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Yang W, Chen S, Cheng X, Xu B, Zeng H, Zou J, Su C, Chen Z. Characteristics of genomic mutations and signaling pathway alterations in thymic epithelial tumors. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1659. [PMID: 34988168 PMCID: PMC8667121 DOI: 10.21037/atm-21-5182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND To elucidate the mechanisms of thymic epithelial tumor (TET) canceration by characterizing genomic mutations and signaling pathway alterations. METHODS Primary tumor and blood samples were collected from 21 patients diagnosed with TETs (thymoma and thymic cancer), 15 of whom were screened by nucleic acid extraction and whole exon sequencing. Bioinformatics was used to comprehensively analyze the sequencing data for these samples, including gene mutation information and the difference of tumor mutation burden (TMB) between thymoma and thymic carcinoma groups. We performed signaling pathway and functional enrichment analysis using the WebGestalt 2017 toolkit. RESULTS ZNF429 (36%) was the gene with the highest mutation frequency in thymic carcinoma. Mutations in BAP1 (14%), ABI1 (7%), BCL9L (7%), and CHEK2 (7%) were exclusively detected in thymic carcinoma, whereas ZNF721 mutations (14%) and PABPC1 (14%) were found exclusively in thymoma. The mean TMB values for thymic carcinoma and thymoma were 0.722 and 0.663 mutations per megabase (Mb), respectively, and these differences were not statistically significant. The ErbB signaling pathway was enriched in the thymoma and intersection groups, and pathways of central carbon metabolism in cancer, longevity regulating and MAPK signaling were only found in the thymoma group, while pathways in cancer (hsa05200) was found in the thymoma and thymic carcinoma groups. CONCLUSIONS Multiple differences in somatic genes and pathways have been identified. Our findings provide insights into differences between thymoma and thymic carcinoma that could aid in designing personalized clinical therapeutic strategies.
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Affiliation(s)
- Weilin Yang
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sai Chen
- Center for Private Medical Service & Healthcare, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinxin Cheng
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bo Xu
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huilan Zeng
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianyong Zou
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunhua Su
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhenguang Chen
- Department of Cardiothoracic Surgery of East Division, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Pinheiro M, Pinto C, Peixoto A, Veiga I, Lopes P, Henrique R, Baldaia H, Carneiro F, Seruca R, Tomlinson I, Kovac M, Heinimann K, Teixeira MR. Target gene mutational pattern in Lynch syndrome colorectal carcinomas according to tumour location and germline mutation. Br J Cancer 2015; 113:686-92. [PMID: 26247575 PMCID: PMC4647680 DOI: 10.1038/bjc.2015.281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/17/2015] [Accepted: 06/25/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND We previously reported that the target genes in sporadic mismatch repair (MMR)-deficient colorectal carcinomas (CRCs) in the distal colon differ from those occurring elsewhere in the colon. This study aimed to compare the target gene mutational pattern in microsatellite instability (MSI) CRC from Lynch syndrome patients stratified by tumour location and germline mutation, as well as with that of sporadic disease. METHODS A series of CRC from Lynch syndrome patients was analysed for MSI in genes predicted to be selective MSI targets and known to be involved in several pathways of colorectal carcinogenesis. RESULTS The most frequently mutated genes belong to the TGF-β superfamily pathway, namely ACVR2A and TGFBR2. A significantly higher frequency of target gene mutations was observed in CRC from patients with germline mutations in MLH1 or MSH2 when compared with MSH6. Mutations in microsatellite sequences (A)7 of BMPR2 and (A)8 of MSH3 were significantly more frequent in the distal CRC. Additionally, we observed differences in MSH3 and TGFBR2 mutational frequency between Lynch syndrome and sporadic MSI CRC regarding tumour location. CONCLUSIONS Our results indicate that the pattern of genetic changes differs in CRC depending on tumour location and between Lynch syndrome and sporadic MSI CRC, suggesting that carcinogenesis can occur by different pathways even if driven by generalised MSI.
