scholarly journals Landscape of Microsatellite Instability Across 39 Cancer Types

2017 ◽  
pp. 1-15 ◽  
Author(s):  
Russell Bonneville ◽  
Melanie A. Krook ◽  
Esko A. Kautto ◽  
Jharna Miya ◽  
Michele R. Wing ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Human Cancer ◽  
The Cancer Genome Atlas ◽  
Repair System ◽  
Multiple Cancer ◽  
External Data ◽  
Mismatch Repair System ◽  
Cancer Types ◽  
Genomic Microsatellites

Purpose Microsatellite instability (MSI) is a pattern of hypermutation that occurs at genomic microsatellites and is caused by defects in the mismatch repair system. Mismatch repair deficiency that leads to MSI has been well described in several types of human cancer, most frequently in colorectal, endometrial, and gastric adenocarcinomas. MSI is known to be both predictive and prognostic, especially in colorectal cancer; however, current clinical guidelines only recommend MSI testing for colorectal and endometrial cancers. Therefore, less is known about the prevalence and extent of MSI among other types of cancer. Methods Using our recently published MSI-calling software, MANTIS, we analyzed whole-exome data from 11,139 tumor-normal pairs from The Cancer Genome Atlas and Therapeutically Applicable Research to Generate Effective Treatments projects and external data sources across 39 cancer types. Within a subset of these cancer types, we assessed mutation burden, mutational signatures, and somatic variants associated with MSI. Results We identified MSI in 3.8% of all cancers assessed—present in 27 of tumor types—most notably adrenocortical carcinoma (ACC), cervical cancer (CESC), and mesothelioma, in which MSI has not yet been well described. In addition, MSI-high ACC and CESC tumors were observed to have a higher average mutational burden than microsatellite-stable ACC and CESC tumors. Conclusion We provide evidence of as-yet-unappreciated MSI in several types of cancer. These findings support an expanded role for clinical MSI testing across multiple cancer types as patients with MSI-positive tumors are predicted to benefit from novel immunotherapies in clinical trials.

scholarly journals Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hanxiao Zhou ◽  
Yue Gao ◽  
Xin Li ◽  
Shipeng Shang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Human Cancer ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Computational Method ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Pathophysiological Mechanism ◽  
Multiple Cancer ◽  
Cancer Types ◽  
Genomic Clusters

Abstract Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types.

scholarly journals Microsatellite instability as a unique characteristic of tumors and a predictor of response to immune therapy

2020 ◽  
Vol 9 (4) ◽  
pp. 59-69 ◽  
Author(s):  
A.  A. Tryakin ◽  
M.  Yu. Fedyanin ◽  
A.  S. Tsukanov ◽  
Yu.  A. Shelygin ◽  
I.  A. Pokataev ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Immune Therapy ◽  
High Sensitivity ◽  
Repair System ◽  
Favorable Prognosis ◽  
Mismatch Repair System ◽  
High Immunogenicity

Deficiency of the mismatch repair system is a unique molecular disorder that occurs in most types of tumors and leads to development of microsatellite instability (MSI) in them. The development of a hypermutated phenotype and related high immunogenicity are typically associated with more favorable prognosis as well as a high sensitivity to immunotherapy with inhibitors of immune checkpoint inhibitors. This review presents the current views on the diagnosis, prognostic and predictive significance of MSI in various tumors, as well as their response to immunotherapy.

Warthin Tumors Do Not Have Microsatellite Instability and Express Normal DNA Mismatch Repair Proteins

2006 ◽  
Vol 130 (1) ◽  
pp. 52-56 ◽  
Author(s):  
Jennifer L. Hunt
Keyword(s):  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Dna Mismatch Repair ◽  
Repair System ◽  
Dna Mismatch ◽  
Epithelial Component ◽  
Repair Enzymes ◽  
Dna Mismatch Repair System ◽  
Mismatch Repair System ◽  
Polymerase Chain

Abstract Context.—Warthin tumors are controversial entities with a poorly understood etiology. Although some investigators have suggested a neoplastic origin, others have supported a developmental anomaly. A recent study described the absence of staining for hMLH1 and hMSH2 proteins in the epithelial component of Warthin tumors, suggesting that they arise secondary to defects in the DNA mismatch repair system. Objective.—To determine if Warthin tumors exhibit evidence of DNA mismatch repair defects. Design.—Immunostains for hMLH1 and hMSH2 were performed using a standard approach. Microdissection of the epithelial component was followed by DNA extraction from the tissue fragments. Polymerase chain reaction and capillary electrophoresis analyses were performed for the following 5 National Cancer Institute–recommended microsatellites: D2s123, D5s346, D17s250, BAT25, and BAT26. Patients.—Twelve patients with Warthin tumors were included. Results.—The immunostains for hMLH1 and hMSH2 showed preserved expression in the nuclei of the epithelial component of all Warthin tumors. No microsatellite instability was detected, and no loss of heterozygosity was seen. Conclusions.—These results are not concordant with previously reported results showing loss of expression of the hMLH1 and hMSH2 DNA mismatch repair enzymes in the epithelial component of Warthin tumors. Furthermore, no microsatellite instability was detected in the 5 loci tested for each tumor in this series. These data demonstrate that Warthin tumors do not have evidence of DNA mismatch repair defects at the genomic or protein expression level.

The Genetics of Hereditary Non-Polyposis Colorectal Cancer

2003 ◽  
Vol 1 (1) ◽  
pp. 137-144 ◽  
Author(s):  
Stephen B. Gruber ◽  
Wendy Kohlmann
Keyword(s):  
Colorectal Cancer ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Molecular Diagnostic ◽  
Repair System ◽  
Molecular Fingerprint ◽  
Dna Mismatch ◽  
Repair Protein ◽  
Mismatch Repair System ◽  
Defective Mismatch Repair

Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant condition accounting for 3% to 5% of all colorectal cancer. HNPCC is caused by germline mutations in the mismatch repair system and is recognized by a characteristic clinical phenotype as well as a hallmark of the tumors termed “microsatellite instability.” Microsatellite instability serves as a molecular fingerprint for defective mismatch repair and has proven to be useful in the molecular diagnostic workup for HNPCC. The crystal structure of the DNA mismatch repair protein MutS has been solved, providing insight into the molecular basis of defective mismatch repair. Genetic testing has become a key component of the treatment of patients and families with HNPCC, and enhanced surveillance for HNPCC has been shown to reduce the rate of colorectal cancer by more than half and improve 10-year survival from 68% to 93%.

Oxidative stress induces inactivation of the DNA mismatch repair system and causes microsatellite instability

2000 ◽  
Vol 118 (4) ◽  
pp. A707
Author(s):  
Christoph Gasche ◽  
Christina L. Chang ◽  
Jennifer Rhees ◽  
Ajay Goel ◽  
Luigi Ricciardiello ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Dna Mismatch Repair ◽  
Repair System ◽  
Dna Mismatch ◽  
Dna Mismatch Repair System ◽  
Mismatch Repair System
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