scholarly journals Mutational signature profiling classifies subtypes of clinically different mismatch repair deficient tumors with a differential immunogenic response potential

2021 ◽  
Author(s):  
Mar Giner-Calabuig ◽  
Seila De Leon ◽  
Julian Wang ◽  
Tara D Fehlmann ◽  
Chinedu Ukaegbu ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Molecular Characterization ◽  
Mutational Signatures ◽  
Mmr Deficiency ◽  
High Level ◽  
Sporadic Tumors ◽  
Generation Sequencing ◽  
Immunogenic Response

ABSTRACTBackgroundMismatch repair (MMR) deficiency is the hallmark of tumors from Lynch syndrome (LS), sporadic MLH1 hypermethylated, and Lynch-like syndrome (LLS), but there is a lack of understanding of the variability in their mutational profiles based on clinical phenotypes. The aim of this study was to perform a molecular characterization to identify novel features that can impact tumor behavior and clinical management.MethodsWe tested 105 MMR-deficient colorectal cancer tumors (25 LS, 35 LLS, and 45 sporadic) for global exome microsatellite instability, cancer mutational signatures, mutational spectrum and neoepitope load.Results78% of tumors showed high contribution of MMR-deficient mutational signatures, high level of global exome microsatellite instability, loss of MLH1/PMS2 protein expression and included sporadic tumors. 22% of tumors showed weaker features of MMR deficiency, 73% lost MSH2/MSH6 expression and included half of LS and LLS tumors. Remarkably, 9% of all tumors lacked global exome microsatellite instability. Lastly, HLA-B07:02 could be triggering the neoantigen presentation in tumors that show the strongest contribution of MMR-deficient tumors.ConclusionsNext-generation sequencing approaches allow for a granular molecular characterization of MMR-deficient tumors, which can be essential to properly diagnose and treat patients with these tumors in the setting of personalized medicine.

scholarly journals Mismatch Repair Deficiency in Colorectal Adenocarcinoma: Clinical, Pathological and Prognostic Features, a Single Center’s Experience of 1002 Cases

2021 ◽  
Author(s):  
Fatma Yildirim ◽  
Murat Sezak ◽  
Tayfun Yoldas ◽  
Bulent Karabulut ◽  
Basak Doganavsargil
Keyword(s):  
Lynch Syndrome ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Tumor Infiltrating Lymphocytes ◽  
Clinicopathological Features ◽  
Prognostic Features ◽  
Mucinous Component ◽  
Significant Difference ◽  
Mmr Deficiency ◽  
High Level

Background and Study Aims: Microsatellite instability pathway caused by loss of DNA “Mismatch Repair genes” (MMR) is responsible of Lynch Syndrome-related tumors and 10-15% of sporadical colorectal cancers. Although MSI-test is regarded as the golden standard for detection of “Lynch Syndrome-related tumors”, there are increasing evidence on similar analytic sensitivity of immunohistochemical evaluations. Patinets and Metods: We retrospectively evaluated 1002 colorectal tumors for loss of DNA MMR protein (MLH1, PMS2, MSH2, MSH6) immunohistochemically. The results were correlated with clinicopathological features and high level-microsatellite instability (MSI-H) related histological parameters. Results: MMR protein expression loss was observed in 9.8% of the cases. MLH1-PMS2 loss (53.2%) was the most common loss followed by MSH2-MSH6 (31.6%), isolated PMS2 loss (12%), and isolated MSH6 loss (2%). MMR deficiency was more frequent under 50 years-old (p<0.0001), in right colon tumors (p<0.0001), poorly differentiated tumors (p<0.0001), tumors with tumor infiltrating lymphocytes (p<0.0001), mucinous component (p=0.001), and medullary component (p<0.0001). Also MMR deficiency was less frequent in tumor with tumor budding (p<0.0001) and dirty necrosis (p<0.0001). The 5 years-survival rate was 55.7%. No significant correlation was found with MMR deficiency and survival. Conclusions: MMR deficiency was observed in 9.8% of the cases with distinct clinicopathological features. The results were consistent with previous studies. Unlike the literature, we did not find any statistically significant difference between MMR deficiency and prognosis.

