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Munté E, Feliubadaló L, Del Valle J, González S, Ramos-Muntada M, Balmaña J, Ramon Y Cajal T, Tuset N, Llort G, Cadiñanos J, Brunet J, Capellá G, Lázaro C, Pineda M. Open-Source Bioinformatic Pipeline to Improve PMS2 Genetic Testing Using Short-Read NGS Data. J Mol Diagn 2024; 26:727-738. [PMID: 38851388 DOI: 10.1016/j.jmoldx.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024] Open
Abstract
The molecular diagnosis of mismatch repair-deficient cancer syndromes is hampered by difficulties in sequencing the PMS2 gene, mainly owing to the PMS2CL pseudogene. Next-generation sequencing short reads cannot be mapped unambiguously by standard pipelines, compromising variant calling accuracy. This study aimed to provide a refined bioinformatic pipeline for PMS2 mutational analysis and explore PMS2 germline pathogenic variant prevalence in an unselected hereditary cancer (HC) cohort. PMS2 mutational analysis was optimized using two cohorts: 192 unselected HC patients for assessing the allelic ratio of paralogous sequence variants, and 13 samples enriched with PMS2 (likely) pathogenic variants screened previously by long-range genomic DNA PCR amplification. Reads were forced to align with the PMS2 reference sequence, except those corresponding to exon 11, where only those intersecting gene-specific invariant positions were considered. Afterward, the refined pipeline's accuracy was validated in a cohort of 40 patients and used to screen 5619 HC patients. Compared with our routine diagnostic pipeline, the PMS2_vaR pipeline showed increased technical sensitivity (0.853 to 0.956, respectively) in the validation cohort, identifying all previously PMS2 pathogenic variants found by long-range genomic DNA PCR amplification. Fifteen HC cohort samples carried a pathogenic PMS2 variant (15 of 5619; 0.285%), doubling the estimated prevalence in the general population. The refined open-source approach improved PMS2 mutational analysis accuracy, allowing its inclusion in the routine next-generation sequencing pipeline streamlining PMS2 screening.
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Affiliation(s)
- Elisabet Munté
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain
| | - Sara González
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Mireia Ramos-Muntada
- Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain; Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Teresa Ramon Y Cajal
- Familial Cancer Clinic, Medical Oncology Service, Hospital Sant Pau, Barcelona, Spain
| | - Noemí Tuset
- Medical Oncology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Gemma Llort
- Department of Medical Oncology Parc Taulí, Hospital Universitari Parc Taulí Sabadell, Barcelona, Spain
| | - Juan Cadiñanos
- R&D Laboratory, Fundación Centro Médico de Asturias-IMOMA, Oviedo, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain; Precision Oncology Group (OncoGir_Pro), Institut d'Investigació Biomèdica de Girona, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain.
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Spain; Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Spain; Ciber Oncología, Instituto Salud Carlos III, Madrid, Spain.
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Prendeville S, Kaur H, Ansari S, Al Qa'qa' S, Stockley TL, Lajkosz K, van der Kwast T, Cheung CC, Selvarajah S. Somatic Tumor Testing in Prostate Cancer: Experience of a Tertiary Care Center Including Pathologist-Driven Reflex Testing of Localized Tumors at Diagnosis. Mod Pathol 2024; 37:100489. [PMID: 38588883 DOI: 10.1016/j.modpat.2024.100489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Somatic tumor testing in prostate cancer (PCa) can guide treatment options by identifying clinically actionable variants in DNA damage repair genes, including acquired variants not detected using germline testing alone. Guidelines currently recommend performing somatic tumor testing in metastatic PCa, whereas there is no consensus on the role of testing in regional disease, and the optimal testing strategy is only evolving. This study evaluates the frequency, distribution, and pathologic correlates of somatic DNA damage repair mutations in metastatic and localized PCa following the implementation of pathologist-driven reflex testing at diagnosis. A cohort of 516 PCa samples were sequenced using a custom next-generation sequencing panel including homologous recombination repair and mismatch repair genes. Variants were classified based on the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines. In total, 183 (35.5%) patients had at least one variant, which is as follows: 72 of 516 (13.9%) patients had at least 1 tier I or tier II variant, whereas 111 of 516 (21.5%) patients had a tier III variant. Tier I/II variant(s) were identified in 27% (12/44) of metastatic biopsy samples and 13% (61/472) of primary samples. Overall, 12% (62/516) of patients had at least 1 tier I/II variant in a homologous recombination repair gene, whereas 2.9% (10/516) had at least 1 tier I/II variant in a mismatch repair gene. The presence of a tier I/II variant was not significantly associated with the grade group (GG) or presence of intraductal/cribriform carcinoma in the primary tumor. Among the 309 reflex-tested hormone-naive primary tumors, tier I/II variants were identified in 10% (31/309) of cases, which is as follows: 9.2% (9/98) GG2; 9% (9/100) GG3; 9.1% (4/44) GG4; and 13.4% (9/67) GG5 cases. Our findings confirm the use of somatic tumor testing in detecting variants of clinical significance in PCa and provide insights that can inform the design of testing strategies. Pathologist-initiated reflex testing streamlines the availability of the results for clinical decision-making; however, pathologic parameters such as GG and the presence of intraductal/cribriform carcinoma may not be reliable to guide patient selection.
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Affiliation(s)
- Susan Prendeville
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Harpreet Kaur
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shervin Ansari
- Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Shifaa' Al Qa'qa'
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Pathology and Forensic Medicine, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Katherine Lajkosz
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Carol C Cheung
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Division of Genome Diagnostics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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Wang Y, Guan ZY, Shi SW, Jiang YR, Zhang J, Yang Y, Wu Q, Wu J, Chen JB, Ying WX, Xu QQ, Fan QX, Wang HF, Zhou L, Wang L, Fang J, Pan JZ, Fang Q. Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell. Nat Commun 2024; 15:1279. [PMID: 38341466 PMCID: PMC10858870 DOI: 10.1038/s41467-024-45659-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.
