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Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability [RNA-sequencing]

ABSTRACT: Approximately 15% of colorectal cancer (CRC) patients present with high levels of microsatellite instability (MSI-H), which is driven by defective mismatch repair (dMMR). While about 20% of MSI-H tumors are associated with the hereditary condition, Lynch syndrome (LS), the majority develop through non-hereditary mechanisms. In recent years, the molecular processes underpinning tumor development in LS patients has been debated, with the longstanding view that dMMR is a secondary process in CRC development of LS patients being questioned. Here, we performed the first multi-omic analysis of normal colon organoids developed from LS and healthy patients to address questions regarding the development of dMMR in LS colon epithelial cells from cancer-free individuals.

ORGANISM(S): Homo sapiens

PROVIDER: GSE211221 | GEO | 2023/06/01

REPOSITORIES: GEO

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Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability [methylation array]

Project description:Approximately 15% of colorectal cancer (CRC) patients present with high levels of microsatellite instability (MSI-H), which is driven by defective mismatch repair (dMMR). While about 20% of MSI-H tumors are associated with the hereditary condition, Lynch syndrome (LS), the majority develop through non-hereditary mechanisms. In recent years, the molecular processes underpinning tumor development in LS patients has been debated, with the longstanding view that dMMR is a secondary process in CRC development of LS patients being questioned. Here, we performed the first multi-omic analysis of normal colon organoids developed from LS and healthy patients to address questions regarding the development of dMMR in LS colon epithelial cells from cancer-free individuals.

2023-06-01 | GSE210018 | GEO

Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model

Project description:DNA mismatch repair deficiency (MMRD) drives microsatellite instability (MSI). Cells with MSI accumulate numerous frameshift mutations. Frameshift mutations affecting cancer-related genes may promote tumorigenesis and, therefore, are shared among independently arising MSI tumors. Consequently, such recurrent frameshift mutations can give rise to shared immunogenic frameshift peptides (FSPs) that represent ideal candidates for a vaccine against MSI cancer. Pathogenic germline variants of mismatch repair genes cause Lynch syndrome (LS), a hereditary cancer syndrome affecting approximately 20-25 million individuals worldwide. LS individuals are at high risk of developing MSI cancer. Previously, we demonstrated safety and immunogenicity of an FSP-based vaccine in a Phase I/IIa clinical trial. However, the cancer-preventive effect of FSP vaccination in the scenario of LS has not been demonstrated so far.

2021-08-30 | GSE175744 | GEO

Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Affymetrix]

Project description:Only a small proportion of cases suspected to have Lynch Syndrome (LS) can be explained by mutation in the mismatch repair (MMR) genes. This study aimed to identify rare CNVs that may contribute to an increased risk for hereditary colorectal cancer in patients with MMR proficiency.

2015-11-30 | GSE72667 | GEO

Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Agilent]

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Systemic circulating microRNA landscape in Lynch syndrome

Project description:Purpose: Lynch syndrome (LS) is a hereditary cancer syndrome. Systemic circulating microRNA expression levels (c-miRnome) in LS carriers have not been characterized previously. This exploratory study characterized the systemic c-miRnomes of LS carriers with or without cancer and compared it to c-miRnomes of sporadic rectal cancer patients and healthy controls. Methods: Blood serum samples of Lynch syndrome carriers without (n=81) or with (n=13) cancer, sporadic rectal cancer patients (n=24) and healthy controls (n=37) were sequenced with NextSeq500. FastQC was used for quality controls. High quality samples with Phred score >25 were selected for downstream analysis. FastX-toolkit was used for trimming and filtering. Mapping of the reads to miRbase (v.22) was conducted with Bowtie with v-mode and best strata parameters for single-end data. Only the uniquely mapped reads were selected for differential expression (DE) analysis. Dimension reduction analysis was conducted with t-SNE. Target gene prediction and pathway analysis was performed with mirWalk and validated with COSMIC-database. Results: An average of 3.2M reads pers sample was achieved. We identified a pool of 228 c-miRs common to all study groups that was used to setup the design matrix for DE analysis. We identified a c-miRnome of 40 DE c-miRs that discern healthy LS carriers from healthy controls but could not distinguish them from cancer patients with or without LS. Our results suggested that hereditary and sporadic carcinogenesis share common biological pathways and alterations in these pathways generate a c-miR response, which can be used to track oncogenic stress at cancer-free state in LS. Conclusion: Our results show that c-miRs hold diagnostic and predictive potential in molecular profiling of human cancers.

