GENOMIC INSTABILITY IN MISMATCH REPAIR DEFICIENT COLORECTAL CANCER
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ABSTRACT:
PROVIDER: EGAS00001002477 | EGA |
REPOSITORIES: EGA
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Project description:We have generated a gene signature of mismatch repair (MMR) deficient intestinal stem cells (ISCs) using whole-genome transcriptomics and proteomics from murine intestinal stem cells and epithelial non-stem cells in a Lynch syndrome mouse model (Msh2-fl/fl;Villin-Cre). Then we have validated this signature in RNA-seq data from LS normal unaffected mucosa (UM), adenomas (AD) and adenomas with high-grade dsyplasia (AD-HGD) and tumors (T). MMR status for LS tumors and adenomas with high-grade dysplasia was categorized as KO, for unaffected mucosa as HET and FAP samples as WT.
2021-06-01 | GSE153385 | GEO
Project description:This clinical trial evaluates the effect of tislelizumab in treating patients with mismatch repair deficient endometrial cancer that has come back (recurrent). Deoxyribonucleic acid (DNA) mismatch repair (MMR) is a system for recognizing and repairing DNA errors and damage. Mismatch repair deficient tumors (dMMR) may have difficulty repairing DNA mutations during replication that may affect tumor’s response to therapy. Immunotherapy with monoclonal antibodies, such as tislelizumab, may help the body’s immune system attack the cancer, and may interfere with the ability of tumor cells to grow and spread. Giving tislelizumab may help treat patients with mismatch repair deficient endometrial cancer.
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Project description:DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects innate DNA polymerase infidelities during replication to maintain genomic integrity. Defects in a subset of MMR genes are associated with hereditary non-polyposis colon cancer and some other sporadic cancers, highlighting the crucial role for MMR in genome maintenance. In E. coli a helicase implicated in the MMR process is well characterized, and named UvrD, whereas in mammals it has not been identified yet, even though the eukaryotic DNA mismatch pathway is analogous to the bacterial one and uses a similar repair mechanism and key components. Here we identify MCM9 as a helicase playing a vital role in MMR in mammals. MCM9 is the last discovered member of the MCM2-9 family, and has been implicated in replication and homologous recombination processes. By an affinity-purification proteomic approach, we found that MCM9 interacts with the MMR initiation complex. Immortalized cells from MCM9 knockout mice showed clear length alterations in their microsatellites, and a dramatic MMR deficiency compared to wild-type cells. We also found that a helicase-dead form of MCM9 is totally unable to restore the MMR deficiency phenotype. Furthermore, using an siRNA approach in human cells, we demonstrated that MCM9 is regulated by MSH2, a protein responsible for mismatch recognition. Our results clearly reveal that MCM9 functions as a helicase for DNA mismatch repair in mammals, and thus is essential for the maintenance of genome stability. Proteomics analysis: FLAG-HA-tagged human MCM9 plus associated proteins were isolated by tandem affinity purification from nuclear extracts of stably-expressing HeLa S3 cells, then analysed by SDS-PAGE and silver staining. Gel lanes were cut into slices, which were processed and analysed separately. Proteins in each gel slice were digested with trypsin, extracted and analysed by LC-MS/MS on a Thermo Scientific LTQ Velos mass spectrometer, generating a series of MS RAW files. Bioinformatics: Peptide and protein identification from MS data was performed using the Sequest program, with a human IPI sequence database (v.3.60). Trypsin was defined as the protease used, a peptide mass tolerance of 2.5 was specified, and all peptide matches have a Sequest Xcorr score ≥0.5.
2015-08-19 | PXD000212 | Pride
Project description:DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient tumors and observed that mutation rates were drastically increased relative to MMR-proficient endometrial tumors.
| EGAS00001000182 | EGA
Project description:The mismatch repair (MMR) family is a highly conserved group of proteins that function in correcting base-base and insertion-deletion mismatches generated during DNA replication. To systematically investigate the mismatch repair pathway, we conducted a proteomic analysis and identified MMR-associated protein complexes using a tandem-affinity purification coupled with mass spectrometry (TAP-MS) method. In total, we identified 262 high-confidence candidate interaction proteins (HCIPs).
2016-02-08 | PXD003014 | Pride
Project description:The mismatch repair (MMR) family is a highly conserved group of proteins that function in correcting base-base and insertion-deletion mismatches generated during DNA replication. To systematically investigate the mismatch repair pathway, we conducted a proteomic analysis and identified MMR-associated protein complexes using a tandem-affinity purification coupled with mass spectrometry (TAP-MS) method. In total, we identified 262 high-confidence candidate interaction proteins (HCIPs).
2016-03-13 | MSV000079578 | MassIVE
Project description:We show that mismatch-repair (MMR) signature mutations can activate colorectal cancer (CRC)-specific enhancers, through analysis of enhancer DNA associated with the active enhancer histone mark H3K27ac. We demonstrate that MMR mutations activate enhancers using a xenograft metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection.
2019-02-07 | GSE126188 | GEO
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
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 | GSE72665 | GEO
Project description:Immune checkpoint inhibitor (ICI) therapy can induce complete responses in mismatch repair-deficient and microsatellite instability-high (d-MMR/MSI-H) colorectal cancers (CRCs). However, the mechanism responsible for pathological complete response (pCR) to immunotherapy has not been completely understood. We utilize single-cell RNA sequencing to examine the immune and stromal cell dynamics in 19 patients with d-MMR/MSI-H CRC treated with the neoadjuvant PD-1 blockade. In tumors with a pCR, the proportions of CD8+ Trm-mitotic, CD4+ Tregs, proinflammatory IL1B monocyte and CCL2+Fibroblast concertedly decrease following treatment, while those of CD8+ Tem, CD4+ Th, CD20+ B and HLA-DRA+ Endothelial cells increase. Proinflammatory features in tumor microenvironment mediate the persistence of residual tumors by modulating CD8+ T cells and other response-associated immune cell populations. Our study provides rich resources and biological insights into the mechanism of successful ICI therapy and potential targets to improve treatment efficacy.
2023-05-11 | GSE205506 | GEO