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Affiliation(s)
- Yu Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Ying Guan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Shao-Wen Shi
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Zhang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Yi Yang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qiong Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Xin Ying
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Feng Wang
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Li Zhou
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Ling Wang
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Jin Fang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China.
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310007, China.
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Yildiz S, Musarurwa TN, Algar U, Chambuso R, Rebello G, Goldberg PA, Ramesar R. Genetic insights: High germline variant rate in an indigenous African cohort with early-onset colorectal cancer. Front Oncol 2023; 13:1253867. [PMID: 37965459 PMCID: PMC10642181 DOI: 10.3389/fonc.2023.1253867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction The increase in incidence of colorectal cancer in young patients of African ancestry coupled with increased aggressiveness has warranted investigation of the heritable nature of these cancers. Only a limited number of published reports of hereditary colorectal cancer in indigenous African populations have been reported and no systematic screening of these groups has been performed previously. We aimed to investigate causative germline variants and to establish the incidence of pathogenic/likely pathogenic germline variants in the known colorectal cancer genes in indigenous African colorectal cancer patients using a next-generation sequencing (NGS) multigene panel. Materials and methods Patients were selected from two hospitals in Cape Town and Johannesburg, South Africa. Patients with unresolved molecular diagnosis with an age of onset below or at 60 years were selected. Germline DNA samples were analyzed using a 14-gene NGS panel on the Ion Torrent platform. Variant calling and annotation were performed, and variants were classified according to the American College of Medical Genetics and Genomics guidelines. Observed variants were verified by Sanger sequencing and/or long-range PCR. Results Out of 107 patients, 25 (23.4%) presented with a pathogenic/likely pathogenic germline variant (PGV). Fourteen PGVs in at least one mismatch repair (MMR) gene were identified and verified in 12 patients (11.2%). Of these MMR gene variants, five were novel. The remaining 10 PGVs were in the APC, BMPR1A, MUTYH, POLD1, and TP53 genes. Conclusion The high incidence of PGVs associated with early-onset colorectal cancer in indigenous African patients has important implications for hereditary colorectal cancer risk management. These findings pave the way for personalized genetic screening programs and cascade testing in South Africa. The next step would involve further screening of the unresolved cases using tools to detect copy number variation, methylation, and whole exome sequencing.
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Affiliation(s)
- Safiye Yildiz
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
| | - Takudzwa N. Musarurwa
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
| | - Ursula Algar
- The Colorectal Unit of the Department of Surgery, Groote Schuur Hospital and the University of Cape Town, Cape Town, South Africa
| | - Ramadhani Chambuso
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
| | - George Rebello
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
| | - Paul A. Goldberg
- The Colorectal Unit of the Department of Surgery, Groote Schuur Hospital and the University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
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Bryant P, Walton Bernstedt S, Thutkawkorapin J, Backman AS, Lindblom A, Lagerstedt-Robinson K. Exome sequencing in a Swedish family with PMS2 mutation with varying penetrance of colorectal cancer: investigating the presence of genetic risk modifiers in colorectal cancer risk. Eur J Cancer Prev 2023; 32:113-118. [PMID: 36134613 DOI: 10.1097/cej.0000000000000769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes, such as the PMS2 gene, and is characterised by a familial accumulation of colorectal cancer. The penetrance of cancer in PMS2 carriers is still not fully elucidated as a colorectal cancer risk has been shown to vary between PMS2 carriers, suggesting the presence of risk modifiers. METHODS Whole exome sequencing was performed in a Swedish family carrying a PMS2 missense mutation [c.2113G>A, p.(Glu705Lys)]. Thirteen genetic sequence variants were further selected and analysed in a case-control study (724 cases and 711 controls). RESULTS The most interesting variant was an 18 bp deletion in gene BAG1. BAG1 has been linked to colorectal tumour progression with poor prognosis and is thought to promote colorectal tumour cell survival through increased NF-κB activity. CONCLUSIONS We conclude the genetic architecture behind the incomplete penetrance of PMS2 is complicated and must be assessed in a genome wide manner using large families and multifactorial analysis.
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Affiliation(s)
- Patrick Bryant
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm
- Science for Life Laboratory Department of Biochemistry and Biophysics, Stockholm University
| | - Sophie Walton Bernstedt
- Department of Medicine, Solna, Karolinska Institutet, Stockholm
- Karolinska University Hospital, Division of Gastroenterology, Medical Unit Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn 20 University, Bangkok, Thailand
| | - Ann-Sofie Backman
- Department of Medicine, Solna, Karolinska Institutet, Stockholm
- Hereditary Cancer, Medical Unit Breast Endocrine and Sarcoma tumour, Karolinska University Hospital
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm
- Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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Poaty H, Bouya LB, Lumaka A, Mongo-Onkouo A, Gassaye D. PMS2 Pathogenic Variant in Lynch Syndrome-Associated Colorectal Cancer with Polyps. Glob Med Genet 2023; 10:1-5. [PMID: 36644715 PMCID: PMC9833889 DOI: 10.1055/s-0042-1759888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/25/2022] [Indexed: 01/13/2023] Open
Abstract
Background Lynch syndrome (LS) is an autosomal dominant condition due to the germline mutation in the mismatch repair (MMR) genes including MLH1 , MSH2 , MSH6, and PMS2 (post-meiotic segregation increased 2). The MMR mutation carriers have high risk for cancers. Pathogenic PMS2 variants are rarely reported in LS-associated colorectal cancer (CRC) with colorectal polyps. The aim of the study was to investigate the genetic etiology of CRC in an individual with CRC with multiple colorectal polyps and a family history of cancers. Patients and Methods The index patient was an African male affected by CRC with multiple colorectal polyps. The clinical diagnostic for LS was based on the Amsterdam II criteria and pedigree. Next-generation sequencing with inherited cancer genes panel was used to detect the pathogenic variant. Results The patient fulfilled the Amsterdam II criteria and the pedigree revealed a family history of recurrent CRC. A deleterious PMS2 germline heterozygous mutation c.2192_2196delTAACT was detected. Conclusion Our study supports the notion that LS may be associated with polyps and shows the predisposition of PMS2 heterozygous mutation in LS-associated CRC at young age.