scholarly journals Correction to: Molecular characterization of a novel citrivirus from citrus using next‑generation sequencing

2018 ◽  
Vol 163 (12) ◽  
pp. 3483-3483
Author(s):  
Mengji Cao ◽  
Ping Li ◽  
Song Zhang ◽  
Fangyun Yang ◽  
Yan Zhou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Characterization ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals The Frequency of DNA Mismatch Repair Deficiency Is Very Low in Surgically Resected Lung Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Naoki Yanagawa ◽  
Noriyuki Yamada ◽  
Ryo Sugimoto ◽  
Mitsumasa Osakabe ◽  
Noriyuki Uesugi ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Protein Expression ◽  
Microsatellite Instability ◽  
Cell Carcinoma ◽  
Mismatch Repair ◽  
Squamous Cell ◽  
Lung Carcinoma ◽  
The Other ◽  
Dna Mismatch ◽  
Mmr Deficiency

IntroductionDNA mismatch repair (MMR) deficiency leads to changes in the length of nucleotide repeat sequences of tumor DNA. In that situation, DNA replicational errors occur and accumulate during DNA replication. As a result, this mechanism frequently affects the coding regions of oncogenes and tumor suppressor genes and causes carcinogenesis. Recently, DNA MMR deficiency has been recognized as a predictive biomarker for immunotherapy. The aim of this study is to examine the frequency of DNA MMR deficiency and clinicopathological characteristics in surgically resected lung carcinoma (LC) and their correlation.MethodsA total of 1153 LCs were examined. Tissue microarrays were constructed. The status of MMR deficiency was evaluated by immunohistochemical analysis of MMR protein expression (hMLH1, hMSH2, hMSH6, and hPMS2). Microsatellite instability analysis, BRAF mutation, and MLH1 methylation analysis were performed for cases that showed MMR deficiency.ResultsOnly 2 of the 1153 cases (0.17%) showed a loss of hMLH1/hPMS2 protein expression. They also had high levels of microsatellite instability (MSI-H), had neither MLH1 promoter methylation nor BRAF mutation, and were male smokers. Histopathologically, one was a squamous cell carcinoma, and the other was combined small cell carcinoma with squamous cell carcinoma. Regarding PD-L1 protein expression, one had high expression, and the other had none.ConclusionThe frequency of MMR deficiency was very low in LC. However, our two cases were non-adenocarcinoma and differed from previous studies. Because of its very low frequency, MMR deficiency is not a practical biomarker to predict the effect of immune checkpoint inhibitors in LC.

Microsatellite Instability, Mismatch Repair Deficiency, and BRAF Mutation in Treatment-Resistant Germ Cell Tumors

2009 ◽  
Vol 27 (13) ◽  
pp. 2129-2136 ◽  
Author(s):  
Friedemann Honecker ◽  
Hendrik Wermann ◽  
Frank Mayer ◽  
Ad J.M. Gillis ◽  
Hans Stoop ◽  
...  
Keyword(s):  
Germ Cell ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Braf Mutation ◽  
Cisplatin Resistance ◽  
Germ Cell Tumors ◽  
Braf V600e ◽  
Braf Mutations ◽  
Kras Mutations ◽  
Mmr Deficiency

