with MM or associated with susceptibility to MM (e.g., a
gene whose mutation contributes specifically to MM formation and/or
progression). Genes associated with susceptibility to MM are
referred to as MM driver genes. For example, genetic abnormalities
detectable in a blood biopsy from a subject having, or at risk of
developing, a plasma cell dyscrasia can be in one or more of the
following MM driver genes: KRAS, NRAS, TP53, DIS3, FAM46C, BRAF,
TRAF3, PRDM1, CYLD, RB1, ACTG1, IRF4, IDH1, INTS12, SP140, LTB,
MAX, HIST1H1E, EGR1, FGFR3, FNDC3A, TNKS, BCL7A, RPL10, GCET2,
RASA2, PLA2G2D, C9orf80, HIST1H3Q CDKN1B, RNF151, C17orf77,
FAM153B, SLC24A1, OR1L8, USP50, CXCR4, KRTDAP, FBXO36, ROBO1, TGDS,
SNX7, MPEG1, DHX32, RYR2, NFKBIA, FSIP2, SI, NECAB3, COASY, EIF4G2,
ZFHX4, CCND1, LRRC16A, YTHDF2, PHOX2B, C15orf59, MOGAT3, EXOG
GRIA2, C4orf43, CCDC144NL, CKM, OR1N2, PRIM2, OR1S2, NDUFAF3,
C20orf112, HIST1H3H, and PNRC1. In some cases a genetic abnormality
is one or more of KRAS (p.G12D), KRAS (p.Q61H), NRAS (p.G12D), BRAF
(p.G469R), IRF4 (p.L116R), SLC24A1 (p.R686G), MPEG1 (p.G537E), and
RYR2 (p.I784V).
[0059] In some cases a biomarker is a genetic abnormality common to
both a blood biopsy and a matched BM biopsy from a subject. Example
1 shows whole exome sequencing of CTCs and matched BM clonal PCs to
demonstrate that 79% of mutations present in CTCs are concordant
with those in BM clonal PCs (see, e.g., FIGS. 5a and 5b). The
mutational profile present in a blood biopsy can indicate disease
progression. For example, detection of a mutational profile that is
common to both a blood biopsy and a matched BM biopsy would
indicate minimal or absent clonal evolution and/or minimal change
or no change in clonal heterogeneity. Mutational profiles common to
blood and BM could contain a single genetic abnormality or a
plurality (e.g., two, three, four, five, six, seven, eight, nine,
10, 12, 15, 20, 25, 30, 40, 50, 70, 100, 150, 200, 300, or 500) of
genetic abnormalities. For example, a mutational profile indicative
of minimal or absent clonal evolution and/or minimal change or no
change in clonal heterogeneity can include a genetic abnormality in
one or more of the following genes: KRAS, NRAS, BRAF, IRF4, MPEG1,
RYR2, SLC24A1, FAT1, BCLAF1, CDC27, HLA-B, NBPF1, and ZFHX3. In
some cases a genetic abnormality is one or more of KRAS (p.G12D),
KRAS (p.Q61H), NRAS (p.G12D), BRAF (p.G469R), IRF4 (p.L116R), MPEG1
(p.G537E), RYR2 (p.I784V), SLC24A1 (p.R686G), FAT1 (p.V3464I or
p.K2895R), BCLAF1 (p.N629S), CDC27 (p.A273G), HLA-B (p.K210N),
NBPF1 (p.D679E, p.K41R, or p.L648V), or ZFHX3 (p.Q2007*, p.H2001N,
or p.F1800L).
[0060] In some embodiments a genetic abnormality is unique to a
blood biopsy relative to a matched BM sample from a subject. Again,
the mutational profile present in a blood biopsy can indicate
disease progression. For example, detection of a mutational profile
that is unique to a blood biopsy relative to a matched BM biopsy
would indicate clonal evolution and/or increased clonal
heterogeneity. In this case, "unique" can be "overlapping" or "not
overlapping." Thus, for example, a unique blood biopsy from a test
subject could have a mutational profile in which some mutations are
the same as those detected in BM from the same test subject and
others are different. Alternatively, a unique blood biopsy from a
test subject could have a mutational profile in which no mutations
are the same as those detected in BM. For example, a mutational
profile indicative of clonal evolution and/or increased clonal
heterogeneity can include a genetic abnormality in one or more of
the following genes: CR1, DPY19L2, TMPRSS13, HBG1, FAM178B, OR6P1,
TNRC6B, PRDM2, HERC3, PIK3R4, PATZ1, ARHGEF33, ELAVL4,
RP11-766F14.2, RBM14, CELF4, FAM104B, SPAG17, HELZ2, DNAH7,
SLC25A23, ZNF98, VGLL1, RRBP1, MUC4, RRN3, MUC2, KRTAP9-2, GPR64,
TPSD1, TAL1, PSMB8, ANPEP, and CCDC108. In some cases a genetic
abnormality is one or more of CR1 (p.R2194* or p.M2208T), DPY19L2
(p.I647V), TMPRSS13 (p.A77G or p.Q78R), HBG1 (p.A137G), FAM178B
(p.D35H), OR6P1 (p.A264S), TNRC6B (p.L383S or T403A), PRDM2
(p.E428*), HERC3 (p.Y864*), PIK3R4 (p.K1136N), PATZ1 (p.P459S),
ARHGEF33 (p.D863E), ELAVL4 (frame shift), RP11-766F14.2 (p.R537C),
RBM14 (p.Q151P), CELF4 (p.N21S), FAM104B (p.R107*), SPAG17
(p.P388T), HELZ2 (p.R1190L), DNAH7 (p.I3394L), SLC25A23 (p.S417F),
ZNF98 (p.Y87C), VGLL1 (p.G35V), RRBP1 (p.G449D), MUC4 (p.S1653I or
p.H3026P), RRN3 (p.P11S or p.R9C), MUC2 (p.T1582R), KRTAP9-2
(p.A41S), GPR64 (p.T359A), TPSD1 (p.A92T), TAL1 (p,L280I), PSMB8
(p.Y93H), ANPEP (p.V726A), and CCDC108 (p.V738D). For example, new
SNVs uniquely identified in CTCs include 6 NS-SNVs in 4 genes (CR1,
DPY19L2, TMPRSS13 and HBG1) that were detected from multiple
patient samples (see, e.g., Example 1). In some cases a NS-SNV is
CR1 (p.R2194* or p.M2208T), DPY19L2 (p.I647V), TMPRSS13 (p.A77G or
p.Q78R), or HBG1 (p.A137G).
[0061] Genetic abnormalities also include any epigenetic
modification which affects a genetic sequence that causes MM or is
associate with susceptibility to MM. Epigenetic modifications
regulated gene expression and/or protein function without changing
the DNA sequence. Epigenetic modifications are well known and can
include, for example, modifications to either DNA (e.g. cytosine
methylation and hydroxymethylation) or proteins (e.g. lysine
acetylation, lysine and arginine methylation, serine and threonine
phosphorylation, and lysine ubiquitination and sumoylation).
Epigenetic modifications can be applied to any biomarker described
herein.
[0062] This disclosure also provides a panel including a plurality
of biomarkers described herein (see, e.g., Example 2). In some
embodiments the panel includes about 80 genes recurrently mutated
in MM and known as oncogenes/tumor suppressor genes, such as NRAS,
KRAS, BRAF and TP53 that occur in about 75% of MM patients. In
addition, the panel can include CNVs and translocations involving
IGH that occur in about 60% of patients; namely t(4;14), t(6;14),
t(11;14), t(14;16), t(14;20). Additional CNVs that are known to
confer an adverse prognosis in MM include 1q21 amp, dell3q and
dell7p.
[0063] In some cases a biomarker is a RNA obtained from exosomes
from a human subject. In some instances, the RNA is miRNA. In
certain embodiments, the miRNA is one or more of let-7b, let-7e,
miR-106a, miR-106b, miR-16, miR-17, miR-181a, miR-18a, miR-20a,
miR-21, miR-25 and miR-744. In certain embodiments, the miRNA is
one or more of let-7e, miR-106a, miR-106b, miR-16, miR-17, miR-18a,
miR-20a, and miR-25. In other embodiments, the miRNA is one or more
of let-7b, let-7e, and miR-16. In certain embodiments, the
expression level of at least: let-7 and miR-16 is assessed. In
certain embodiments, the expression level of at least: let-7b,
let-7e, and miR-16 is assessed. In other embodiments, the
expression level of at least: let-7e, miR-106a, miR-106b, miR-16,
miR-17, miR-18a, miR-20a, and miR-25 is determined. The expression
levels of an RNA or miRNA can be determined by, e.g., quantitative
RT-PCR. In some instances, the RNA (e.g., miRNA) biomarker analysis
is done alongside the International Staging System (based on
albumin and beta-2 microglobulin levels in peripheral blood at the
time, or at substantially the same time as, the exosomes are
isolated from the subject) and/or analysis of chromosomal
abnormalities (e.g., t(4:14), 17p deletion, 1q21
amplification).
Detecting/Measuring a Biomarker
[0064] Detection of one or more biomarkers in a blood biopsy may
represent a non-invasive method to evaluate plasma cell dyscrasias.
For example, detection of one or more biomarkers is useful for
diagnosis, prognosis, staging, monitoring, and/or personalization
or therapy related to plasma cell dyscrasias.
[0065] Determining the presence of one or more biomarkers may
include analysis of all or part of a genome or may include analysis
of all or part of an exome. Determining the presence of one or more
biomarkers may include analysis of one or more (e.g., 2, 3, 4, 5,
6, 7, 8, 9, 10, 12, 15, 20, 25, 30, 35, 40, 50, 75, 100, 150, 200,
300, 400, 500, 1,000, 2,000, 3,000, 4,000, 5,000, or 10,000 or
more) genes of interest.
[0066] In embodiments where the biomarker is a CTC, the CTC can be
detected by any manner known in the art. The presence of CTCs can
be detected, for example, using flow cytometry (e.g.,
multiparameter flow cytometry). An exemplary flow cytometry method
for detecting CTCs in blood biopsies is described in Example 1.
Briefly, CTCs were identified on the basis of intermediate/strong
CD38 expression, strong CD138 expression, down-regulation of CD19,
and down-regulation of CD45, with or without over-expression of
CD56 or CD28.
[0067] In embodiments where the biomarker is a genetic abnormality,
the biomarker can be detected by any manner known in the art. The
presence of a translocation can be detected by, for example,
cytogenetic analyses such as karyotyping and analysis of G-banded
chromosomes (e.g., via fluorescent in situ hybridization (FISH) or
comparative genomic hybridization (CGH)). The presence of a CNV can
be detected by, for example, software programs such as Samtools
v0.1.18, VarScan v2.3.7, and/or DNAcopy (Seshan and Olshen 2010;
bioconductor.org/) See, for example, the methods described in
Example 1. The presence of a NS-SNV can be detected by, for
example, by standard sequence techniques and/or by software
programs such as MuTect (Cibulskis et al., 2013 Nature
Biotechnology 31:213-219) See, for example, the methods described
in Example 1.