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Affiliation(s)
- Henriette Poaty
- Embryology and Genetic Laboratory, Faculty of Health Sciences, Marien Ngouabi University, Brazzaville, Congo,Department of Clinical Sciences, Institute of Research on Health Sciences, Brazzaville, Congo,Address for correspondence Henriette Poaty, MD Embryology and Genetic Laboratory, Faculty of Health Sciences, Marien Ngouabi UniversityBP 2672, BrazzavilleRepublic of Congo
| | - Lauria Batamba Bouya
- Embryology and Genetic Laboratory, Faculty of Health Sciences, Marien Ngouabi University, Brazzaville, Congo
| | - Aimé Lumaka
- Centre de Génétique de l'Université de Kinshasa, DR Congo,Service de Génétique Humaine, Sart Tilman, Avenue de l'Hôpital 13, 4000, Liège, Belgium
| | - Arnaud Mongo-Onkouo
- Embryology and Genetic Laboratory, Faculty of Health Sciences, Marien Ngouabi University, Brazzaville, Congo,Gastro-Enterology and Internal Medicine Service, CHU Brazzaville, Congo
| | - Deby Gassaye
- Embryology and Genetic Laboratory, Faculty of Health Sciences, Marien Ngouabi University, Brazzaville, Congo,Gastro-Enterology and Internal Medicine Service, CHU Brazzaville, Congo
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7
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Sekine Y, Iwasaki Y, Hakozaki N, Endo M, Kamatani Y, Matsuda K, Murakami Y, Sano T, Akamatsu S, Kobayashi T, Nakagawa H, Numakura K, Narita S, Habuchi T, Momozawa Y. Prevalence and risk estimation of cancer-predisposing genes for upper urinary tract urothelial carcinoma in Japanese. Jpn J Clin Oncol 2022; 52:1441-1445. [PMID: 36093724 DOI: 10.1093/jjco/hyac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/12/2022] [Indexed: 11/12/2022] Open
Abstract
Upper urinary tract urothelial carcinoma is a rare cancer that has been associated with mismatch repair genes such as MLH1, MSH2, MSH6 and PMS2. In addition, patients with pathogenic variants of cancer-predisposing genes such as BRCA1 and BRCA2 have been reported. However, how cancer-predisposing genes affect the risk of upper urinary tract urothelial carcinoma in the Japanese population remains unclear. Thus, we performed a case-control sequencing study of 27 cancer-predisposing genes in 208 upper urinary tract urothelial carcinoma patients and 37 727 controls. Only MSH6 and MSH2 were observed with a value of P < 0.05. However, there was no difference in the prevalence of pathogenic variants of BRCA1/2, which does not support the use of a poly adenosine diphosphate-ribose polymerase inhibitor in patients with upper urinary tract urothelial carcinoma. Only mismatch repair genes were associated with patients with upper urinary tract urothelial carcinoma, but the prevalence of pathogenic variants in mismatch repair genes was lower than that reported in previous studies from other populations.
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Affiliation(s)
- Yuya Sekine
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.,Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Nozomi Hakozaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takeshi Sano
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shusuke Akamatsu
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuyuki Numakura
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shintaro Narita
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Tomonori Habuchi
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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8
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Usui Y, Iwasaki Y, Matsuo K, Endo M, Kamatani Y, Hirata M, Sugano K, Yoshida T, Matsuda K, Murakami Y, Maeda Y, Nakagawa H, Momozawa Y. Association between germline pathogenic variants in cancer-predisposing genes and lymphoma risk. Cancer Sci 2022; 113:3972-3979. [PMID: 36065483 PMCID: PMC9633290 DOI: 10.1111/cas.15522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 11/28/2022] Open
Abstract
The application of advanced molecular technology has significantly expanded lymphoma classification, allowing risk stratification and treatment optimization. Limited evidence suggests the presence of a genetic predisposition in lymphoma, indicating the potential for better individualized clinical management based on a novel lymphoma classification. Herein, we examined the impact of germline pathogenic variants in 27 cancer‐predisposing genes with lymphoma risk and explored the clinical characteristics of pathogenic variant carriers. This study included 2,066 lymphoma patients and 38,153 cancer‐free controls from the Japanese population. Following quality control of sequencing data, samples from 1,982 lymphoma patients and 37,592 controls were further analyzed. We identified 309 pathogenic variants among 4,850 variants in the 27 cancer‐predisposing genes. Pathogenic variants in the following four cancer‐predisposing genes were associated with a high risk of lymphoma: ATM (odds ratio [OR], 2.63; 95% confidence interval [CI], 1.25–5.51; p = 1.06 × 10−2), BRCA1 (OR, 5.88; 95% CI, 2.65–13.02; p = 1.27 × 10−5), BRCA2 (OR, 2.94; 95% CI, 1.60–5.42; p = 5.25 × 10−4), and TP53 (OR, 5.22; 95% CI, 1.43–19.02; p = 1.23 × 10−2). The proportion of carriers of these genes was 1.6% of lymphoma patients. Furthermore, pathogenic variants in these genes were especially associated with a higher risk of mantle cell lymphoma (OR, 21.57; 95% CI, 7.59–61.26; p = 8.07 × 10−9). These results provide novel insights concerning monogenic form into lymphoma classification. Some lymphoma patients may benefit from surveillance and targeted treatment, such as other neoplasms.