Purpose Mismatch repair (MMR) deficiency and microsatellite instability (MSI) are associated with cisplatin resistance in human germ cell tumors (GCTs). BRAF mutation (V600E) is found in MSI colorectal cancers. The role of RAS/RAF pathway mutations in GCT treatment response is unknown. Patients and Methods Two patient cohorts were investigated: 100 control GCTs (50 seminomas and 50 nonseminomas) and 35 cisplatin-based chemotherapy-resistant GCTs. MMR proteins were analyzed by immunohistochemistry, and eight microsatellite loci were examined for MSI. Tumors were assessed for specific BRAF and KRAS mutations. Results Resistant tumors showed a higher incidence of MSI than controls: 26% versus 0% in two or more loci (P < .0001). All resistant tumors were wild-type KRAS, and two controls (2%) contained a KRAS mutation. There was a significantly higher incidence of BRAF V600E mutation in resistant tumors compared with controls: 26% versus 1% (P < .0001). BRAF mutations were highly correlated with MSI (P = .006), and MSI and mutated BRAF were correlated with weak or absent staining for hMLH1 (P = .017 and P = .008). Low or absent staining of hMLH1 was correlated with promoter hypermethylation (P < .001). Tumors lacking expression of hMLH1 or MSH6 were significantly more frequent in resistant GCTs than in controls (P = .001 and 0.0036, respectively). Within the subgroup of resistant tumors, patients with MSI showed a trend to longer progression-free survival (P = .068). Conclusion We report for the first time a correlation between a gene mutation—BRAF V600E—and cisplatin resistance in nonseminomatous GCTs. Furthermore, a correlation between MMR deficiency, MSI, and treatment failure is confirmed.

scholarly journals Understanding Inherited Risk in Unselected Newly Diagnosed Patients With Endometrial Cancer

2019 ◽  
pp. 1-15
Author(s):  
Karen A. Cadoo ◽  
Diana L. Mandelker ◽  
Semanti Mukherjee ◽  
Carolyn Stewart ◽  
Deborah DeLair ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Next Generation Sequencing ◽  
Lynch Syndrome ◽  
Microsatellite Instability ◽  
Mismatch Repair ◽  
Cancer Predisposition ◽  
Next Generation ◽  
Germline Variants ◽  
Predisposition Genes ◽  
Generation Sequencing

PURPOSE Mutations in DNA mismatch repair genes and PTEN, diagnostic of Lynch and Cowden syndromes, respectively, represent the only established inherited predisposition genes in endometrial cancer to date. The prevalence of other cancer predisposition genes remains unclear. We determined the prevalence of pathogenic germline variants in unselected patients with endometrial cancer scheduled for surgical consultation. PATIENTS AND METHODS Patients prospectively consented (April 2016 to May 2017) to an institutional review board–approved protocol of tumor-normal sequencing via a custom next-generation sequencing panel—the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets—that yielded germline results for more than 75 cancer predisposition genes. Tumors were assessed for microsatellite instability. Per institutional standards, all tumors underwent Lynch syndrome screening via immunohistochemistry (IHC) for mismatch repair proteins. RESULTS Of 156 patients who consented to germline genetic testing, 118 (76%) had stage I disease. In 104 patients (67%), tumors were endometrioid, and 60 (58%) of those tumors were grade 1. Twenty-four pathogenic germline variants were identified in 22 patients (14%): seven (4.5%) had highly penetrant cancer syndromes and 15 (9.6%) had variants in low-penetrance, moderate-penetrance, or recessive genes. Of these, five (21%) were in Lynch syndrome genes (two MSH6, two PMS2, and one MLH1). All five tumors had concordant IHC staining; two (40%) were definitively microsatellite instability–high by next-generation sequencing. One patient had a known BRCA1 mutation, and one had an SMARCA4 deletion. The remaining 17 variants (71%) were incremental findings in low- and moderate-penetrance variants or genes associated with recessive disease. CONCLUSION In unselected patients with predominantly low-risk, early-stage endometrial cancer, germline multigene panel testing identified cancer predisposition gene variants in 14%. This finding may have implications for future cancer screening and risk-reduction recommendations. Universal IHC screening for Lynch syndrome successfully identifies the majority (71%) of high-penetrance germline mutations.

scholarly journals Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing

PLoS ONE ◽  
2019 ◽  
Vol 14 (11) ◽  
pp. e0224379 ◽  
Author(s):  
You Jin Chun ◽  
Jae Woo Choi ◽  
Min Hee Hong ◽  
Dongmin Jung ◽  
Hyeonju Son ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Adenocarcinoma ◽  
Molecular Characterization ◽  
Next Generation ◽  
Korean Patients ◽  
Generation Sequencing
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