[0068] The genetic abnormality can be detected in any genetic
material derived from the plasma cell dyscrasia found in the blood
biopsy. For example, a blood biopsy of a person having a plasma
cell dyscrasia can include, for example, circulating free DNA
(cfDNA), a circulating exosome, or a circulating tumor cell (CTC)
which originated from the plasma cell dyscrasia. In some cases, the
genetic material may need to be isolated from a circulating exosome
or from a CTC. Methods of isolating genetic material are well
known. In some cases, isolation of the genetic material may include
treating the starting material (e.g., a blood biopsy) to lyse red
blood cells followed by the removal of proteins and other
contaminants and finally recovery of the DNA (see, e.g., Example
1). In some cases genetic material is amplified prior to analysis.
Methods of amplification are well known and may include whole
genome amplification as described in Example 1.
[0069] In some cases, the genetic material is circulating free DNA
(cfDNA) released by tumor cells (e.g., MM cells) into the
bloodstream. Recent studies indicate that cfDNA may be more
accurate in the assessment of clonal heterogeneity in solid tumors
compared to CTCs (Murtaza et al., 2013 Nature 497:108-112), since
cfDNA may reflect a broader representation of the different clones
present in multiple sites of the bone marrow. Thus, one or more
biomarkers can be detected in cfDNA (see, e.g., Example 2).
[0070] In some cases, the genetic material is derived from
extracellular vesicles (EVs). EVs can carry cargo such as
mitochondrial DNA (mtDNA), single-stranded DNA, double-stranded DNA
(dsDNA) and/or mRNA. Tumor EVs have been shown to carry oncogene
amplifications (i.e., c-Myc) have been detected in EVs
(Lazaro-Ibanez et al., 2014 The Prostate 74:1379-1390) and DNA that
reflects the genetic status of the tumor (Kahlert et al., 2014 The
Journal of Biological Chemistry 289:3869-3875). EVs include,
without limitation, exosomes, ectosomes, and, apoptotic bodies. In
some cases the EV is an exosome. In some cases, the genetic
material is isolated from an EV. Thus, one or more biomarkers can
be detected in DNA isolated from a circulating exosome (see, e.g.,
Example 3).
[0071] In some cases the genetic material is derived from a CTC.
Whole exome sequencing of CTCs and matched BM clonal PCs
demonstrated that 79% of mutations present in CTCs are concordant
with those in BM clonal PCs. In some cases, the genetic material is
isolated from a CTC. Thus, one or more biomarkers can be detected
in DNA from a CTC (see, e.g., Example 1).
[0072] In some cases, the genetic material is RNA (e.g., miRNA)
derived from exosomes of the human subject. The expression levels
of an RNA or miRNA can be determined by any method known in the
art, e.g., quantitative RT-PCR.
Methods of Use
[0073] Provided herein are methods for using the biomarkers
described herein. The methods described herein are useful in
determining whether a human subject has, or is at risk of
developing, a plasma cell dyscrasia. The methods described herein
may be applied to any appropriate subject having, or at risk of
developing, a plasma cell dyscrasia. Non-limiting examples of a
subject having, or at risk of developing, a plasma cell dyscrasia
include humans, non-human primates, horses, bovine species, porcine
species, dogs, cats, rabbits, rats, and mice. In some embodiments,
a subject having, or at risk of developing, a plasma cell dyscrasia
is a human. For example, the methods described herein can be
applied to a human subject having, or at risk of developing,
MM.
[0074] In some embodiments, the method comprises
detecting/measuring a biomarker. The mutational profile present in
a blood biopsy can indicate a number of things. For example, the
presence of a biomarker as provided herein can be used to determine
a diagnosis, prognosis, or stage of a plasma cell dyscrasia based
on the presence of the biomarkers in a blood biopsy. The presence
of a biomarker as provided herein can be used to monitor a plasma
cell dyscrasia for disease progression, to determine the efficacy
of a therapeutic agent, and/or to determine an appropriate targeted
therapy for the plasma cell dyscrasia.
[0075] This application provides methods for diagnosing plasma cell
dyscrasia based on detection of at least one biomarker in a blood
biopsy from a human subject. In some cases, a genetic abnormality
is a useful biomarker for diagnosing a plasma cell dyscrasia (e.g.,
MM). A method can include detecting at least one genetic
abnormality associated with a plasma cell dyscrasia in cfDNA, DNA
from a circulation exosome, or DNA from a CTC from a human subject.
For example, detection of at least one genetic abnormality in a
gene associated with MM indicates that the human subject has MM. A
method of determining whether a human subject has, or is at risk of
developing, a plasma cell dyscrasia (e.g., MM) can include
detecting at least one genetic abnormality described herein in
cfDNA, DNA from a CTC, or DNA from a circulating exosome from the
human subject. Detection of the at least one genetic abnormality
indicates that the human subject has, or is at risk of developing,
MM. In some cases, detecting at least one translocation in a gene
associated with MM (e.g., t(4;14), t(6;14), t(11;14), t(14;16), or
t(14;20)) indicates that the human subject has, or is at risk of
developing, MM. In some cases, detecting at least one copy number
variation in a gene associated with MM (e.g., 1q21 amplification,
1p32 deletion, 13q deletion, 16q deletion, or 17p deletion)
indicates that the human subject has, or is at risk of developing,
MM. In some cases, detecting at least one SNV in a gene associated
with MM (e.g., KRAS (p.G12D), KRAS (p.Q61H), NRAS (p.G12D), BRAF
(p.G469R), IRF4 (p.L116R), MPEG1 (p.G537E), RYR2 (p.I784V), SLC24A1
(p.R686G), FAT1 (p.V3464I or p.K2895R), BCLAF1 (p.N629S), CDC27
(p.A273G), HLA-B (p.K210N), NBPF1 (p.D679E, p.K41R, or p.L648V), or
ZFHX3 (p.Q2007*, p.H2001N, or p.F1800L)) indicates that the human
subject has a clonal MM which has not progressed. In some cases
detecting at least one SNV in a gene associated with MM (e.g., CR1
(p.R2194* or p.M2208T), DPY19L2 (p.I647V), TMPRSS13 (p.A77G or
p.Q78R), or HBG1 (p.A137G)) indicates that the human subject has MM
which has undergone clonal evolution and/or has increased clonal
heterogeneity. The method can also include treating the human
subject with a therapeutic agent.
[0076] This document provides methods for determining a prognosis
of a plasma cell dyscrasia based on detection of at least one
biomarker in a blood biopsy from a human subject. In some cases, a
CTC is a useful biomarker for determining a prognosis for a human
subject having MM. A method of determining a prognosis of a human
subject having MM can include detecting CTCs present in a blood
biopsy from the human subject. For example, detection of CTCs
(i.e., >0.001% CTCs relative to white blood cells present in a
blood biopsy) in the blood biopsy indicates a poor prognosis (e.g.,
disease progression), and absence of CTC detection in the blood
biopsy indicates a better prognosis (e.g., better progression-free
survival); see, e.g., Example 1 and FIG. 1c. A trend of increasing
CTC counts also indicates poor overall survival (see, e.g., Example
1 and FIG. 1e). A higher percentage of CTC in the peripheral blood
is associated with poor prognosis and survival. In some cases, a
genetic abnormality is a useful biomarker for determining a
prognosis for a human subject having or at risk of developing MM. A
method can include detecting at least one genetic abnormality
associated with a plasma cell dyscrasia in cfDNA, DNA from a
circulating exosome, or DNA from a CTC from a human subject. For
example, detection of at least one genetic abnormality in a gene
associated with MM indicates that the human subject is at risk of
developing MM. A method of determining whether a human subject is
at risk of developing a plasma cell dyscrasia can include
determining whether cfDNA, DNA from a circulating exosome, or DNA
from a CTC from a blood biopsy from the subject has one or more
gene abnormalities described herein.
[0077] This document provides methods for staging a plasma cell
dyscrasia based on detection of at least one biomarker in a blood
biopsy from a human subject. In some cases, a CTC is a useful
biomarker for determining a stage of MM in a human subject. A
method of staging MM in a human subject can include measuring a
percentage of CTCs relative to white blood cells present in a blood
biopsy from the human subject. For example, a low percentage of
CTCs is associated with a precursor state such as monoclonal
gammopathy of undetermined significance (MGUS) or smoldering
multiple myeloma (SMM) while an increased percentage of CTCs is
associated with symptomatic MM or PCL.
[0078] This document provides methods for monitoring the
progression of a plasma cell dyscrasia based on detection of at
least one biomarker in a blood biopsy from a human subject. A
method of monitoring a plasma cell dyscrasia in a human subject can
include detecting at least one genetic abnormality in cfDNA, DNA
from a CTC, or DNA from a circulating exosome. Detection of the at
least one genetic abnormality indicates progression of the plasma
cell dyscrasia. For example, detecting at least one SNV in a gene
associated with MM (e.g., KRAS (p.G12D), KRAS (p.Q61H), NRAS
(p.G12D), BRAF (p.G469R), IRF4 (p.L116R), MPEG1 (p.G537E), RYR2
(p.I784V), SLC24A1 (p.R686G), FAT1 (p.V3464I or p.K2895R), BCLAF1
(p.N629S), CDC27 (p.A273G), HLA-B (p.K210N), NBPF1 (p.D679E,
p.K41R, or p.L648V), or ZFHX3 (p.Q2007*, p.H2001N, or p.F1800L))
which is also detected in a matched BM biopsy indicates that the
human subject has a clonal MM which has not progressed. For
example, detecting at least one SNV in a gene associated with MM
(e.g., CR1 (p.R2194* or p.M2208T), DPY19L2 (p.I647V), TMPRSS13
(p.A77G or p.Q78R), or HBG1 (p.A137G)) in a blood biopsy which
cannot be detected in a matched BM biopsy indicates that the human
subject has MM which has undergone clonal evolution and/or has
increased clonal heterogeneity.
[0079] This document provides methods for determining the efficacy
of a therapeutic agent based on detection of at least one biomarker
in a blood biopsy from a human subject. In some cases, a CTCs is a
useful biomarker for determining the efficacy of a therapeutic
agent. A method of determining treatment efficacy of a therapeutic
agent in a human subject having MM can include measuring a
percentage of CTCs relative to white blood cells present in a first
blood biopsy from the human subject obtained prior to
administration of the therapeutic agent, measuring a percentage of
CTCs relative to white blood cells present in a second blood biopsy
from the human subject obtained after administration of the
therapeutic agent, and comparing the percentage of CTCs in the
first blood biopsy to the percentage of CTCs in the second blood
biopsy. A decrease in the percentage of CTCs in the second blood
biopsy relative to the percentage of CTCs in the first blood biopsy
is indicative that the therapeutic agent is effective treatment. No
change in the percentage of CTCs or an increase in the percentage
of CTCs in the second blood biopsy relative to the percentage of
CTCs in the first blood biopsy is indicative that the therapeutic
agent is ineffective.