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Affiliation(s)
- Yoshiaki Usui
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Hematology, Oncology and Respiratory Medicine, Okayama University Medical School, Okayama, Japan.,Division of Cancer Information and Control, Department of Preventive Medicine, Aichi Cancer Center, Nagoya, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center, Nagoya, Japan.,Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kokichi Sugano
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan.,Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation, Tokyo, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshinobu Maeda
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceuticals Sciences, Okayama, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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9
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Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, Takata S, Inai C, Aoi T, Mizukoshi M, Maejima K, Hirata M, Murakami Y, Kamatani Y, Kubo M, Akagi K, Matsuda K, Nakagawa H, Momozawa Y. Population-based Screening for Hereditary Colorectal Cancer Variants in Japan. Clin Gastroenterol Hepatol 2022; 20:2132-2141.e9. [PMID: 33309985 DOI: 10.1016/j.cgh.2020.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) is one of the most common cancers in the world. A small proportion of CRCs can be attributed to recognizable hereditary germline variants of known CRC susceptibility genes. To better understand cancer risk, it is necessary to explore the prevalence of hereditary CRC and pathogenic variants of multiple cancer-predisposing genes in non-European populations. METHODS We analyzed the coding regions of 27 cancer-predisposing genes in 12,503 unselected Japanese CRC patients and 23,705 controls by target sequencing and genome-wide SNP chip. Their clinical significance was assessed using ClinVar and the guidelines by ACMG/AMP. RESULTS We identified 4,804 variants in the 27 genes and annotated them as pathogenic in 397 and benign variants in 941, of which 43.6% were novel. In total, 3.3% of the unselected CRC patients and 1.5% of the controls had a pathogenic variant. The pathogenic variants of MSH2 (odds ratio (OR) = 18.1), MLH1 (OR = 8.6), MSH6 (OR = 4.9), APC (OR = 49.4), BRIP1 (OR=3.6), BRCA1 (OR = 2.6), BRCA2 (OR = 1.9), and TP53 (OR = 1.7) were significantly associated with CRC development in the Japanese population (P-values<0.01, FDR<0.05). These pathogenic variants were significantly associated with diagnosis age and personal/family history of cancer. In total, at least 3.5% of the Japanese CRC population had a pathogenic variant or CNV of the 27 cancer-predisposing genes, indicating hereditary cancers. CONCLUSIONS This largest study of CRC heredity in Asia can contribute to the development of guidelines for genetic testing and variant interpretation for heritable CRCs.
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Affiliation(s)
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | | | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program, RIKEN, Yokohama; Artificial intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba
| | | | - Chihiro Inai
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Tomomi Aoi
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | - Makoto Hirata
- Institute of Medical Science, University of Tokyo, Tokyo
| | | | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama
| | - Koichi Matsuda
- Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan
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10
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Comprehensive assessment of germline pathogenic variant detection in tumor-only sequencing. Ann Oncol 2022; 33:426-433. [PMID: 35074424 PMCID: PMC9172914 DOI: 10.1016/j.annonc.2022.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022] Open
Abstract
Background: Tumor-only sequencing, implemented for the identification of somatic variants, is oftentimes used for the detection of actionable germline variants. We sought to determine whether tumor-only sequencing assays are suitable for detection of actionable germline variants, given their importance for the delivery of targeted therapies and risk-reducing measures. Patients and methods: The detection of germline variants affecting moderate- and high-penetrance cancer susceptibility genes (CSGs) by tumor-only sequencing was compared to clinical germline testing in 21 333 cancer patients who underwent tumor and germline testing using the Food and Drug Administration (FDA)-authorized Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay. Seven homologous recombination deficiency (HRD), two DNA damage response (DDR) and four mismatch repair (MMR) genes, as well as NF1, RB1 and TP53 were included in the analysis. FDA-authorized and New York State Department of Health-approved sequencing methods for germline, tumor/normal and tumor-only sequencing assays and analytical pipelines were employed. Results: In patients who underwent tumor and germline sequencing, as compared to clinical genetic testing, tumor-only sequencing failed to detect 10.5% of clinically actionable pathogenic germline variants in CSGs, including 18.8%, 12.8% and 7.3% of germline variants in MMR, DDR and HRD genes, respectively. The sensitivity for detection of pathogenic germline variants by tumor-only sequencing was 89.5%. Whilst the vast majority of pathogenic germline exonic single-nucleotide variants (SNVs) and small indels were detected by tumor-only sequencing, large percentages of germline copy number variants, intronic variants and repetitive element insertions were not detected. Conclusions: Tumor-only sequencing is adequate for the detection of clinically actionable germline variants, particularly for SNVs and small indels; however, a small subset of alterations affecting HRD, DDR and MMR genes may not be detected optimally. Therefore, for high-risk patients with negative tumor-only sequencing results, clinical genetic testing could be considered given the impact of these variants on therapy and genetic counseling.
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11
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Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS. The context-specific role of germline pathogenicity in tumorigenesis. Nat Genet 2021; 53:1577-1585. [PMID: 34741162 PMCID: PMC8957388 DOI: 10.1038/s41588-021-00949-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/09/2021] [Indexed: 11/08/2022]
Abstract
Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.
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Affiliation(s)
- Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Chaitanya Bandlamudi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip Jonsson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Hwee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JianJiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roy Cambria
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semanti Mukherjee
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen A Cadoo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria I Carlo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Walsh
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
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12
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Smithgall MC, Remotti H, Hsiao SJ, Mansukhani M, Liu-Jarin X, Fernandes H. Investigation of discrepant mismatch repair immunohistochemistry and microsatellite instability polymerase chain reaction test results for gynecologic cancers using next-generation sequencing. Hum Pathol 2021; 119:41-50. [PMID: 34666078 DOI: 10.1016/j.humpath.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022]
Abstract
Gynecologic cancers are routinely screened for DNA mismatch repair (MMR) gene mutations using immunohistochemistry (IHC) and/or polymerase chain reaction (PCR) for microsatellite instability (MSI) to enable selection of immune checkpoint inhibitor therapy and screen for Lynch syndrome. The limited data that compare IHC and MSI in endometrial tumors have shown discordance rates of 5-10%. We reviewed MMR/MSI results in gynecologic cancers and used next-generation sequencing (NGS) to interrogate discrepancies. Of the 328 cases with both IHC and MSI results, 256 (78.0%) were microsatellite stable (MSS) with preserved MMR (pMMR), 64 (19.5%) cases were MSI-High (MSI-H) with MMR deficient (dMMR), 2 cases showed subclonal loss of MLH1 and PMS2 with MSI-H, and 6 cases were discordant. Overall, there was a 98.2% (322/328) IHC/MSI concordance. Discordant cases were retested and/or subject to NGS. Of the six discrepant cases, five showed dMMR with MSS and one showed pMMR with MSI-H. One dMMR/MSI-L case showed loss of PMS2 with a germline pathogenic mutation. The pMMR/MSI-H case was found to harbor pathogenic variants in MLH1 and MSH6. One of the two cases with subclonal populations demonstrated MSI-H in the dMMR area and MSS in the pMMR area. These results emphasize the importance of selecting the appropriate tumor tissue for both IHC and molecular testing and demonstrate that NGS can help resolve discrepant MMR and MSI results.
