Methods and compositions for prediction of therapeutic efficacy of cancer treatments and cancer prognosis

Patent metadata

Field	Value
Publication number	US-12188097-B2
Application number	US-202318330112-A
Country	US
Kind code	B2
Filing date	Jun 6, 2023
Priority date	Apr 15, 2015
Publication date	Jan 7, 2025
Grant date	Jan 7, 2025

Abstract

The invention generally relates to methods and compositions for the prediction of therapeutic efficacy of cancer treatments and the prognosis of cancer. The invention discloses markers that are associated with favorable and unfavorable outcomes, respectively, in certain cancer treatments and are useful as prognostic markers for cancer. Methods involving these markers are disclosed for predicting cancer therapy benefit and prognosing clinical outcome for cancer patients.

First claim

The invention claimed is:

1. A method of treating a human cancer patient having a CLDN18.2-positive tumor, said method comprising
a. determining or having determined a genotype for at least one single-nucleotide polymorphism in a sample obtained from the cancer patient, the at least one single-nucleotide polymorphism including FCGR3A rs396991;
b. identifying the cancer patient as a likely responder to treatment with an anti-CLDN18.2 antibody based on the patient having a heterozygous FCGR3A rs396991 [TG] genotype or a homozygous FCGR3A rs396991 [TT] genotype; and
c. administering the anti-CLDN18.2 antibody to the human cancer patient.

2. The method of claim 1 , wherein the antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 or an antigen-binding fragment thereof and a light chain having the amino acid sequence of SEQ ID NO: 24 or an antigen-binding fragment thereof.

3. The method of claim 1 , wherein the antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 and a light chain having the amino acid sequence of SEQ ID NO: 24.

4. The method of claim 3 , wherein the cancer is gastroesophageal cancer.

5. The method of claim 4 , wherein the cancer is metastatic gastroesophageal cancer.

6. The method of claim 4 , wherein the cancer is an advanced adenocarcinoma of the stomach or the lower esophagus.

7. The method of claim 1 , further comprising determining or having determined a genotype for at least one additional single-nucleotide polymorphism in the sample, wherein the at least one additional single-nucleotide polymorphism is MUC1 rs4072037, DNMT3A rs1550117, SMAD4 rs12456284, EGF rs4444903, CDH1 rs16260, or ERCC1 rs11615.

8. The method of claim 1 , wherein the sample is a blood sample.

9. A method of treating a human cancer patient, said method comprising:
administering an anti-CLDN18.2 antibody to the patient, wherein the patient has been determined to have a heterozygous FCGR3A rs396991 [TG] genotype or a homozygous FCGR3A rs396991 [TT] genotype.

10. The method of claim 9 , wherein the anti-CLDN18.2 antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 or an antigen-binding fragment thereof and a light chain having the amino acid sequence of SEQ ID NO: 24 or an antigen-binding fragment thereof.

11. The method of claim 9 , wherein the anti-CLDN18.2 antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 and a light chain having the amino acid sequence of SEQ ID NO: 24.

12. The method of claim 11 , wherein the cancer is gastroesophageal cancer.

13. The method of claim 12 , wherein the cancer is metastatic gastroesophageal cancer.

14. The method of claim 12 , wherein the cancer is an advanced adenocarcinoma of the stomach or the lower esophagus.

15. The method of claim 9 , wherein the cancer is gastroesophageal cancer.

16. The method of claim 15 , wherein the cancer is metastatic gastroesophageal cancer.

17. The method of claim 9 , wherein the patient has been determined to have a homozygous MUC1 rs4072037 [AA] genotype, a heterozygous DNMT3A rs1550117 [GA] genotype, a heterozygous SMAD4 rs12456284 [GA] genotype, a homozygous EGF rs4444903 [AA] genotype, a homozygous CDH1 rs16260 [AA] genotype, or a homozygous ERCC1 rs11615 [TT] genotype.

18. A method of detecting a state of a single-nucleotide polymorphism (SNP) in a human patient having a CLDN18.2-positive cancer, said method comprising:
obtaining a sample from a patient having a CLDN18.2-positive cancer, the sample comprising genomic DNA, wherein the patient has been determined to have a CLDN18.2-positive cancer; and
detecting which nucleotide is present at both alleles of FCGR3A rs396991 in the sample, wherein the detecting comprises (i) contacting a detection reagent with a target FCGR3A rs396991-containing nucleic acid and (ii) detecting hybridization between the detection reagent and the target FCGR3A rs396991-containing nucleic acid, wherein the state of the FCGR3A rs396991 SNP is homozygous [GG], homozygous [TT], or heterozygous [TG];
identifying the patient as a likely responder to treatment with an anti-CLDN18.2 antibody based on the patient having a heterozygous FCGR3A rs396991 [TG] genotype or a homozygous FCGR3A rs396991 [TT] genotype; and
administering the anti-CLDN18.2 antibody to the patient.

19. The method of claim 18 , wherein the anti-CLDN18.2 antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 or an antigen-binding fragment thereof and a light chain having the amino acid sequence of SEQ ID NO: 24 or an antigen-binding fragment thereof.

20. The method of claim 18 , wherein the anti-CLDN18.2 antibody comprises a heavy chain having the amino acid sequence of SEQ ID NO: 17 or 51 and a light chain having the amino acid sequence of SEQ ID NO: 24.

21. The method of claim 20 , wherein the cancer is gastroesophageal cancer.

22. The method of claim 21 , wherein the cancer is metastatic gastroesophageal cancer.

23. The method of claim 21 , wherein the cancer is an advanced adenocarcinoma of the stomach or the lower esophagus.

24. The method of claim 18 , further comprising detecting which nucleotide is present at both alleles of at least one additional single-nucleotide polymorphism (SNP) in the sample, wherein the detecting comprises (i) contacting a detection reagent with a target SNP-containing nucleic acid and (ii) detecting hybridization between the detection reagent and the target SNP-containing nucleic acid;
wherein the at least one additional SNP is MUC1 rs4072037, DNMT3A rs1550117, SMAD4 rs12456284, EGF rs4444903, CDH1 rs16260, or ERCC1 rs11615.

Assignees

• Astellas Pharma Inc
• Tron Translationale Onkologie An Der Univ Der Johannes Gutenberg Univ Mainz Ggmbh
• Tron Translationale Onkologie An Der Univ Der Johannes Gutenberg Univ Mainz

Inventors

• Sahin Ugur
• Tureci Ozlem
• Maurus Daniel

Classifications

• C12Q2600/106

  Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q2600/118

  Prognosis of disease development · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title