[0080] This document provides methods for treating a human subject
having, or at risk of developing, a plasma cell dyscrasia based on
the presence of the biomarkers in a blood biopsy. Methods for
treating a human subject include a targeted therapy (also referred
to as personalized medicine) based on a particular biomarker
detected in a blood biopsy from the human subject. In some cases, a
genetic abnormality is a useful biomarker for determining a
targeted therapy. A targeted therapy can be designed to target a
gene product (e.g., a protein) expressed by the genetic
abnormality. For example, a BRAF inhibitor can be used to treat a
human subject identified as having a genetic abnormality in the
BRAF gene. A method can include detecting at least one genetic
abnormality described herein in cfDNA, DNA from a CTC, or DNA/RNA
from a circulating exosome from a human subject. Detection of at
least one genetic abnormality in a gene associated with MM
indicates that the human subject is a candidate for a therapeutic
agent targeted to a gene produce of the gene associated with MM. A
targeted therapy can also be designed to target a gene product
(e.g., a protein) expressed by a gene associated with the genetic
abnormality. As used herein, a gene product associated with the
genetic abnormality is a protein in the same gene regulatory
network or the same signal transduction pathway as the gene product
expressed by the genetic abnormality. For example, a plasma cell
dyscrasia having a genetic abnormality can respond to a therapy
that targets a first gene product of the genetic abnormality (e.g.,
BRAF), but may also respond to a therapy that targets a second gene
product of another gene in the same signal transduction pathway
(e.g., KRAS, NRAS, MEK, and/or MPAK).
[0081] The treatment methods described above for any of the plasma
cell dyscrasias can also include additional and/or alternative
treatment (e.g., chemotherapy, radiation therapy, targeted therapy,
immunotherapy, and stem cell transplants) either before,
substantially at the same time as, or after the indicated
treatment. Non-limiting examples of chemotherapeutic agents
commonly used for MM include, for example, a proteasome inhibitor
(e.g., Velcade.RTM. (bortezomib) or Kyprolis.TM. (carfilzomib)), an
oral agent (e.g., Thalomid.RTM. (thalidomide) or Revlimid.RTM.
(lenalidomide)), a chemotherapy agent (e.g., Doxil.RTM.
(doxorubicin)), steroids (e.g., corticosteroids, dexamethasone, or
prednisone), and bisphosphonates (e.g., pamidronate or zoledronic
acid for individuals with osteolytic lesions, osteoporosis, or
osteopenia). Non-limiting examples of additional chemotherapeutic
agents include, but are not limited to, an alkylating agent (e.g.,
busulfan, chlorambucil, cisplatin, cyclophosphamide (cytoxan),
dacarbazine, ifosfamide, mechlorethamine (mustargen), and
melphalan), a topoisomerase inhibitor, an antimetabolite (e.g.,
5-fluorouracil (5-FU), cytarabine (Ara-C), fludarabine,
gemcitabine, and methotrexate), an anthracycline, an antitumor
antibiotic (e.g., bleomycin, dactinomycin, daunorubicin,
doxorubicin (Adriamycin), and idarubicin), an epipodophyllotoxin,
nitrosoureas (e.g., carmustine and lomustine), topotecan,
irinotecan, doxorubicin, etoposide, mitoxantrone, bleomycin,
busultan, mitomycin C, cisplatin, carboplatin, oxaliplatin and
docetaxel. Non-limiting examples of immunotherapies commonly used
for MM include interferon and immunoglobulin. Non-limiting examples
of stem cell transplants commonly used for MM include
transplantation of autologous (the subject's own) or allogeneic
(from a donor) hematopoietic stem cells derived from, for example,
bone marrow, peripheral blood, or umbilical cord blood. The methods
described above for any of the plasma cell dyscrasias can include a
single additional and/or alternative treatment or any combination
of additional and/or alternative treatments.
[0082] The invention will be further described in the following
examples, which do not limit the scope of the invention described
in the claims.
Examples
Example 1. Mutational Profile and Prognostic Relevance of
Circulating Tumor Cells in Multiple Myeloma
[0083] Circulating tumor cells (CTCs) have prognostic relevance in
patients with MM and their mutational profile mirrors the genomic
variants present within the bone marrow malignant plasma cells;
thereby defining a new role for CTCs in the prognostic and
molecular profiling of MM patients.
Introduction
[0084] Recent studies of massive parallel sequencing of tumor cells
obtained from the bone marrow (BM) of patients with multiple
myeloma (MM) have demonstrated significant clonal heterogeneity in
MM with a median of five clones present in each sample (Lohr et
al., 2014 Cancer Cell 25:91-101; Bolli et al., 2014 Nature
Communications 5:2997; Cone et al., 2015 Blood 125:1870-1876). The
most frequently observed mutations were seen in KRAS, NRAS, DIS3,
TP53, FAM46C and BRAF (Lohr et al., 2014 Cancer Cell 25:91-101;
Bolli et al., 2014 Nature Communications 5:2997; Cone et al., 2015
Blood 125:1870-1876). Driver mutations in the same pathways were
demonstrated to be mutually exclusive in individual cells
(Leiserson et al., 2013 PLoS Computational Biology 9:e1003054), but
multiple mutations within the same pathway (e.g., KRAS, NRAS, and
BRAF) have been observed in different subclones from the same
patients (Lohr et al., 2014 Cancer Cell 25:91-101).
Results
Detection Rate and Prognostic Relevance of CTC in MM Patients.
[0085] Before investigating if CTCs could represent a reliable
non-invasive alternative to perform genomic characterization of MM
patients, their applicability for prognosis at different disease
stages of MM was first defined. Using sensitive multiparameter flow
cytometry (MFC), we showed that CTCs were detectable in 40/50 (80%)
newly-diagnosed MM patients, 27 out of 64 samples (42.2%) relapsed
non sequential samples and 44 out of 66 samples (66.7%) in the
sequential samples collected. Significant differences were observed
between newly diagnosed patients (median of 0.017%; range,
0.001%-8%) and relapsed MM (Median of 0.003%, range, 0-72%,
p=0.028) and between relapsed MM and patients in response post
therapy or on maintenance therapy (p=2.56.times.10.sup.-6)
patients, (FIG. 1a and Table 2). For MM patients, we further
examined the correlation between monoclonal protein measurements of
tumor burden (M-spike) at the time of sample acquisition and
determination of the percentage of CTCs. As shown in FIG. 1b, there
was a weak correlation between M spike value and level of CTCs in
the PB (R.sup.2=0.20, p=1.07.times.10.sup.-6). Accordingly, the
screening for CTCs is applicable to all patients with MM
independent of the level of M spike.
TABLE-US-00001 TABLE 1 Patient characteristics* Age at the time of
Number of DNA Patient sample collection % BM CTCs Total CTCs
extracted Cytogenetics/ ID in 2014 involvement % CTCs (cells/.mu.L)
harvested (ng) FISH** 413 51 33 0.24 25 86,000 160 +1q 431 50 18
0.32 13.4 48,800 157 None 434 50 36 0.08 5.9 26,300 232 t(4; 14)
447 59 46 0.06 3 5,200 176 +1q/del(1p)/ del(IgH) 448 58 77 0.05 3.4
15,000 294 del(17p) 453 64 70 2 107 300,000 1,022 +1q 457 58 95
0.04 1.68 11,400 279 del(1p32) 461 52 11 0.51 13.8 37,100 259 t(4;
14)/+1q *All samples collected from March to May 2014
**Cytogenetics and FISH are examined for the following markers:
1p/1q and t(4; 14) and t(14/16) and del(17p)
[0086] We then focused on 50 newly diagnosed transplant-ineligible
patients prospectively enrolled on the PETHEMA/GEM2010MAS65
clinical trial to address the role of sensitive baseline monitoring
of CTCs. With a median follow-up of approximately 3 years, 19 of
the 40 cases displaying PB CTCs had relapsed (median time-to
progression of 31 months); by contrast, only 1 of the 10 patients
with undetectable CTCs has relapsed (median time-to progression not
reached; log-rank P-value=0.081, FIG. 1C).
[0087] After demonstrating an association between detectable CTCs
and progression-free survival, we further investigated whether
dynamic changes in the kinetics of CTCs in sequential PB samples
was also predictive of outcome. We examined 66 sequential clinical
samples obtained from 28 patients who were seen at the Dana-Farber
Cancer Institute (DFCI) in the years 2011-2012 (Table 3).
TABLE-US-00002 TABLE 2 Patient characteristics of samples analyzed
with one time point of CTCs (non-sequential cases) at DFCI. Non
sequential Characteristic (n = 64) Sex Male 30 (46.9%) Female 34
(53.1%) Median age (range) 59.5 (35-75) Diagnosis MM 64 (100%)
Subcategory (MM) Relapsed 17 (56.6%) On Maintenance 28 (43.8%)
Post-therapy in response 19 (29.7%) Treatment No 34 (53.1%)
Maintenance therapy 30 (46.9%) Follow-up Medina duration of
follow-up (range), days 1050 (27-1145) Death during follow-up 17
(26.6%)
TABLE-US-00003 TABLE 3 Patient characteristics of sequential
samples analyzed at DFCI. Sequential Characteristic (n = 28) Sex
Male 16 (57.1%) Female 12 (42.9%) Median age (range) 63.5 (40-87)
Diagnosis SMM 3 (11.0%) MM 25 (87.7%) Subcategory (MM) Relapsed 18
(72.0%) Maintenance 4 (16.0%) Post-therapy in response 3 (12.0%)
Treatment at the time of CTC sample Yes 16 (57.1%) No 8 (28.6%)
Maintenance therapy 4 (14.3%) Follow-up Median duration of
follow-up (range), days 795 (20-1118) Death during follow-up 15
(53.6%) Laboratory data Median serum M Protein (range), g/dL 1.86
(0-9.56) Median B2M (range), d/dL 3.15 (1.40-22.3) CTC monitoring
Total number of samples 66 Median duration between sequential
samples 43 (13-105) (range), days Number of CTC analysis/patient
Median = 2 n = 2 21 n = 3 5 n = 4 1
There was a median of 3 samples per patient (range, 2-5) and we
determined the CTC trend for each patient using linear regression.
Given the slopes were not normally distributed, we adopted median
absolute deviation (MAD) as a robust measure of the variability.