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Affiliation(s)
- Marie C Smithgall
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Helen Remotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Xiaolin Liu-Jarin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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13
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Rocha ML, Schmid KW, Czapiewski P. The prevalence of DNA microsatellite instability in anaplastic thyroid carcinoma - systematic review and discussion of current therapeutic options. Contemp Oncol (Pozn) 2021; 25:213-223. [PMID: 34729042 PMCID: PMC8547184 DOI: 10.5114/wo.2021.110052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION Anaplastic thyroid carcinoma is a rare, rapidly progressing, highly aggressive thyroid malignancy. Responses to immune checkpoint inhibitors in mismatch repair-deficient/microsatellite instability-high tumours of other locations have shown promising results, and with the extended approval of the PD-1 receptor inhibitor pembrolizumab by the Food and Drug Administration, also anaplastic thyroid cancer (ATC) requires analysis for microsatellite instability (MSI) status. MATERIAL AND METHODS Systematic research for relevant literature was conducted in different databases. Prevalence, detection methods, and the potential prognostic/predictive value of MSI in view of the available targeted therapies were of special focus. RESULTS Selected citations revealed the prevalence of MSI in 7.4%, with mutations in the MSH2 gene (33%) being the most frequent, followed by MSH6 (25%) and MLH1 (16.7%) occurring in the following combinations: MLH1-MSH2 (8.3%), MSH2-MSH6 (8.3%), and MLH3-MSH5 (8.3%). No mutations in the PMS2 gene were reported. Sixty-six co-mutations in 9 cases were found, with TP53 (88.9%), NF1 (44.4 %), ATM (33.3%), and RB1 (33.3%) being the most frequent. No RAS mutations were noted. Survival ranged between 2.8 and 48 months, and patient age varied between 49 and 84 years. There are insufficient and heterogenous data concerning the predictive or prognostic value of mismatch repair-deficient/microsatellite instability status. CONCLUSIONS Tumour molecular profiling is fundamental in ATC for predictive, prognostic, as well as therapeutic reasons, and analysis of MSI status is strongly suggested because a small subgroup show the MSI signature and might profit from recently approved targeted therapies.
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Affiliation(s)
- Maria Linda Rocha
- Institute of Pathology Königs Wusterhausen, Königs Wusterhausen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Piotr Czapiewski
- Institute of Pathology, Dessau Medical Centre, Dessau, Germany
- Institute of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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14
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Mizukami K, Iwasaki Y, Kawakami E, Hirata M, Kamatani Y, Matsuda K, Endo M, Sugano K, Yoshida T, Murakami Y, Nakagawa H, Spurdle AB, Momozawa Y. Genetic characterization of pancreatic cancer patients and prediction of carrier status of germline pathogenic variants in cancer-predisposing genes. EBioMedicine 2020; 60:103033. [PMID: 32980694 PMCID: PMC7519363 DOI: 10.1016/j.ebiom.2020.103033] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND National Comprehensive Cancer Network (NCCN) recently recommended germline genetic testing for all pancreatic cancer patients. However, the genes targeted by genetic testing and the feasibility of selecting patients likely to carry pathogenic variants have not been sufficiently verified. The purpose of this study was to genetically characterize Japanese patients and examine whether the current guideline is applicable in this population. METHODS Using targeted sequencing, we analyzed the coding regions of 27 cancer-predisposing genes in 1,005 pancreatic cancer patients and 23,705 controls in Japan. We compared the pathogenic variant frequency between cases and controls and documented the demographic and clinical characteristics of carrier patients. We then examined if it was possible to use machine learning to predict carrier status based on those characteristics. FINDINGS We identified 205 pathogenic variants across the 27 genes. Pathogenic variants in BRCA2, ATM, and BRCA1 were significantly associated with pancreatic cancer. Characteristics associated with carrier status were inconsistent with previous investigations. Machine learning classifiers had a low performance in determining the carrier status of pancreatic cancer patients, while the same classifiers, when applied to breast cancer data as a positive control, had a higher performance that was comparable to that of the NCCN guideline. INTERPRETATION Our findings support the clinical significance of multigene panel testing for pancreatic cancer and indicate that at least 3.4% of Japanese patients may respond to poly (ADP ribose) polymerase inhibitor treatments. The difficulty in predicting carrier status suggests that offering germline genetic testing for all pancreatic cancer patients is reasonable. FUNDING AMED under Grant Number JP19kk0305010 and Australian National Health and Medical Research funding (ID177524).
