U.S. patent application number 16/886059 was filed with the patent office on 2020-10-29 for methods and kits for the molecular subtyping of tumors.
The applicant listed for this patent is BioNTech AG, Stratifyer Molecular Pathology GmbH. Invention is credited to Christoph Kneip, Ralph Wirtz.
Application Number | 20200340065 16/886059 |
Document ID | / |
Family ID | 1000004945943 |
Filed Date | 2020-10-29 |
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United States Patent
Application |
20200340065 |
Kind Code |
A1 |
Wirtz; Ralph ; et
al. |
October 29, 2020 |
METHODS AND KITS FOR THE MOLECULAR SUBTYPING OF TUMORS
Abstract
The present invention relates to an in vitro method of
identifying a molecular subtype of a tumor in a cancer patient and
to a method of stratifying a cancer patient for tumor treatment.
The present invention further relates to kits that are useful for
identifying a molecular subtype of a tumor in a cancer patient.
Inventors: |
Wirtz; Ralph; (Koln, DE)
; Kneip; Christoph; (Berlin, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BioNTech AG
Stratifyer Molecular Pathology GmbH |
Mainz
Koln |
|
DE
DE |
|
|
Family ID: |
1000004945943 |
Appl. No.: |
16/886059 |
Filed: |
May 28, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14912813 |
Feb 18, 2016 |
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PCT/EP2014/067675 |
Aug 19, 2014 |
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16886059 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/6886 20130101;
C12Q 2600/106 20130101; C12Q 2600/112 20130101; C12Q 2600/158
20130101 |
International
Class: |
C12Q 1/6886 20060101
C12Q001/6886 |
Foreign Application Data
Date |
Code |
Application Number |
Aug 19, 2013 |
EP |
PCT/EP2013/002487 |
Claims
1.-8. (canceled)
39. A kit for identifying a molecular subtype of a tumor in a
cancer patient by means of reverse transcription (RT) quantitative
PCR, said kit comprising: at least one pair of HER2-specific
primers and at least one HER2-specific probe; at least one pair of
ESR1-specific primers and at least one ESR1-specific probe; at
least one pair of PGR-specific primers and at least one
PGR-specific probe; and at least one pair of Ki67-specific primers
and at least one Ki67-specific probe.
40. The kit of claim 39, wherein the quantitative PCR is
fluorescence-based quantitative real-time PCR.
41. The kit of claim 39, wherein detection of the probe is based on
amplification-mediated probe displacement.
42. The kit of claim 41, wherein the probe is a dual-label probe
comprising a fluorescence reporter moiety and a fluorescence
quencher moiety.
43. The kit of claim 39, further comprising a reverse transcriptase
and a DNA polymerase.
44. The kit of claim 43, wherein the reverse transcriptase and the
polymerase are provided in the form of an enzyme-mix which allows a
one-step reverse transcription (RT) quantitative PCR.
45. The kit of claim 39, further comprising at least one pair of
reference gene-specific primers and at least one reference
gene-specific probe.
46. The kit of claim 45, wherein the reference gene is one or more
selected from the group comprising CALM2, B2M, RPL37A, GUSB, HPRT1
and GAPDH.
47. The kit of claim 39, further comprising at least one control
RNA sample.
48. The kit of claim 39, wherein the primers provide an amplicon
size of less than 120 bp.
49. The kit of claim 39, wherein the ESR1-specific primers have a
length of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 1 and 2, and/or wherein
the HER2-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 4 and 5, and/or wherein the Ki67-specific primers have a
length of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 7 and 8, and/or wherein
the PGR-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 10 and 11.
50. The kit of claim 39, wherein the ESR1-specific probe has a
length of 20 to 35 nucleotides and comprises at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 3, and/or wherein the
HER2-specific probe has a length of 20 to 35 nucleotides and
comprises at least 15 contiguous nucleotides of the sequence of SEQ
ID NO: 6, and/or wherein the Ki67-specific probe has a length of 20
to 35 nucleotides and comprises at least 15 contiguous nucleotides
of the sequence of SEQ ID NO: 9, and/or wherein the PGR-specific
probe has a length of 20 to 35 nucleotides and comprises at least
15 contiguous nucleotides of the sequence of SEQ ID NO: 12.
51. The kit of claim 39, wherein the tumor is a solid tumor.
52. The kit of claim 39, wherein the tumor is a breast tumor or is
derived from a breast tumor.
53. The kit of claim 39, wherein the cancer is breast cancer.
54. The kit of claim 39, further comprising at least one pair of
RACGAP1-specific primers and at least one RACGAP1-specific
probe
55. The kit of claim 39, wherein the kit comprises: a pair of
HER2-specific primers and an HER2-specific probe; a pair of
ESR1-specific primers and an ESR1-specific probe; a pair of
Ki67-specific primers and a Ki67-specific probe; and a pair of
PGR-specific primers and a PGR-specific probe, wherein the
ESR1-specific primers have the sequences of SEQ ID NOs: 1 and 2,
wherein the HER2-specific primers have the sequences of SEQ ID NOs:
4 and 5, wherein the Ki67-specific primers have the sequences of
SEQ ID NOs: 7 and 8, and wherein the PGR-specific primers have the
sequences of SEQ ID NOs: 10 and 11.
56. The kit of claim 54, wherein the RACGAP1-specific primers
provide an amplicon size of less than 120 bp.
57. The kit of claim 55, wherein the ESR1-specific probe has the
sequence of SEQ ID NO: 3, the HER2-specific probe has the sequence
of SEQ ID NO: 6, the Ki67-specific probe has the sequence of SEQ ID
NO: 9, or the PGR-specific probe has the sequence of SEQ ID NO:
12.
58. The kit of claim 55, wherein the ESR1-specific probe has the
sequence of SEQ ID NO: 3, the HER2-specific probe has the sequence
of SEQ ID NO: 6, the Ki67-specific probe has the sequence of SEQ ID
NO: 9, and the PGR-specific probe has the sequence of SEQ ID NO:
12.
Description
TECHNICAL FIELD OF THE INVENTION
[0001] The present invention relates to an in vitro method of
identifying a molecular subtype of a tumor in a cancer patient and
to a method of stratifying a cancer patient for tumor treatment.
The present invention further relates to kits that are useful for
identifying a molecular subtype of a tumor in a cancer patient.
BACKGROUND OF THE INVENTION
[0002] Tumor prognosis and prediction of therapy response is
closely related to the molecular subtype of the tumor. The current
worldwide applied standard methodology for the detection of the
receptor status of cancers, e.g., breast cancers, is
immunohistochemistry (IHC) from formalin-fixed and
paraffin-embedded (FFPE) biopsy or resection tissue. Currently,
administration of endocrine or targeted systemic treatment (i.e.
trastuzumab) is mostly based on IHC.
[0003] FFPE sample preparation and subsequent immunohistochemical
staining with specific antibodies is a technology currently only
performed in pathology laboratories. From microscopic examination
of FFPE tumor tissues besides interpretation of staining results,
pathologists derive further clinically essential information on
tumor biology and tumor spread. Furthermore, the pathologist's
interpretation of FFPE tissue examination can be considered an
essential column in clinical decision making. In many countries
pathologists are an integral part of the so-called case conference
in breast cancer management decisions. Although IHC could easily be
performed in centralized settings, personal opinion and experience
of the examining pathologist is highly valued in the individual
case decision.
[0004] However, several studies have demonstrated significant
inter-observer variability and technical variability in up to 40%
of immunohistochemistry results. Moreover, immunohistochemistry
only allows a qualitative or, in some cases, a semi-quantitative
statement regarding the respective receptor status.
[0005] Therefore, there is a need for a reliable, objective,
quantitative and reproducible test system for the molecular
subtyping of tumors, e.g. breast tumors, which facilitates the
selection of suitable tumor treatment regimens (patient
stratification), and allows prognosis and prediction of therapy
success and assessment of a patient's risk for distant metastasis.
Moreover, such test system should allow for decentralized testing
that is suitable for a significant proportion of cancer
patients.
SUMMARY OF THE INVENTION
[0006] In one aspect, the invention relates to an in vitro method
of identifying a molecular subtype of a tumor in a cancer patient,
said method comprising the steps: [0007] (a) determining the
expression level of RNA transcript of human epidermal growth factor
receptor 2 (HER2) in a sample of the tumor; [0008] (b) determining
the expression level of RNA transcript of estrogen receptor (ESR1)
in a sample of the tumor; [0009] (c) determining the expression
level of RNA transcript of progesterone receptor (PGR) in a sample
of the tumor; and [0010] (d) determining the expression level of
RNA transcript of proliferation antigen Ki-67 (Ki67) in a sample of
the tumor; and/or [0011] (e) determining the expression level of
RNA transcript of RacGTPase-activating protein 1 (RACGAP1) in a
sample of the tumor.
[0012] In one embodiment, determining the expression level of RNA
transcript of HER2, ESR1, PGR and Ki67 and/or RACGAP1 comprises
determining whether the expression level of RNA transcript of HER2,
ESR1, PGR and Ki67 and/or RACGAP1 is lower or higher than a defined
expression threshold of RNA transcript of HER2, ESR1, PGR and Ki67
and/or RACGAP1.
[0013] In one embodiment, step (a) is performed before steps (b),
(c) and (d) and/or (e). In one embodiment, step (d) and/or step (e)
are performed after steps (a), (b) and (c).
[0014] In one embodiment, step (a) is performed before step (b),
step (b) is performed before step (c), and step (c) is performed
before step (d) and/or step (e).
[0015] In one embodiment, the molecular subtype is selected from
the group comprising HER2-positive, triple-negative, luminal A and
luminal B.
[0016] In one embodiment, an expression level of RNA transcript of
HER2 which is higher than a defined expression threshold of RNA
transcript of HER2 identifies the molecular subtype of the tumor as
HER2-positive.
[0017] In one embodiment, [0018] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0019] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0020] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0021] an expression level
of RNA transcript of Ki67 which is lower or higher than a defined
expression threshold of RNA transcript of Ki67 identify the
molecular subtype of the tumor as triple-negative.
[0022] In one embodiment, the molecular subtype is luminal A or
luminal B.
[0023] In one embodiment, [0024] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0025] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0026] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0027] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0028] In one embodiment, [0029] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0030] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0031] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0032] an expression level
of RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal A.
[0033] In one embodiment, [0034] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0035] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0036] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0037] an expression level
of RNA transcript of Ki67 which is lower or higher than a defined
expression threshold of RNA transcript of Ki67 identify the
molecular subtype of the tumor as luminal B.
[0038] In one embodiment, [0039] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0040] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0041] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0042] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0043] In one embodiment, [0044] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0045] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0046] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0047] an expression level
of RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal A.
[0048] In one embodiment, [0049] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0050] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0051] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0052] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0053] In one embodiment, the molecular subtype luminal A is
associated with a probability of distant recurrence-free survival 5
years after treatment which is at least 11%, preferably at least
13% higher than the probability of distant recurrence-free survival
5 years after treatment associated with molecular subtype luminal B
and/or with a probability of survival 5 years after treatment which
is at least 7%, preferably at least 9% higher than the probability
of survival 5 years after treatment associated with molecular
subtype luminal B.
[0054] In one embodiment, the method comprises step (d), and [0055]
an expression level of RNA transcript of ESR1 which is higher than
a defined expression threshold of RNA transcript of ESR1 and [0056]
an expression level of RNA transcript of Ki67 which is higher than
a defined expression threshold of RNA transcript of Ki67 indicates
an increased risk of poor clinical outcome for the cancer patient,
in particular an increased risk of distant metastasis.
[0057] In one embodiment, the method comprises step (e), and an
expression level of RNA transcript of RACGAP1 which is higher than
a defined expression threshold of RNA transcript of RACGAP1
indicates an increased risk of poor clinical outcome for the cancer
patient.
[0058] In one embodiment, the method comprises steps (d) and (e),
and [0059] an expression level of RNA transcript of Ki67 which is
lower than a defined expression threshold of RNA transcript of Ki67
and [0060] an expression level of RNA transcript of RACGAP1 which
is higher than a defined expression threshold of RNA transcript of
RACGAP1 indicates an increased risk of poor clinical outcome for
the cancer patient.
[0061] In one embodiment, the method comprises steps (d) and (e),
and [0062] an expression level of RNA transcript of Ki67 which is
higher than a defined expression threshold of RNA transcript of
Ki67 and [0063] an expression level of RNA transcript of RACGAP1
which is higher than a defined expression threshold of RNA
transcript of RACGAP1 indicates a further increased risk of poor
clinical outcome for the cancer patient.
[0064] In one embodiment, poor clinical outcome comprises a
relative reduction in or more of survival, recurrence-free survival
and distant recurrence-free survival.
[0065] In one embodiment, the tumor is a solid tumor.
[0066] In one embodiment, the tumor is a breast tumor or is derived
from a breast tumor.
[0067] In one embodiment, the cancer is breast cancer.
[0068] In one embodiment, the sample is RNA extracted from the
tumor.
[0069] In one embodiment, the expression level of RNA transcript is
determined by reverse transcription (RT) quantitative PCR.
[0070] In one embodiment, the quantitative PCR is
fluorescence-based quantitative real-time PCR.
[0071] In one embodiment, the method comprises the use of
ESR1-specific primers having a length of 15 to 30 nucleotides and
comprising at least 10 contiguous nucleotides of the sequences of
SEQ ID NOs: 1 and 2, and/or HER2-specific primers having a length
of 15 to 30 nucleotides and comprising at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 4 and 5, and/or
Ki67-specific primers having a length of 15 to 30 nucleotides and
comprising at least 10 contiguous nucleotides of the sequences of
SEQ ID NOs: 7 and 8, and/or PGR-specific primers having a length of
15 to 30 nucleotides and comprising at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 10 and 11, and/or
RACGAP1-specific primers having a length of 15 to 30 nucleotides
and comprising at least 10 contiguous nucleotides of the sequences
of SEQ ID NOs: 13 and 14.
[0072] In one embodiment, the method comprises the use of an
ESR1-specific probe having a length of 20 to 35 nucleotides and
comprising at least 15 contiguous nucleotides of the sequence of
SEQ ID NO: 3, and/or a HER2-specific probe having a length of 20 to
35 nucleotides and comprising at least 15 contiguous nucleotides of
the sequence of SEQ ID NO: 6, and/or a Ki67-specific probe having a
length of 20 to 35 nucleotides and comprising at least 15
contiguous nucleotides of the sequence of SEQ ID NO: 9, and/or a
PGR-specific probe having a length of 20 to 35 nucleotides and
comprising at least 15 contiguous nucleotides of the sequence of
SEQ ID NO: 12, and/or a RACGAP1-specific probe having a length of
20 to 35 nucleotides and comprising at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 15.
[0073] In one embodiment, the expression level is normalized
against the (mean) expression level of one or more reference genes
in the sample of the tumor.
[0074] In one embodiment, the one or more reference genes are
selected from the group comprising CALM2, B2M, RPL37A, GUSB, HPRT1
and GAPDH.