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Affiliation(s)
- Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
| | - Isabel Veiga
- Department of Genetics, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
| | - Paula Lopes
- Department of Pathology, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, University of Porto, Largo Professor Abel Salazar, 4099-003 Porto, Portugal
| | - Helena Baldaia
- Department of Pathology, Centro Hospitalar de São João, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Fátima Carneiro
- Department of Pathology, Centro Hospitalar de São João, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Medical Faculty of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Raquel Seruca
- Medical Faculty of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Michal Kovac
- Research Group Human Genomics, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
- Medical Genetics, University Hospital Basel, Burgfelderstrasse 101, 4055 Basel, Switzerland
| | - Karl Heinimann
- Research Group Human Genomics, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
- Medical Genetics, University Hospital Basel, Burgfelderstrasse 101, 4055 Basel, Switzerland
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Rua Doutor António Bernardino Almeida, 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, University of Porto, Largo Professor Abel Salazar, 4099-003 Porto, Portugal
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Metcalf AM, Spurdle AB. Endometrial tumour BRAF mutations and MLH1 promoter methylation as predictors of germline mismatch repair gene mutation status: a literature review. Fam Cancer 2015; 13:1-12. [PMID: 23880961 DOI: 10.1007/s10689-013-9671-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Colorectal cancer (CRC) that displays high microsatellite instability (MSI-H) can be caused by either germline mutations in mismatch repair (MMR) genes, or non-inherited transcriptional silencing of the MLH1 promoter. A correlation between MLH1 promoter methylation, specifically the 'C' region, and BRAF V600E status has been reported in CRC studies. Germline MMR mutations also greatly increase risk of endometrial cancer (EC), but no systematic review has been undertaken to determine if these tumour markers may be useful predictors of MMR mutation status in EC patients. Endometrial cancer cohorts meeting review inclusion criteria encompassed 2675 tumours from 20 studies for BRAF V600E, and 447 tumours from 11 studies for MLH1 methylation testing. BRAF V600E mutations were reported in 4/2675 (0.1%) endometrial tumours of unknown MMR mutation status, and there were 7/823 (0.9%) total sequence variants in exon 11 and 27/1012 (2.7%) in exon 15. Promoter MLH1 methylation was not observed in tumours from 32 MLH1 mutation carriers, or for 13 MSH2 or MSH6 mutation carriers. MMR mutation-negative individuals with tumour MLH1 and PMS2 IHC loss displayed MLH1 methylation in 48/51 (94%) of tumours. We have also detailed specific examples that show the importance of MLH1 promoter region, assay design, and quantification of methylation. This review shows that BRAF mutations occurs so infrequently in endometrial tumours they can be discounted as a useful marker for predicting MMR-negative mutation status, and further studies of endometrial cohorts with known MMR mutation status are necessary to quantify the utility of tumour MLH1 promoter methylation as a marker of negative germline MMR mutation status in EC patients.