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Affiliation(s)
- Keijiro Mizukami
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program, RIKEN, Yokohama, Kanagawa, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Makoto Hirata
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo Japan
| | - Yoichiro Kamatani
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kokichi Sugano
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo Japan; Division of Cancer Prevention and Genetic Counseling, Genome Center, Tochigi Cancer Center, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo Japan
| | | | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Amanda B Spurdle
- Division of Genetics and Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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15
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DNA Mismatch Repair Gene Variants in Sporadic Solid Cancers. Int J Mol Sci 2020; 21:ijms21155561. [PMID: 32756484 PMCID: PMC7432688 DOI: 10.3390/ijms21155561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
The phenotypic effects of single nucleotide polymorphisms (SNPs) in the development of sporadic solid cancers are still scarce. The aim of this review was to summarise and analyse published data on the associations between SNPs in mismatch repair genes and various cancers. The mismatch repair system plays a unique role in the control of the genetic integrity and it is often inactivated (germline and somatic mutations and hypermethylation) in cancer patients. Here, we focused on germline variants in mismatch repair genes and found the outcomes rather controversial: some SNPs are sometimes ascribed as protective, while other studies reported their pathological effects. Regarding the complexity of cancer as one disease, we attempted to ascertain if particular polymorphisms exert the effect in the same direction in the development and treatment of different malignancies, although it is still not straightforward to conclude whether polymorphisms always play a clear positive role or a negative one. Most recent and robust genome-wide studies suggest that risk of cancer is modulated by variants in mismatch repair genes, for example in colorectal cancer. Our study shows that rs1800734 in MLH1 or rs2303428 in MSH2 may influence the development of different malignancies. The lack of functional studies on many DNA mismatch repair SNPs as well as their interactions are not explored yet. Notably, the concerted action of more variants in one individual may be protective or harmful. Further, complex interactions of DNA mismatch repair variations with both the environment and microenvironment in the cancer pathogenesis will deserve further attention.
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Rasool M, Pushparaj PN, Mirza Z, Imran Naseer M, Abusamra H, Alquaiti M, Shaabad M, Sibiany AMS, Gauthaman K, Al-Qahtani MH, Karim S. Array comparative genomic hybridization based identification of key genetic alterations at 2p21-p16.3 (MSH2, MSH6, EPCAM), 3p23-p14.2 (MLH1), 7p22.1 (PMS2) and 1p34.1-p33 (MUTYH) regions in hereditary non polyposis colorectal cancer (Lynch syndrome) in the Kingdom of Saudi Arabia. Saudi J Biol Sci 2020; 27:157-162. [PMID: 31889830 PMCID: PMC6933242 DOI: 10.1016/j.sjbs.2019.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/14/2019] [Indexed: 12/12/2022] Open
Abstract
Lynch syndrome is inherited in an autosomal dominant mode. Lynch syndrome is caused by impairment of one or more of the various genes (most frequently MLH1 and MSH2) involved in mismatch repair. In this study, whole genome comparative genomic hybridization array (array CGH) based genomic analysis was performed on twelve Saudi Lynch syndrome patients. A total of 124 chromosomal alterations (structural loss) were identified at mean log2 ratio cut off value of ±0.25. We also found structural loss in 2p21-p16.3, 3p23-p14.2, 7p22.1 and 1p34.1-p33 regions. These findings were subsequently validated by real time quantitative PCR showing downregulation of MSH2, MSH6, EPCAM, MLH1, PMS2 and MUTYH genes. These findings shall help in establishing database for alterations in mismatch repair genes underlying Lynch syndrome in Saudi population as well as to determine the incidence ratio of these disorders. Guided counselling will subsequently lead to the prevention and eradication of Lynch Syndrome in the local population.
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Affiliation(s)
- Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba Abusamra
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maha Alquaiti
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manal Shaabad
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Kalamegam Gauthaman
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Hussein Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding author at: CEGMR, KAU, Jeddah, Saudi Arabia.
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Okkels H, Lagerstedt-Robinsson K, Wikman FP, Hansen TVO, Lolas I, Lindberg LJ, Krarup HB. Detection of PMS2 Mutations by Screening Hereditary Nonpolyposis Colon Cancer Families from Denmark and Sweden. Genet Test Mol Biomarkers 2019; 23:688-695. [PMID: 31433215 DOI: 10.1089/gtmb.2018.0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background and Aims: Hereditary nonpolyposis colon cancer (HNPCC) and Lynch syndrome (LS) are characterized by defects in the mismatch repair (MMR) system, which protects the integrity of the genome. Pathogenic variants in four MMR genes (MLH1, MSH2, MSH6, and PMS2) are responsible for LS, an autosomal, dominant hereditary disease that occurs with a frequency of 2-5% among all colorectal cancer cases. It has been estimated that ∼2-5% of all pathogenic variants found in the four MMR genes in LS cases are detected in the PMS2 gene. An overview of detected variants is presented here. Materials and Methods: Long-range (LR) PMS2 polymerase chain reaction (PCR) and PMS2 multiplex ligation probe amplification (MLPA) assays were used to detect PMS2 variants in ∼1500 probands. In a subset of the probands, pathogenic PMS2 variants were detected by next-generation sequencing, and all detected variants were confirmed by LR-PCR combined with an MLPA assay. Results: A summary of PMS2 mutation analyses performed on colon cancer patients from molecular diagnostic laboratories in Denmark and Sweden is presented. By screening ∼1500 HNPCC probands, a total of 40 different PMS2 variants were detected in 71 probands (5%); 20 variants were classified as pathogenic (C5), 2 variants as likely pathogenic (C4), 15 variants as variants of unknown significance (VUSs) (C3), 1 variant as likely benign (C2), and 2 variants as benign (C1). In total, 22/71 (31%) of the probands carried a pathogenic sequence variant. Among the probands with isolated loss of pPMS2 expression, the fraction of pathogenic variants was 20/35 (55%). Conclusions: Approximately 5% of the probands found in the Danish and Swedish populations presented here carried a PMS2 variant. In this study, six novel pathogenic variants and seven VUSs are reported.