Then a cutoff was defined as (Median+MAD), and samples with slopes
greater than this cutoff were classified as the "CTC UP" group
(n=10); this group was then compared to samples, in which such
trend was not observed (n=18), (FIG. 1d). As shown in FIG. 1e,
increasing CTC counts were associated with poor overall survival
(p-value=0.012), indicating that both the absolute numbers of CTCs
and trend of CTC are predictive of outcome in MM. Mutational
Profile of CTCs in Patients with MM
[0088] After demonstrating that CTCs can be readily detected in the
majority of MM patients, we then determined the mutational profile
of CTCs and compared it to that of patient-paired BM clonal PCs by
analyzing 8 MM patients with matched flow-sorted BM and PB tumor
cells and germline non-tumor cell DNA from PB T-lymphocytes. All
patients had newly-diagnosed, untreated MM diagnosed in 2014, and
their characteristics are shown in Table 1. Purified BM and PB
clonal PCs were obtained by flow-sorting as described in the
methods section. The experiment was designed to sequence the whole
exome of BM clonal PCs and CTCs up to 200.times., and germline
cells up to 50.times.. For samples with minimal numbers of CTCs
(N=8), whole genome amplification (WGA) was performed and two
independent libraries were constructed from the sample, followed by
sequencing up to 100.times. for each duplicate. The mean coverage
in the samples exceeded the designed target, as shown in Table 4
and FIG. 2.
TABLE-US-00004 TABLE 4 Overall quality control of sequenced samples
using BamUtil tool. Total- Mapping- Proper- Read Rate Pair DupRat
Mean Sample (M) (%) (%) (%) Coverage MM413_BM 160.33 97.37 95.1
22.6 287.28 MM413_CTC_A 77.34 92.77 89.1 29.25 113.06 MM413_CTC_B
84.34 93.47 90.2 24.17 134.8 MM413_GL 35.38 97.78 95.86 6.9 77.2
MM431_BM 163.62 97.83 95.96 22.03 299.42 MM431_CTC_A 78.41 93.3
89.54 25.26 122.38 MM431_CTC_B 89.98 92.94 89.01 34.05 122.72
MM431_GL 39.98 98.81 97.46 8.33 88.22 MM434_BM 205.37 96.35 93.42
32.66 311.2 MM434_CTC_A 93.96 94.07 90.32 33.84 132.04 MM434_CTC_B
86.18 94.17 90.72 35.01 119.62 MM434_GL 33.44 96.47 93.6 9.22 88.54
MM447_BM 165.67 96.91 94.29 28.87 269.22 MM447_CTC_A 86.46 93.23
89.17 31.25 123.54 MM447_CTC_B 84.97 93.55 89.72 34.92 116.04
MM447_GL 43.86 96.76 94.05 11.71 88.1 MM448_BM 214.93 96.45 93.72
32.65 327.14 MM448_CTC_A 87.04 92.65 88.42 30.19 124.44 MM448_CTC_B
88.29 67.52 81.04 31.74 106.88 MM448_GL 51.06 95.67 92.28 12.97
98.06 MM453_BM 186.92 96.51 93.64 31.41 289.66 MM453_CTC 180.93
96.58 93.72 31.6 280.06 MM453_GL 47.36 95.29 91.46 14.16 88.58
MM457_BM 166.17 99 98.31 30.51 280.86 MM457_CTC_A 79.55 92.86 88.61
31.18 112.6 MM457_CTC_B 85.1 92.53 88.06 33.61 115.08 MM457_GL
46.67 96.96 94.44 12.07 93.94 MM461_BM_A 95.87 91.03 86.05 34.63
122.74 MM461_BM_B 94.02 90.72 85.62 34.1 120.32 MM461_CTC_A 85.01
90.49 84.95 35.5 105.38 MM461_CTC_B 85.71 91.68 86.8 32.65 114.84
MM461_GL 50.21 94.97 91 14.39 92.88 The total number of reads
(TotalReads), mapping rate (MappingRate), percentage of proper
pairs (ProperPair), duplication rate (DupRate) and mean coverage
are shown. A and B in the sample names represent two parallel WGA
libraries. GL = germline.
Single nucleotide variants (SNVs) were called by MuTect (Cibulskis
et al., 2013 Nature Biotechnology 31:213-219) with default
parameters, with an additional filter that requires at least 3 high
quality reads supporting alternative variants. For samples with
WGA, only SNVs shared in both parallel libraries were used. We
identified a median of 223 and 118 SNVs in patient-paired BM clonal
PCs and CTCs, respectively (FIG. 3a). Thus more variants were
identified in BM samples, but this was not unexpected since we only
retained variants shared between the two WGA libraries in the CTC
samples, which increased specificity but reduced sensitivity. When
we analyzed the mutational variants by type, we found that the
percentages of each type in BM myeloma PCs and CTCs were similar in
all but one patient (MM413), FIG. 3b. Similar findings were
observed when breakdown of variants by nucleotide change was
examined (FIG. 3c-d).
[0089] We then compared the distribution of allele fraction (AF),
which is indicative of clonal heterogeneity, and demonstrated
similar bimodal patterns in both BM and PB tumor cells (FIG. 3e).
We further compared shared SNVs between BM myeloma clonal PCs and
CTCs (FIG. 30. As shown by regression lines and slope values, there
was a statistically significant linear correlation (p-value
<2.times.10.sup.-14 for all patients); all slopes were close to
1 except for sample MM447, in which the AF was 1.8-fold higher in
the BM compared to that in CTC sample. We hypothesized that sample
MM447 was contaminated with non-malignant cells and therefore
examined the coverage patterns of BM and PB tumor cells in IGHV
regions. Interestingly, MM447 was the only sample that demonstrated
different patterns in matched BM clonal PCs and CTC (FIG. 4),
indicating that sequencing of the IGHV region could be used to
determine contamination with non-malignant cells when mutational
profiles are being assessed in minimal numbers of CTCs.
Concordance of Somatic Variants Found in Matched BM Clonal PCs and
CTCs.
[0090] We further compared the number of SNVs shared between BM
clonal PCs and CTCs and found that 79% of CTC-SNVs were also
identified in the BM counterpart (FIGS. 5a-b). We then investigated
specific mutations implicated in MM and curated from public
databases (Omberg et al., 2013 Nature Genetics 45:1121-1126; Cancer
Genome Atlas Research et al., 2013 Nature Genetics 45:1113-1120)
(Methods and Table 5).
TABLE-US-00005 TABLE 5 Curated MM and pan cancer driver genes.
Group Genes MM drivers KRAS NRAS TP53 DIS3 FAM46C BRAF TRAF3 PRDM1
CYLD RB1 ACTG1 IRF4 IDH1 INTS12 Potential MM SP140 LTB MAX HIST1H1E
EGR1 FGFR3 FNDC3A TNKS BCL7A RPL10 drivers GCET2 RASA2 PLA2G2D
C9orf80 HIST1H3G CDKN1B RNF151 C17orf77 FAM153B SLC24A1 OR1L8 USP50
CXCR4 KRTDAP FBXO36 ROBO1 TGD8 SNX7 MPEG1 DHX32 RYR2 NFKBIA FSIP2
SI NECAB3 COASY EIF4G2 ZFHX4 CCND1 LRRC16A YTHDF2 PHOX2B C15orf59
MOGAT3 EXOG GRIA2 C4orf43 CCDC144NL CKM OR1N2 PRIM2 OR1S2 NDUFAF3
C20orf112 HIST1H3H PNRC1 Pan cancer ACO1 ACVR1B ACVR2B ADNP AJUBA
AKT1 ALK ALKBH6 ALPK2 ANK3 drivers APC APOL2 ARHGAP35 ARID1A ARID2
ARID5B ASXL1 ASXL2 ATM ATP5B AXIN2 AZGP1 B2M BAP1 BCLAF1 BCOR BHMT2
BRCA1 BRE C3orf70 CAP2 CARD11 CASP8 CBFB CCDC120 CCDC6 CD1D CD70
CD79B CDC27 CDH1 CDK12 CDK4 CDKN1A CDKN2A CEBPA CEP76 CHD4 CHD8
CNBD1 CNKSR1 COLSA1 COLSA3 CREBBP CTCF CTNNB1 CUL4B CUX1 DDX3X DDX5
DIAPH1 DNAH12 DNER DNMT3A EGFR EIF2S2 ELF3 EP300 EPHA2 ERBB2 ERBB3
ERCC2 EZH1 EZH2 EZR FAM166A FAT1 FBXW7 FGFBP1 FGFR2 FLG FLT3 FOXA1
FOXQ1 FRMD7 GATA3 GNA13 GNB1 GNPTAB GOT1 GPS2 GUSB HIST1H3B
HIST1H4E HLA-A HLA-B HRAS HSP90AB1 IDH1 IDH2 IL7R ING1 INPPL1
INTS12 IPO7 IRF6 ITGB7 ITPKB KDM5C KDM6A KEAP1 KEL KIT KLHL8 LCTL
MAP2K1 MAP2K4 MAP3K1 MAP4K3 MBD1 MED12 MED33 MET MGA MICALCL MLL
MLL2 MLL3 MLL4 MORC4 MPO MTOR MUC17 MXRA5 MYB MYCN MYD88 MYOCD
NBPF1 NCOR1 NF1 NFE2L2 NOTCH1 NPM1 NSD1 NTN4 NUP210L ODAM OMA1
OR4A16 OR52N1 OTUD7A PAPD5 PBRM1 PCBP1 PDAP1 PDCD2L PDSS2 PHF6
PIK3CA PIK3R1 PLCG2 POLE POU2AF1 POU2F2 PPM1D PPP2R1A PPP6C PTEN
PTPN11 QKI RAB40A RAC1 RAD21 RASA1 RBM10 RHEB RHOA RIT1 RPL5 RPS15
RPS2 RSBN1L RUNX1 RXRA SACS SELP SEPT12 SERPINB13 SETD2 SETDB1
SF3B1 SFRS2 SGK1 SIRT4 SLC1A3 SLC26A3 SLC44A3 SLC4A5 SMAD2 SMAD4
SMARCA4 SMARCB1 SMC1A SMC3 SNX25 SOS1 SOX17 SPEN SPOP STAG2 STK11
STK19 STX2 TAP1 TBC1D12 TBL1XR1 TBX3 TCEB1 TCF7L2 TCP11L2 TDRD10
TET2 TGFBR2 TIMM17A TNF TNFRSF14 TPS3BP1 TPX2 TRIM23 TSC1 TTLL9
TXNDC8 U2AF1 VHL WASF3 WT1 XIRP2 XPO1 ZFHX3 ZNF180 ZNF471 ZNF483
ZNP620 ZNF750 ZRANB3
Among 70 MM-related genes and 246 pan-cancer driver genes (Omberg
et al., 2013 Nature Genetics 45:1121-1126; Cancer Genome Atlas
Research et al., 2013 Nature Genetics 45:1113-1120), a total of 18
non-synonymous single nucleotide variants (NS-SNVs) in 13 genes
were identified in our cohort (FIG. 5c). Most of these NS-SNVs were
simultaneously detected in matched BM clonal PCs and CTCs from the
same patients. As expected, the genes with the highest frequency in
MM such as KRAS, NRAS, and BRAF were present in these samples, and
were shared between patient-paired BM clonal PCs and CTCs with
similar allele fractions, as shown by the 95% confidence interval
for each mutation. As indicated earlier, the only exception was for
patient MM447, in which there was potential contamination with
non-malignant cells. Further validation using whole exome
sequencing of 5 additional samples of CTCs that did not have
matched BM samples but were sequenced without WGA was performed
(FIG. 5C and FIG. 6).