[0075] In a further aspect, the invention relates to a method of
stratifying a cancer patient for tumor treatment, said method
comprising, as a first step, identifying a molecular subtype of a
tumor in the cancer patient using the in vitro method as defined
above and, as a second step, selecting a tumor treatment regimen
based on the molecular subtype identified by the in vitro
method.
[0076] In one embodiment, the molecular subtype is selected from
the group comprising HER2-positive, triple-negative, luminal A and
luminal B.
[0077] In one embodiment, [0078] the molecular subtype is
HER2-positive, and the tumor treatment regimen comprises
administration of anti-HER2 antibodies and chemotherapeutic agents;
[0079] the molecular subtype is triple-negative, and the tumor
treatment regimen comprises administration of chemotherapeutic
agents; [0080] the molecular subtype is luminal A, and the tumor
treatment regimen comprises endocrine therapy; or [0081] the
molecular subtype is luminal B, and the tumor treatment regimen
comprises endocrine therapy and, optionally, administration of
chemotherapeutic agents.
[0082] In one embodiment, the molecular subtype is luminal B, and
the tumor treatment regimen comprises administration of
chemotherapeutic agents.
[0083] In one embodiment, the molecular subtype is luminal B, and
the tumor treatment regimen comprises administration of a taxane,
preferably docetaxel.
[0084] In one embodiment, the taxane is administered in combination
with fluorouracil, epirubicin and cyclophosphamide (FEC).
[0085] In one embodiment, the tumor is a solid tumor.
[0086] In one embodiment, the tumor is a breast tumor or is derived
from a breast tumor.
[0087] In one embodiment, the cancer is breast cancer.
[0088] In a further aspect, the present invention relates to a
method of treatment of cancer, said method comprising, as a first
step, stratifying a cancer patient for tumor treatment using the in
vitro method as defined above, and, as a second step, providing the
selected tumor treatment regimen to the cancer patient.
[0089] In a further aspect, the present invention relates to a kit
useful for identifying a molecular subtype of a tumor in a cancer
patient by means of reverse transcription (RT) quantitative PCR,
said kit comprising: [0090] at least one pair of HER2-specific
primers and at least one HER2-specific probe; [0091] at least one
pair of ESR1-specific primers and at least one ESR1-specific probe;
[0092] at least one pair of PGR-specific primers and at least one
PGR-specific probe; and [0093] at least one pair of Ki67-specific
primers and at least one Ki67-specific probe; and/or [0094] at
least one pair of RACGAP1-specific primers and at least one
RACGAP1-specific probe.
[0095] In one embodiment, the quantitative PCR is
fluorescence-based quantitative real-time PCR.
[0096] In one embodiment, detection of the probe is based on
amplification-mediated probe displacement.
[0097] In one embodiment, the probe is a dual-label probe
comprising a fluorescence reporter moiety and a fluorescence
quencher moiety.
[0098] In one embodiment, the kit further comprises a reverse
transcriptase and a DNA polymerase.
[0099] In one embodiment, the reverse transcriptase and the
polymerase are provided in the form of an enzyme-mix which allows a
one-step reverse transcription (RT) quantitative PCR.
[0100] In one embodiment, the kit further comprises at least one
pair of reference gene-specific primers and at least one reference
gene-specific probe.
[0101] In one embodiment, the reference gene is one or more
selected from the group comprising CALM2, B2M, RPL37A, GUSB, HPRT1
and GAPDH.
[0102] In one embodiment, the kit further comprises at least one
control RNA sample. In one embodiment, the primers provide an
amplicon size of less than 120 bp.
[0103] In one embodiment, the ESR1-specific primers have a length
of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 1 and 2, and/or the
HER2-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 4 and 5, and/or the Ki67-specific primers have a length of
15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 7 and 8, and/or the
PGR-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 10 and 11, and/or the RACGAP1-specific primers have a
length of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 13 and 14.
[0104] In one embodiment, the ESR1-specific probe has a length of
20 to 35 nucleotides and comprises at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 3, and/or the
HER2-specific probe has a length of 20 to 35 nucleotides and
comprises at least 15 contiguous nucleotides of the sequence of SEQ
ID NO: 6, and/or the Ki67-specific probe has a length of 20 to 35
nucleotides and comprises at least 15 contiguous nucleotides of the
sequence of SEQ ID NO: 9, and/or the PGR-specific probe has a
length of 20 to 35 nucleotides and comprises at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 12, and/or the
RACGAP1-specific probe has a length of 20 to 35 nucleotides and
comprises at least 15 contiguous nucleotides of the sequence of SEQ
ID NO: 15.
[0105] In one embodiment, the tumor is a solid tumor.
[0106] In one embodiment, the tumor is a breast tumor or is derived
from a breast tumor.
[0107] In one embodiment, the cancer is breast cancer.
[0108] In another aspect, the present invention relates to the use
of a kit as defined above for identifying a molecular subtype of a
tumor in a cancer patient.
[0109] In another aspect, the present invention relates to the use
of a kit as defined above for assessing a cancer patient's risk for
distant metastasis.
BRIEF DESCRIPTION OF THE FIGURES
[0110] FIG. 1 outlines potential uses for the methods of the
present invention as a back up for conventional methods of subtype
classification (e.g. IHC) and as a supplement to conventional
methods of patient stratification.
[0111] FIGS. 2A-B depict a partitioning test to evaluate the
prognostic and predictive value of the expression level of HER2,
ESR1, PGR, Ki67 and RACGAP1 mRNA for the 5-years survival rate of
breast cancer patients. Available data from 855 tumors were first
stratified by HER2 mRNA expression level to identify HER2-positive
tumors (>cut-off value 38). HER2-negative tumors were further
stratified by ESR1 mRNA expression level. FIG. 2A shows that
ESR1-positive tumors (>cut-off value 34) were further stratified
by Ki67 mRNA expression level (cut-off value 31,7) followed by PGR
mRNA expression level (cut-off value 30,2). FIG. 2B shows that,
alternatively, ESR1-positive tumors (>cut-off value 34) were
further stratified by PGR mRNA expression level (cut-off value
30,2) followed Ki67 mRNA expression level (cut-off value 31,7).
Kaplan-Meier analyses of these data are shown in FIGS. 3 and 4.
FIG. 2C shows that Ki67-positive and Ki67-negative tumors were
stratified by RACGAP1 mRNA expression level (cut-off value 34,2).
To improve the number of patients for further analysis of RACGAP1,
no data for PGR are given in the picture. The further consideration
of PGR does not alter the overall outcome with respect to RACGAP1.
The data (see Table 3) shows that RACGAP1 mRNA expression levels
below or above the defined threshold are associated with
particularly significant differences in the 5-years survival
rate.
[0112] FIG. 3 depicts a Kaplan Meier analysis of survival of breast
cancer patients with HER2-positive (HER2), luminal A (LumA),
luminal B (LumB) or triple-negative (TNT) tumors, wherein the
molecular subtype of the tumor was identified in accordance with
the present invention, based on the mRNA expression levels of HER2,
ESR1, PGR and Ki67. The luminal A subtype, as defined by the
present inventors, is associated with an overall survival rate of
97% after 5 years (vs. 87% for luminal B and HER2-positive tumors
and 84% for triple-negative tumors).
[0113] FIG. 4 depicts a Kaplan Meier analysis of distant metastasis
free survival ("DMFS"; distant recurrence X years after surgery) of
breast cancer patients with HER2-positive (HER2), luminal A (LumA),
luminal B (LumB) or triple-negative (TNT) tumors, wherein the
molecular subtype of the tumor was identified in accordance with
the present invention, based on the mRNA expression levels of HER2,
ESR1, PGR and Ki67. The luminal A subtype, as defined by the
present inventors, is associated with a DMFS rate of 92% after 5
years (vs. 78% for luminal B, HER2-positive and triple-negative
tumors).
[0114] FIG. 5 depicts a multivariate Cox regression analysis of
DMFS comparing molecular subtyping by immunohistochemistry
(Sotiriou et al. (2009), N Engl J Med, 360(8):790-800) with
molecular subtyping using the method in accordance with the present
invention, based on the mRNA expression levels of HER2, ESR1, PGR
and Ki67. The analysis clearly shows the superiority of the method
of the present invention, as the immunohistochemical subtyping
looses its significance when the results obtained by the method of
the present invention are included in the Cox proportional hazards
model.
[0115] FIGS. 6 to 9 show the 40-MCT values of the markers HER2,
ESR1, PGR and Ki67 as determined by RT-qPCR for patient samples 1
to 6 and lots 1 to 3.
[0116] FIGS. 10A-B depict a Kaplan Meier analysis of the overall
survival of patients with luminal B tumors. FIG. 10A shows that
when defined by RT-qPCR, patients with luminal B cancer treated
with docetaxel-FEC survive significantly longer than when treated
with vinorelbine-FEC (97% vs. 89% respectively, Hazard Ratio [HR]
0.241; CI: 0.090-0.642). FIG. 10B shows that the tumor subtype is
defined by IHC, the benefit of docetaxel for luminal B patients
cannot be shown (95% vs. 92%, HR 0.617; CI 0.235-1.623).
[0117] FIGS. 11A-B depict a Kaplan Meier analysis of the overall
survival of patients with luminal B tumors, adjusted for tumor
histologic type by Cox Regression as specified in the SAP. FIG. 11A
shows that the prediction of the docetaxel benefit by RT-qPCR kit
remains significant (97% vs. 88%, HR 0.232; CI 0.087-0.624). FIG.
11B shows that subtyping by IHC is not predictive for a docetaxel
benefit (96% vs. 92%, HR 0.510; CI 0.184-1.414).
[0118] FIGS. 12A-B depict a Kaplan Meier analysis of distant
metastasis free survival (DMFS) of luminal B tumor patients. FIG.
12A shows that when defined by RT-qPCR, luminal B patients have a
higher probability to remain free of distant metastasis when
treated with docetaxel-FEC as compared to vinorelbine-FEC (89% vs.
78% respectively, HR 0.471; CI 0.263-0.843). FIG. 12B shows that
when luminal B tumors are defined by IHC, survival differences are
not observed between different treatment regimens (87% vs. 86%, HR
0.938 CI 0.474-1.856).
[0119] FIGS. 13A-B depict a Kaplan Meier analysis of distant
metastasis free survival of patients with luminal B tumors,
adjusted for number of metastatic lymph nodes, tumor size and
histologic type by Cox Regression as specified in the SAP. FIG. 13A
shows that by using the subtyping assay of the present invention
the effect remains significant (90 vs. 78%, HR 0.409; CI
0.219-0.764). FIG. 13B shows that by contrast there is no effect
when tumor subtyping occurs by IHC (89% vs. 85%, HR 0.674; CI
0.307-1.481).
[0120] FIGS. 14A-B depict a Kaplan Meier analysis of the overall
survival of HER2-positive tumor patients. FIG. 14A shows that when
defined by RT-qPCR, HER2-positive patients do not have better
overall survival rates when treated with docetaxel as compared to
vinorelbine (87 vs. 91%, HR 1.320; CI 0.556-3.132). FIG. 14B shows
similar results are shown for tumors subtyped by IHC (86% vs. 89%,
HR 1.175; CI 0.518-2.663).
[0121] FIGS. 15A-B depict a Kaplan Meier analysis of distant
metastasis free survival of HER2-positive tumors. FIG. 15A shows
that when defined by the method of the present invention,
HER2-positive patients do not differ in distant metastasis free
survival when treated with docetaxel as compared to vinorelbine (80
vs. 81%, HR 1.070; CI 0.551-2.076). FIG. 15B shows that similarly,
when defined by IHC, differently treated HER2-positive patients do
not show differences in survival (78% vs. 77%, HR 0.975; CI
0.516-1.843).
[0122] FIGS. 16A-B depict a Kaplan Meier analysis of overall
survival of luminal A tumors. FIG. 16A shows that when defined by
RT-qPCR, luminal A patients tend to have inferior overall survival
rates when treated with docetaxel as compared to vinorelbine (95%
vs. 98%, HR 2.471; CI 0.477-12.809). FIG. 16B shows that by
contrast, when defined by IHC, luminal A patients show a weak, yet
non-significant trend towards longer overall survival (97 vs. 93%
HR 0.443; CI 0.114-1.716) when treated with docetaxel as compared
to vinorelbine.
[0123] FIGS. 17A-B depict a Kaplan Meier analysis of distant
metastasis free survival of luminal A tumor patients. FIG. 17A
shows that when_defined by RT-qPCR, luminal A patients do not
differ in distant metastasis free survival upon treatment with
docetaxel or vinorelbine (92% vs. 90%, HR 0.826; CI 0.336-2.033).
FIG. 17B shows IHC-subtyped patients treated with docetaxel as
compared to vinorelbine show a weak, yet non-significant trend
towards longer distant metastasis free survival (93% vs. 88%, HR
0.553; CI 0.221-1.386).
[0124] FIGS. 18A-B depict a Kaplan Meier analysis of overall
survival of TNBC tumor patients. FIG. 18A shows that defined by
RT-qPCR, patients bearing TNBC exhibit no difference in overall
survival upon treatment with docetaxel or vinorelbine (84% vs. 83%,
HR 0.949; CI 0.338-2.665). FIG. 18B shows that defined by IHC, TNBC
patients show a weak, yet non-significant trend towards longer
overall survival (88% vs. 80%, HR 0.552; CI 0.207-1.472).
[0125] FIGS. 19A-B depict a Kaplan Meier analysis of distant
metastasis free survival of TNBC tumor patients. FIG. 19A shows
that differently treated RT-qPCR-defined TNBC patients do not
significantly differ in distant metastasis free survival (74% vs.
78%, HR 1.211; CI 0.523-2.802). FIG. 19B shows that IHC-defined
TNBC patients show a weak, yet non-significant trend towards longer
distant metastasis free survival (82% vs. 72%, HR 0.615; CI
0.284-1.333) when treated with docetaxel as compared to
vinorelbine.
[0126] FIGS. 20A-D show IHC assessment results. FIG. 20 A shows a
scatterplot of continuous Ki67 estimations by IHC (as depicted by %
positive cells on the y-axis) and RT-qPCR (as depicted by
40-.DELTA..DELTA.CT on the x-axis). Lines illustrate the predefined
cut-off values of the statistical analysis plan (horizontal: IHC
20%; vertical: RT-qPCR 34.8 40-.DELTA..DELTA.CT). FIG. 20B
summarizes concordances and discordances between RT-qPCR and IHC
based categorization (positive [pos] vs. negative [neg]). FIG. 20C
shows Kappa statistics revealing a highly significant correlation
(p<0.0001), but moderate concordance between methods. FIG. 20D
shows the positive and negative percent agreement (PPA and NPA,
respectively) when testing Ki67 by RT-qPCR vs. IHC.
[0127] FIG. 21 depicts a Kaplan Meier analysis of distant
metastasis free survival of patients with estrogen receptor
positive tumors and discordant Ki67 results between RT-qPCR and
IHC.