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Affiliation(s)
- Henrik Okkels
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Kristina Lagerstedt-Robinsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Friedrik P Wikman
- Department of Molecular Medicine (MOMA), Århus University Hospital, Århus, Denmark
| | - Thomas V O Hansen
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark.,Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ihab Lolas
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Lars Joachim Lindberg
- The Danish HNPCC Registry, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Henrik B Krarup
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
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18
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Bowles KR, Mancini-DiNardo D, Coffee B, Cox HC, Qian Y, Elias M, Singh N, Judkins T, Leclair B, Roa BB. Hereditary cancer testing challenges: assembling the analytical pieces to solve the patient clinical puzzle. Future Oncol 2018; 15:65-79. [PMID: 30113232 DOI: 10.2217/fon-2018-0476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expanded genetic test utilization to guide cancer management has driven the development of larger gene panels and greater diversity in the patient population pursuing testing, resulting in increased identification of atypical or technically challenging genetic findings. To ensure appropriate patient care, it is critical that genetic tests adequately identify and characterize these findings. We describe genetic testing challenges frequently encountered by our laboratory and the methodologies we employ to improve test accuracy for the identification and characterization of atypical genetic findings. While these findings may be individually rare, 15,745 (9%) individuals tested by our laboratory for hereditary cancer risk had an atypical genetic finding, highlighting the importance of employing highly accurate and comprehensive methods in clinical genetic testing.
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Affiliation(s)
- Karla R Bowles
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Yaping Qian
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Maria Elias
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Nanda Singh
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Thaddeus Judkins
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benoît Leclair
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benjamin B Roa
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
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19
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Pujar NK, Premakshi HG, Laad S, Pattar SV, Mirjankar M, Kamanavalli CM. Biodegradation of chlorpropham and its major products by Bacillus licheniformis NKC-1. World J Microbiol Biotechnol 2018; 34:112. [DOI: 10.1007/s11274-018-2494-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/30/2018] [Indexed: 11/25/2022]
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20
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Blount J, Prakash A. The changing landscape of Lynch syndrome due to PMS2 mutations. Clin Genet 2018; 94:61-69. [PMID: 29286535 PMCID: PMC5995637 DOI: 10.1111/cge.13205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations.
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Affiliation(s)
- Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
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21
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Zheng J, Huang B, Nie X, Zhu Y, Han N, Li Y. The clinicopathological features and prognosis of tumor MSI in East Asian colorectal cancer patients using NCI panel. Future Oncol 2018; 14:1355-1364. [PMID: 29366338 DOI: 10.2217/fon-2017-0662] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AIM To compare test results obtained from a PCR assay for the National Cancer Institute (NCI) five loci criteria for detecting microsatellite instability (MSI) with those obtained from immunohistochemistry of mismatch repair and a five-mononucleotide site amplification system in East Asian patients with colorectal cancer. PATIENTS & METHODS A total of 245 East Asian patients with colorectal cancer were studied retrospectively at our institution. RESULTS The consistency of the NCI panel PCR method compared with detection of mismatch repair protein expression by immunohistochemistry was 0.898. High level MSI (MSI-H) status was correlated with the Tumor, Node, Metastasis stage, tumor location site, metastasis, tumor grade, mucinous histological type and BRAF-type mutations. CONCLUSION The NCI panel PCR assay has excellent sensitivity and specificity for detecting MSI in an East Asian population.
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Affiliation(s)
- Jianmin Zheng
- Department of Pathology, Changhai Hospital of Shanghai, 168 Changhai Road, Shanghai 200433, PR China
| | - Bangxing Huang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430022, PR China
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430022, PR China
| | - Yan Zhu
- Department of Pathology, Changhai Hospital of Shanghai, 168 Changhai Road, Shanghai 200433, PR China
| | - Ningning Han
- Department of Clinical Medicine, Shanghai Tongshu Biotech Co. Ltd, Shanghai 200120, PR China
| | - Yan Li
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430022, PR China
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22
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Alpert L, Pai RK, Srivastava A, McKinnon W, Wilcox R, Yantiss RK, Arcega R, Wang HL, Robert ME, Liu X, Pai RK, Zhao L, Westerhoff M, Hampel H, Kupfer S, Setia N, Xiao SY, Hart J, Frankel WL. Colorectal Carcinomas With Isolated Loss of PMS2 Staining by Immunohistochemistry. Arch Pathol Lab Med 2018; 142:523-528. [DOI: 10.5858/arpa.2017-0156-oa] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
Isolated loss of PMS2 staining is an uncommon immunophenotype in colorectal carcinomas, accounting for approximately 4% of tumors with microsatellite instability. Limited information regarding these tumors is available in the literature.
Objective.—
To compare the clinicopathologic features of colorectal carcinomas with isolated PMS2 loss by immunohistochemistry to those with other forms of mismatch repair deficiency.
Design.—
Ninety-three colorectal carcinomas with isolated PMS2 loss by immunohistochemistry and 193 with other forms of mismatch repair deficiency were identified. Forty (43%) of the isolated PMS2 loss cases and 35 control cases (18%) had a known germline mutation or a clinical diagnosis of Lynch syndrome.
Results.—
Overall, isolated PMS2-loss tumors occurred in significantly younger patients (P < .001) and in fewer female patients (P = .006). These tumors were significantly less likely to be right-sided (P = .001), high-grade (P = .01), or display histologic features of microsatellite instability (P < .001). The isolated PMS2-loss group also exhibited increased odds of disease-specific death (odds ratio [OR], 3.09; 95% CI, 1.41–6.85; P = .007). When the analysis was restricted to germline mutation/Lynch syndrome cases and controls, no significant differences were detected for age, sex, tumor location, tumor grade, histologic features, or distant metastases, although a trend toward increased odds of disease-specific death in the isolated PMS2-loss group was evident (OR, 3.87; 95% CI, 0.89–27.04; P = .10).
