US-20260125490-A1 - Methods for Determining the Likelihood of Survival and for Predicting Likelihood of Metastasis in Cancer Patients

US20260125490A1US 20260125490 A1US20260125490 A1US 20260125490A1US-20260125490-A1

Abstract

The present invention relates generally to methods of accurately quantifying HER2 and/or p95 expression in subjects with a HER2 positive cancer and indicating the risk of brain relapse in such patients.

Inventors

Weidong Huang
Gundo Diedrich
LAURIE GOODMAN
Ali Mukherjee
Gordon Parry
Stephen J. Williams
Jodi Weidler
Jeff Sperinde
Mojgan Haddad
Michael Bates
John William Winslow
Xueguang Jin
Gerald J. Wallweber
JENNIFER W. COOK

Assignees

LABORATORY CORPORATION OF AMERICA HOLDINGS

Dates

Publication Date: 20260507
Application Date: 20250905

Claims (20)

1 - 39 . (canceled)
40 . A method for determining whether a subject with a HER2 positive cancer is likely to respond to treatment with a Her-2 pathway targeted therapy, comprising the steps of: (a) measuring the amount of p95-HER2 in a biological sample of the subject's cancer using a proximity assay using a p95-HER2-specific antibody, wherein the p95-HER2-specific antibody competes for binding to p95-HER2 with an antibody produced by a hybridoma cell line selected from the group consisting of hybridoma cell lines having ATCC accession number PTA-9738 (p95.D3.4), PTA-9739 (p95.D8.2), and PTA-9740 (p95.D9.1); (b) determining whether the amount of p95-HER2 in the subject's sample is below a p95-HER2 cutoff, wherein the p95-HER2 cutoff comprises at least one of (i) a level of p95-HER2 expression at least two-fold greater than control cancer cells lines having basal levels of p95-HER2 expression or (ii) a level of p95-HER2 expression corresponding to at least a top 30th-50th percentile of p95-HER2 expression in a reference cohort of subjects having the Her-2 positive cancer; and (c) indicating that the subject is more likely to respond to a Her-2 pathway targeted therapy targeted to the extracellular domain of Her-2 if the amount of p95-HER2 in the biological sample is below the p95-HER2 cutoff as compared to if the p95-HER2 in the biological sample is above the p95-HER2 cutoff.
41 . The method of claim 40 , wherein step (a) of measuring the amount of p95-HER2 in the biological sample comprises the steps of: (i) contacting the biological sample with a p95-HER2 binding composition that specifically binds to p95-HER2, wherein the p95-HER2 binding composition comprises the p95-HER2-specific antibody; (ii) contacting the p95-HER2 binding composition with a tagged binding composition, wherein the tagged binding composition comprises a molecular tag attached thereto via a cleavable linkage, and wherein the tagged binding composition specifically binds to the p95-HER2 binding composition; (iii) cleaving the cleavable linker of the tagged binding composition, thereby releasing the molecular tag; and (iv) quantitating the released molecular tag to determine the amount of p95-HER2 in the biological sample.
42 . The method of claim 40 , wherein the p95-HER2 cutoff comprises a level of p95-HER2 expression corresponding to at least a top 40th percentile of p95-HER2 expression in a reference cohort of subjects having the Her-2 positive cancer.
43 . The method of claim 40 , wherein the p95-HER2 cutoff comprises a level of p95-HER2 expression corresponding to at least a top 30th percentile of p95-HER2 expression in a reference cohort of subjects having the Her-2 positive cancer.
44 . The method of claim 40 , further comprising: (d) indicating that the subject is more likely to respond to a Her-2 pathway targeted therapy targeted to the intracellular domain of Her-2 if the amount of p95-HER2 in the biological sample is above the p95-HER2 cutoff as compared to a Her-2 pathway targeted therapy targeted to the extracellular domain of Her-2.
45 . The method of claim 44 , wherein the Her-2 pathway targeted agent targeted to the intracellular domain of Her-2 comprises a tyrosine kinase inhibitor.
46 . The method of claim 44 , wherein the Her-2 pathway targeted agent targeted to the intracellular domain of Her-2 comprises at least one of lapatinib, canertinib, mubritinib, AEE-788, HKI-272, BIBW-2992, or BMS-599626.
47 . A method of treating a subject having a HER2-positive cancer, the method comprising the steps of: selecting a subject who has been determined to have an amount of p95-HER2 in a biological sample of the subject's HER2-positive tumor above a predetermined cutoff by: (a) a p95-HER2 monoclonal antibody competes for binding the p95-HER2 protein with an antibody produced by a hybridoma cell line having ATCC accession number PTA-9740 (p95.D9.1), PTA-9738 (p95.D3.4), or PTA-9739 (p95.D8.2); (b) providing a binding compound that binds to the p95-HER2 monoclonal antibody, wherein the binding compound comprises a molecular tag covalently attached thereto via a cleavable linkage; (c) quantifying the amount of p95-HER2 protein in a sample from the subject by the steps of (i) incubating the sample with the p95-HER2 monoclonal antibody and the binding compound, (ii) treating the sample with a cleaving agent to release the molecular tag from the binding compound, and (iii) measuring the amount of released molecular tag as indicative of the amount of p95-HER2 protein in the sample; and (d) comparing the amount of p95-HER2 protein in the sample determined in step (c) with the predetermined cutoff, wherein the predetermined cutoff comprises at least one of (i) a level of p95-HER2 protein expression at least two-fold greater than a control cancer cell line having a basal level of p95-HER2 expression, (ii) a level of p95-HER2 protein expression corresponding to at least a top 30th percentile of p95-HER2 protein expression in a reference cohort of subjects having the HER2 positive cancer; and administering a HER2-acting agent and a second form of cancer treatment to the subject, wherein the p95-HER2 protein has a first amino acid corresponding to methionine 611 of HER2 protein.
