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US-20260125767-A1 - HER2 HETEROGENEITY AS A BIOMARKER IN CANCER

US20260125767A1US 20260125767 A1US20260125767 A1US 20260125767A1US-20260125767-A1

Abstract

A method for predicting responsiveness to a HER2-directed therapy by assessing HER2 heterogeneity in a tumor includes contacting a sample of the tumor with a biomarker-specific reagent that specifically binds to HER2 protein and detecting HER2 protein in the sample, contacting the sample of the tumor with a first nucleic acid probe that specifically binds HER2 genomic DNA and detecting HER2 gene amplification status in the sample, contacting the sample of the tumor with a second nucleic acid probe that specifically binds HER2 RNA and detecting HER2 RNA status in the sample scoring the HER2 protein (IHC), HER2 gene (DISH), and HER2 RNA (RNA-ISH), predicting that the tumor is responsive to the HER2-directed therapy if the tumor reveals a first foci having a first score and a second score, in which the first score and the second score are not the same.

Inventors

  • Adrian E. Murillo
  • Hiro Nitta
  • Donald G. Munroe
  • Amy A. LO
  • Takeshi Kuwata
  • Akio KAITO
  • Atsushi Ochiai

Assignees

  • GENENTECH, INC.
  • NATIONAL CANCER CENTER
  • VENTANA MEDICAL SYSTEMS, INC.

Dates

Publication Date
20260507
Application Date
20251231

Claims (20)