[0091] We next investigated the differences in AF distribution in
CTCs and BM clonal PCs that could be potentially attributed to the
presence of unique SNVs in each fraction. We identified several
unique mutations present in CTC or BM clonal PCs (FIGS. 7-8); of
those, up to 39 NS-SNV were identified as CTC-specific (FIG. 7),
and 6 NS-SNVs in 4 genes (CR1, DPY19L2, TMPRSS13 and HBG1) were
detected in CTC from multiple patient samples. We evaluated copy
number variations (CNVs) and compared them between matched BM and
PB tumor cells across paired samples. For samples in which WGA was
performed, we called CNVs using the two parallel libraries
separately and only retained shared CNVs. As described in the Table
6, a significant concordance between BM clonal PCs and CTCs was
observed.
TABLE-US-00006 TABLE 6 Concordance of CNVs found in BM and CTC. #
CNVs # CNVs % BM CNVs Patient in CTC in BM found in CTC Notes MM413
730 139 68.35% WGA for CTC MM431 873 100 85.00% WGA for CTC MM434
1048 127 46.46% WGA for CTC MM447 728 202 29.21% WGA for CTC MM448
962 178 72.47% WGA tor CTC MM453 166 158 82.28% No WGA for BM and
CTC MM457 975 101 34.65% WGA for CTC MM461 1306 1297 43.79% WGA for
both CTC and BM
In sample MM453, for which no WGA was applied on BM or CTC, we were
able to detect more than 80% of CNVs shared between BM and CTC
samples. Previously reported MM-related CNVs such as 1q21
amplification and 16q deletion were present both BM clonal PCs and
CTCs from this patient (FIG. 5d) (Corre et al., 2015 Blood
125:1870-1876; Walker et al., 2010 Blood 116:e56-65; Mohamed et
al., 2007 American Journal of Hematology 82:1080-1087; Jenner et
al., 2007 Blood 110:3291-3300). In samples with WGA, such as those
from patient MM431, there were about 100 CNVs found in the BM
sample and 85% of those were also found in CTC.
DISCUSSION
[0092] In MM, there is a marked fluctuation of different clones
throughout patients' clinical course implying that multiple bone
marrow aspirates are needed to determine the genomic profile of
patients, specifically with the development of new targeted
therapies for actionable mutations (e.g., B-RAF inhibitors for
patients with B-RAF mutations). Accordingly, the primary objectives
of our study was to determine the overall applicability of
performing genomic characterization of MM patients non-invasively,
and define if the mutation profile of CTCs reflected that of
patient-paired BM clonal PCs.
[0093] Our results reveal that in MM, PB CTCs can be used as a
non-invasive biomarker to perform mutational profiling of MM
samples with an overlap of 79% of the mutations present in matched
BM clonal PCs from the same patients. A higher number of SNVs were
identified in BM samples, which can be partially explained because
WGA performed in CTCs may have actually eliminated mutations that
could have been detected otherwise, since we only called for
mutations that were present in both WGA duplicates. However, this
is a standard method used to avoid false mutation calls, and WGA
was applied to most PB samples due to low number of CTCs.
Conversely, we observed 21% of CTC-specific mutations, and 4 (CR1,
DPY19L2, TMPRSS13 and HBG1) were noted in multiple patient samples.
It should be noted that key driver genes were identified in both BM
and CTC (BRAF, KRAS and NRAS); indicating that although the
mutation landscape of CTCs does not completely overlap with that of
BM myeloma PCs, the clinically relevant information is fully
represented in peripheral blood CTCs.
[0094] The ability to use peripheral blood (PB) samples to
determine the mutational landscape of MM patients during disease
presentation and progression eliminates the need for multiple
invasive BM aspirates to determine genomic alterations and monitor
clonal evolution during disease progression and after therapeutic
interventions.
[0095] Our study defines the clinical significance of sensitive CTC
monitoring by measuring larger numbers of cells with higher
sensitivity, among uniformly treated patients enrolled in
prospective clinical trials or using sequential peripheral blood
samples. Of note, even by using sensitive MFC immunophenotyping,
CTCs remain undetectable in a small fraction of MM patients which
showed lower relapse rates compared to cases in which CTCs do
circulate in PB; conversely, patients with increasing CTC levels in
sequential samples had significantly inferior survival. Thus, MFC
represents a widely available technique for a fast and sensitive
screening of CTCs that not only affords prognostic information, but
also guides the laboratory for the feasibility of subsequent
deep-sequencing studies in patients with detectable CTCs, thereby
avoiding unnecessary sequencing costs among patients with
undetectable CTCs.
[0096] Our results delineate the clinical value of sensitive
monitoring of CTCs, and should encourage CTC enumeration in larger
series of patients to establish the role of serial CTC monitoring
in the management of patients with MM. Together, this study defines
a new role for CTCs in the prognostic and molecular profiling of MM
patients, and provides the rationale for an integrated
flow-molecular algorithm to detect CTCs in PB and identify
candidate patients for non-invasive genomic characterization to
predict outcomes.
Material and Methods
Patient Sample Collection and Study Approval
[0097] For CTC enumeration studies by MFC, we obtained samples from
50 newly diagnosed patients with symptomatic MM who were
prospectively enrolled on the Spanish clinical trial
PETHEMA/GEM2010MAS65 (sequential chemotherapy with 9 cycles of
bortezomib-melphalan-prednisone (VMP) followed by 9 cycles of
lenalidomide-low dose dexamethasone (Rd) n=27, or alternating
cycles of VMP and Rd up to 18 cycles, n=32).
[0098] In addition, we prospectively collected samples from
patients seen in the clinic at Dana-Farber Cancer Institute (DFCI)
from 2011-2012. A total of 64 unique patients with MM with relapsed
disease or in remission/on maintenance therapy were included in
this study. In addition, 28 patients had sequential samples of CTCs
(N=66 samples) that were used to determine the association of
sequential CTC changes with overall survival.
[0099] For whole exome sequencing studies, we obtained 8 samples of
newly diagnosed untreated patients whose bone marrow, CTC and
germline T lymphocytes were available and selected for exome
sequencing. Additional whole exome sequencing studies were
performed in 5 patients with flow-sorted CTCs but without available
BM clonal PCs.
[0100] The review boards of participating centers approved the
study, which was conducted according to the Declaration of Helsinki
and International Conference on Harmonization Guidelines for Good
Clinical Practice. All patients provided written informed
consent.
Detection of CTCs by Multiparameter Flow Cytometry (MFC)
[0101] The detection of CTCs in EDTA-anticoagulated PB samples
collected from the 50 elderly, newly-diagnosed,
transplant-ineligible MM patients prospectively enrolled in the
GEM2010MAS65 trial was performed following the guidelines of the
European Myeloma Network, and was based on a singular combination
of antigens that allows the identification of aberrant phenotypes
in MM patients. Accordingly, MFC studies were performed using a
4-color monoclonal antibody combinations
(CD38-FITC/CD56-PE/CD19-PerCPCy5.5/CD45-APC) as previously
described in prior publications for sensitive detection of minimal
residual disease (Paiva et al., 2015 Blood 125:3059-3068; Paiva et
al., 2015 Haematologica 100:e53-55; Paiva et al., 2012 Blood
119:687-691).
[0102] Noteworthy, the identification of phenotypically aberrant
myeloma PCs in PB (i.e.: CTCs) is easier than MRD monitoring in
post-treatment BM samples since normal circulating PCs in PB are
homogeneously positive for CD19 and CD45; furthermore,
CTC-screening in PB was performed after determining
patient-specific aberrant immunophenotypes in matched BM myeloma
PCs. CTCs were initially identified on the basis of
intermediate/strong CD38 expression and low/intermediate side
scatter signals; discrimination between myeloma and normal PCs was
performed by the recognition of aberrant phenotypic expression
profiles such as simultaneous down-regulation of CD19, CD38 and
CD45, with or without over-expression of CD56. For patients in whom
CD45 or CD19 was positively expressed, lack of CD19 or CD45,
respectively, dim CD38 intensity and/or bright CD56 staining (equal
or higher than that of natural-killer cells) allowed identification
of myeloma PCs in the vast majority of cases. Data acquisition was
performed in a FACSCantoII flow cytometers (Becton Dickinson
Biosciences--BDB--San Jose, Calif.) using the FACSDiva 6.1 software
(BDB), and allowing for 2.times.10.sup.6 leucocytes/tube to be
selectively stored. Data analysis was performed using the Infinicyt
software (Cytognos SL, Salamanca, Spain), and the presence of CTCs
was established after the identification of a cluster with 20 or
more myeloma PCs, at a sensitivity level of 10.sup.-5. Noteworthy,
the discrimination between plasma cells with normal phenotypes vs.
those phenotypically aberrant (e.g., CTCs) is irrespective of the
individual patients' aberrant phenotypic profile. Thus, the
sensitivity of the assay depends exclusively on the number of cells
analyzed, and the sensitivity is stable providing that
.gtoreq.2.000.000 leukocytes are measured (using a cut-off of 20
myeloma PCs in 2.000.000 leukocytes to define a cluster of CTCs;
limit of detection of 10.sup.-5).
[0103] For the DFCI samples, whole blood samples were treated with
Red Blood Cell Lysis Solution (Miltenyi Biotec) to obtain the total
fraction of leukocytes. Leukocytes were labeled with a combination
of antihuman CD45-APC-Cy7, CD19-PE-Cy7, CD38-V450,
CD56-BrilliantViolet (BD), CD138-PC5 and CD28-FITC (Beckman
Coulter), and subsequently the cells were analyzed using FACSaria
II flowcytometer (BD Biosciences). CTCs were identified on the
basis of intermediate/strong CD38 expression and strong CD138
expression with aberrant phenotypic expression profiles such as
simultaneous down-regulation of CD19 and CD45, with or without
over-expression of CD56 or CD28. For the sake of consistency, CTC
enumeration was performed similarly across all samples from
participating DFCI and Spanish centers, after independent and
blinded review of raw FCS files.
Whole Exome Sequencing
[0104] BM myeloma PCs and CTCs were sorted from paired BM and PB
from 8 patients with symptomatic MM using a FACSAriaIIb sorter (BD
Biosciences). Both tumor fractions were sorted according to the
individual patient-specific aberrant phenotypes, and PB
T-lymphocytes were simultaneously collected for germline control.
