Frameshift mutations in peripheral blood as a biomarker for surveillance of lynch syndrome

BACKGROUND

Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline mutations in DNA mismatch repair (MMR) genes, which lead to high microsatellite instability (MSI-H) and frameshift mutations (FSMs) at coding mononucleotide repeats (cMNRs) in the genome. Recurrent FSMs in these regions are thought to play a central role in the increased risk of various cancers. However, there are no biomarkers currently available for the surveillance of MSI-H-associated cancers.

METHODS

An FSM-based biomarker panel was developed and validated by targeted next generation sequencing of supernatant DNA from cultured MSI-H colorectal cancer cells. This supported selection of 122-FSM targets as potential biomarkers. This biomarker panel was then tested using matched tumor, adjacent normal tissue, and buffy coat (53 samples), and blood-derived cell-free DNA (cfDNA; 38 samples) obtained from 45 cases of MSI-H/MMR deficient (MMRd) patients/carriers. cfDNA from 84 healthy individuals was also sequenced to assess background noise.

RESULTS

Recurrent FSMs at cMNRs were detectable not only in tumors, but also in cfDNA from MSI-H/MMRd cases including a LS carrier with a varying range of target detection (up to 85.2%), whereas they were virtually undetectable in healthy individuals. ROC analysis showed high sensitivity and specificity (AUC = 0.94) of the investigated panel.

CONCLUSIONS

We demonstrated that FSMs can be detected in cfDNA from MSI-H/MMRd cases and asymptomatic carriers. The 122-target FSM panel described here has promise as a tool for improved surveillance of MSI-H/MMRd carriers with the potential to reduce the frequency of invasive screening methods for this high-cancer-risk cohort.

Organoids and metastatic orthotopic mouse model for mismatch repair-deficient colorectal cancer

Background

Genome integrity is essential for the survival of an organism. DNA mismatch repair (MMR) genes (e.g., MLH1, MSH2, MSH6, and PMS2) play a critical role in the DNA damage response pathway for genome integrity maintenance. Germline mutations of MMR genes can lead to Lynch syndrome or constitutional mismatch repair deficiency syndrome, resulting in an increased lifetime risk of developing cancer characterized by high microsatellite instability (MSI-H) and high mutation burden. Although immunotherapy has been approved for MMR-deficient (MMRd) cancer patients, the overall response rate needs to be improved and other management options are needed.

Methods

To better understand the biology of MMRd cancers, elucidate the resistance mechanisms to immune modulation, and develop vaccines and therapeutic testing platforms for this high-risk population, we generated organoids and an orthotopic mouse model from intestine tumors developed in a Msh2-deficient mouse model, and followed with a detailed characterization.

Results

The organoids were shown to be of epithelial origin with stem cell features, to have a high frameshift mutation frequency with MSI-H and chromosome instability, and intra- and inter-tumor heterogeneity. An orthotopic model using intra-cecal implantation of tumor fragments derived from organoids showed progressive tumor growth, resulting in the development of adenocarcinomas mixed with mucinous features and distant metastasis in liver and lymph node.

Conclusions

The established organoids with characteristics of MSI-H cancers can be used to study MMRd cancer biology. The orthotopic model, with its distant metastasis and expressing frameshift peptides, is suitable for evaluating the efficacy of neoantigen-based vaccines or anticancer drugs in combination with other therapies.

Abstract 6518: Time course genomic characterization reveals progressive accumulation of mutations during tumor development in a Lynch syndrome mouse model

DNA mismatch repair (MMR) genes (e.g., MLH1, MSH2, MSH6, PMS2, and EPCAM) play an important role in maintaining genomic stability during DNA replication and recombination. Deficiency in MMR resulting from mutations in these genes leads to mutations in microsatellite regions throughout the genome (microsatellite instability; MSI) and in cancer driver oncogenes or tumor suppressor genes, which accumulate over time and eventually lead to cancer formation. Monoallelic germline mutation in MMR genes causes Lynch syndrome (LS). Among LS-related cancer types, the lifetime risk for colorectal cancer (CRC) is the highest (~80%). Frameshift mutations (FSMs) in coding microsatellites produce neoantigens, which have been shown to elicit immune responses. It was thus postulated that they can serve as vaccine targets. To develop a prophylactic vaccine and prevention strategy for this high-risk population, we characterized a LS mouse model (Msh2LoxP/LoxP;Villin-Cre) to determine whether these mice recapitulate the human LS oncogenic process. We found that tumor development was already notable at 7-8 months of age and median survival was 11.5 months. Histopathological analysis showed that tumors were adenoma or adenocarcinoma mixed with mucinous features. Using a targeted sequencing approach, a panel of FSMs in mononucleotide regions were identified in both tumors and histologically normal mucosa, suggesting that Msh2 deletion and FSMs were not sufficient for tumor development. In addition, Apc, Ctnnb, and Trp53 mutations were also observed with low frequency in organoids derived from these tumors, indicating that other driver mutations may be required for tumor initiation and progression, and most FSMs detected in tumors and mucosa were probably passenger mutations. To determine if fecal samples can be used to monitor the FSM load, fecal DNA from different time points was sequenced. We found that FSMs can be detected at 1month of age although the number of FSMs was relatively low compared to that from older mice, indicating that FSMs accumulate over time. MSI detection via fragment analysis confirmed that these tumors were MSI-H. Interestingly, mucosa and fecal samples from a time course study showed progressive increase in microsatellite instability, suggesting the possibility of using MSI score for disease monitoring. Our preliminary data indicates that combined fecal FSM status and MSI score can be potentially used as a biomarker to monitor the tumor development and disease progression for LS colorectal cancer.