[0128] Other objects, advantages and features of the present
invention will become apparent from the following detailed
description, in particular when considered in conjunction with the
accompanying figures.
DETAILED DESCRIPTION OF THE INVENTION
[0129] Although the present invention is described in detail below,
it is to be understood that this invention is not limited to the
particular methodologies, protocols and reagents described herein
as these may vary. It is also to be understood that the terminology
used herein is for the purpose of describing particular embodiments
only, and is not intended to limit the scope of the present
invention which will be limited only by the appended claims. Unless
defined otherwise, all technical and scientific terms used herein
have the same meanings as commonly understood by one of ordinary
skill in the art.
[0130] In the following, the elements of the present invention will
be described. These elements are listed with specific embodiments,
however, it should be understood that they may be combined in any
manner and in any number to create additional embodiments. The
variously described examples and preferred embodiments should not
be construed to limit the present invention to only the explicitly
described embodiments. This description should be understood to
support and encompass embodiments which combine the explicitly
described embodiments with any number of the disclosed and/or
preferred elements. Furthermore, any permutations and combinations
of all described elements in this application should be considered
disclosed by the description of the present application unless the
context indicates otherwise.
[0131] Preferably, the terms used herein are defined as described
in "A multilingual glossary of biotechnological terms: (IUPAC
Recommendations)", H. G. W. Leuenberger, B. Nagel, and H. Kolb',
Eds., Helvetica Chimica Acta, CH-4010 Basel, Switzerland,
(1995).
[0132] The practice of the present invention will employ, unless
otherwise indicated, conventional methods of chemistry,
biochemistry, cell biology, immunology, and recombinant DNA
techniques which are explained in the literature in the field (cf.,
e.g., Molecular Cloning: A Laboratory Manual, 2.sup.nd Edition, J.
Sambrook et al. eds., Cold Spring Harbor Laboratory Press, Cold
Spring Harbor 1989).
[0133] Throughout this specification and the claims which follow,
unless the context requires otherwise, the word "comprise", and
variations such as "comprises" and "comprising", will be understood
to imply the inclusion of a stated member, integer or step or group
of members, integers or steps but not the exclusion of any other
member, integer or step or group of members, integers or steps
although in some embodiments such other member, integer or step or
group of members, integers or steps may be excluded, i.e. the
subject-matter consists in the inclusion of a stated member,
integer or step or group of members, integers or steps. The terms
"a" and "an" and "the" and similar reference used in the context of
describing the invention (especially in the context of the claims)
are to be construed to cover both the singular and the plural,
unless otherwise indicated herein or clearly contradicted by
context. Recitation of ranges of values herein is merely intended
to serve as a shorthand method of referring individually to each
separate value falling within the range. Unless otherwise indicated
herein, each individual value is incorporated into the
specification as if it were individually recited herein. All
methods described herein can be performed in any suitable order
unless otherwise indicated herein or otherwise clearly contradicted
by context. The use of any and all examples, or exemplary language
(e.g., "such as"), provided herein is intended merely to better
illustrate the invention and does not pose a limitation on the
scope of the invention otherwise claimed. No language in the
specification should be construed as indicating any non-claimed
element essential to the practice of the invention.
[0134] Several documents are cited throughout the text of this
specification. Each of the documents cited herein (including all
patents, patent applications, scientific publications,
manufacturer's specifications, instructions, etc.), whether supra
or infra, are hereby incorporated by reference in their entirety.
Nothing herein is to be construed as an admission that the
invention is not entitled to antedate such disclosure by virtue of
prior invention.
[0135] In one aspect, the invention relates to an in vitro method
of identifying a molecular subtype of a tumor in a cancer patient,
said method comprising the steps: [0136] (a) determining the
expression level of RNA transcript of human epidermal growth factor
receptor 2 (HER2) in a sample of the tumor; [0137] (b) determining
the expression level of RNA transcript of estrogen receptor (ESR1)
in a sample of the tumor; [0138] (c) determining the expression
level of RNA transcript of progesterone receptor (PGR) in a sample
of the tumor; and [0139] (d) determining the expression level of
RNA transcript of proliferation antigen Ki-67 (Ki67) in a sample of
the tumor; and/or [0140] (e) determining the expression level of
RNA transcript of RacGTPase-activating protein 1 (RACGAP1) in a
sample of the tumor.
[0141] In one embodiment, said method does not comprise the
determination of the expression level, in particular the expression
level of RNA transcript, of one or more additional non-reference
genes. In other words, no expression level, in particular no
expression level of RNA transcript, of a gene other than HER2,
ESR1, PGR and Ki67 and/or RACGAP1 and one or more reference genes
is determined.
[0142] In one embodiment, said method does not comprise any other
diagnostic steps, such as histological grading or determining the
lymph nodal status.
[0143] The term "tumor", as used herein, refers to all neoplastic
cell growth and proliferation whether malignant or benign, and all
pre-cancerous and cancerous cells and tissues. In one embodiment of
the present invention, the tumor is a solid tumor. In one
embodiment, the tumor is a breast tumor or is derived from a breast
tumor (e.g. by metastasis).
[0144] As used herein, "cancer" includes a disease characterized by
aberrantly regulated cellular growth, proliferation,
differentiation, adhesion, and/or migration. The term "cancer"
according to the invention comprises leukemias, seminomas,
melanomas, teratomas, lymphomas, neuroblastomas, gliomas, rectal
cancer, endometrial cancer, kidney cancer, adrenal cancer, thyroid
cancer, blood cancer, skin cancer, cancer of the brain, cervical
cancer, intestinal cancer, liver cancer, colon cancer, stomach
cancer, intestine cancer, head and neck cancer, gastrointestinal
cancer, lymph node cancer, esophagus cancer, colorectal cancer,
pancreas cancer, ear, nose and throat (ENT) cancer, breast cancer,
prostate cancer, cancer of the uterus, ovarian cancer and lung
cancer and the metastases thereof. Examples thereof are lung
carcinomas, mamma carcinomas, prostate carcinomas, colon
carcinomas, renal cell carcinomas, cervical carcinomas, or
metastases of the cancer types or tumors described above. The term
cancer according to the invention also comprises cancer metastases.
In one embodiment, the cancer is breast cancer.
[0145] The term "breast cancer" relates to a type of cancer
originating from breast tissue, most commonly from the inner lining
of milk ducts or the lobules that supply the ducts with milk.
Cancers originating from ducts are known as ductal carcinomas,
while those originating from lobules are known as lobular
carcinomas. Occasionally, breast cancer presents as metastatic
disease. Common sites of metastasis include bone, liver, lung and
brain. Breast cancer occurs in humans and other mammals. While the
overwhelming majority of human cases occur in women, male breast
cancer can also occur. Treatment of breast cancer may include
surgery, medications (hormonal therapy and chemotherapy), radiation
and/or immunotherapy/targeted therapy.
[0146] The term "patient", as used herein, refers to any organism
such as vertebrate, particularly any mammal, including both a human
and another mammal, e.g., an animal such as a rodent, a rabbit, or
a monkey. The rodent may be a mouse, rat, hamster, guinea pig, or
chinchilla. Preferably, the patient is a human.
[0147] According to the present invention, the term "RNA
transcript" includes and preferably relates to "mRNA" which means
"messenger RNA" and relates to a "transcript" which encodes a
peptide or protein. mRNA typically comprises a 5' non translated
region (5'-UTR), a protein or peptide coding region and a 3' non
translated region (3'-UTR). mRNA has a limited halftime in cells
and in vitro.
[0148] The gene HER2 (also referred to as ERBB2; location: 17q12,
annotation: chromosome: 17; NC 000017.10) encodes a member of the
epidermal growth factor (EGF) receptor family of receptor tyrosine
kinases. Amplification and/or overexpression of this gene have been
reported in numerous cancers, including breast and ovarian tumors.
In the NCBI database, two mRNA variants for HER2 are listed which
code for two protein versions. Protein and mRNA sequences can be
found under the accession numbers NM_001005862.1 (receptor
tyrosine-protein kinase erbB-2 isoform b) and NM_004448.2 (receptor
tyrosine-protein kinase erbB-2 isoform a precursor). HER2 gene
amplification occurs in approx. 10-20% of primary breast
carcinomas.
[0149] The gene ESR1 (location: 6q25, annotation: chromosome 6,
NC_000006.11) encodes an estrogen receptor (ER), a ligand-activated
transcription factor composed of several domains important for
hormone binding, DNA binding, and activation of transcription.
Estrogen receptors are known to be involved in pathological
processes including breast cancer, endometrial cancer, and
osteoporosis. Four ESR1 mRNA variants are known, wherein the
transcript variants differ in the 5' UTR and/or use different
promoters, but each variant codes for the same protein. 70-80% of
all breast cancers are ER positive.
[0150] The gene PGR (also referred to as PR; location: 11q22-q23,
annotation: chromosome: 11; NC_000011.9) encodes the progesterone
receptor. Steroid hormones such as progesterone and their receptors
are involved in the regulation of eukaryotic gene expression and
affect cellular proliferation and differentiation in target
tissues. This gene uses two distinct promoters and translation
start sites in the first exon to produce two mRNA isoforms, A and
B. The two isoforms are identical except for the additional 165
amino acids found in the N-terminus of isoform B. 40% of breast
tumors are positive for PGR.
[0151] The gene Ki-67 (Ki67; location: 10q26.2, annotation:
chromosome: 10; NC_000010.10) encodes a nuclear protein that is
associated with and may be necessary for cellular proliferation.
Two mRNA variants have been described. A related pseudogene exists
on chromosome 10. Approximately 25% of breast tumors are positive
for Ki67.
[0152] The gene RACGAP1 (location: 12q13.12, annotation:
chromosome: 12; NC_000012.11) encodes for RacGTPase-activating
protein 1. Three splice variants have been described, all encoding
for the same protein. RACGAP1 is a component of the central
spindlin complex and plays key roles in controlling growth-related
processes and differentiation.
[0153] The term "expression level", as used herein, refers to the
expression of a particular gene (i.e. HER2, ESR1, PGR, Ki67 or
RACGAP1) so as to produce transcript and/or protein. According to
the present invention, the expression level is determined on the
RNA transcript level, in particular mRNA level (transcriptional
level), for example, by measuring the transcribed mRNA (e.g., via
northern blot), by reverse transcription (RT) quantitative PCR or
by directly staining the mRNA (e.g., via in situ
hybridization).
[0154] In one embodiment, the term "sample of the tumor" refers to
a tumor tissue sample isolated from the cancer patient (e.g., a
biopsy or resection tissue of the tumor). In a preferred
embodiment, the tumor tissue sample is a cryo-section of a tumor
tissue sample or is a chemically fixed tumor tissue sample. In a
more preferred embodiment, the tumor tissue sample is a
formalin-fixed and paraffin-embedded (FFPE) tumor tissue sample. In
one embodiment, the sample of the tumor is (total) RNA extracted
from the tumor tissue sample.
[0155] In a particularly preferred embodiment, the sample of the
tumor is (total) RNA extracted from a FFPE tumor tissue sample.
Those skilled in the art are able to perform RNA extraction
procedures. For example, total RNA from a 5 to 10 .mu.m curl of
FFPE tumor tissue can be extracted using the High Pure RNA Paraffin
Kit (Roche, Basel, Switzerland) or, preferably, the XTRAKT RNA
Extraction Kit XL (Stratifyer Molecular Pathology, Cologne,
Germany). It is also possible to store the sample material to be
used/tested in a freezer and to carry out the method of the present
invention at an appropriate point in time after thawing the
respective sample material. The sample may be obtained from the
cancer patient prior to initiation of a therapeutic treatment,
during the therapeutic treatment, and/or after the therapeutic
treatment, i.e. prior to, during or following the administration of
cancer therapy.
[0156] The term "molecular subtype of a tumor", as used herein,
refers to subtypes of a tumor that are characterized by distinct
molecular profiles, e.g., gene expression profiles. In one
embodiment, the molecular subtype is selected from the group
comprising HER2-positive, triple-negative (also referred to as
"basal-like"), luminal A and luminal B. The term "basal-like"
refers to the fact that such tumors have some similarity in gene
expression to that of basal epithelial cells. The term "luminal"
derives from the similarity in gene expression between the tumors
and the luminal epithelium.
[0157] The molecular subtypes differ markedly in clinical outcome
and response to therapy. In one embodiment, the molecular subtype
luminal A, as defined herein, is associated with a probability of
distant recurrence-free survival 5 years after treatment which is
at least 11%, preferably at least 13% higher than the probability
of distant recurrence-free survival 5 years after treatment
associated with molecular subtype luminal B and/or with a
probability of survival 5 years after treatment which is at least
7%, preferably at least 9% higher than the probability of survival
5 years after treatment associated with molecular subtype luminal
B.
[0158] The term "(therapeutic) treatment", in particular in
connection with the treatment of cancer as used herein, relates to
any treatment which improves the health status and/or prolongs
(increases) the lifespan of a patient. Said treatment may eliminate
cancer, reduce the size or the number of tumors in a patient,
arrest or slow the development of cancer in a patient, inhibit or
slow the development of new cancer in a patient, decrease the
frequency or severity of symptoms in a patient, and/or decrease
recurrences in a patient who currently has or who previously has
had cancer. In one embodiment, the terms "treatment" and
"therapeutic treatment" are meant to refer to one or more of
surgical removal of the primary tumor, chemotherapy, hormonal
therapy, radiation therapy and immunotherapy/targeted therapy.
Adjuvant therapy is a treatment that is given in addition to the
primary, main or initial treatment. The surgeries and complex
treatment regimens used in cancer therapy have led the term to be
used mainly to describe adjuvant cancer treatments. An example of
adjuvant therapy is the additional treatment (e.g., chemotherapy)
usually given after surgery (post-surgically), where all detectable
disease has been removed, but where there remains a statistical
risk of relapse due to occult disease. Neoadjuvant therapy is
treatment given before the primary, main or initial treatment
(e.g., pre-surgical chemotherapy).
[0159] In accordance with the present invention, the step of
"determining the expression level of RNA transcript" may comprise
(i) measuring the expression level of RNA transcript and (ii)
analyzing the measured expression level of RNA transcript (e.g., by
comparison to a reference expression level, such as a defined
expression threshold), wherein the order of measuring the
expression level of RNA transcript of HER2, ESR1, PGR and Ki67
and/or RACGAP1 is independent of the order of analyzing the
measured expression level of RNA transcript of HER2, ESR1, PGR and
Ki67 and/or RACGAP1.