Genomic DNA was extracted using QIAamp DNA micro kit (QIAGEN,
Valencia, Calif.) according to the manufacturer's protocols and
double stranded DNA concentration was quantified using PicoGreen
dsDNA Assay kit (Life Technology). The cell number of CTC used and
total amount of genomic DNA obtained are shown in Table 7.
TABLE-US-00007 TABLE 7 Number of cells and DNA quantity of
sequenced samples. Sam- Cell number DNA quantity (ng) ple BM T- BM
T- ID CTCs PCs Cells CTCs PCs Cells 413 86,000 20,000,000 3,600,000
160 4,170 348 431 48,000 1,172,000 4,000,000 157 2,241 7,553 434
26,300 2,095,000 7,400,000 232 2,761 4,673 447 5,200 216,000
842,000 176 1,465 1,073 448 15,000 1,300,000 5,000,000 294 1,642
8,334 453 300,000 110,000 2,300,000 1,022 101 2,343 457 11,400
100,000 1,400,000 279 513 2,930 461 37,100 840,000 2,000,000 259
829 1,688
[0105] For cases in which the total amount of DNA extracted from BM
myeloma PCs (n=1) and CTCs (n=7) was limited, the gDNA was
amplified using GenomePlex Whole Genome Amplification (WGA) Kits
(Sigma-Aldrich) according to manufacturer's introduction. To
capture the coding regions, we used the SureSelectQXT Target
Enrichment kit (Agilent, Santa Clara, Calif.). All sequencing was
performed on the illumina HiSeq 2000 platform (illumina) at the New
York Genome Center, New York, N.Y., USA or at the Broad Institute,
Cambridge, Mass.
Curation of MM and Pan-Cancer Driver Genes
[0106] Cancer driver genes were curated from published larger scale
WES studies specifically; pan cancer driver genes were retrieved
from tumor portal (http://www.tumorportal.org), which defines
driver genes as those with statistical significance (Q-value
<0). MM drivers were curated from MM tumor portal
(www.broadinstitute.org/mmgp) or recent integrative studies of MM
(Lohr et al., 2014 Cancer Cell 25:91-101; Bolli et al., 2014 Nature
Communications 5:2997).
Read Mapping and Variant Analysis
[0107] Paired-end 125 bp reads were aligned to the GRCh37 human
reference using the Burrows-Wheeler Aligner (BWA-ALN v0.6.2) and
processed using the best-practices pipeline that includes marking
of duplicate reads by the use of Picard tools (v1.83), realignment
around indels, and base recalibration via the Genome Analysis
Toolkit (GATK v2.7.4). Single nucleotide variants (SNVs) were
called by MuTect (v1.5) using default parameters, with an
additional filter that requires at least 3 high quality reads
supporting alternative variants. As whole genome amplification
introduces random errors, two libraries were constructed in
parallel for samples with WGA, and only the shared SNVs identified
in both libraries were kept for subsequent analysis.
Quality Control of Sequencing Data
[0108] To evaluate the overall quality of sequenced samples, we
used BamUtil (http://genome.sph.umich.edu/wiki/BamUtil) to
calculate various statistics, including the total number of reads,
mapping rate, percentage of proper pairs, and duplication rate.
Given that the SureSelectQXT v4 platform covers around 51M, a mean
coverage was calculated for each sample. Since exome sequencing
results in uneven coverage, the mean coverage is usually too simple
a statistic to describe the overall quality. We thus evaluated the
distribution of the mean coverage across all targeted regions. The
DepthOfCoverage function from GATK (v2.74) was used with the "-mmq
10" parameter. By doing so we removed all unmapped reads,
duplicated reads and reads with low mapping quality (<10).
Somatic Copy Number Identification
[0109] Samtools v0.1.18 was used to calculate coverage at the base
pair level. Reads with low mapping quality (-q 1) were removed.
VarScan v2.3.7 was used to compare read depths between BM/CTC and
germline samples for contiguous regions of coverage. After
normalizing for the total sequencing depth, the relative copy
number change was inferred as the log 2 ratio for each contiguous
region. The DNAcopy (Seshan and Olshen 2010) library from
BioConductor (http://www.bioconductor.org/) was applied to identify
copy number changes with significance. The resulting p-values were
adjusted for multiple testing and represented as false discovery
rates (FDR). Regions with 10 or more fragments, log 2 ratio >0.5
or <-0.5 and FDR <0.1% were selected.
Characterizing the Shared and Unique SNVs in BM Clonal Cells and
CTCs
[0110] Since SNVs were identified by comparing tumor to normal
genomes, the detection power at a specific locus is determined by
the coverage of this locus at both tumor genome and normal genomes.
MuTect currently uses cutoffs of at least 14 reads in the tumor and
at least 8 in the normal to define whether the gene in question is
sufficiently covered in the tumor and normal samples to be
sensitive enough to call mutations. For a fair comparison, we only
focused on the loci that were covered in both the CTC and BM
samples. Furthermore, for samples with WGA, we required that the
interrogated loci were covered by both libraries.
Survival Analysis
[0111] Survival time was measured from the time of CTC collection
to the date of an event (death, progression or last visit). Curves
were plotted by the Kaplan-Meier method, and the log-rank test was
used to estimate the statistical significance of differences
observed between curves. For the sequential cohort, we tested the
association of survival of MM patients with CTC trends by
performing linear regression (CTC.about.time) and using the
obtained slopes to represent CTC trends. Since the slopes were not
normally distributed, we adopted the median absolute deviation
(MAD) as a robust measure of the variability. Then a cutoff was
defined as (Median+MAD), and samples with slopes greater than this
cutoff were classified as the "CTC UP" group that was then compared
to other samples. All analysis was performed in the R statistical
computing environment (http://www.r-project.org/).
Example 2. Biomarker Panel
[0112] We developed a targeted sequencing panel for MM by using
Hybrid Capture to detect somatic mutations, translocations and copy
number variations (CNV) in MM patients. The panel was developed
using whole exome sequencing databases published to date (Lohr et
al., 2014 Cancer Cell 25:91-101; Bolli et al., 2014 Nature
Communications 5:2997; Chapman et al., 2011 Nature 471:467-472) and
defined genes recurrently mutated in MM and known as
oncogenes/tumor suppressor genes, such as NRAS, KRAS, BRAF and TP53
(FIG. 9). 75% of patients with MM presented with at least one of
these mutations. In addition, the panel covers CNVs and
translocations involving IGH that occur in about 60% of patients;
namely t(4;14), t(6;14), t(11;14), t(14;16), t(14;20). CNVs
specifically covered include 1q21 amp, dell3q and dell7p that are
known to confer an adverse prognosis in MM.
[0113] We tested our panel on 10 matched serum and bone marrow
samples of patients with MM. To examine mutations in cfDNA, serum
and plasma samples were centrifuged at 2,000.times.g for 10 minutes
to remove cell debris. cfDNA was extracted with Qiagen circulating
nucleic acid kit and 50-100 ng cfDNA quantified by nanodrop was
isolated. Prior to library preparation, DNA was fragmented (Covaris
sonication) to 250 bp and further purified using Agencourt AMPure
XP beads. Size-selected DNA was then ligated to specific adaptors
during library preparation (Rubicon kit). Each library was made
with sample-specific barcodes and quantified using qPCR. The bone
marrow and cfDNA samples were pooled separately in equimolar
concentrations to a total of 500 ng for custom enrichment using the
Agilent SureSelect hybrid capture kit. The captures were pooled and
sequenced in one lane of an Illumina HiSeq 2500 in Rapid Run Mode.
Pooled sample reads were de-convoluted (de-multiplexed) and sorted
using the Picard tools. Reads were aligned to the reference
sequence b37 edition from the Human Genome Reference Consortium
using Burrows-Wheeler Aligner (BWA). The alignments were further
refined using the Genome Analysis Toolkit (GATK) tool. Mutation
analysis for single nucleotide variants (SNV) was performed using
MuTect v1.1.4 and annotated by Oncotator. Insertions and deletions
(InDels) were called using Indel Locator
(http://www.broadinstitute.org/cancer/cga/indelocator). The allelic
fraction from duplicate cfDNA samples were compared with tumor DNA
(from CD138+ bone marrow cells) from the same patients at the same
time point. We found high consistency of non-synonymous SNV calls
between replicates of cfDNA and between tumor and matching cfDNA
samples. Duplicate samples were compared between each other and
with matched tumor DNA samples. We were able to identify mutations
at as low AF as 0.22% as illustrated by a KRAS Q61H mutation, also
detected in the matched tumor DNA sample. Correlation within 2
duplicates was more than 0.85 for AF<1%, without false positive
mutation call. Duplicate samples were compared between each other
and with matched tumor DNA samples. Because of low allelic fraction
in the cfDNA, we changed the Mutect settings of fraction of
contamination to 0.2%, and were able to detect mutations in the
cfDNA fraction that were present in the bone marrow samples.
Example 3. Genomic Exosomal DNA (exoDNA) and Progression from
MGUS/Smoldering MM to MM
[0114] Cells were cultured in media supplemented with 10%
exosome-depleted FBS. FBS was depleted of bovine exosomes by
ultracentrifugation at 100,000.times.g for 17 hours. Supernatant
fractions collected from 48 hour cell cultures were pelleted by
centrifugation at 300.times.g for 10 minutes. The supernatant was
collected and centrifuged at 2,000.times.g for 10 minutes followed
by a centrifugation step of 10,000.times.g at 4.degree. C. for 10
minutes to discard cellular debris. Afterward, the medium was
filtered using a 0.22 .mu.m pore filter (Millex GP). Exosomes were
then harvested by centrifugation at 100,000.times.g for 70 minutes.
The exosome pellet was resuspended in PBS and collected by
ultracentrifugation at 100,000.times.g for 70 minutes (Beckman 32Ti
rotor). The exosome pellet was pooled in 500 .mu.L of PBS and
incubated with 10 .mu.l of DNase I (1 unit/.mu.L, catalog number
M6101, Promega) at 37.degree. C. for 30 minutes. Subsequently, 50
.mu.L of DNase stop solution (catalog number M199A, Promega) were
added, and the samples were heated at 65.degree. C. in a water bath
for 5 minutes. Next, the pooled exosome pellet was washed in 11 mL
of PBS, and a second step of ultracentrifugation was performed at
160,000.times.g at 4.degree. C. for 2 hours. After aspiration of
the supernatant, the exosome pellet was suspended in PBS. For
functional assays where exosomes were used, the concentration of
total proteins contained in each exosome pellet was quantified
using the BCA assay (Pierce); exosome quantities are therefore
expressed as micrograms of containing proteins.