2022-04-25 | GSE198834 | GEO

Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RNA-Seq)

Project description:Colorectal cancer (CRC) remains the third most common cancer in the US, with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1. DNA methylation and transcriptome analysis was used to evaluate the rhesus macaque as a model organism to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans. NIH grant(s): Grant ID: 5 P30 CA016672-44 Grant title: Cancer Center Support Grant Affiliation: The University of Texas MD Anderson Cancer Center Grantor: NCI

2022-03-31 | GSE178381 | GEO

Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RRBS)

Project description:Colorectal cancer (CRC) remains the third most common cancer in the US, with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1. DNA methylation and transcriptome analysis was performed to evaluate the rhesus macaque as a model organism to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans. NIH grant(s): Grant ID: 5 P30 CA016672-44 Grant title: Cancer Center Support Grant Affiliation: The University of Texas MD Anderson Cancer Center Grantor: NCI

2022-03-31 | GSE178377 | GEO

Distinct tumorigenic pathways within hereditary nonpolyposis colorectal cancer

Project description:Gene expression profiling has discriminated between sporadic microsatellite instable (MSI) and microsatellite stable (MSS) colorectal cancers (CRCs), whereas the expression pattern of familial colorectal cancer type X (FCCTX) and Lynch syndrome (LS) associated CRCs remain largely unknown. The purpose of this study is to use gene expression profiling of formalin-fixed paraffin-embedded (FFPE) tumor specimens from FCCTX, LS and sporadic CRC as a control to detect expression patterns and to identify signaling pathways differing between FCCTX and LS tumors.

2012-03-08 | GSE36335 | GEO

HNPCC-Sys: Molecular Characterization of Lynch Syndromes

Project description:<p>Lynch Syndrome (LS) tumors are characterized by constitutional mutations in DNA mismatch-repair genes. Colorectal cancers (CRCs) are the predominant tumor type in patients with LS. Here, we have used whole-genome and transcriptome sequencing of LS- CRC to find similarities and differences of mutation and gene expression characteristics between LS-CRC and sporadic CRC (data provided by <a href="./study.cgi?study_id=phs000178">TCGA via dbGaP</a>). Furthermore, we were interested in the molecular heterogeneity of LS-CRC. We have performed a molecular characterization of LS-tumors and of matched tumor-distant reference colonic mucosa based on whole-genome DNA- and RNA-sequencing analyses. Our data indicates the existence of two subgroups of LS-CRCs, G1 and G2, where G1 tumors show a higher number of somatic mutations, higher microsatellite slippage and a different mutation spectrum.</p>

| phs001407 | dbGaP

Naproxen Chemoprevention Promotes Immune Activation In Lynch Syndrome Colorectal Mucosa

Project description:Lynch syndrome (LS) patients are at markedly increased risk for colorectal cancer. It is being increasingly recognized that the immune system plays an essential role in LS tumor development. Therefore, immune interception strategies are emerging as a novel way to prevent cancer in LS. This phase Ib, placebo-controlled, randomized clinical trial and a co-clinical trial using a LS mouse model and patient-derived organoids aims to evaluate the safety and tolerability as well as to discover novel molecular pathways involved in the activity of Naproxen as chemoprevention in LS patients.

2020-06-25 | GSE144381 | GEO

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