48 . The method of claim 47 , wherein the predetermined cutoff comprises a level of p95-HER2 protein expression corresponding to at least a top 40th percentile of p95-HER2 protein expression in a reference cohort of subjects having the HER2 positive cancer.
49 . The method of claim 47 , wherein the second form of cancer treatment comprises at least one of a HER2-targeted small molecule drug, chemotherapy, or radiation therapy.
50 . The method of claim 47 , wherein the HER2-positive cancer of the subject has been characterized as HER2-positive based on at least one of an elevated level of HER2 gene expression, an elevated level of HER2 protein level, or HER2 gene amplification.
51 . The method of claim 47 , wherein the subject has been characterized as HER2-positive by quantifying the amount of HER2 in the sample using a quantitative immunoassay and determining if the amount of HER2 in the sample is above median amount of HER2 determined in the reference population of subjects having the HER2-positive cancer.
52 . The method of claim 47 , wherein the HER2-positive cancer of the subject comprises breast cancer.
53 . The method of claim 47 , wherein the HER2-acting agent is a monoclonal antibody, optionally, the monoclonal antibody is trastuzumab.
54 . A method for determining whether a subject with a HER2 positive cancer is likely to respond to treatment with a HER2 acting agent, more likely to have a long time course for unfavorable significant events related to HER2 positive cancer to occur, and/or less likely to have an unfavorable significant event in the time course of disease-during the treatment with the HER2 acting agent, wherein the HER2 acting agent is a HER2 antibody or a small molecule kinase inhibitor, comprising: (a) providing a biological sample from the subject's cancer; (b) measuring the amount of HER3 in the biological sample using a HER3 antibody in a proximity assay, wherein the HER3 antibody competes for binding to HER3 with an antibody selected from the group consisting of (i) a monoclonal antibody comprising (a) a light chain variable region comprising CDR1, CDR2 and CDR3 having the sequences as set forth in SEQ ID NOs: 13, 14 and 15, respectively, and (b) a heavy chain variable region comprising CDR1, CDR2 and CDR3 having the sequences as set forth in SEQ ID NOs: 16, 17 and 18, respectively; or (ii) a monoclonal antibody comprising (a) a light chain variable region comprising CDR1, CDR2 and CDR3 having the sequences as set forth in SEQ ID NOs: 19, 20 and 21, respectively, and (b) a heavy chain variable region comprising CDR1, CDR2 and CDR3 having the sequences as set forth in SEQ ID NOs: 22, 23 and 24, respectively; (c) determining that the subject is more likely to respond to the HER2 acting agent, more likely to have a long time course for unfavorable significant events to occur, and/or less likely to have an unfavorable significant event in the time course of disease during the treatment with the HER2 acting agent if the amount of HER3 in the biological sample is below a HER3 cutoff than if the amount of HER3 in the biological sample is above the HER3 cutoff, the HER3 cutoff having been determined by positional scanning analysis of a cohort of subjects having HER2 positive cancer of the same kind as the subject.
55 . The method of claim 54 , wherein the cutoff is a median of HER3 levels in the cohort of subjects having HER2 positive cancer of the same kind as the subject, wherein optionally the likeliness to respond to the HER2 acting agent is measured by at least one of overall survival, time to progression, disease-free survival, progression-free survival (PFS), time to distant reoccurrence (TTDR), hazard ratio, or objective tumor response or clinical benefit using the RECIST criteria.
56 . The method of claim 54 , wherein measuring the amount of HER3 in the biological sample comprises measuring at least one of total HER3 protein, HER3 homodimers, or HER3 heterodimers.
57 . The method of claim 54 , wherein the proximity assay comprises the steps of: a) contacting the biological sample with the HER3 antibody; b) contacting the HER3 antibody with a tagged antibody, wherein the tagged antibody comprises a molecular tag attached thereto via a cleavable linkage, and wherein the tagged antibody is capable of specifically binding to the HER3 antibody; c) cleaving the cleavable linker of the tagged antibody, thereby releasing the molecular tag; and d) quantitating the released molecular tag to determine the amount of HER3 protein in the biological sample.