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Affiliation(s)
- Alexander M Metcalf
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research, Herston, QLD, 4006, Australia
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Gossage L, Murtaza M, Slatter AF, Lichtenstein CP, Warren A, Haynes B, Marass F, Roberts I, Shanahan SJ, Claas A, Dunham A, May AP, Rosenfeld N, Forshew T, Eisen T. Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma. Genes Chromosomes Cancer 2014; 53:38-51. [PMID: 24166983 DOI: 10.1002/gcc.22116] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022] Open
Abstract
VHL is mutated in the majority of patients with clear cell renal cell carcinoma (ccRCC), with conflicting clinical relevance. Recent studies have identified recurrent mutations in histone modifying and chromatin remodeling genes, including BAP1, PBRM1, SETD2, KDM6A, and JARID1c. Current evidence suggests that BAP1 mutations are associated with aggressive disease. The clinical significance of the remaining genes is unknown. In this study, targeted sequencing of VHL and JARID1c (entire genes) and coding regions of BAP1, PBRM1, SETD2, and KDM6A was performed on 132 ccRCCs and matched normal tissues. Associations between mutations and clinical and pathological outcomes were interrogated. Inactivation of VHL (coding mutation or promoter methylation) was seen in 75% of ccRCCs. Somatic noncoding VHL alterations were identified in 29% of ccRCCs and may be associated with improved overall survival. BAP1 (11%), PBRM1 (33%), SETD2 (16%), JARID1c (4%), and KDM6A (3%) mutations were identified. BAP1-mutated tumors were associated with metastatic disease at presentation (P = 0.023), advanced clinical stage (P = 0.042) and a trend towards shorter recurrence free survival (P = 0.059) when compared with tumors exclusively mutated for PBRM1. Our results support those of recent publications pointing towards a role for BAP1 and PBRM1 mutations in risk stratifying ccRCCs. Further investigation of noncoding alterations in VHL is warranted.
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Affiliation(s)
- Lucy Gossage
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
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Luthra R, Patel KP, Reddy NG, Haghshenas V, Routbort MJ, Harmon MA, Barkoh BA, Kanagal-Shamanna R, Ravandi F, Cortes JE, Kantarjian HM, Medeiros LJ, Singh RR. Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: applicability for diagnostics and disease monitoring. Haematologica 2013; 99:465-73. [PMID: 24142997 DOI: 10.3324/haematol.2013.093765] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Routine molecular testing in acute myeloid leukemia involves screening several genes of therapeutic and prognostic significance for mutations. A comprehensive analysis using single-gene assays requires large amounts of DNA, is cumbersome and timely consolidation of results for clinical reporting is challenging. High throughput, next-generation sequencing platforms widely used in research have not been tested vigorously for clinical application. Here we describe the clinical application of MiSeq, a next-generation sequencing platform to screen mutational hotspots in 54 cancer-related genes including genes relevant in acute myeloid leukemia (NRAS, KRAS, FLT3, NPM1, DNMT3A, IDH1/2, JAK2, KIT and EZH2). We sequenced 63 samples from patients with acute myeloid leukemia/myelodysplastic syndrome using MiSeq and compared the results with those obtained using another next-generation sequencing platform, Ion-Torrent Personal Genome Machine and other conventional testing platforms. MiSeq detected a total of 100 single nucleotide variants and 23 NPM1 insertions that were confirmed by Ion Torrent or conventional platforms, indicating complete concordance. FLT3-internal tandem duplications (n=10) were not detected; however, re-analysis of the MiSeq output by Pindel, an indel detection algorithm, did detect them. Dilution studies of cancer cell-line DNA showed that the quantitative accuracy of mutation detection was up to an allelic frequency of 1.5% with a high level of inter- and intra-run assay reproducibility, suggesting potential utility for monitoring response to therapy, clonal heterogeneity and evolution. Examples demonstrating the advantages of MiSeq over conventional platforms for disease monitoring are provided. Easy work-flow, high throughput multiplexing capability, 4-day turnaround time and simultaneous assessment of routinely tested and emerging markers make MiSeq highly applicable for clinical molecular testing in acute myeloid leukemia.