  1. 1 . A method for predicting responsiveness to a HER2-directed therapy by assessing HER2 heterogeneity in a tumor, comprising: contacting a sample of the tumor with a biomarker-specific reagent that specifically binds to HER2 protein and detecting HER2 protein in the sample, contacting the sample of the tumor with a first nucleic acid probe that specifically binds HER2 genomic DNA, and detecting HER2 gene amplification status in the sample, contacting the sample of the tumor with a second nucleic acid probe that specifically binds HER2 RNA, and detecting HER2 RNA status in the sample, scoring the HER2 protein (IHC), HER2 gene (DISH), and HER2 RNA (RNA-ISH), wherein scoring is categorized as: Group A for samples exhibiting IHC 3+, DISH+, and RNA-ISH+, Group B for samples exhibiting IHC 3+, DISH−, and RNA-ISH−, Group C for samples exhibiting IHC 2+, DISH+, and RNA-ISH+, Group D for samples exhibiting IHC 2+, DISH−, and RNA-ISH−, Group E for samples exhibiting IHC 0, 1+, DISH+, and, RNA-ISH+, and Group F for samples exhibiting IHC 0, 1+, DISH−, and RNA-ISH−, predicting that the tumor is responsive to the HER2-directed therapy if the tumor reveals a first foci having a first score selected from Group A to Group F and a second foci having a second score selected from Group A to Group F, wherein the first score and the second score are not the same.
  2. 2 . The method of claim 1 , wherein the contacting a sample of the tumor with a biomarker-specific reagent and the contacting the sample of the tumor with a first nucleic acid probe are both performed on a first section of the sample and the contacting the sample of the tumor with a second nucleic acid probe is performed on a second section of the sample, wherein the second section is a serial section of the first section.
  3. 3 . The method of claim 1 , wherein the contacting a sample of the tumor with a biomarker-specific reagent is performed on a first section of the sample, the contacting the sample of the tumor with a first nucleic acid probe is performed on a second section of the sample, and the contacting the sample of the tumor with a second nucleic acid probe is performed on a third section of the sample, wherein the first, the second, and the third sections are serial sections.
  4. 4 . The method of claim 1 , further comprising dissecting IHC 0, 1+ tumor cells from the sample and determining HER2 RNA levels in the dissected tumor cells.
  5. 5 . The method of claim 4 , wherein the dissecting is by microdissection or mesodissection.
  6. 6 . The method of claim 4 , wherein the determining is by RT-PCR or qRT-PCR.
  7. 7 . The method of claim 1 , wherein the sample is a surgical tissue sample.
  8. 8 . The method of claim 1 , wherein the tumor is a solid tumor selected from the group consisting of gastric cancer, breast cancer, lung cancer, salivary gland cancer, ovarian cancer, pancreatic cancer, endometrial cancer, colorectal cancer, oesophageal cancer, bladder cancer, biliary tract cancer, uterine cervical cancer, and head and neck squamous cell cancer.
  9. 9 . The method of claim 8 , wherein the tumor is gastric cancer.
  10. 10 . The method of claim 9 , wherein the Group E samples are located at mucosal and invasive cancer areas of submucosa and disrupted muscularis propria.
  11. 11 . The method of claim 9 , wherein the tumor sample is scored as invasive if the first score is Group F and the second score is Group E.
  12. 12 . The method of claim 1 , wherein the HER-2 directed therapy is selected from the group consisting of trastuzumab, trastuzumab emtansine, pertuzumab, neratinib, and lapatinib.
  13. 13 . The method of claim 1 , wherein the predicting step is based on scores obtained from an invasive region of the tumor.
  14. 14 . A method for predicting responsiveness to a HER2-directed therapy by assessing HER2 heterogeneity in a tumor, comprising contacting a sample of the tumor with the biomarker-specific reagent that specifically binds to HER2 protein and detecting HER2 protein in the sample, and contacting the sample of the tumor with a nucleic acid probe that specifically binds HER2 RNA and detecting HER2 RNA status in the sample, scoring the HER2 protein (IHC) and HER2 RNA (RNA-ISH), wherein the scoring is categorized as: Group A for samples exhibiting IHC 3+ and RNA-ISH+, Group B for samples exhibiting IHC 3+ and RNA-ISH−, Group C for samples exhibiting IHC 2+ and RNA-ISH+, Group D for samples exhibiting IHC 2+ and RNA-ISH−, Group E for samples exhibiting IHC 0, 1+ and RNA-ISH+, and Group F for samples exhibiting IHC 0, 1+ and RNA-ISH−, and the predicting that the tumor is responsive to the HER2-directed therapy if the tumor reveals a first foci having a first score selected from Group A to Group F and a second foci having a second score selected from Group A to Group F, wherein the first score and the second score are not the same.
  15. 15 . The method of claim 14 , wherein the contacting a sample of the tumor with the biomarker-specific reagent and the contacting the sample of the tumor with the nucleic acid probe are performed on a same section of the sample.
  16. 16 . A method of identifying HER2 heterogeneity in a tumor, comprising contacting a sample of the tumor with a biomarker-specific reagent that specifically binds to HER2 protein and detecting HER2 protein in the sample, contacting the sample of the tumor with a nucleic acid probe that specifically binds HER2 RNA and detecting HER2 RNA status in the sample, wherein, if the HER2 protein is not homogenously detected, evaluating the HER2 RNA status at an invasive margin, identifying the HER2 heterogeneity, if the HER2 RNA status is negative at the invasive margin.