[0115] The DNA was extracted using the QIAamp DNA micro kit
according to the manufacturer's instructions. Finally, the DNA was
eluted in distilled water and stored at -20.degree. C. until
processing. The amount of DNA from cell medium-derived exosomes was
quantified using PicoGreen.RTM. (Quant-iT.TM. PicoGreen.RTM. dsDNA
assay kit, catalog number P11496, Life Technologies).
[0116] PCR analysis was performed with exoDNA using the specific
designed primers. PCR was performed in a mixture of 5 .mu.L of
10.times. Accuprime Pfx Reaction mix, 1.5 .mu.L each of
forward/reverse primers (10 .mu.L), template DNA, 0.4 .mu.L of
Accuprime pfx (25 U/.mu.L), and distilled water was added to the
reaction. Amplification was carried out in a 2720 Thermocycler
(ABI) under the following conditions: 95.degree. C. for 2 minutes;
35 cycles of 95.degree. C. for 15 seconds, 55.degree. C. for 30
seconds, 68.degree. C. for 1 minute; 68.degree. C. for 5 minutes;
endless 4.degree. C. PCR products were purified using the QIAquick
PCR purification kit. Subsequently, a sequencing reaction was
performed using BigDye terminator kit (v3.1, Life Technologies).
Sequencing products were separated on an ABI 3730 automated
sequencer.
Example 4. Prognostic Role of Circulating Exosomal miRNAs in
Multiple Myeloma
[0117] In this example, the prognostic significance of circulating
exosomal microRNAs (miRNAs) in MM was examined.
INTRODUCTION
[0118] Multiple Myeloma (MM) is a hematological malignancy
characterized by a clonal proliferation of plasma cells in the bone
marrow microenvironment. However, the clinical and biological
heterogeneity of this malignancy leads to variable responses to
therapy and outcomes. With a vast increase in therapeutic choices
in MM and improved outcomes, the issue of risk stratification to
dissect this heterogeneity is becoming more critical as it may lead
to tailored therapies for different groups of patients. It is
helpful to have prognostic biomarkers that reflect tumor burden and
stage of the disease, tumor biology (such as chromosomal
abnormalities and gene expression signatures), or factors present
in the host that indicate fitness to therapy.
[0119] The most widely used prognostic factors in MM are currently
the International Staging System (ISS) (Griepp et al., J. Clin.
Oncol., 23:3412-20 (2005)) based on albumin and beta-2
microglobulin levels in the peripheral blood at the time of
diagnosis--and chromosomal abnormalities such as t(4:14), 17p
deletion and 1q21 amplification (Avet-Loiseau et al., Leukemia,
27:711-7 (2013)). A new revised ISS (R-ISS) system has been
proposed that includes poor risk cytogenetics and LDH for improved
characterization of patients with poor survival (Palumbo et al., J.
Clin. Oncol., 33:2863-9 (2015)). However, despite these advances,
patients within similar prognostic groups display heterogeneous
outcomes indicating that current prognostic factors used in MM are
suboptimal in stratifying patients with poor risk features.
Combining information about cytogenetic abnormalities and ISS with
other molecular markers may therefore further improve their
prognostic value.
Results
Characterization of Circulating Exosomes in MM
[0120] Peripheral blood circulating exosomes from MM patients and
normal controls were first characterized. After isolation of
circulating exosomes, the presence of exosomes was confirmed by
transmission electron microscopy with immunogold labeling for CD63
and CD81, specific markers of exosomes. The diameter of isolated
exosomes was confirmed to be around 120 nm by Nanosight analysis
(data not shown).
[0121] To define the content of exosomes in terms of small RNAs, a
small RNA sequencing was performed from circulating exosomes of 10
newly diagnosed MM patients and 5 healthy individuals. The large
majority of mappable RNAs were miRNAs (88% in MM samples and 86% in
healthy donor samples). The rest of the RNAs were represented by
small nuclear and nucleolar RNA (sno/snRNA), ribosomal RNA (rRNA),
messenger RNA (mRNA), long noncoding RNA (lincRNA) and unclassified
RNA (miscRNA). There was no difference in terms of distribution of
small exosomal RNA between MM and healthy donor samples (FIG. 10A).
2044 miRNAs were identified, among which 91 were downregulated and
67 were up-regulated in circulating exosomes of MM patients
compared to healthy control samples with a FDR <5% (FIG. 10B). A
hierarchical clustering, based on the differentially expressed
miRNAs, successfully separated samples from MM patients and normal
donors (FIG. 10C). The results of these miRNAs were confirmed by
qPCR indicating that specific miRNAs were downregulated in MM
exosomes compared to normal healthy controls (FIG. 10D). These
results suggest the presence of specific miRNAs expressed in
circulating exosomes that enables differentiation between normal
and malignant samples.
Relationship Between Exosomal miRNAs and PFS in MM
[0122] It was then aimed to determine the prognostic role of
exosomal miRNAs after adjusting for ISS and cytogenetics. 22 miRNAs
were selected based on their differential expression in MM samples
and biological relevance based on studies of tumor samples in MM
(data not shown). The goal was to identify a clinically significant
prognostic signature of circulating exosomal miRNA in patients with
newly diagnosed MM. Therefore, serum samples of 156 patients were
obtained with newly diagnosed MM who were uniformly treated with
Bortezomib and dexamethasone (from the IFM group). The clinical
characteristics of the patients are listed in Table 8.
TABLE-US-00008 TABLE 8 Clinical characteristics of patients. N =
156 N % Age, median (range) 56 (34-73) Sex, male 89 57 IGH IgG 81
52 IgA 36 23 IgD 2 1 No heavy chain 22 14 No data 15 10 IGL Kappa
94 60 Lambda 41 26 No data 21 14 ISS 1 63 40 2 56 36 3 33 21 No
data 4 3 FISH* 13q deletion 59 40 t(4; 14) 14 10 17p deletion 5 3
Poor risk** 17 12 Progression-free survival Relapse or death 111 71
3 years PFS, % (CI) 50 (42-28) Overall survival Deaths 27 17 3
years OS, % (CI) 97 (95-99) Follow-up Median FU, years (CI) 5.6
(5.4-5.9) *Del13q: unknown for 7 subjects; t(4; 14): unknown for 14
subjects. Del17p: unknown for 5 subjects. Poor risk cytogenetics
for 16 subjects. **Poor risk cytogenetics include t(4; 14) and/or
del17p.
All serum samples were harvested at diagnosis, before initiation of
therapy. The median follow up of the cohort was 5.6 years (range,
5.4-5.9).
[0123] A custom quantitative RT-PCR Taqman low-density array (TLDA)
was performed to assess the clinical significance of the 22
selected miRNAs. From univariate analysis, several miRNAs were
significantly associated with worse PFS, specifically let-7b,
let-7e, miR-106a, miR-106b, miR-16, miR-17, miR-181a, miR-18a,
miR-20a, miR-21, miR-25 and miR-744 (FIG. 11A). Each of these
miRNAs had a hazard ratio <1, indicating a worse outcome for
patients with a low expression of the miRNA. Moreover, these miRNAs
remained significantly associated with PFS even when ISS and
cytogenetics was accounted for (FIG. 11B). The effect of the miRNAs
on PFS was illustrated by Kaplan-Meier curves with dichotomized
miRNAs at the median (FIG. 11C). These data indicate that specific
miRNAs can be critical in defining worse prognosis in patients with
newly diagnosed MM even when one accounts for the usual prognostic
factors used in these patients such as ISS and cytogenetics.
Multivariable Analysis
[0124] To evaluate the impact of all of the miRNAs together with
ISS and cytogenetics in a multivariable model, a principal
component (PC) analysis was used. This approach was used because of
the high correlation of the miRNAs. It reduces the dimensionality
and the multi-collinearity of the variables. Using this approach,
six PCs were identified--as defined by linear combinations of the
miRNAs. While all of the miRNAs were used to compute the principal
components, the miRNAs that primarily defined the PC were
determined. Considering that the miRNAs with the largest
coefficients contribute the most to a PC, the following miRNAs
primarily define each PC: 1st PC (let-7e, miR-106a, miR-106b,
miR-16, miR-17, miR-18a, miR-20a and miR-25), 2nd PC (miR-19a and
miR-19b), 3rd PC (miR-10b and miR-125b), 4th PC (miR-19b and
miR-223), 5th PC (miR-125b and miR-181a) and 6th PC (miR-744 and
miR-125a).
[0125] The six PCs were then used together with ISS and
cytogenetics in a multivariable Cox PH model. PC1 was the most
significant variable of the model (Table 9 and FIG. 12A).
TABLE-US-00009 TABLE 9 Multivariable Cox PH model of exosomal miRNA
PC signatures and progression-free survival. Variable HR (95% CI) P
value ISS II vs. I 0.58 (0.35; 0.96) 0.07 III vs. I 1.38 (0.77;
2.47) 0.27 Del17p and/or t(4; 14) 0.99 (0.53; 1.8) 0.99 PC1 1.1
(1.03; 1.18) 0.003 PC2 0.85 (0.72; 1.01) 0.06 PC3 0.78 (0.65; 0.94)
0.01 PC4 1.22 (1.01; 1.49) 0.04 PC5 1.19 (0.95; 1.49) 0.12 PC6 0.99
(0.78; 1.25) 0.96 * Missing indicators were used for unknown
cytogenetics
[0126] Patients with a high PC1 signature had a shorter PFS
compared to low PC1 signature (median PFS of 2.5 [95% CI: 2.2-3.2]
vs. 3.62 [95% CI: 3.0-4.6], respectively, p=0.004), (FIG. 12B). To
further evaluate the effect of the PCI signature by ISS subgroups,
we stratified the patients with ISS I, II and III diseases. The PC1
miRNAs signature had a significant effect on PFS for ISS I/II
patients but not for ISS III patients (ISS I p=0.03, ISS II
p<0.001, ISS III p=0.69).
[0127] Together, this data indicates that the circulating exosomal
miRNAs as a group, defined by the PCs, adds to the prognostic
relevance of ISS and cytogenetics to further stratify patients with
poor outcome.
Discussion
[0128] In this study, a novel prognostic biomarker based on miRNAs
from circulating exosomes was examined to improve the prediction of
PFS in patients with MM. The results of the experiment described
above show that circulating exosomes harbor specific miRNA content
in MM compared to healthy donors. Furthermore, an exosomal miRNA
signature predicts the PFS of patients with MM in an independent
manner, and improves on the prognostic value of ISS and cytogenetic
status in MM.
[0129] Established markers of prognosis in MM include the ISS and
cytogenetics. The ISS classification is based on non-clonal markers
instead that are albumin and beta-2 microglobulin (B2M). Although
B2M is a useful marker of the tumor burden, it is not specific
enough to define the clinical and biological heterogeneity of
patients with MM. Cytogenetics and several gene expression
signatures are truly reflective of the molecular and biological
characteristics of the tumor clone. However, these are only
performed on tumor cells obtained from bone marrow biopsies.