[0160] In one embodiment, determining the expression level of RNA
transcript of HER2, ESR1, PGR and Ki67 and/or RACGAP1 comprises
determining whether the expression level of RNA transcript of HER2,
ESR1, PGR and Ki67 and/or RACGAP1 is lower or higher than a defined
expression threshold of RNA transcript of HER2, ESR1, PGR and Ki67
and/or RACGAP1. In cases where the expression level is equal to the
defined expression threshold, the expression level is considered to
belong to the group of expression levels that are higher than the
defined expression threshold. Thus, the wording "higher than a
defined expression threshold", as used herein, includes expression
levels that are higher than or equal to the defined expression
threshold. Expression levels that are "higher than a defined
expression threshold" may also be referred to as
"expression-positive", whereas expression levels that are "lower
than a defined expression threshold" may also be referred to as
"expression-negative"
[0161] The term "defined expression threshold of RNA transcript",
as used herein, may refer to the mean cut-off value (in short:
cut-off) calculated from a number of samples, said number of
samples being obtained from a number of subjects, in particular,
subjects having cancer. To obtain the threshold, the number of
subjects may include subjects having tumors of different molecular
subtypes, e.g., subjects having HER2-positive tumors and/or
subjects having triple-negative tumors and/or subjects having
luminal A tumors and/or subjects having luminal B tumors. The
threshold may represent an amount or concentration of the RNA
transcript. In one embodiment, the threshold is given as CT (cycle
threshold) value (see below). In one embodiment, the (relative)
expression level and expression threshold are expressed as
40-.DELTA.CT or 40-.DELTA..DELTA.CT values (see below).
[0162] The term "subject", as used herein, relates to any organism
such as vertebrate, particularly any mammal, including both a human
and another mammal, e.g. an animal such as a rodent, a rabbit, or a
monkey. The rodent may be a mouse, rat, hamster, guinea pig, or
chinchilla. Preferably, the subject is a human. In one embodiment,
a subject is a subject with or suspected of having a disease, in
particular cancer, also designated "patient" herein. For the
determination of the mean cut-off value, at least two subjects,
preferably at least 5, at least 10, at least 20, at least 30, at
least 40, at least 50, at least 60, at least 70, at least 80, at
least 90, at least 100, at least 200, at least 300, at least 400,
at least 500, at least 600, at least 700, at least 800, at least
900, at least 1000, at least 1500, or at least 2000 subjects, are
tested.
[0163] As various clinical studies have already been conducted with
the gene markers used in accordance with the present invention, a
concordance study in a training-testing setting will be sufficient
for the definition and validation of a clinical cut-off/threshold
for dichotomization of quantitative results in
"expression-positive" or "expression-negative". Thus, in one
embodiment, the cut-off/threshold is defined based on one or more
previous clinical studies. Moreover, additional clinical studies
may be conducted for the establishment and validation of the
cut-off/threshold. The cut-off/threshold may be determined/defined
by techniques known in the art.
[0164] In one embodiment, the cut-off/threshold is
determined/defined on the basis of clinico-pathologic parameters,
such as IHC-ISH, and/or the data for overall survival (OS),
disease-free survival (DFS), and distant metastasis free survival
(DMFS), and disease-specific survival (DSS) in training cohorts
(e.g., HE10-97, Pentheroudakis et al. (2009), Breast Cancer Res
Treat, 116: 131-143) by portioning tests (e.g., SAS Software
JMP.RTM. 9.0.0) and validated in independent clinical trial
cohorts, e.g., FFPE tissue samples of the FinHER study (Joensuu et
al. (2006), N Engl J Med, 354: 809-820).
[0165] In one embodiment, the 40-.DELTA.CT value is calculated as
follows: 40--[CT of the respective biomarker (i.e. HER2, ESR1, PGR
and Ki67 and/or RACGAP1) of a patient sample--CT of a reference
gene (e.g., CALM2) of a patient sample] (=calculation method 1). If
more than one reference gene is used, the 40-.DELTA.CT value is
calculated as follows: 40--(CT of the respective biomarker of a
patient sample--mean CT of selected reference genes of a patient
sample) (=calculation method 2). Alternatively, a
40-.DELTA..DELTA.CT value can be used, wherein the
40-.DELTA..DELTA.CT can be calculated as follows:
.DELTA..DELTA.CT=40-[(CT biomarker of a patient sample-CT biomarker
of a reference sample)-(CT reference gene of patient sample-CT
reference gene of a reference sample)] (=calculation method 3);
e.g., 40-.DELTA..DELTA.CT=40-[(CT Ki67 patient sample-CT Ki67
reference sample)-(CT CALM2 of a patient sample-CT CALM2 of a
reference sample)]. In one embodiment, CALM2 is used as reference
gene.
[0166] In an exemplary embodiment, the mean cut-off value is given
as a 40-.DELTA.CT value according to calculation method 2, wherein
the mean cut-off value for HER2 is a 40-.DELTA.CT value of 38, the
mean cut-off value for ESR1 is a 40-.DELTA.CT value of 34, the mean
cut-off value for PGR is a 40-.DELTA.CT value of 30,2, the mean
cut-off value for Ki67 is a 40-.DELTA.CT value of 31,7, and the
mean cut-off value for RACGAP1 is a 40-.DELTA.CT value of 34,2.
[0167] In another embodiment, the relative expression level of the
biomarkers is given as a 40-.DELTA..DELTA.CT value, which is
calculated as follows: 40-[(CT biomarker of a patient sample-CT
reference gene of the patient sample)-(CT biomarker of a control
sample-CT reference gene of the control sample)] (=calculation
method 4); e.g., 40-.DELTA..DELTA.CT=40-[(CT Ki67 patient sample-CT
Mean CombRef patient sample)-(CT Ki67 control sample-CT Mean
CombRef control sample)]. In one embodiment, the CT is the median
CT. The CT of the reference gene can be the CT of a single
reference gene or the mean CT of two or more reference genes
(referred to as Mean CombRef). Preferably, the same control sample
(also referred to as calibrator) is used in all analyses and leads
to the same RT-qPCR or qPCR results. In one embodiment, the control
sample is a cell line RNA, an in vitro transcribed artificial RNA
or an equimolar mixture of DNA oligonucleotides, representing the
biomarker mRNA or cDNA or the biomarker amplicon or a part of the
biomarker amplicon with a constant ratio. In one embodiment, CALM2
and B2M are used as reference genes and a positive control (e.g.,
in vitro transcribed artificial RNA) is used as control sample
(calibrator).
[0168] In an exemplary embodiment, the mean cut-off value is given
as a 40-.DELTA..DELTA.CT value according to calculation method 4,
wherein the mean cut-off value for HER2 is a 40-.DELTA..DELTA.CT
value of 40.90, the mean cut-off value for ESR1 is a
40-.DELTA..DELTA.CT value of 38.20, the mean cut-off value for PGR
is a 40-.DELTA..DELTA.CT value of 34.90 and the mean cut-off value
for Ki67 is a 40-.DELTA..DELTA.CT value of 34.80 on a Versant kPCR
Instrument AD module (Siemens).
[0169] In another exemplary embodiment, the mean cut-off value is
given as a 40-.DELTA..DELTA.CT value according to calculation
method 4, wherein the mean cut-off value for HER2 is a
40-.DELTA..DELTA.T value of 41.1, the cut-off value for ESR1 is a
40-.DELTA..DELTA.CT value of 38.00, the cut-off value for PGR is a
40-.DELTA..DELTA.CT value of 35.50 and the cut-off value for Ki67
is a 40-.DELTA..DELTA.CT value of 35.50 on a LightCycler.RTM. 480
instrument II (Roche).
[0170] In one embodiment, steps (a), (b), (c) and (d) and/or (e)
are performed in random order. In one embodiment, step (a) is
performed before steps (b), (c) and (d) and/or (e). In one
embodiment, step (d) and/or step (e) are performed after steps (a),
(b) and (c). In one embodiment, step (a) is performed before step
(b), step (b) is performed before step (c), and step (c) is
performed before step (d) and/or step (e).
[0171] In one embodiment, an expression level of RNA transcript of
HER2 which is higher than a defined expression threshold of RNA
transcript of HER2 identifies the molecular subtype of the tumor as
HER2-positive.
[0172] In one embodiment, [0173] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0174] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0175] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0176] an expression level
of RNA transcript of Ki67 which is lower or higher than a defined
expression threshold of RNA transcript of Ki67 identify the
molecular subtype of the tumor as triple-negative.
[0177] In one embodiment, the molecular subtype is luminal A or
luminal B.
[0178] In one embodiment, [0179] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0180] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0181] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0182] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0183] In one embodiment, [0184] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0185] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0186] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0187] an expression level
of RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal A.
[0188] In one embodiment, [0189] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0190] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0191] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0192] an expression level
of RNA transcript of Ki67 which is lower or higher than a defined
expression threshold of RNA transcript of Ki67 identify the
molecular subtype of the tumor as luminal B.
[0193] In one embodiment, [0194] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0195] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0196] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0197] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0198] In one embodiment, [0199] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0200] an expression level of
RNA transcript of ESR1 which is lower than a defined expression
threshold of RNA transcript of ESR1; [0201] an expression level of
RNA transcript of PGR which is higher than a defined expression
threshold of RNA transcript of PGR; and [0202] an expression level
of RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal A.
[0203] In one embodiment, [0204] an expression level of RNA
transcript of HER2 which is lower than a defined expression
threshold of RNA transcript of HER2; [0205] an expression level of
RNA transcript of ESR1 which is higher than a defined expression
threshold of RNA transcript of ESR1; [0206] an expression level of
RNA transcript of PGR which is lower than a defined expression
threshold of RNA transcript of PGR; and [0207] an expression level
of RNA transcript of Ki67 which is higher than a defined expression
threshold of RNA transcript of Ki67 identify the molecular subtype
of the tumor as luminal B.
[0208] In one embodiment, the method comprises step (d), and [0209]
an expression level of RNA transcript of ESR1 which is higher than
a defined expression threshold of RNA transcript of ESR1 and [0210]
an expression level of RNA transcript of Ki67 which is higher than
a defined expression threshold of RNA transcript of Ki67 indicates
an increased risk of poor clinical outcome for the cancer patient,
in particular an increased risk of distant metastasis.
[0211] In one embodiment, the method comprises step (e), and an
expression level of RNA transcript of RACGAP1 which is higher than
a defined expression threshold of RNA transcript of RACGAP1
indicates an increased risk of poor clinical outcome for the cancer
patient (as compared to the risk of a cancer patient with a tumor
having an expression level of RNA transcript of RACGAP1 which is
lower than the defined expression threshold of RNA transcript of
RACGAP1).
[0212] The determination of the expression level of RNA transcript
of both Ki67 and RACGAP1 provides more precise information
regarding the clinical outcome of a cancer patient, wherein,
generally, an increased expression level of RNA transcript of
either Ki67 or RACGAP1 indicates an increased risk of poor clinical
outcome for the cancer patient (as compared to the risk of a cancer
patient with a tumor having an expression level of RNA transcript
of Ki67 or RACGAP1 which is lower than the defined expression
threshold of RNA transcript of Ki67 or RACGAP1).
[0213] In one embodiment, the method comprises steps (d) and (e),
and [0214] an expression level of RNA transcript of Ki67 which is
lower than a defined expression threshold of RNA transcript of Ki67
and [0215] an expression level of RNA transcript of RACGAP1 which
is higher than a defined expression threshold of RNA transcript of
RACGAP1 indicates an increased risk of poor clinical outcome for
the cancer patient.
[0216] In one embodiment, the method comprises steps (d) and (e),
and [0217] an expression level of RNA transcript of Ki67 which is
higher than a defined expression threshold of RNA transcript of
Ki67 and [0218] an expression level of RNA transcript of RACGAP1
which is higher than a defined expression threshold of RNA
transcript of RACGAP1 indicates a further increased risk of poor
clinical outcome for the cancer patient (as compared to the
increased risk of a cancer patient with a tumor having an
expression level of RNA transcript of Ki67 which is lower than a
defined expression threshold of RNA transcript of Ki67 and an
expression level of RNA transcript of RACGAP1 which is higher than
the defined expression threshold of RNA transcript of RACGAP1,
wherein, preferably, the further increase refers to an increase by
at least 5%, more preferably by at least 10%).
[0219] The term "clinical outcome" is defined as the clinical
result of a disease, in particular following a treatment, e.g.,
reduction or amelioration of symptoms. In one embodiment, poor
clinical outcome comprises a relative reduction in or more of
survival, recurrence-free survival and distant recurrence-free
survival. The term "recurrence" with respect to cancer includes
re-occurrence of tumor cells at the same site and organ of the
origin disease, metastasis that can appear even many years after
the initial diagnosis and therapy of cancer, or to local events
such as infiltration of tumor cells into regional lymph nodes.
"Distant recurrence" refers to a scenario, where the cancer cells
have spread (metastasized) to a distant part (i.e., another organ)
of the body beyond the regional lymph nodes. Recurrence-free
survival is generally defined as the time from randomization to the
first of recurrence, relapse, second cancer, or death.
[0220] The term "metastasis" is meant to refer to the spread of
cancer cells from their original site to another part of the body.
The formation of metastasis is a very complex process and depends
on detachment of malignant cells from the primary tumor, invasion
of the extracellular matrix, penetration of the endothelial
basement membranes to enter the body cavity and vessels, and then,
after being transported by the blood, infiltration of target
organs. Finally, the growth of a new tumor at the target site
depends on angiogenesis. Tumor metastasis often occurs even after
the removal of the primary tumor because tumor cells or components
may remain and develop metastatic potential.
[0221] In one embodiment, an "increased risk of poor clinical
outcome" refers to a probability of survival 5 years after
treatment which is at least 20% lower, preferably at least 25%
lower than the probability of survival 5 years after treatment of a
cancer patient with a tumor having [0222] an expression level of
RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 and [0223] an expression level
of RNA transcript of RACGAP1 which is lower than a defined
expression threshold of RNA transcript of RACGAP1.
[0224] In one embodiment, a "further increased risk of poor
clinical outcome" refers to a probability of survival 5 years after
treatment which is at least 30% lower, preferably at least 35%
lower than the probability of survival 5 years after treatment of a
cancer patient with a tumor having [0225] an expression level of
RNA transcript of Ki67 which is lower than a defined expression
threshold of RNA transcript of Ki67 and [0226] an expression level
of RNA transcript of RACGAP1 which is lower than a defined
expression threshold of RNA transcript of RACGAP1.
[0227] In one embodiment, the expression level of RNA transcript is
determined by reverse transcription (RT) quantitative PCR
(RT-qPCR). As RNA cannot be directly amplified in PCR, it must be
reverse transcribed into cDNA using the enzyme reverse
transcriptase. For this purpose, a one-step RT-qPCR can be
utilized, which combines the reactions of reverse transcription
with DNA amplification by PCR in the same reaction. In one-step
RT-qPCR, the RNA template is mixed in a reaction mix containing
reverse transcriptase, DNA polymerase, primers and probes, dNTPs,
salts and detergents. In a first PCR step, the target RNA is
reverse transcribed by reverse transcriptase using the target
specific reverse primers. Afterwards, the cDNA is amplified using
the primers/probes and DNA polymerase.