  17. 17 . The method of claim 16 , wherein the contacting a sample of the tumor with a biomarker-specific reagent is performed on a first section of the sample and the contacting the sample of the tumor with a nucleic acid probe is performed on a second section of the sample, wherein the first and the second sections are serial sections.
  18. 18 . The method of claim 16 , wherein the tumor is a solid tumor selecting from the group consisting of gastric cancer, breast cancer, lung cancer, salivary gland cancer, ovarian cancer, pancreatic cancer, endometrial cancer, colorectal cancer, oesophageal cancer, bladder cancer, biliary tract cancer, uterine cervical cancer, and head and neck squamous cell cancer.
  19. 19 . The method of claim 18 , wherein the tumor is gastric cancer.
  20. 20 . The method of claim 18 , wherein the invasive margin is located at mucosal and invasive cancer areas of submucosa and disrupted muscularis propria.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a Divisional Application of U.S. application Ser. No. 17/100,357, filed 20 Nov. 2020, which is a By-Pass Continuation based on International Patent Application No. PCT/EP2019/062972, filed 20 May 2019, which claims priority to U.S. Provisional Patent Application No. 62/674,566, filed May 21, 2018, the content of which is incorporated herein by reference in its entirety. BACKGROUND 1. Field The present disclosure relates to methods of measuring tissue heterogeneity and using the same as a biomarker and predictive tool in the diagnosis and treatment of gastric cancer. 2. Description of Related Art HER2 (human epidermal growth factor 2) is a membrane-bound tyrosine kinase in the ERBB family. The HER2 monomeric protein has three main regions: the extracellular amino-terminal region comprising four domains (I-IV), the hydrophobic transmembrane domain and the carboxy-terminal kinase domain comprising the juxtamembrane domain, tyrosine kinase and C-terminal tail with autophosphorylation sites. It has no known ligand, and heterodimerizes with other members of ERBB family on ligand binding to stimulate various intracellular signal transduction pathways involved in cell growth. HER2 protein overexpression, gene amplification and mutation have been identified in a variety of cancer types. Evaluation of HER2 status is critical as a companion diagnostic for anti-HER2 targeted therapeutics. There are two different strategies for targeting HER2 that have been successfully employed in the clinic: (1) antibodies directed against the extracellular domain of the receptor and (2) small molecule Tyrosine Kinase Inhibitors (TKIs) acting on the intracellular kinase domain. Several agents targeting HER2-positive malignancies have been approved, including trastuzumab and pertuzumab (humanized monoclonal antibodies); lapatinib and afatinib (dual EGFR/HER2 inhibitors); and ado-trastuzumab emtansine (T-DMI) (an antibody-cytotoxic conjugate that combines the HER2-targeting antitumour property of trastuzumab with the cytotoxic microtubule-depolymerizing compound DM1). The presence of HER2 alterations in diverse cancers provides novel therapeutic opportunities. U.S. 2017/0082627 discloses methods for predicting the response to a HER2-directed therapy and for scoring a breast cancer tumor sample including contacting the sample with an antibody that specifically binds HER2 protein and detecting presence and/or amount of HER2 protein and contacting the sample with a nucleic acid probe that specifically binds to HER2 genomic DNA and detecting presence and/or amount of HER2 genomic DNA (such as HER2 gene copy number). Methods may also include detection of a centromere nucleic acid (such as chromosome 17 centromere DNA) and contacting the sample with an antibody that specifically binds ER protein and detecting presence and/or amount of ER protein in the same sample. Nishida et al. (Gastric Cancer, 2015 July;18 (3): 458-66. Epub 2014 Jun. 11) discloses, using the tissue microarray technique, the HER2 status of each gastric cancer cases may be evaluated by immunohistochemistry (IHC), brightfield dual-color in situ hybridization (DISH), and gene-protein assay (GPA), which allows the simultaneous analysis of HER2 protein and gene status on a single slide. Intratumoral phenotypic and genotypic heterogeneity may be evaluated by comparing the HER2 statuses of two tissue cores from each case. The solution to this technical problem is provided by the embodiments characterized in the claims. BRIEF SUMMARY The present disclosure generally relates to methods of identifying HER2 heterogeneity based on HER2 protein and one or more of HER2 RNA and HER2 gene amplification. The present disclosure also relates to methods of identifying HER2 protein-negative and HER2 RNA-positive tumor cells that are mainly localized at the invasive regions of the tumor, and thus this sub-population of HER2-positive tumor cells may be a good region-of-interest (ROI) to focus on for diagnosis. The present application relates to methods for predicting responsiveness to a HER2-directed therapy by assessing HER2 heterogeneity in a tumor, comprising contacting a sample of the tumor with a biomarker-specific reagent that specifically binds to HER2 protein and detecting HER2 protein in the sample, and contacting the sample of the tumor with a nucleic acid probe that specifically binds HER2 RNA and detecting HER2 RNA status in the sample scoring the HER2 protein (IHC), and HER2 RNA (RNA-ISH), in which scoring is categorized as: Group A for samples exhibiting IHC 3+ and RNA-ISH+,Group B for samples exhibiting IHC 3+ and RNA-ISH−,Group C for samples exhibiting IHC 2+ and RNA-ISH+,Group D for samples exhibiting IHC 2+ and RNA-ISH−,Group E for samples exhibiting IHC 0, 1+ and RNA-ISH+, andGroup F for samples exhibiting IHC 0, 1+ and RNA-ISH−, predicting that the tumor is responsive to the HER2-directed therapy if the tumor reveals