58 . The method of claim 54 , further comprising: (i) measuring the amount of p95-HER2 in the biological sample; (ii) determining whether the amount of p95-HER2 in the biological sample is above a p95-HER2 cutoff; and (iii) determining that the subject is more likely to respond to the HER2 acting agent, more likely to have a long time course for unfavorable significant events to occur during treatment with the HER2 acting agent, and/or less likely to have an unfavorable significant event during treatment with the HER2 acting agent if the amount of p95-HER2 in the biological sample is below the p95-HER2 cutoff than if the amount of HER3, the amount of p95-HER2, or both, in the biological sample are above their respective cutoffs.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a continuation of U.S. patent application Ser. No. 17/855,437, filed Jun. 30, 2022, which is a continuation of U.S. patent application Ser. No. 16/166,878, filed Oct. 22, 2018, which is a continuation-in-part application of U.S. patent application Ser. No. 13/476,735, filed May 21, 2012, which claims the benefit of and priority under 35 U.S.C. § 119 (c) to U.S. Provisional Patent Application Ser. No. 61/488,028, filed May 19, 2011. These applications are each incorporated herein by reference in their entireties. This application is a continuation of U.S. patent application Ser. No. 17/855,437, filed Jun. 30, 2022, which is a continuation of U.S. patent application Ser. No. 16/166,878, filed Oct. 22, 2018, which is a continuation-in-part application of U.S. patent application Ser. No. 14/737,742, filed Jun. 12, 2015, and issued as U.S. Pat. No. 10,273,308 on Apr. 30, 2018, which is a continuation of U.S. patent application Ser. No. 13/911,329, filed Jun. 6, 2013, and issued as U.S. Pat. No. 9,081,019 on Jul. 14, 2015, which is a divisional of U.S. patent application Ser. No. 12/629,037, filed Dec. 1, 2009, and issued as U.S. Pat. No. 8,470,542 on Jun. 25, 2013, which claims the benefit of and priority under 35 U.S.C. § 119 (c) to U.S. Provisional Application No. 61/118,975, filed Dec. 1, 2008, U.S. Provisional Application No. 61/182,282, filed May 29, 2009, and U.S. Provisional Application No. 61/187,960, filed Jun. 17, 2009. These applications are each incorporated herein by reference in their entireties. This application is a continuation of U.S. patent application Ser. No. 17/855,437, filed Jun. 30, 2022, which is a continuation-in-part application of U.S. patent application Ser. No. 15/681,895, filed Aug. 21, 2017, which is a continuation of U.S. patent application Ser. No. 14/802,170, filed Jul. 17, 2015, and issued as U.S. Pat. No. 9,766,242 on Sep. 19, 2017, which is a continuation of U.S. patent application Ser. No. 13/670,508, filed Nov. 7, 2012, and issued as U.S. Pat. No. 9,110,066 on Aug. 18, 2015, which is a divisional application of U.S. patent application Ser. No. 12/688,798, filed Jan. 15, 2010, and issued as U.S. Pat. No. 8,349,574 on Jan. 8, 2013, which claims the benefit of and priority under 35 U.S.C. § 119 (c) to U.S. Provisional Application No. 61/176,630, filed May 8, 2009, U.S. Provisional Application No. 61/187,962, filed Jun. 17, 2009, and U.S. Provisional Application No. 61/145,029, filed Jan. 15, 2009. These applications are each incorporated herein by reference in their entireties. FIELD The present invention relates generally to methods of accurately quantifying total HER2 or p95 expression in patients with a HER2 positive cancer, such as advanced breast cancer, and correlating HER2 or p95 expression with the risk of brain relapse in such patients. BACKGROUND Brain metastases accompanying breast cancer are associated with particularly poor prognosis. Brain metastases seriously affect quality of life and are relatively resistant to systemic therapies. Breast cancer is the second most common cause of brain metastases. Though the biological basis is not yet fully understood, patients with HER2-positive breast cancer are at a particularly high risk of brain metastases. However, currently there are no clinical or biological features that have been shown to consistently associate with a propensity to develop brain relapse in HER2-positive advanced breast cancer patients. Similarly, no robust molecular marker to predict brain relapse has been developed. Current methodologies for determining of HER2 status include immunohistochemistry (IHC) to detect HER2 protein overexpression, fluorescence in situ hybridization (FISH), or chromogenic in situ hybridization to detect amplification of the HER2 gene. However, considerable controversy still exists regarding the accuracy, reliability, and inter-observer variability of these assay methods. For example, the assessment of HER2 expression by IHC is inherently subjective and semi-quantitative (scored as 0, 1+, 2+, 3+). The FISH test, where HER2 gene copy number is counted, is more quantitative analytically, but multiple clinical studies have failed to demonstrate a relationship between HER2 gene copy number and response to clinical treatment. Using currently available techniques, it is estimated that approximately 20% of HER2 testing may be inaccurate. Currently, the standard component of systemic therapy in HER2-positive breast cancer patients is trastuzumab, a monoclonal antibody against the extracellular domain of the HER2 receptor. However, due to a high molecular weight (approx. 145,000 Da), and physical and chemical properties, trastuzumab does not cross the blood-brain barrier and is ineffective in preventing and treating brain metastases. In addition, a subgroup of HER2-overexpressing tumors also have p95 HER2 (p95), an N-terminal truncated version of HER2 that has shed the ecto