[0228] In one embodiment, the quantitative PCR is
fluorescence-based quantitative real-time PCR. The
fluorescence-based quantitative real-time PCR comprises the use of
a fluorescently labeled probe. Preferably, the fluorescently
labeled probe consists of an oligonucleotide labeled with both a
fluorescent reporter dye and a quencher dye (=dual-label probe).
Suitable fluorescent reporter and quencher dyes/moieties are known
to a person skilled in the art and include, but are not limited to
the reporter dyes/moieties 6-FAM.TM., JOE.TM., CyS.RTM., Cy3.RTM.
and the quencher dyes/moieties dabcyl, TAMRA.TM., BHQ.TM.-1, -2 or
-3. Amplification of the probe-specific product causes cleavage of
the probe (=amplification-mediated probe displacement), thereby
generating an increase in reporter fluorescence. The increase of
fluorescence in the reaction is directly proportional to the
increase of target amplificates. By using the LightCycler 480 II
system (Roche) or the Versant kPCR system (Siemens) or the Mx3005P
system (Agilent Technologies) or equivalent real-time instruments
for detection of fluorescence originating from the probe, one can
measure the increase in fluorescence in real-time. Analysis output
is a CT value of each target. The CT (cycle threshold) value is
determined by the number of PCR amplification cycles, after which
the fluorescence signal of the probe exceeds a certain background
signal, wherein the CT value is a measure for the amount of target
molecules in the sample before the PCR amplification. Preferably,
CT-values are further analyzed with appropriate software (e.g.,
Microsoft Excel.TM.) or statistical software packages (e.g., SAS
JMP.RTM. 9.0.0, GraphPad Prism4, Genedata Expressionist.TM.). The
CT value can either be converted to an absolute target molecule
amount (e.g., ng/.mu.l or molecules/.mu.l) based on the CT results
of a standard curve with known target concentrations.
Alternatively, the target amount can be reported as x-fold
decreased or increased amount based on a reference (=.DELTA.CT).
Low .DELTA.CT values (small difference) indicate higher amounts of
target relative to the reference compared to high .DELTA.CT (big
difference). It is suitable to re-calculate the .DELTA.CT by
subtracting it from a fixed value (such as the number of PCR
cycles, e.g. 40). The result is a value with direct correlation to
target amount (high value=high amount) and expressed as
40-.DELTA.CT values, wherein one integer refers to a doubling of
the target amount (e.g., a value of 34 indicates an amount which is
twice as much as that with a value of 33). Depending on the desired
reproducibility and precision of the system, it is possible to
panel multiple reference assays or to re-calculate/normalize the
.DELTA.CT of the sample with the .DELTA.CT of a calibrator (1 point
calibration; Pfaffl (2001), Nucleic Acid Res., 29(9):e45). By using
different fluorophores for specific probes it is also possible to
multiplex different target assays in the same reaction. During PCR,
each target in the multiplex is amplified in parallel, but
separately detected utilizing the different fluorescent
emission.
[0229] Preferably, primers for use in accordance with the present
invention have a length of 15 to 30 nucleotides, in particular
deoxyribonucleotides. In one embodiment, the primers are designed
so as to (1) be specific for the target mRNA-sequence (i.e. HER2,
ESR1, PGR and Ki67 and/or RACGAP1), (2) provide an amplicon size of
less than 120 bp (preferably less than 100 bp), (3) detect all
known protein-encoding splicing variants, (4) not include known
polymorphisms (e.g., single nucleotide polymorphisms, SNPs), (5) be
mRNA-specific (consideration of exons/introns; preferably no
amplification of DNA), (6) have no tendency to dimerize and/or (7)
have a melting temperature T.sub.m in the range of from 58.degree.
C. to 62.degree. C. (preferably, T.sub.m is approximately
60.degree. C.).
[0230] As used herein, the term "nucleotide" includes native
(naturally occurring) nucleotides, which include a nitrogenous base
selected from the group consisting of adenine (A), thymidine (T),
cytosine (C), guanine (G) and uracil (U), a sugar selected from the
group of ribose, arabinose, xylose, and pyranose, and deoxyribose
(the combination of the base and sugar generally referred to as a
"nucleoside"), and one to three phosphate groups, and which can
form phosphodiester internucleosidyl linkages. Further, as used
herein, "nucleotide" refers to nucleotide analogues. As used
herein, "nucleotide analogue" shall mean an analogue of A, G, C, T
or U (that is, an analogue of a nucleotide comprising the base A,
G, C, T or U) which is recognized by DNA or RNA polymerase
(whichever is applicable) and incorporated into a strand of DNA or
RNA (whichever is appropriate). Examples of such nucleotide
analogues include, without limitation, 5-propynyl pyrimidines
(i.e., 5-propynyl-dTTP and 5-propynyl-dCTP), 7-deaza purines (i.e.,
7-deaza-dATP and 7-deaza-dGTP), aminoallyl-dNTPs, biotin-AA-dNTPs,
2-amino-dATP, 5-methyl-dCTP, 5-iodo-dUTP, 5-bromo-dUTP,
5-fluoro-dUTP, N4-methyl-dCTP, 2-thio-dTTP, 4-thio-dTTP and
alpha-thio-dNTPs. Also included are labelled analogues, e.g.
fluorescent analogues such as DEAC-propylenediamine (PDA)-ATP,
analogues based on morpholino nucleoside analogues as well as
locked nucleic acid (LNA) analogues.
[0231] The wording "specific for the target mRNA-sequence", as used
in connection with primers for use in accordance with the present
invention, is meant to refer to the ability of the primer to
hybridize (i.e. anneal) to the cDNA of the target mRNA-sequence
under appropriate conditions of temperature and solution ionic
strength, in particular PCR conditions. The conditions of
temperature and solution ionic strength determine the stringency of
hybridization. Hybridization requires that the two nucleic acids
(i.e. primer and cDNA) contain complementary sequences, although
depending on the stringency of the hybridization, mismatches
between bases are possible. In one embodiment, "appropriate
conditions of temperature and solution ionic strength" refer to a
temperature in the range of from 58.degree. C. to 62.degree. C.
(preferably a temperature of approximately 60.degree. C.) and a
solution ionic strength commonly used in PCR reaction mixtures. In
one embodiment, the sequence of the primer is 80%, preferably 85%,
more preferably 90%, even more preferably 95%, 96%, 97%, 98%, 99%
or 100% complementary to the corresponding sequence of the cDNA of
the target mRNA-sequence, as determined by sequence comparison
algorithms known in the art.
[0232] In one embodiment, the primer hybridzes to the cDNA of the
target mRNA-sequence under stringent or moderately stringent
hybridization conditions. "Stingent hybridization conditions", as
defined herein, involve hybridizing at 68.degree. C. in 5.times.
SSC/5.times. Denhardt's solution/1,0% SDS, and washing in
0,2.times. SSC/0,1% SDS at room temperature, or involve the
art-recognized equivalent thereof (e.g., conditions in which a
hybridization is carried out at 60.degree. C. in 2,5.times.SSC
buffer, followed by several washing steps at 37.degree. C. in a low
buffer concentration, and remains stable). "Moderately stringent
hybridization conditions", as defined herein, involve including
washing in 3.times. SSC at 42.degree. C., or the art-recognized
equivalent thereof. The parameters of salt concentration and
temperature can be varied to achieve the optimal level of identity
between the primer and the target nucleic acid. Guidance regarding
such conditions is available in the art, for example, by Sambrook
et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring
Harbor Press, N.Y.; and Ausubel et al. (eds.), 1995, Current
Protocols in Molecular Biology, (John Wiley and Sons, N.Y.).
[0233] In one embodiment, the method of the present invention
comprises the use of ESR1-specific primers having a length of 15 to
30 nucleotides and comprising at least 10 contiguous nucleotides of
the sequences of SEQ ID NOs: 1 and 2, and/or HER2-specific primers
having a length of 15 to 30 nucleotides and comprising at least 10
contiguous nucleotides of the sequences of SEQ ID NOs: 4 and 5,
and/or Ki67-specific primers having a length of 15 to 30
nucleotides and comprising at least 10 contiguous nucleotides of
the sequences of SEQ ID NOs: 7 and 8, and/or PGR-specific primers
having a length of 15 to 30 nucleotides and comprising at least 10
contiguous nucleotides of the sequences of SEQ ID NOs: 10 and 11,
and/or RACGAP1-specific primers having a length of 15 to 30
nucleotides and comprising at least 10 contiguous nucleotides of
the sequences of SEQ ID NOs: 13 and 14. In one embodiment, the
specific primers comprise at least 15 contiguous nucleotides of the
sequences indicated above.
[0234] In one embodiment, the method comprises the use of
ESR1-specific primers having the sequences of SEQ ID NOs: 1 and 2,
and/or HER2-specific primers having the sequences of SEQ ID NOs: 4
and 5, and/or Ki67-specific primers having the sequences of SEQ ID
NOs: 7 and 8, and/or PGR-specific primers having the sequences of
SEQ ID NOs: 10 and 11, and/or RACGAP1-specific primers having the
sequences of SEQ ID NOs: 13 and 14.
[0235] Preferably, probes for use in accordance with the present
invention have a length of 20 to 35 nucleotides, in particular
deoxyribonucleotides. In one embodiment, the probes are designed so
as to (1) be specific for the target mRNA-sequence (i.e. HER2,
ESR1, PGR and Ki67 and/or RACGAP1), (2) not include known
polymorphisms (e.g., single nucleotide polymorphisms, SNPs) and/or
(3) have a melting temperature T.sub.m, which is approximately
5.degree. C. to 8.degree. C. higher than the melting temperature
T.sub.m of the corresponding primer(s).
[0236] The wording "specific for the target mRNA-sequence", as used
in connection with probes for use in accordance with the present
invention, is meant to refer to the ability of the probe to
hybridize (i.e. anneal) to the (amplified) cDNA of the target
mRNA-sequence under appropriate conditions of temperature and
solution ionic strength, in particular PCR conditions. The
conditions of temperature and solution ionic strength determine the
stringency of hybridization. Hybridization requires that the two
nucleic acids (i.e. probe and cDNA) contain complementary
sequences, although depending on the stringency of the
hybridization, mismatches between bases are possible. In one
embodiment, "appropriate conditions of temperature and solution
ionic strength" refer to a temperature in the range of from
63.degree. C. to 70.degree. C. and a solution ionic strength
commonly used in PCR reaction mixtures. In one embodiment, the
sequence of the probe is 80%, preferably 85%, more preferably 90%,
even more preferably 95%, 96%, 97%, 98%, 99% or 100% complementary
to the corresponding sequence of the (amplified) cDNA of the target
mRNA-sequence, as determined by sequence comparison algorithms
known in the art.
[0237] In one embodiment, the probe hybridizes to the (amplified)
cDNA of the target mRNA-sequence under stringent or moderately
stringent hybridization conditions as defined above.
[0238] In one embodiment, the method comprises the use of an
ESR1-specific probe having a length of 20 to 35 nucleotides and
comprising at least 15 contiguous nucleotides of the sequence of
SEQ ID NO: 3, and/or a HER2-specific probe having a length of 20 to
35 nucleotides and comprising at least 15 contiguous nucleotides of
the sequence of SEQ ID NO: 6, and/or a Ki67-specific probe having a
length of 20 to 35 nucleotides and comprising at least 15
contiguous nucleotides of the sequence of SEQ ID NO: 9, and/or a
PGR-specific probe having a length of 20 to 35 nucleotides and
comprising at least 15 contiguous nucleotides of the sequence of
SEQ ID NO: 12, and/or a RACGAP1-specific probe having a length of
20 to 35 nucleotides and comprising at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 15. In one embodiment,
the specific probes comprise at least 20 contiguous nucleotides of
the sequences indicated above.
[0239] In one embodiment, the method comprises the use of an
ESR1-specific probe having the sequence of SEQ ID NO: 3, and/or a
HER2-specific probe having the sequence of SEQ ID NO: 6, and/or a
Ki67-specific probe having the sequence of SEQ ID NO: 9, and/or a
PGR-specific probe having the sequence of SEQ ID NO: 12, and/or a
RACGAP1-specific probe having the sequence of SEQ ID NO: 15.
[0240] Preferably, the probes as defined above are dual-label
probes comprising a fluorescence reporter moiety and a fluorescence
quencher moiety.
[0241] In one embodiment, the expression level is normalized
against the (mean) expression level of one or more reference genes
in the sample of the tumor. The term "reference gene", as used
herein, is meant to refer to a gene which has a relatively
invariable level of expression on the RNA transcript/mRNA level in
the system which is being examined, i.e. cancer. Such gene may be
referred to as housekeeping gene. In one embodiment, the one or
more reference genes are selected from the group comprising CALM2,
B2M, RPL37A, GUSB, HPRT1 and GAPDH, preferably CALM2 and/or
B2M.
[0242] As used herein, CALM2 refers to calmodulin-2, phosphorylase
kinase, delta (Ref Seq. (mRNA): NM_001743), B2M refers to beta-2
microglobulin (Ref. Seq. (mRNA): NM_004048), RPL37A refers to 60S
ribosomal protein L37a (Ref Seq. (mRNA): NM_000998), GUSB refers to
beta-glucuronidase (Ref. Seq. (mRNA): NM_000181), HPRT1 refers to
hypoxanthine-phosphoribosyl-transferase 1 (Ref Seq. (mRNA):
NM_000194) and GAPDH refers to
glycerinaldehyde-3-phosphate-dehydrogenase (Ref. Seq. (mRNA):
NM_002046).
[0243] In a further aspect, the invention relates to a method of
stratifying a cancer patient for tumor treatment, said method
comprising, as a first step, identifying a molecular subtype of a
tumor in the cancer patient using the in vitro method as defined
above and, as a second step, selecting a tumor treatment regimen
based on the molecular subtype identified by the in vitro
method.
[0244] "Stratifying a cancer patient for tumor treatment" in
accordance with the present invention comprises the allocation of
the cancer patient to a patient group having a particular molecular
tumor subtype, which then allows the medical practitioner to select
the most suitable tumor treatment regimen.
[0245] In one embodiment, said method of stratifying a cancer
patient for tumor treatment does not comprise any other diagnostic
steps, such as histological grading or determining the lymph nodal
status, besides the step of identifying the molecular subtype of
the tumor in the cancer patient using the in vitro method as
defined above.
[0246] In one embodiment, the molecular subtype is selected from
the group comprising HER2-positive, triple-negative, luminal A and
luminal B.
[0247] In one embodiment, [0248] the molecular subtype is
HER2-positive, and the tumor treatment regimen comprises
administration of anti-HER2 antibodies and chemotherapeutic agents;
[0249] the molecular subtype is triple-negative, and the tumor
treatment regimen comprises administration of chemotherapeutic
agents; [0250] the molecular subtype is luminal A, and the tumor
treatment regimen comprises endocrine therapy; or [0251] the
molecular subtype is luminal B, and the tumor treatment regimen
comprises endocrine therapy and, optionally, administration of
chemotherapeutic agents.