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Corso G, Pascale V, Flauti G, Ferrara F, Marrelli D, Roviello F. Oncogenic mutations and microsatellite instability phenotype predict specific anatomical subsite in colorectal cancer patients. Eur J Hum Genet 2013; 21:1383-8. [PMID: 23572025 DOI: 10.1038/ejhg.2013.66] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/06/2013] [Accepted: 02/14/2013] [Indexed: 02/08/2023] Open
Abstract
In colorectal cancer (CRC) oncogenic mutations such as KRAS alterations, are considered standard molecular biomarkers that predict the clinical benefit for targeted intervention with epidermal growth factor receptor (EGFR) inhibitors. In addition, these mutations are associated with specific anatomical area in colon tumor development, as BRAF mutations with the microsatellite instability (MSI). In this translational study, we aimed to assess the mutation frequencies of the EGFR (hotspot area and polyadenine deletions A13_del), KRAS, BRAF(V600E), and PIK3CA oncogenes in a series of 280 CRC patients. MSI phenotypes are also considered in this series. All patients' clinicopathological data were assessed for statistical analysis and its associations were validated. We verified multiple associations between oncogenic mutations and determined clinicopathological tumor features (1) EGFR A13_deletions are associated with right colon carcinoma (P<0.005), mucinous histotype (P=0.042), G3 grading (P=0.024), and MSI status (P<0.005); (2) PIK3CA mutations are related mucinous histotype (P=0.021); (3) KRAS(G12) and KRAS(G13) mutations are correlated, respectively, with the left and right colon cancer development (P<0.005), and finally (4) MSI is associated with right colon tumors (P<0.005). Mostly, we verified a higher frequency rate of the KRAS(G13) and EGFR A13_del oncogene mutations in right colon cancer; whereas KRAS(G12) codon mutation occurs more frequently in left colon cancers. In particular, we assessed that right vs left colon cancer are associated with specific molecular characteristics. These evidences, in association with clinicopathological data, can delineate novel approaches for the CRC classification and targeted intervention.
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Affiliation(s)
- Giovanni Corso
- Department of Human Pathology and Oncology, Section of General Surgery and Surgical Oncology, University of Siena, Siena, Italy
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Sarafan-Vasseur N, Sefrioui D, Tougeron D, Lamy A, Blanchard F, Le Pessot F, Di Fiore F, Michel P, Bézieau S, Latouche JB, Frebourg T, Sesboüé R. Genetic variations of the A13/A14 repeat located within the EGFR 3' untranslated region have no oncogenic effect in patients with colorectal cancer. BMC Cancer 2013; 13:183. [PMID: 23565769 PMCID: PMC3626788 DOI: 10.1186/1471-2407-13-183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/21/2013] [Indexed: 01/06/2023] Open
Abstract
Background The EGFR 3′ untranslated region (UTR) harbors a polyadenine repeat which is polymorphic (A13/A14) and undergoes somatic deletions in microsatellite instability (MSI) colorectal cancer (CRC). These mutations could be oncogenic in colorectal tissue since they were shown to result into increased EGFR mRNA stability in CRC cell lines. Methods First, we determined in a case control study including 429 CRC patients corresponding to different groups selected or not on age of tumor onset and/or familial history and/or MSI, whether or not, the germline EGFR A13/A14 polymorphism constitutes a genetic risk factor for CRC; second, we investigated the frequency of somatic mutations of this repeat in 179 CRC and their impact on EGFR expression. Results No statistically significant difference in allelic frequencies of the EGFR polyA repeat polymorphism was observed between CRC patients and controls. Somatic mutations affecting the EGFR 3′UTR polyA tract were detected in 47/80 (58.8%) MSI CRC versus 0/99 microsatellite stable (MSS) tumors. Comparative analysis in 21 CRC samples of EGFR expression, between tumor and non malignant tissues, using two independent methods showed that somatic mutations of the EGFR polyA repeat did not result into an EGFR mRNA increase. Conclusion Germline and somatic genetic variations occurring within the EGFR 3′ UTR polyA tract have no impact on CRC genetic risk and EGFR expression, respectively. Genotyping of the EGFR polyA tract has no clinical utility to identify patients with a high risk for CRC or patients who could benefit from anti-EGFR antibodies.
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Affiliation(s)
- Nasrin Sarafan-Vasseur
- Inserm U1079, Institute for Biomedical Research and Innovation, University of Rouen, 22 Boulevard Gambetta, CS 76183, Rouen Cedex 76183, France
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