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Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma.

ABSTRACT: Purpose:Tumor metastasis remains the leading cause of cancer-related mortality in biliary tract cancer. The etiology and mechanism of bile tract carcinoma metastasis are unclear. Methods:The primary tumor and blood samples of 14 patients with biliary tract cancer were collected, followed by nucleic acid extraction and library construction. Target sequencing with 556 panel genes and WES were performed to detect the hot spot genes variations. Bioinformatics was used to comprehensively analyze the sequencing data of these samples, including the differences of tumor mutation burden and signaling pathways. Results:The results showed that the mutation frequency of TP53 gene was the highest and the mutations of CTNNB1, EPHA7, ARID2, and PIK3CA were only found in metastatic samples. The TMB mean values of metastatic and non-metastatic groups were 12.97 and 10.38 mutations per Mb, respectively. There were significant differences in the enrichment pathways of cellular components between the tumor metastasis and non-metastatic samples. Conclusions:We identified multiple pathway differences, which helps us better understand metastatic biliary tumors and design clinical therapy for personalized medicine.

SUBMITTER: Li Q

PROVIDER: S-EPMC7487098 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma.

Li Qi Q Zhang Qifan Q Cheng Xiao X Weng Xie X Chen Mian M Hu Xiaoyun X Huang Jing J Chen Jinzhang J

Journal of oncology 20200904

<h4>Purpose</h4>Tumor metastasis remains the leading cause of cancer-related mortality in biliary tract cancer. The etiology and mechanism of bile tract carcinoma metastasis are unclear.<h4>Methods</h4>The primary tumor and blood samples of 14 patients with biliary tract cancer were collected, followed by nucleic acid extraction and library construction. Target sequencing with 556 panel genes and WES were performed to detect the hot spot genes variations. Bioinformatics was used to comprehensive ...[more]

PMID: 32952556

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Project description:IntroductionMultiple primary melanomas (MPM) occur up to 8% of patients with cutaneous malignant melanoma (CMM). They are often sporadic harbouring several somatic mutations, but also familial cases harbouring a CDKN2A germline mutation have been describe in Caucasian populations. The aim of this study was to investigate the incidence, the distribution patterns and the impact of known and unknown germline and somatic mutations in patients with MPM from Italy.Materials and methodsOne-hundred and two MPM patients were enrolled for germline mutation analysis, and five patients with at least four MPMs were identified for somatic mutation analysis. The demographic, pathologic and clinical features were retrieved from medical records. Molecular analysis for both germline and somatic mutations was performed in genomic DNA from peripheral blood and tissue samples, respectively, through a next generation sequencing approach, using a specific multiple-gene panel constructed by the Italian Melanoma Intergroup for somatic analysis and a commercial cancer hotspot panel for somatic analysis.ResultsCDKN2A mutations were detected in 6/16 (37.5%) and 3/86 (3.5%) MPM cases with and without family history for melanoma, respectively. Furthermore, multiple MC1R and, to a lesser extent, ATM variants have been identified. BAP1 variants were found only in MPM patients from southern Italy. The most frequent somatic variants were the pathogenic BRAFV600E and TP53, followed by KIT, PIK3CA, KDR, and NRAS. Single APC, ERBB4, MET, JAK3 and other variants with unknown function were also detected.ConclusionsCDNK2A mutation is the most relevant susceptibility mutation in Italian patients with MPM, especially those with a family history for CMM. The prevalence of this mutation and other sequence variants identified in this study varies among specific sub-populations. Furthermore, some heterogeneity in driver somatic mutations between sporadic MPMs has been observed, as well as in a number of associated sequence variants the clinical impact of which needs to be further elucidated.

Project description:BackgroundBiliary tract cancers (BTCs) are uncommon and are associated with a dismal prognosis. Combinations of gemcitabine and platinum chemotherapy (gemcitabine and platinum-based therapy [GP]) form the standard approach for treating advanced BTC. To characterize the spectrum of mutations and to identify potential biomarkers for a GP response in BTC, this study evaluated the genomic landscape and assessed whether mutations affecting DNA repair were associated with GP resistance.MethodsPretreatment, formalin-fixed, paraffin-embedded samples from 183 BTC patients treated with GP were analyzed. Cox regression models were used to determine the association between mutations, progression-free survival (PFS), and overall survival (OS).ResultsWhen genes with an incidence > 10% were considered, no individual gene was independently predictive of a GP response. In patients with unresectable BTC who received GP as their first-line therapy, the joint status of cyclin-dependent kinase inhibitor 2A (CDKN2A), tumor protein 53 (TP53), and AT-rich interaction domain 1A (ARID1A) was associated with PFS (P = .0004) and OS (P ≤ .0001). Patients with mutations in CDKN2A and TP53 were identified as a poor-prognosis cohort with a median PFS of 2.63 months and a median OS of 5.22 months. Patients with mutant ARID1A, regardless of the single-mutation status of TP53 or CDKN2A, had similar outcomes. A patient who exhibited mutations in all 3 genes had a median PFS of 20.37 months, and OS was not reached.ConclusionsIn the largest exploratory analysis of this kind for BTC, 3 prevalent, mutually exclusive mutations represent distinct patient cohorts. These mutations are prognostic and may represent a predictive biomarker for a GP response. Prospective studies to validate these findings are needed, and they should include the incorporation of therapies that exploit the genomic instability observed with these mutations in BTC. Cancer 2016;122:3657-66. © 2016 American Cancer Society.

Dataset Information

Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma.

Publications

Next-Generation Sequencing Characterizes the Landscape of Somatic Mutations and Pathways in Metastatic Bile Tract Carcinoma.

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