[0252] Monoclonal anti-HER2 antibodies include trastuzumab
(Herceptin.RTM.) and pertuzumab (Perjeta.RTM.), which may be
administered alone or combination. Trastuzumab is effective only in
cancers where HER2 is over-expressed. Other monoclonal antibodies,
such as ertumaxomab (Rexomun.RTM.), are presently undergoing
clinical trials. The anti-HER2 antibodies can further be modified
to comprise a therapeutic moiety/agent, such as a cytotoxic agent,
a drug (e.g., an immunosuppressant), a chemotherapeutic agent or a
radionuclide, or a radioisotope. A cytotoxin or cytotoxic agent
includes any agent that is detrimental to and, in particular, kills
cells. Examples include mertansine (DM1), taxol, cytochalasin B,
gramicidin D, ethidium bromide, emetine, mitomycin, etoposide,
tenoposide, vincristine, vinblastine, colchicin, doxorubicin,
daunorubicin, dihydroxy anthracin, dione, mitoxantrone,
mithramycin, actinomycin D, amanitin, 1-dehydrotestosterone,
glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and
puromycin and analogs or homologs thereof. Other suitable
therapeutic agents for forming antibody conjugates include, but are
not limited to, antimetabolites (e.g., methotrexate,
6-mercaptopurine, 6-thioguanine, cytarabine, fludarabin,
5-fluorouracil decarbazine), alkylating agents (e.g.,
mechlorethamine, thioepachlorambucil, melphalan, carmustine (BSNU)
and lomustine (CCNU), cyclophosphamide, busulfan, dibromomannitol,
streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II)
(DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly
daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin
(formerly actinomycin), bleomycin, mithramycin, and anthramycin
(AMC)), and anti-mitotic agents (e.g., vincristine and
vinblastine). In a preferred embodiment, the therapeutic agent is a
cytotoxic agent or a radiotoxic agent. In another embodiment, the
therapeutic agent is an immunosuppressant. In yet another
embodiment, the therapeutic agent is GM-CSF. In a preferred
embodiment, the therapeutic agent is doxorubicin, cisplatin,
bleomycin, sulfate, carmustine, chlorambucil, cyclophosphamide or
ricin A. Further therapeutic moieties include therapeutic moieties
acting on mRNA and/or protein synthesis. Several inhibitors of
transcription are known. For instance, actinomycin D, which is both
a transcriptional inhibitor and a DNA damage agent, intercalates
within the DNA and thus inhibits the initiation stage of
transcription. Flavopiridol targets the elongation stage of
transcription. a-Arnanitin binds directly to RNA polymerase II,
which leads to the inhibition of both initiation and elongation
stages. Anti-HER2 Antibodies also can be conjugated to a
radioisotope, e.g., iodine-131, yttrium-90 or indium-111, to
generate cytotoxic radiopharmaceuticals. An alternative to the
administration of anti-HER2 antibodies is the administration of
small compounds targeting HER2, such as lapatinib (Tykerb.RTM. or
Tyverb.RTM.).
[0253] Chemotherapeutic agents according to the invention include
cytostatic compounds and cytotoxic compounds. Traditional
chemotherapeutic agents act by killing cells that divide rapidly,
one of the main properties of most cancer cells. According to the
invention, the term "chemotherapeutic agent" includes taxanes,
platinum compounds, nucleoside analogs, camptothecin analogs,
anthracyclines and anthracycline analogs, etoposide, bleomycin,
vinorelbine, cyclophosphamide, antimetabolites, anti-mitotics, and
alkylating agents, including the agents disclosed above in
connection with antibody conjugates, and combinations thereof.
According to the invention a reference to a chemotherapeutic agent
is to include any prodrug such as ester, salt or derivative such as
a conjugate of said agent. Examples are conjugates of said agent
with a carrier substance, e.g., protein-bound paclitaxel such as
albumin-bound paclitaxel. Preferably, salts of said agent are
pharmaceutically acceptable. Chemotherapeutic agents are often
given in combinations, usually for 3-6 months. One of the most
common treatments is cyclophosphamide plus doxorubicin (adriamycin;
belonging to the group of anthracyclines and anthracycline
analogs), known as AC. Sometimes, a taxane drug, such as docetaxel,
is added, and the regime is then known as CAT; taxane attacks the
microtubules in cancer cells. Another common treatment, which
produces equivalent results, is cyclophosphamide, methotrexate,
which is an antimetabolite, and fluorouracil, which is a nucleoside
analog (CMF). Another standard chemotherapeutic treatment comprises
fluorouracil, epirubicin and cyclophosphamide (FEC), which may be
supplemented with docetaxel or vinorelbine.
[0254] Endocrine therapy (anti-hormonal treatment) targets cancers
that require estrogen to continue growing by administration of
drugs that either block/down-regulate estrogen and/or progesterone
receptors, e.g., tamoxifen (Nolvadex.RTM.) or fulvestrant
(Faslodex.RTM.), or alternatively block the production of estrogen
with an aromatase inhibitor, e.g., anastrozole (Arimidex.RTM.) or
letrozole (Femara.RTM.). Aromatase inhibitors, however, are only
suitable for post-menopausal patients. This is because the active
aromatase in postmenopausal women is different from the prevalent
form in premenopausal women, and therefore these agents are
ineffective in inhibiting the predominant aromatase of
premenopausal women.
[0255] In one embodiment, the molecular subtype is luminal B, and
the tumor treatment regimen comprises administration of
chemotherapeutic agents.
[0256] In one embodiment, the molecular subtype is luminal B, and
the tumor treatment regimen comprises administration of a taxane,
preferably docetaxel.
[0257] In one embodiment, the taxane is administered in combination
with fluorouracil, epirubicin and cyclophosphamide (FEC).
[0258] In a further aspect, the present invention relates to a
method of treatment of cancer, said method comprising, as a first
step, stratifying a cancer patient for tumor treatment using the in
vitro method as defined above, and, as a second step, providing the
selected tumor treatment regimen to the cancer patient. The tumor
treatment regimen is selected based on the molecular subtype
identified by the in vitro method as defined above.
[0259] In one embodiment, said method comprises using quantitative
results obtained by the in vitro method as defined above for direct
decision-making in favor of or against adjuvant/neoadjuvant
chemotherapy.
[0260] In yet a further aspect, the present invention relates to a
kit useful for identifying a molecular subtype of a tumor in a
cancer patient by means of reverse transcription (RT) quantitative
PCR, said kit comprising: [0261] at least one pair of HER2-specific
primers and at least one HER2-specific probe; [0262] at least one
pair of ESR1-specific primers and at least one ESR1-specific probe;
[0263] at least one pair of PGR-specific primers and at least one
PGR-specific probe; and [0264] at least one pair of Ki67-specific
primers and at least one Ki67-specific probe; and/or [0265] at
least one pair of RACGAP1-specific primers and at least one
RACGAP1-specific probe.
[0266] In one embodiment, the quantitative PCR is
fluorescence-based quantitative real-time PCR.
[0267] In one embodiment, detection of the probe is based on
amplification-mediated probe displacement.
[0268] In one embodiment, the probe is a dual-label probe
comprising a fluorescence reporter moiety and a fluorescence
quencher moiety.
[0269] In one embodiment, the kit further comprises a reverse
transcriptase and a DNA polymerase.
[0270] In one embodiment, the reverse transcriptase and the
polymerase are provided in the form of an enzyme-mix which allows a
one-step reverse transcription (RT) quantitative PCR.
[0271] In one embodiment, the kit further comprises at least one
pair of reference gene-specific primers and at least one reference
gene-specific probe. In one embodiment, the reference gene is one
or more selected from the group comprising CALM2, B2M, RPL37A,
GUSB, HPRT1 and GAPDH, preferably CALM2 and/or B2M.
[0272] In one embodiment, the kit further comprises at least one
control RNA sample. In one embodiment, the at least one control RNA
sample is used as a positive control and/or a control sample
(calibrator), wherein, preferably, the at least one control RNA
sample comprises synthetic mRNA coding for one or more gene
products (or parts thereof) of one or more genes selected from the
group comprising HER2, ESR1, PGR, Ki67, RACGAP1 and one or more
reference genes. In one embodiment, the one or more reference genes
are selected from the group comprising CALM2, B2M, RPL37A, GUSB,
HPRT1 and GAPDH, preferably CALM2 and/or B2M.
[0273] In one embodiment, the kit may further comprise a DNase and
a DNase reaction buffer.
[0274] Preferably, the primers and probes are as defined further
above in connection with the in vitro method of the present
invention.
[0275] In one embodiment, the primers provide an amplicon size of
less than 120 bp, preferably less than 100 bp.
[0276] In one embodiment, the ESR1-specific primers have a length
of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 1 and 2, and/or the
HER2-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 4 and 5, and/or the Ki67-specific primers have a length of
15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 7 and 8, and/or the
PGR-specific primers have a length of 15 to 30 nucleotides and
comprise at least 10 contiguous nucleotides of the sequences of SEQ
ID NOs: 10 and 11, and/or the RACGAP1-specific primers have a
length of 15 to 30 nucleotides and comprise at least 10 contiguous
nucleotides of the sequences of SEQ ID NOs: 13 and 14. In one
embodiment, the specific primers comprise at least 15 contiguous
nucleotides of the sequences indicated above.
[0277] In one embodiment, the ESR1-specific primers have the
sequences of SEQ ID NOs: 1 and 2, and/or the HER2-specific primers
have the sequences of SEQ ID NOs: 4 and 5, and/or the Ki67-specific
primers have the sequences of SEQ ID NOs: 7 and 8, and/or the
PGR-specific primers have the sequences of SEQ ID NOs: 10 and 11,
and/or the RACGAP1-specific primers have a the sequences of SEQ ID
NOs: 13 and 14.
[0278] In one embodiment, the ESR1-specific probe has a length of
20 to 35 nucleotides and comprises at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 3, and/or the
HER2-specific probe has a length of 20 to 35 nucleotides and
comprises at least 15 contiguous nucleotides of the sequence of SEQ
ID NO: 6, and/or the Ki67-specific probe has a length of 20 to 35
nucleotides and comprises at least 15 contiguous nucleotides of the
sequence of SEQ ID NO: 9, and/or the PGR-specific probe has a
length of 20 to 35 nucleotides and comprises at least 15 contiguous
nucleotides of the sequence of SEQ ID NO: 12, and/or the
RACGAP1-specific probe has a length of 20 to 35 nucleotides and
comprises at least 15 contiguous nucleotides of the sequence of SEQ
ID NO: 15. In one embodiment, the specific probes comprise at least
20 contiguous nucleotides of the sequences indicated above.
[0279] In one embodiment, the ESR1-specific probe has the sequence
of SEQ ID NO: 3, and/or the HER2-specific probe has the sequence of
SEQ ID NO: 6, and/or the Ki67-specific probe has the sequence of
SEQ ID NO: 9, and/or the PGR-specific probe has the sequence of SEQ
ID NO: 12, and/or the RACGAP1-specific probe has the sequence of
SEQ ID NO: 15.
[0280] Preferably, the probes as defined above are dual-label
probes comprising a fluorescence reporter moiety and a fluorescence
quencher moiety.
[0281] In one embodiment, the tumor is a solid tumor. In one
embodiment, the tumor is a breast tumor or is derived from a breast
tumor (e.g. by metastasis). In one embodiment, the cancer is breast
cancer.
[0282] As used herein, the term "kit of parts (in short: kit)"
refers to an article of manufacture comprising one or more
containers and, optionally, a data carrier. Said one or more
containers may be filled with one or more of the above mentioned
means or reagents. Additional containers may be included in the kit
that contain, e.g., diluents, buffers and further reagents such as
dNTPs. Said data carrier may be a non-electronical data carrier,
e.g., a graphical data carrier such as an information leaflet, an
information sheet, a bar code or an access code, or an electronical
data carrier such as a floppy disk, a compact disk (CD), a digital
versatile disk (DVD), a microchip or another semiconductor-based
electronical data carrier. The access code may allow the access to
a database, e.g., an internet database, a centralized, or a
decentralized database. Said data carrier may comprise instructions
for the use of the kit in the methods of the invention. The data
carrier may comprise a threshold value or reference level of RNA
transcript, e.g., mRNA. In case that the data carrier comprises an
access code which allows the access to a database, said threshold
value or reference level is deposited in this database. In
addition, the data carrier may comprise information or instructions
on how to carry out the methods of the present invention.
[0283] In another aspect, the present invention relates to the use
of a kit as defined above for identifying a molecular subtype of a
tumor in a cancer patient.
[0284] In another aspect, the present invention relates to the use
of a kit as defined above for assessing a cancer patient's risk for
distant metastasis.
[0285] The present invention overcomes major disadvantages of the
current standard and state of the art diagnostic method
immunohistochemistry and more recent methods.
[0286] The present invention allows reliable molecular subtyping of
tumors, in particular breast tumors, which then allows the medical
practitioner to select the most suitable tumor treatment
regimen.
[0287] Thanks to the preferred order of the assessment of the four
or five markers (preferably, the expression level of RNA transcript
of HER2 is determined first) there is no misclassification of
HER2-positive into luminal A and B subtypes, a problem that often
occurs if the subtyping is based on hierarchal cluster analysis or
correlation analysis (Perou et al. (2000), Nature, 406:747-752;
TCGA (Cancer Genome Atlas Network) (2012), Nature, 490:61-70).
Furthermore, there is no misclassification of false-positive and
clinically HER2-negative tumors, which, according to Perou et al.,
may occur in up to 30% of these cases.
[0288] The present invention provides methods and kits to
confirm/reassess uncertain or contradictory results of an
immunochemical analysis, especially in the following breast cancer
patient groups as identified by IHC: ESR1/PGR negative (approx. 30%
of all breast cancer patients), ESR1/PGR weakly positive (approx.
15% of all breast cancer patients), HER2 3+ (tumor biopsy IHC, not
confirmed by dissection tumor IHC; approx. 15% of all breast cancer
patients) and HER 2+ (approx. 20% of all breast cancer
patients).
[0289] The methods and kits of the present invention facilitate
direct decision-making in favor of or against adjuvant/neoadjuvant
chemotherapy in luminal breast cancer due to the distinction of
luminal A and luminal B subtypes by reliable detection of Ki67-
and/or RACGAP1 RNA transcript. This is particularly helpful for
patients having ESR1/PGR positive and up to grade 2 tumors (approx.
50% of all breast cancer patients).
[0290] The present invention allows a distinction of luminal A and
luminal B tumors with clearly differing overall survival and
distant metastasis free survival rates. While luminal B patients
have a continuously high risk of metastasis, particularly in the
first five years after treatment (e.g. surgery), the risk of
luminal A patients is constantly and clearly lower. Thus, the
methods and kits also allow for the assessment of a patient's risk
for distant metastasis.
[0291] By using the methods of the present invention, approximately
77% of the luminal tumors in the FinHER study (Joensuu et al.
