Methods and compositions for diagnosing and treating, germline mismatch repair deficiencies, lynch syndrome and assessing germline risks of cancer

Patent metadata

Field	Value
Publication number	US-12331345-B2
Application number	US-202217674400-A
Country	US
Kind code	B2
Filing date	Feb 17, 2022
Priority date	Feb 17, 2021
Publication date	Jun 17, 2025
Grant date	Jun 17, 2025

Abstract

Heritable pathogenic variants in the mismatch repair (MMR) pathway, also known as Lynch Syndrome (LS), can lead to the development of colon cancer and other cancers. Following mismatch, a complex of proteins consisting of MLH1, MSH2, MSH6 and PMS2 translocate into the nucleus to signal recruitment of repair mechanisms. Flow cytometry-based, functional variant assays (FVAs), were developed to determine whether variants in these MMR repair genes and/or other related genes would augment the nuclear translocation of MLH1 and MSH2 and downstream nuclear phosphorylation of ATM and ATR in response to DNA mismatches. Each assay distinguished pathogenic variants in MMR repair genes (MLH1, MSH2, PMS2 and MSH6) from benign controls. The combination of multiple assays provided robust separation between heterozygous pathogenic variant carriers and benign controls. The ability to produce distinct molecular phenotypes by these assays suggest FVA assays of MMR pathways could be used to identify LS and associated risk of colon and other cancers and could act as an adjunct to MMR gene sequencing panels in categorizing variants.

First claim

The invention claimed is:

1. A method for screening a population of cells from a human subject for functionality of the mismatch repair (MMR) pathway, the method comprising:
(a) contacting the population of cells with a DNA mismatch-inducing agent;
(b) measuring via flow-cytometry in the population of cells at least one functional activity of the mismatch repair (MMR) pathway, wherein the at least one functional activity comprises nuclear localization of mutL homologue 1 (MLH1) and mutS homologue 2 (MSH2);
(c) comparing the nuclear localization of MLH1 and MSH2 in the population of cells contacted with the DNA mismatch-inducing agent with the nuclear localization of MLH1 and MSH2 from a control population of cells treated with the DNA mismatch-inducing agent and having a normal functioning MMR pathway; and
(d) categorizing the MMR pathway as having loss of function or as having a partial-loss of function, based on the comparing step (c);
wherein having loss of function or partial-loss of function of the MMR pathway indicates the subject as having Lynch Syndrome and one or more preventative interventions selected from colonoscopy, chemotherapy, chemoprevention, radiotherapy, immunotherapy, gene therapy, or surgery is administered to the subject having Lynch Syndrome.

2. The method of claim 1 , wherein the population of cells comprises an introduced genetic variant or an expression plasmid.

3. The method of claim 1 , wherein the DNA mismatch inducing agent is selected from the group consisting of SN1 DNA alkylators, 8-oxoguanine, 6-thioguanine (6-TG), fluoropyrimidines, cisplatin, radiomimetic agents, radiation, and UV light.

4. The method of claim 3 , wherein:
(a) the SN1 DNA alkylators are selected from the group consisting of N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), N-methyl-N-nitroso-p-toluenesulfonamide, methylnitrosourea (MNU), procarbazine, and temozolomide;
(b) the fluoropyrimidines are selected from the group consisting of 5-fluorouracil (FU), and 5-fluoro-2′-deoxyuridine (FdU); and
(c) the radiomimetic agents are selected from the group consisting of Diepoxybutane, Mitomycin C, and Bleomycin.

5. The method of claim 4 , wherein the SN1 DNA alkylator is N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), or N-methyl-N-nitroso-p-toluenesulfonamide, or both N-methyl-N′-nitro-N-nitrosoguanidine and N-methyl-N-nitroso-p-toluenesulfonamide.

6. The method of claim 1 , wherein the at least one functional activity of the MMR pathway further comprises BRCA1 associated RING domain 1 (BARD1) nuclear localization, postmeiotic segregation increased 2 (PMS2) nuclear localization, BRCA2 DNA repair associated (BRCA2) nuclear localization, p53 phosphorylation, ATM serine/threonine kinase (ATM) phosphorylation, or ATR serine/threonine kinase (ATR) phosphorylation.

Assignees

• Morgan And Mendel Genomics Inc
• Albert Einstein College Medicine

Inventors

• Ostrer Harry
• Loke Johnny C
• Alim Ishraq

Classifications

• G01N33/57535

  of the large intestine, e.g. colon, rectum or anus · CPC title

• G01N33/5758

  involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites · CPC title

• C12Q1/6804

  Nucleic acid analysis using immunogens (immunoassay G01N33/53) · CPC title

• G01N33/5035

  on sub-cellular localization · CPC title

• G01N15/14

  Optical investigation techniques, e.g. flow cytometry · CPC title