Therefore, there is a need to develop non-invasive biomarkers that
reflect the molecular aspect of the disease.
[0130] Cell-free miRNAs are attractive as prognostic biomarkers
because they are non-invasive. However, many circulating miRNAs are
passively released from apoptotic and necrotic cells, and therefore
may not truly reflect the biological changes that occur in these
tumor cells. In contrast, exosomes are actively secreted in the
peripheral blood by different cell types including cancer cells and
are biologically relevant as they promote tumorigenesis through
miRNA transfer. Cancer exosomes are capable of cell-independent
miRNA processing and transfer of mature miRNAs into recipient
cells; they thus mediate significant transcriptome alterations in
target cells and lead to induction of proliferation and the
conversion of non-tumorigenic cells into tumor-forming cells. This
indicates that exosomes carry specifically selected miRNAs as well
as their own miRNA biogenesis machinery. Therefore, exosomal miRNAs
truly represent specific molecular biomarkers in contrast to
cell-free miRNAs. The exosomal PC1 signature includes: let-7e,
miR-106a, miR-106b, miR-16, miR-17, miR-18a, miR-20a, and miR-25.
Among them, three important family of miRNAs can be identified: the
let-7 family, the miR-17-92 cluster, and the miR-106 family.
[0131] In summary, the data in this example provide an
unprecedented finding of the prognostic significance of an exosomal
miRNA signature in patients with MM. This exosomal miRNA signature
can effectively classify patients with MM into groups at low and
high risk of progression, and adds to the prognostic value of ISS
and cytogenetics in MM. These results need to be validated in other
independent prospective cohorts specifically with other therapeutic
agents used in MM.
Materials and Methods
[0132] Plasma Samples from Patients with MM
[0133] 156 serum samples were obtained from the Intergroupe
Francophone du Myelome (IFM) collected between Jun. 14, 2006 and
Dec. 16, 2008 for this study. All patients were newly diagnosed
with MM, uniformly followed and treated with a combination of
Bortezomib and Dexamethasone followed by high dose Melphalan and
autologous stem cell transplant. None of the patients received
therapy before the collection of blood samples. Criteria of
diagnosis, clinical staging and risk stratification were assessed
according to the International Myeloma Working Group (IMWG)
guidelines (Kyle et al., Leukemia, 23:3-9 (2009)). The median
follow-up was 5.6 years (95% CI 5.4-5.9). Patients provided written
informed consent in accordance with the Declaration of Helsinki. In
addition, samples from 5 healthy volunteers over the age of 40 (for
age-matched comparison) were used for RNA sequencing studies.
Circulating Exosome Isolation
[0134] Circulating exosomes were isolated as described previously
(Taylor et al., Methods Mol Biol., 728:235-46 (2011)). Exosomes
were isolated from serum samples using a combined centrifugation
and exosome isolation reagent method. Serum was isolated by
centrifugation at 300 g for 10 min and further spun down at 2,000 g
for 10 min and 10,000 g for 10 min, to remove dead cells and cell
debris, respectively. Exosomes were harvested by adding an exosome
isolation reagent for 30 min (ExoQuick solution) before
centrifugation at 1,500 g for 30 min.
Electron Microscopy
[0135] Exosomes were characterized by electron microscopy using
CD61 and CD81, as follows:
[0136] pelleted exosomes were fixed with 2% paraformaldehyde in 0.1
M phosphate buffer (pH 7.4), then processed for ultrathin
sectioning and immunogold labeling using anti-CD63 and anti-CD81
antibodies and protein A coupled with 10- or 15-nm gold particles.
Sections were observed at 80 kV on a TecnaiG.beta. Spirit BioTWIN
Transmission electron microscope (FEI), and images were recorded
with an AMT 2 k CCD camera.
RNA Extraction and RNA Sequencing
[0137] Total RNA was extracted from exosome pellets using the
miRNeasy Micro Kit (Qiagen). Small RNA libraries were prepared and
amplified using the NEBNext small RNA Library Prep Set (New England
BioLabs). Amplified libraries were resolved on a 10% polyacrylamide
gel for size selection. The 140 to 160 nucleotide bands correspond
to adapter-ligated constructs derived from the 21 to 40 nucleotide
RNA fragments were excised and recovered in DNA elution buffer. The
average size distribution of each library was determined using
Agilent Bioanalyzer with High Sensitivity Chip Kit (Agilent) and
quantified on ABI 7900HT Fast RT-PCR instrument using the KAPA
Library Quantification kit (Kapa Biosystems). Each library was
adjusted to final concentration of 2 nM, pooled, and sequenced on
an Illumina HiSeq 2000 sequencer for single read 50 cycles at the
Center for Cancer Computational Biology at Dana-Farber Cancer
Institute. The BCL files were demultiplexed using CASAVA 1.8.2
(Illumina) into fastq files. Raw sequencing reads were then
analyzed by miRDeep2 to quantify known small RNA species.
Taqman Low-Density Array
[0138] For quantitative RT-PCR, a custom Taqman Low-Density Array
(Life Technology) was designed. RNA concentrations were measured
with a Qubit miRNA assay and 5 ng of miRNA was reverse transcribed
using a miRNA RT kit (Taqman, Life Technology) and pre-amplified
with a custom pool of primers and a Preamp Master Mix (Taqman, Life
Technology). Quantitative PCR reactions were done with the Taqman
Universal Master Mix II reagent in Custom Taqman Array Cards (384
well plate pre-loaded with 24 specific primers of interest) on a
ViiA.TM. 7 Real-Time PCR System (Life Technology). All assays were
done in duplicate and a subset of samples was also run in
duplicates to test reproducibility. All Ct values above 35 cycles
were considered as undetectable. qRT-PCR data was normalized using
a robust global median normalization as described previously
(D'Haene et al., Methods Mol. Biol., 822:261-72 (2012)). Each plate
was adjusted by a normalization factor as the difference between
the global median Ct value and the plate median Ct value. The
expression of miRNAs with .DELTA.Ct was calculated in which the
maximal Ct value for a miRNA is subtracted from the specific value
for this miRNA. The average of the replicate expression values of
the miRNAs were used in the analysis.
Statistical Analysis
[0139] The primary outcome of interest was progression-free
survival (PFS). The limited number of survival events (27 deaths)
in this cohort precluded the analysis of overall survival (OS). The
Cox Proportional Hazards (Cox PH) model was used to evaluate the
effect on PFS of a) ISS and cytogenetics alone, b) each miRNA
individually and c) each miRNA individually with ISS and
cytogenetics. In these analyses, the miRNAs are included as
continuous variables and ISS and cytogenetics as categorical
variables. To illustrate the effect of the miRNAs on PFS
graphically, the miRNAs were dichotomized at the median based on
low versus high expression and the PFS was estimated and compared
using the Kaplan Meier method and the log-rank test. Given the high
correlation (Pearson correlation) of the miRNAs, a multivariate
model with all variables was not considered. Instead principal
components analysis (PCA) was used to reduce the dimensionality and
multi-collinearity, and then the principal components (PC) that
explained 80% of the original variation in the data were used in a
Cox PH model to predict PFS with and without ISS and cytogenetics.
In the PCA, the original data were centered and scaled. From the
analysis, six principal components were determined to explain 80%
of the variation in the data. While all of the miRNAs were used to
calculate the PCs included in the Cox PH model, the magnitude of
the coefficients were evaluated to determine the miRNAs that most
influenced each PC. The likelihood ratio test was used to evaluate
the added value when the miRNA PC was added to a Cox PH model with
ISS and poor risk cytogenetics. Analyses comparing impact of miRNA
PC on outcome were also performed by ISS. Sensitivity and
specificity of the signature was evaluated using receiver operator
characteristics (ROC) curve. All statistical analyses were
performed in R. The following functions were used in the analysis:
coxph function of the survival package for Cox PH model, prcomp
from the stats packages, risksetROC and risksetAUC functions from
the risksetROC package for ROC analysis.
Example 5. Whole-Exome Sequencing and Targeted Deep Sequencing of
cfDNA Enables a Comprehensive Mutational Profiling of Multiple
Myeloma
[0140] We performed next generation sequencing of matched Cell-free
DNA (cfDNA)/tumor DNA (tDNA) samples for 63 patients with newly
diagnosed or relapsed MM, SMM, or MGUS. Whole-Exome Sequencing
(WES) was performed on 30 matched samples cfDNA/tDNA/germline DNA
from 10 patients with more than 5% of tumor fraction. Libraries
were hybridized to the Nextera Rapid Capture Exome kit (Illumina)
and then sequenced on HiSeq 4000 (Illumina). Targeted deep
sequencing was performed on 32 matched cfDNA/tDNA samples from 15
patients using the HaloPlex HS technology (Agilent), allowing for
molecular barcoding. Libraries were constructed according to the
manufacturer's instructions and sequenced on HiSeq 2500. Sequencing
data were analyzed using the Firehose pipelines, including MuTect,
ABSOLUTE, RecapSeg, GISTIC and MutSig.
[0141] To assess whether cfDNA can capture the genetic diversity of
MM and inform clinical management, we performed WES of matched
cfDNA/tDNA/germline DNA samples for 10 patients (mean target
coverage 194.times.). Copy number alterations (CNAs) assessed by
WES (ReCapSeg) were consistent between cfDNA and tumor DNA.
Similarly, focal CNAs assessed by GISTIC were consistent between
tDNA and cfDNA. We then examined the overlap of somatic single
nucleotide variants (SSNVs) between WES of cfDNA and matched tDNA.
We found most (54-100%) of clonal and subclonal SSNVs that were
detected in the tumor or cfDNA were confirmed to be present in
cfDNA or tumor, respectively, FIGS. 13 and 14. To assess whether
targeted deep sequencing of cfDNA could be a good proxy for tumor
biopsy we used a targeted deep sequencing approach of known MM
driver genes. Libraries were prepared using unique molecular
barcodes to avoid high duplication rates, for 32 matched cfDNA/tDNA
samples from 15 MM patients. We found similar frequencies of
altered MM driver genes in both cfDNA and tDNA, including KRAS,
NRAS, and TP53 as shown in FIG. 15, indicating that cfDNA can be
used for precision medicine.
[0142] Our study demonstrates that both WES and targeted deep
sequencing of cfDNA are consistently representative of tumor DNA
alterations in terms of CNAs, focal CNAs and SNVs. This approach
can therefore be used to longitudinally follow clonal evolution
across the course of the disease and precision medicine in patients
with MM.
OTHER EMBODIMENTS
[0143] It is to be understood that while the disclosure has been
described in conjunction with the detailed description thereof, the
foregoing description is intended to illustrate and not limit the
scope of the disclosure, which is defined by the scope of the
appended claims. Other aspects, advantages, and modifications are
within the scope of the following claims.
* * * * *
References