(2006), N Engl J Med, 354:809-820) are allocated to the low risk
group luminal A, and there are no intermediate risk groups.
Furthermore, the classification into luminal A and luminal B
reduces the significance of histological grading and nodal status,
two parameters that are usually very important for tumor prognosis.
Therefore, uncertainties regarding the therapy of grade 2 tumors
are resolved in a clinically relevant manner.
[0292] The methods and kits of the present invention also allow for
the prediction of response to systemic therapy thanks to the
quantitative determination of the RNA transcript expression level
of ESR1, HER2, Ki67 and, optionally, RACGAP1. This is particularly
helpful for patients having invasive breast cancer >1 cm with
uncertain IHC (approx. 40% of all breast cancer patients).
[0293] Novelties of the present invention include not only the
mRNA-based estimation of breast cancer biomarkers, but also the
algorithmic definition of subtypes. The inclusion of mandatory PGR
positivity for luminal A definition in addition to low Ki67 is an
original criterion, not included in the 2011 St. Gallen clinical
guidelines at the time of the invention. In addition, tumors
displaying HER2 mRNA expression exceeding the predefined cut-off
are classified as HER2-positives irrespective of ESR1/PGR status
which also deviates from the 2011 international guidelines, which
are still in effect. All these new aspects contribute to the
predictive value of the RT-qPCR-based approach and kit of the
present invention. In fact, these novelties, technical in terms of
RT-qPCR--based biomarker estimation and theoretical in terms of the
classification algorithm, provide a more accurate and meaningful
subtyping of patients in the FinHer clinical trial, which
ultimately provides a predictive tool for docetaxel benefit in an
adjuvant therapy setting.
[0294] Taken together, the present invention serves currently
largely unmet clinical needs for a reliable, reproducible and
quantitative assessment of prognosis and prediction of therapy
success in at least 50% of all breast cancer patients (see also
FIG. 1).
[0295] The present invention is further illustrated by the
following examples which are not be construed as limiting the scope
of the invention.
EXAMPLES
Example 1: Determination of mRNA Expression Levels by Reverse
Transcription (RT) Quantitative PCR (RT-qPCR)
[0296] RNA was isolated from paraffin-embedded, formalin-fixed
tissues (=FFPE tissues). More particularly, total RNA from a 5 to
10 .mu.m curl of FFPE tumor tissue was extracted using the High
Pure RNA Paraffin Kit (Roche, Basel, Switzerland) or the XTRAKT RNA
Extraction Kit XL (Stratifyer Molecular Pathology, Cologne,
Germany), quantified by the Ribogreen RNA Quantitation Assay
(Molecular Probes, Eugene, Oreg.) and qualified by real-time
fluorescence RT-PCR of a fragment of the reference gene RPL37A. It
was recognized that differences exist between different extraction
technologies when comparing quantitative data of target genes of
sequential slices by different methodologies. For the purpose of
the present invention the use of the XTRAKT RNA Extraction Kit XL
was preferred. In general 2.5 .mu.l RNA of each qualified
extraction (approx. 50-100 ng) was assayed by qRT-PCR as described
below.
[0297] For a detailed analysis of gene expression by quantitative
RT-PCR methods, primers flanking the region of interest and a
fluorescent labeled probe hybridizing in-between were utilized.
Target specific primers and probes were selected using the NCBI
prime designing tool (www.ncbi.nlm.nih.go). RNA specific
primer/probe sequences were used to enable RNA specific
measurements by locating primer/probe sequences across exon/exon
boundaries.
[0298] Furthermore, primer/probes were selected not to bind to
sequence regions with known polymorphisms (SNPs). In case multiple
isoforms of the same gene exist, primers were selected to amplify
all relevant splice variants. All primer pairs were checked for
specificity by conventional PCR reactions. After further
optimization of the primers/probes, the primers and probes listed
in Table 1 gave the best results. These primers/probes are superior
to primers/probes known from the prior art, e.g. in terms of
specificity and amplification efficiency. To standardize the amount
of sample RNA, the genes CALM2 and B2M were selected as reference
genes, since they were not differentially regulated in the samples
analyzed.
TABLE-US-00001 TABLE 1 Used primers and probes. Name Sequence (5'
.fwdarw. 3') Purification 5' Modification 3' Modification ESR_F
AGAGGGTGCCAGGCTTTGT HPLC none none (SEQ ID NO: 1) ESR_R
AGGATCTCTAGCCAGGCACATT HPLC none none (SEQ ID NO: 2) ESR_P
TTTGACCCTCCATGATCAGGTCCACCT HPLC JOE TAMRA (SEQ ID NO: 3) HER2_F
GAACTCACCTACCTGCCCACC HPLC none none (SEQ ID NO: 4) HER2_R
GACCTGCCTCACTTGGTTGTG HPLC none none (SEQ ID NO: 5) HER2_P
CCAGGAGGTGCAGGGCTACGTG HPLC 6-FAM Dabcyl (SEQ ID NO: 6) KI67_F
CGAGACGCCTGGTTACTATCAA HPLC none none (SEQ ID NO: 7) KI67_R
GGATACGGATGTCACATTCAATACC HPLC none none (SEQ ID NO: 8) KI67_P
ACGGTCCCCACTTTCCCCTGAGC HPLC 6-FAM Dabcyl (SEQ ID NO: 9) PGR_F
AAACTTCTTGATAACTTGCATGATCTT HPLC none none (SEQ ID NO: 10) PGR_R
CAATAACTTCAGACATCATTTCTGG HPLC none none (SEQ ID NO: 11) PGR_P
CGGGACTGGATAAATGTATTCAAGCAGTAC HPLC 6-FAM Dabcyl (SEQ ID NO: 12)
RAC_F GAATGTGCGGAATCTGTTTGAG HPLC none none (SEQ ID NO: 13) RAC_R
TCGCCAACTGGATAAATTGGA HPLC none none (SEQ ID NO: 14) RAC_P
ACTGAGAATCTCCACCCGGCGCA HPLC JOE TAMRA (SEQ ID NO: 15) B2M_F
GTATGCCTGCCGTGTGAACC HPLC none none (SEQ ID NO: 16) B2M_R
GGCATCTTCAAACCTCCATGAT HPLC none none (SEQ ID NO: 17) B2M_P
AGTGGGATCGAGACATGTAAGCAGC HPLC JOE TAMRA (SEQ ID NO: 18) CALM2_F
AGGAGGCGAATTAGTCCGA HPLC none none (SEQ ID NO: 19) CALM2_R
GCTCTTCAGTCAGTTGGTCA HPLC none none (SEQ ID NO: 20) CALM2_P
TCGCGTCTCGGAAACCGGTAGC HPLC JOE TAMRA (SEQ ID NO: 21)
TagMan.RTM. validation experiments were performed showing that the
efficiencies of the target and the control amplifications are
approximately equal which is a prerequisite for the relative
quantification of gene expression by the comparative .DELTA.CT
method. To perform the expression analysis of genes of interest
within a biological sample, 4.times. duplex assay-mixtures were
prepared by mixing the respective primer/probes of two specific
assays. For separate detection of CT values the assay probes were
modified with different fluorescent probes. Each 4.times. assay-mix
contained 2 .mu.M of unmodified forward and reverse primer and 1,2
.mu.M of probe. For each reaction 2,5 .mu.l total RNA extracted
from FFPE sections (see above) was mixed with 2,5 .mu.l assays-mix,
2,5 .mu.l enzyme-mix and 2,5 .mu.l water in one well of a
96-well-Optical Reaction Plate. Measurements of the PCR reaction
were done according to the instructions of the manufacturer with a
Versant kPCR Cycler (Siemens) or a Light Cycler 480 (Roche) under
appropriate conditions (5 min. 50.degree. C., 20 sec. 95.degree.
C., 15 sec. 95.degree. C., 1 min 60.degree. C.; 40 cycles). Prior
to the measurement of so far unclassified biological samples
control, experiments with, e.g., cell lines, healthy control
samples, samples of defined molecular tumor subtypes can be used
for standardization of the experimental conditions.
Example 2: Molecular Subtyping of Tumors Based on the mRNA
Expression Levels of HER2, ESR1, PGR, Ki67 and, Optionally,
RACGAP1
[0299] For the evaluation of breast tumors, 855 out of 1010 breast
cancer patients of the FinHER study (Joensuu et al. (2006), N Engl
J Med, 354:809-820) could be used. The mean cut-off values (given
as 40-.DELTA.CT values) were as follows: HER2: 38; ESR1: 34; PGR:
30,2; Ki67: 31,7; and RACGAP1: 34,2. The cut-off values for HER2
and ESR1 were determined based on evaluation of previous studies
(Koutras et al. (2008), Brit. J. of Canc., 99:1775-1785;
Pentheroudakis et al. (2009), Breast Cancer Res Treat 2009,
116:131-143) using 268 samples and were applied to the FinHER study
(proportional hazards model validation). CALM2 served as reference
gene.
[0300] Based on the mRNA expression level of HER2, ESR1, PGR and
Ki67 (neg/low indicates an expression level which is lower than the
defined expression threshold; pos/increased indicates an expression
level which is higher than the defined expression threshold) tumors
are allocated to the molecular subtypes HER2-positive (HER2),
luminal A (LumA), luminal B (LumB) and triple-negative (TNT). As
shown in Table 2, the molecular subtyping of tumors in accordance
with the present invention differs from those that are based on
prior art methods, e.g., immunohistochemistry (Goldhirsch et al.
(2011), Annals of Oncology, 22:1736-1747, St. Gallen International
Expert Consensus on the Primary Therapy of Early Breast Cancer
2011) and analysis of only three gene markers (Sotiriou et al.
(2009), N Engl J Med, 360(8):790-800).
TABLE-US-00002 TABLE 2 Molecular subtyping of tumors. Present
Goldhirsch Sotiriou HER2 ESR1 PGR Ki67 Invention et al. (2011) et
al. (2009) neg neg neg low TNT TNT basal-like neg neg neg increased
TNT TNT basal-like neg pos pos low LumA LumA LumA neg neg pos low
LumA LumA LumB neg neg pos increased LumB LumB LumB neg pos neg low
LumB LumA LumB neg pos pos increased LumB LumB LumB neg pos neg
increased LumB LumB LumB pos pos pos increased HER2 LumB HER2 pos
pos pos low HER2 LumB HER2 pos pos neg low HER2 LumB HER2 pos neg
neg low HER2 HER2 HER2 pos neg neg increased HER2 HER2 HER2
[0301] FIG. 2 shows a partitioning test to evaluate the prognostic
and predictive value of the expression level of HER2, ESR1, PGR,
Ki67 and RACGAP1 mRNA for the 5-years survival rate of breast
cancer patients. These data show that RACGAP1 mRNA expression
levels below or above the defined threshold are associated with
particularly significant differences in the 5-years survival rate.
More particularly, an increased level of RACGAP1 mRNA expression
reduces the probability of survival significantly. Probability of
survival is further reduced if the mRNA expression of RACGAP1 is
increased and Ki67 mRNA expression is low (see Table 3). With
current analytical procedures, these risk patients (who would
require a different kind of follow-up care, e.g., examination with
particular imaging methods) remain undiscovered.
TABLE-US-00003 TABLE 3 5-years Ki67 RCGAP1 Survival increased
increased 50% increased low 84% low increased 63% low low 91%
increased unaccounted 78% low unaccounted 90% RACGAP1/K167 mRNA
expression and probability of survival.
[0302] Using Kaplan Meier analysis the inventors analyzed the
survival of patients with HER2-positive, luminal A, luminal B and
triple-negative tumors, respectively, wherein the molecular subtype
of the tumor was identified in accordance with the present
invention, i.e. based on the mRNA expression levels of HER2, ESR1,
PGR and Ki67. As shown in FIG. 3, the luminal A subtype, as defined
by the present inventors, is associated with an overall survival
rate of 97% after 5 years (vs. 87% for luminal B and HER2-positive
tumors and 84% for triple-negative tumors).
[0303] The inventors further analyzed distant metastasis free
survival ("DMFS"; distant recurrence X years after surgery) of
patients with HER2-positive, luminal A, luminal B and
triple-negative tumors, respectively, wherein the molecular subtype
of the tumor was identified in accordance with the present
invention. As shown in FIG. 4, the luminal A subtype, as defined by
the present inventors, is associated with a distant metastasis free
survival rate of 92% after 5 years (vs. 78% for luminal B,
HER2-positive and triple-negative tumors).
[0304] In a multivariate analysis of overall survival with the most
important histopathological standard parameters (tumor size, nodal
status and histological grading) the molecular subtyping in
accordance with the present invention turned out to be highly
significant, whereas both histological grading and nodal status
lost their significance.
[0305] Finally, a multivariate Cox regression analysis of DMFS
comparing the molecular subtyping by immunohistochemistry (Sotiriou
et al. (2009), N Engl J Med, 360(8):790-800) with the molecular
subtyping by the method in accordance with the present invention,
based on the mRNA expression levels of HER2, ESR1, PGR and Ki67,
was performed (FIG. 5). The analysis clearly shows the superiority
of the method of the present invention, as the immunohistochemical
subtyping looses its significance when the results obtained by the
method of the present invention are included in the Cox
proportional hazards model.
Example 3: Measurement of mRNA Expression Levels of Biomarkers
HER2, ESR1, PGR, Ki67 by Reverse Transcription (RT) Quantitative
PCR (RT-qPCR) and Molecular Subtype Determination
[0306] RNA was isolated from FFPE tissues. More particularly, total
RNA from 10 .mu.m sections of FFPE breast tumor tissue were
extracted using the XTRAKT RNA Extraction Kit (Stratifyer Molecular
Pathology, Cologne, Germany). RNA eluates were directly used
without determination of concentration. 2.5 .mu.l RNA of each
extraction was assayed by RT-qPCR as described below.
[0307] For RT-qPCR, primers flanking the region of interest and a
5'-fluorescently labeled hydrolysis probe with a 3'-TAMRA or-Dabcyl
Quencher were used for each target. Primers and probes used are
listed in Table 1. To correct for different amounts of sample RNA,
the genes CALM2 and B2M were used as reference genes for
normalization of expression results. RT-qPCR was performed in
duplexes in the following combinations, HER2/ESR1, Ki67/B2M and
PGR/CALM2. Each of the three 4.times. assay mixes contained 2 .mu.M
of unmodified forward and reverse primer and 1.2 .mu.M of probe.
For each assay, a master mix with 2.5 .mu.l assay-mix, 2.5
.parallel.l 4.times. enzyme-mix (TaqManFast Virus 1-Step MasterMix,
Life Technologies), and 2.5 .mu.l water per reaction was prepared
and 7.5 .mu.l of each master mix distributed into a kPCR 96-well
reaction plate in triplicates. 2.5 .mu.l total RNA extracted from
FFPE sections (see above) or, alternatively, positive (IVT RNA) or
negative control (water) was added to each well. Analysis of RNA
eluates derived from three patient samples was done with three lots
of assay mixes and enzyme mixes. Measurement of the 1-step RT-qPCR
reactions was done according to the instructions of the
manufacturer with a Versant kPCR Cycler (Siemens) with the
following thermal profile: 5 min 50.degree. C., 20 sec 95.degree.