Funded by the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261201500003I

Citation Format: Yurong Song, Shaneen Baxter, Lisheng Dai, Chelsea Sanders, Holli Loomans-Kropp, Brandon Somerville, Ryan N. Baugher, Stephanie D. Mellott, Todd B. Young, Heidi E. Lawhorn, Teri M. Plona, Bingfang Xu, Lei Wei, Qiang Hu, Song Liu, Alan Hutson, Baktiar Karim, Simone Difilippantonio, Ligia Pinto, Matthias Kloor, Steven M. Lipkin, Shizuko Sei, Robert H. Shoemaker. Time course genomic characterization reveals progressive accumulation of mutations during tumor development in a Lynch syndrome mouse model. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6518.

Mesothelioma Mouse Models with Mixed Genomic States of Chromosome and Microsatellite Instability

Simple Summary

Only a limited number of murine mesothelioma cell lines have been developed to date. We sought to expand this number and to characterize the models in detail to enable studying mesothelioma biology in vivo. Two cell lines were identified as showing well-defined mesothelioma biomarkers and being suitable for preclinical use. In the course of our studies, we observed a mixed phenotype of chromosomal instability and microsatellite instability not previously reported in mouse models. Moreover, microsatellite markers were detectable in the plasma of tumor-bearing animals, which potentially can be used as non-invasive biomarkers for early cancer detection and monitoring the effects of interventions.

Abstract

Malignant mesothelioma (MMe) is a rare malignancy originating from the linings of the pleural, peritoneal and pericardial cavities. The best-defined risk factor is exposure to carcinogenic mineral fibers (e.g., asbestos). Genomic studies have revealed that the most frequent genetic lesions in human MMe are mutations in tumor suppressor genes. Several genetically engineered mouse models have been generated by introducing the same genetic lesions found in human MMe. However, most of these models require specialized breeding facilities and long-term exposure of mice to asbestos for MMe development. Thus, an alternative model with high tumor penetrance without asbestos is urgently needed. We characterized an orthotopic model using MMe cells derived from Cdkn2a^+/−;Nf2^+/− mice chronically injected with asbestos. These MMe cells were tumorigenic upon intraperitoneal injection. Moreover, MMe cells showed mixed chromosome and microsatellite instability, supporting the notion that genomic instability is relevant in MMe pathogenesis. In addition, microsatellite markers were detectable in the plasma of tumor-bearing mice, indicating a potential use for early cancer detection and monitoring the effects of interventions. This orthotopic model with rapid development of MMe without asbestos exposure represents genomic instability and specific molecular targets for therapeutic or preventive interventions to enable preclinical proof of concept for the intervention in an immunocompetent setting.

A novel mouse model of PMS2 founder mutation that causes mismatch repair defect due to aberrant splicing

Hereditary non-polyposis colorectal cancer, now known as Lynch syndrome (LS) is one of the most common cancer predisposition syndromes and is caused by germline pathogenic variants (GPVs) in DNA mismatch repair (MMR) genes. A common founder GPV in PMS2 in the Canadian Inuit population, NM_000535.5: c.2002A>G, leads to a benign missense (p.I668V) but also acts as a de novo splice site that creates a 5 bp deletion resulting in a truncated protein (p.I668*). Individuals homozygous for this GPV are predisposed to atypical constitutional MMR deficiency with a delayed onset of first primary malignancy. We have generated mice with an equivalent germline mutation (Pms2c.1993A>G) and demonstrate that it results in a splicing defect similar to those observed in humans. Homozygous mutant mice are viable like the Pms2 null mice. However, unlike the Pms2 null mice, these mutant mice are fertile, like humans homozygous for this variant. Furthermore, these mice exhibit a significant increase in microsatellite instability and intestinal adenomas on an Apc mutant background. Rectification of the splicing defect in human and murine fibroblasts using antisense morpholinos suggests that this novel mouse model can be valuable in evaluating the efficacy aimed at targeting the splicing defect in PMS2 that is highly prevalent among the Canadian Inuits.

Pharmacogenomics Implementation at the National Institutes of Health Clinical Center

The National Institutes of Health Clinical Center (NIH CC) is the largest hospital in the United States devoted entirely to clinical research, with a highly diverse spectrum of patients. Patient safety and clinical quality are major goals of the hospital, and therapy is often complicated by multiple cotherapies and comorbidities. To this end, we implemented a pharmacogenomics program in 2 phases. In the first phase, we implemented genotyping for HLA-A and HLA-B gene variations with clinical decision support (CDS) for abacavir, carbamazepine, and allopurinol. In the second phase, we implemented genotyping for drug-metabolizing enzymes and transporters: SLCO1B1 for CDS of simvastatin and TPMT for CDS of mercaptopurine, azathioprine, and thioguanine. The purpose of this review is to describe the implementation process, which involves clinical, laboratory, informatics, and policy decisions pertinent to the NIH CC.