C. one cycle each and 15 sec 95 .degree. C., 1 min 60.degree. C.
for 40 cycles.
[0308] 6 patient samples along with the positive and negative
controls were analyzed with three lots of assay mixes.
40-.DELTA..DELTA.CT values were calculated according to the
description given above (calculation method 4). FIGS. 6 to 9 show
the 40-.DELTA..DELTA.CT values for each marker, for each sample and
lot. The cut-off values (given as 40-.DELTA..DELTA.CT values) for
the classification of the biomarkers in positive or negative were
as follows: HER2: 40.90; ESR1: 38.20; PGR: 34.90; Ki67: 34.80. The
molecular subtype was defined as shown in Table 4.
TABLE-US-00004 TABLE 4 HER2 ESR1 PGR KI67 Subtype pos pos pos pos
HER2+ pos pos pos neg HER2+ pos pos neg neg HER2+ pos neg pos neg
HER2+ pos neg pos pos HER2+ pos pos neg pos HER2+ pos neg neg pos
HER2+ pos neg neg neg HER2+ neg pos pos pos Luminal-B neg pos pos
neg Luminal-A neg pos neg neg Luminal-B neg neg pos neg Luminal-A
neg neg pos pos Luminal-B neg pos neg pos Luminal-B neg neg neg pos
Triple negative neg neg neg neg Triple negative Molecular subtyping
of patient samples.
TABLE-US-00005 TABLE 5 40-.DELTA..DELTA.CT values and subtype
calling for assay mix lot 1. Sub- Lot 1 HER2 ESR1 PGR KI67 HER2
ESR1 PGR KI67 type Sam- 37.13 33.64 32.05 36.90 neg neg neg pos
TNBC ple 1 Sam- 38.86 33.86 32.60 38.72 neg neg neg pos TNBC ple 2
Sam- 42.75 37.84 32.08 37.43 pos neg neg pos HER2+ ple 3 Sam- 39.11
40.07 38.22 37.13 neg pos pos pos LumB ple 4 Sam- 41.55 37.87 35.89
33.85 pos neg pos neg HER2+ ple 5 Sam- 39.40 40.14 40.63 34.64 neg
pos pos neg LumA ple 6
TABLE-US-00006 TABLE 6 40-.DELTA..DELTA.CT values and subtype
calling for assay mix lot 2. Sub- Lot 2 HER2 ESR1 PGR KI67 HER2
ESR1 PGR KI67 type Sam- 36.49 32.61 30.77 36.61 neg neg neg pos
TNBC ple 1 Sam- 38.66 33.24 31.62 38.60 neg neg neg pos TNBC ple 2
Sam- 42.71 37.85 31.19 37.44 pos neg neg pos HER2+ ple 3 Sam- 38.98
39.84 37.73 37.43 neg pos pos pos LumB ple 4 Sam- 41.72 37.13 35.12
34.08 pos neg pos neg HER2+ ple 5 Sam- 39.63 40.32 40.30 33.83 neg
pos pos neg LumA ple 6
TABLE-US-00007 TABLE 7 40-.DELTA..DELTA.CT values and subtype
calling for assay mix lot 3. Sub- Lot 3 HER2 ESR1 PGR KI67 HER2
ESR1 PGR KI67 type Sam- 36.77 33.46 30.90 36.60 neg neg neg pos
TNBC ple 1 Sam- 38.46 33.27 31.52 38.51 neg neg neg pos TNBC ple 2
Sam- 42.84 37.78 31.22 37.44 pos neg neg pos HER2+ ple 3 Sam- 38.78
39.56 37.97 37.73 neg pos pos pos LumB ple 4 Sam- 41.17 37.79 35.18
34.13 pos neg pos neg HER2+ ple 5 Sam- 39.16 40.36 40.01 33.96 neg
pos pos neg LumA ple 6
[0309] Only slight differences of the results between different
reagent lots can be observed. Assay performance was very robust and
reproducible for all markers. Tables 5 to 7 show the
40-.DELTA..DELTA.CT values and the positive or negative result for
each marker and the translation into the respective subtype as
defined in Table 4 (see also Table 2). Marker results (pos/neg) and
subtypes were consistent for all 6 samples measured with three
different reagent lots.
Example 4: Comparison of Breast Cancer Subtyping by RT-qPCR and IHC
in Terms of the Clinical Outcome
[0310] FIGS. 10 to 19 depict Kaplan-Meier survival curves for
different tumor subtypes (luminal B, HER2-positive, luminal A, and
triple-negative breast cancer [TNBC]) treated with different
chemotherapy agents (docetaxel or vinorelbine). Subytpes defined by
RT-qPCR according to the present invention are shown in panel A,
whereas subtypes defined by IHC are shown in panel B. Dotted lines
mark the 5 year time point for outcome calculations.
[0311] The data presented in FIGS. 10 to 19 collectively highlight
the superiority of the novel RNA-based classification of breast
cancer by RT-qPCR as compared to the conventional protein-based
IHC. The data indicate a significant benefit of docetaxel treatment
for luminal B tumors. In contrast, IHC-based subtyping failed to
show a significant benefit in any subtype with some trends in
luminal A, luminal B and triple-negative breast cancer patients.
However, as these 3 subtypes comprise .about.80% of all patients,
the IHC-based subtyping did not provide any clinically useful
predictive information.
[0312] Importantly, RT-qPCR-defined patients with luminal B tumors
derive a statistically significant and exclusive benefit from
docetaxel as compared to vinorelbine upon combined treatment with
fluorouracil, epirubicin and cyclophosphamide (FEC). These patients
remain free of metastasis and live significantly longer when
treated with docetaxel, whereas their outcome is clearly worse when
receiving vinorelbine. This difference in outcome between the two
chemotherapeutic regimens is not observed in any other subtype
except for luminal B. Interestingly, docetaxel appears to be even
inferior to vinorelbine for luminal A tumors. Although this effect
does not reach statistical significance, it clearly excludes a
possible beneficial effect of docetaxel treatment in luminal A
patients as it is seen in luminal B patients identified by
RT-qPCR.
[0313] In contrast, when patients are subtyped by IHC, the effect
exerted on clinical outcome by the type of regimen is equivocal,
due to inaccurate classification. This in turn generates a variety
of inconclusive trends that cannot be relied upon for clinical
decision making. In conclusion, the present invention undisputably
identifies a specific group of breast cancer patients who respond
favorably to docetaxel but not to vinorelbine, thus showing
predictive power for luminal B tumors in this particular setting.
This is a very important property for a diagnostic assay, given
that, as was shown in the FinHER clinical trial, docetaxel is more
commonly associated with adverse effects than vinorelbinea, a fact
that necessitated a reduction of the scheduled starting dose.
[0314] Therefore, the present invention can be used to assist in
proper allocation of treatments in breast cancer. In particular, as
shown for the first time in the context of a randomized clinical
trial, breast cancer subtying by RT-qPCR allows to limit
docetaxel-containing regimens to patients bearing luminal B tumors,
which are more responsive to docetaxel treatment, and to consider
alternative chemotherapeutics for patients with other tumor
subtypes.
Example 5: Comparison of RT-qPCR and Conventional IHC Staining in
Terms of their Sensitivity Towards Ki67
[0315] A considerable number of cases (16.58%) are Ki67 negative by
IHC, but are Ki67 positive by RT-qPCR. This demonstrates the higher
sensitivity and robustness of the mRNA determination by the present
invention as compared to the protein-based assessment of the prior
art. In part, this may be due to multiple technical limitations of
the IHC-based method (e.g., lack of protein preservation due to
fixation and/or antigen retrieval issues, analysis time after
tissue cutting, etc.) or staining interpretation problems (e.g.,
interpretation of faint nuclei stains).
[0316] Due to the higher sensitivity of the RNA-based assessment of
Ki67 by RT-qPCR, the concordance with IHC assessment of Ki67 is
only moderate (see FIG. 20 A, C). Moreover, this results in a low
NPA for the present invention (53.82%), when local IHC assessment
is used as reference method (FIG. 20 D). By contrast the PPA is
high, as RT-qPCR identifies the majority of positive IHC cases
(94.2%). In conclusion, both methods significantly correlate
(p<0,0001), but are only moderately concordant.
[0317] Table 8 is a contingency table displaying interrelations
between RT-qPCR-based and IHC-based subtypes in the FinHer study
population, wherein N is the number of observations, % (cell) is
the overall frequency of the 16 potential subtype combinations, %
(col.) is the distribution of RT-qPCR subtypes within IHC subtypes,
and % (row) is the distribution of IHC subtypes within subtypes
defined by the present application. Setting IHC subtypes as a
"reference standard", concordance is highest for TNBCs (85.71%) and
HER2-positives (79.43%) and lowest for luminal A (65.38%) and
luminal B (61.22%) tumors.
TABLE-US-00008 TABLE 8 Interrelations between RT- qPCR-based and
ICH-based subtypes in the FinHer study population. Tumor material
HER2+ Luminal-A Luminal-B subtype % % % % % % % % % Crosstabulation
N (cell) (col.) (row) N (cell) (col.) (row) N (cell) (col.) (row)
Tumor HER2+ 139 19.41 79.43 85.28 5 0.70 3.21 3.07 12 1.68 4.08
7.36 material Luminal-A 12 1.68 6.86 6.35 102 14.25 65.38 53.97 75
10.47 25.51 39.68 subtype Luminal-B 17 2.37 9.71 6.77 48 6.70 30.77
19.12 180 25.14 61.22 71.71 (FinHer) Triple 7 0.98 4.00 6.19 1 0.14
0.64 0.88 27 3.77 9.18 23.89 Negative Total 175 24.44 100.00 24.44
156 21.79 100.00 21.79 294 41.06 100.00 41.06 Tumor material Triple
Negative Total subtype % % % % % % Crosstabulation N (cell) (col.)
(row) N (cell) (col.) (row) Tumor HER2+ 7 0.96 7.69 4.29 163 22.77
22.77 100.00 material Luminal-A 0 0.00 0.00 0.00 189 26.40 26.40
100.00 subtype Luminal-B 6 0.84 6.59 2.39 251 35.06 35.06 100.00
(FinHer) Triple 78 10.89 85.71 69.03 113 15.78 15.78 100.00
Negative Total 91 12.71 100.00 12.71 716 100.00 100.00 100.00
Example 6: RT-qPCR- and IHC-Based Subtyping Mainly Differ in
Luminal B Assessment
[0318] The higher sensitivity of the RT-qPCR-based assessment of
Ki67 results in a substantial difference in determining luminal A
and luminal B patients, when compared to IHC-based assessment,
while using the same algorithm to combine ESR1, PGR, HER2 and Ki67
for subtyping.
[0319] Of the 189 breast cancer patients that were classified as
being luminal A by IHC methods, only 53.97% were also classified as
being luminal A by RT-qPCR, while 39.68% turned out to be luminal B
patients. In contrast, only 6.35% were reclassified as being
HER2-positive and 0% turned out to be triple-negative. Moreover, of
the 251 patients that were classified as being luminal B by IHC
methods, 71.71% were also classified as being luminal B by RT-qPCR,
while 19.12% turned out to be luminal A patients. In contrast,
6.77% were reclassified as being HER2-positive and 2.39% turned out
to be triple-negative. Conversely, only 61.22% of the tumors that
were classified as being luminal B by RT-qPCR were also classified
by conventional IHC as being luminal B.
[0320] These data illustrate the modest concordance observed
between the two assays for determining docetaxel-sensitive luminal
B tumors, which is mainly caused by the limited sensitivity and/or
robustness of the semi-quantitative assessment of Ki67 by IHC.
Example 7: High Ki67 Determined by RT-qPCR, but Low Ki67 Determined
by IHC are Associated with Higher Risk of Distant Metastasis
[0321] The approach of the present invention proves to have
additional discriminatory power when considering a population
comprising only ER-positive cases as determined by IHC. In this
case, Ki67 was found to be discordant between the IHC- and
RT-qPCR-based assays. As the determination of Ki67 by RT-qPCR and
IHC was concordant in 514 out of 686 available data sets (74.92%),
the number of samples for proving superiority of the mRNA based
assessment is limited (n=172).
[0322] However, despite the small number of samples, Ki67
positivity by RT-qPCR indicates an increased risk for developing
distant metastases in discordant cases. As shown in FIG. 21 A, at 5
years follow-up 5% of ER-positive patients with low Ki67 mRNA
expression developed distant metastasis, while 15% of patients
exhibiting high Ki67 mRNA expression suffered distant metastasis
(HR 3.315). This trend was unaffected by multivariate analysis
(FIG. 21 B).
[0323] This demonstrates that the higher sensitivity with respect
to Ki67 assessment of the approach of the present invention
provides additional prognostic information as compared to
conventional IHC staining.
Sequence CWU 1
1
21119DNAArtificial SequenceESR_F 1agagggtgcc aggctttgt
19222DNAArtificial SequenceESR_R 2aggatctcta gccaggcaca tt
22327DNAArtificial SequenceESR_P 3tttgaccctc catgatcagg tccacct
27421DNAArtificial SequenceHER2_F 4gaactcacct acctgcccac c
21521DNAArtificial SequenceHER2_R 5gacctgcctc acttggttgt g
21622DNAArtificial SequenceHER2_P 6ccaggaggtg cagggctacg tg
22722DNAArtificial SequenceKI67_F 7cgagacgcct ggttactatc aa
22825DNAArtificial SequenceKI67_R 8ggatacggat gtcacattca atacc
25923DNAArtificial SequenceKI67_P 9acggtcccca ctttcccctg agc
231027DNAArtificial SequencePGR_F 10aaacttcttg ataacttgca tgatctt
271125DNAArtificial SequencePGR_R 11caataacttc agacatcatt tctgg
251230DNAArtificial SequencePGR_P 12cgggactgga taaatgtatt
caagcagtac 301322DNAArtificial SequenceRAC_F 13gaatgtgcgg
aatctgtttg ag 221421DNAArtificial SequenceRAC_R 14tcgccaactg
gataaattgg a 211523DNAArtificial SequenceRAC_P 15actgagaatc
tccacccggc gca 231620DNAArtificial SequenceB2M_F 16gtatgcctgc
cgtgtgaacc 201722DNAArtificial SequenceB2M_R 17ggcatcttca
aacctccatg at 221825DNAArtificial SequenceB2M_P 18agtgggatcg
agacatgtaa gcagc 251919DNAArtificial SequenceCALM2_F 19aggaggcgaa
ttagtccga 192020DNAArtificial SequenceCALM2_R 20gctcttcagt
cagttggtca 202122DNAArtificial SequenceCALM2_P 21tcgcgtctcg
gaaaccggta gc 22
* * * * *