Conclusions.—
Unusual clinicopathologic features observed in colorectal carcinomas with isolated PMS2 loss are likely related to the high proportion of cases caused by germline mutations. Isolated PMS2-loss tumors may demonstrate more aggressive behavior than other tumors with microsatellite instability, but larger studies are needed to investigate that possibility further.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wendy L. Frankel
- From the Departments of Pathology (Drs Alpert, Setia, Xiao, and Hart) and Medicine (Dr Kupfer), University of Chicago, Chicago, Illinois; the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Reetesh Pai); the Department of Pathology, Brigham and Womens Hospital, Boston, Massachusetts (Dr Srivastava); the Departments of Medicine (Ms McKinnon) and Patho
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23
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Lorans M, Dow E, Macrae FA, Winship IM, Buchanan DD. Update on Hereditary Colorectal Cancer: Improving the Clinical Utility of Multigene Panel Testing. Clin Colorectal Cancer 2018; 17:e293-e305. [PMID: 29454559 DOI: 10.1016/j.clcc.2018.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the most common cancers, is a major public health issue globally, especially in Westernized countries. Up to 35% of CRCs are thought to be due to heritable factors, but currently only 5% to 10% of CRCs are attributable to high-risk mutations in known CRC susceptibility genes, predominantly the mismatch repair genes (Lynch syndrome) and adenomatous polyposis coli gene (APC; familial adenomatous polyposis). In this era of precision medicine, high-risk mutation carriers, when identified, can be offered various risk management options that prevent cancers and improve survival, including risk-reducing medication, screening for early detection, and surgery. The practice of clinical genetics is currently transitioning from phenotype-directed single gene testing to multigene panels, now offered by numerous providers. For CRC, the genes included across these panels vary, ranging from well established, clinically actionable susceptibility genes with quantified magnitude of risk, to genes that lack extensive validation or have less evidence of association with CRC and, therefore, have minimal clinical utility. The current lack of consensus regarding inclusion of genes in CRC panels presents challenges in patient counseling and management, particularly when a variant in a less validated gene is identified. Furthermore, there remain considerable challenges regarding variant interpretation even for the well established CRC susceptibility genes. Ironically though, only through more widespread testing and the accumulation of large international data sets will sufficient information be generated to (i) enable well powered studies to determine if a gene is associated with CRC susceptibility, (ii) to develop better models for variant interpretation and (iii) to facilitate clinical translation.
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Affiliation(s)
- Marie Lorans
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eryn Dow
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Finlay A Macrae
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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Germline Mutations in MLH1 Leading to Isolated Loss of PMS2 Expression in Lynch Syndrome: Implications for Diagnostics in the Clinic. Am J Surg Pathol 2017; 41:861-864. [DOI: 10.1097/pas.0000000000000827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Rey JM, Ducros V, Pujol P, Wang Q, Buisine MP, Aissaoui H, Maudelonde T, Olschwang S. Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing. J Mol Diagn 2017; 19:589-601. [PMID: 28502729 DOI: 10.1016/j.jmoldx.2017.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/03/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of genetic alterations is important for family risk assessment in colorectal cancers. Next-generation sequencing (NGS) technologies provide useful tools for single-nucleotide and copy number variation (CNV) identification in many genes and samples simultaneously. Herein, we present the validation of current Multiplicom MASTR designs of mismatch repair combined to familial adenomatous polyposis genes in a single PCR reamplification test for eight DNA samples simultaneously on a MiSeq apparatus. Blood samples obtained from 224 patients were analyzed. We correctly identified the 97 mutations selected among 48 samples tested in a validation cohort. PMS2 NGS analysis of the eight positive controls identified single-nucleotide variations not detected with targeted referent methods. As NGS method could not discriminate if some of them were assigned to PMS2 or pseudogenes, only CNV analysis with multiplex ligand probe-dependent amplification confirmation was retained for clinical use. Twenty-seven new variants of unknown significance, 21 disease-causing variants, and two CNVs were detected among the 176 patient samples analyzed in diagnosis routine. MUTYH disease-causing mutations were identified in two patient samples assessed for mismatch repair testing, confirming that this method facilitates accurate and rapid individual risk assessments. In one sample, the MUTYH mutation was associated with a MSH6 disease-causing mutation, suggesting that this method is helpful to identify additional cancer risk modifiers and provides a useful tool to optimize clinical issues.
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Affiliation(s)
- Jean-Marc Rey
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France.
| | - Vincent Ducros
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Pascal Pujol
- Oncogenetic Department, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Qing Wang
- Laboratoire de Génétique Constitutionnelle des Cancers Fréquents, Léon Bérard Center, Lyon, France
| | - Marie-Pierre Buisine
- Laboratoire de Biochimie et Biologie Moléculaire, Oncologie et Génétique Moléculaire, Center de Biologie Pathologie, CHRU Lille, Lille, France
| | | | - Thierry Maudelonde
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Arnaud de Villeneuve Hospital, Montpellier, France; Montpellier University, EA2415, Institut Universitaire de Recherche Clinique, Montpellier, France
| | - Sylviane Olschwang
- INSERM UMR_S910, Aix-Marseille University, Ramsay Générale de Santé Clairval Hospital, Marseille, France
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Wang WC, Lee YT, Lai YC. PMS2 gene mutation results in DNA mismatch repair system failure in a case of adult granulosa cell tumor. J Ovarian Res 2017; 10:22. [PMID: 28347324 PMCID: PMC5369012 DOI: 10.1186/s13048-017-0317-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/22/2017] [Indexed: 12/19/2022] Open
Abstract
Background Granulosa cell tumors are rare ovarian malignancies. Their characteristics include unpredictable indolent growth with malignant potential and late recurrence. Approximately 95% are of adult type. Recent molecular studies have characterized the FOXL2 402C > G mutation in adult granulosa cell tumor. Our previous case report showed that unique FOXL2 402C > G mutation and defective DNA mismatch repair system are associated with the development of adult granulosa cell tumor. Findings In this study, the DNA sequences of four genes, MSH2, MLH1, MSH6, and PMS2, in the DNA mismatch repair system were determined via direct sequencing to elucidate the exact mechanism for the development of this granulosa cell tumor. The results showed that two missense germline mutations, T485K and N775L, inactivate the PMS2 gene. Conclusions The results of this case study indicated that although FOXL2 402C > G mutation determines the development of granulosa cell tumor, PMS2 mutation may be the initial driver of carcinogenesis. Immunohistochemistry-based tumor testing for mismatch repair gene expression may be necessary for granulosa cell tumors to determine their malignant potential or if they are part of Lynch syndrome.
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Affiliation(s)
- Wen-Chung Wang
- Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung, Taiwan
| | - Ya-Ting Lee
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Road, Taichung, 402, Taiwan, Republic of China
| | - Yen-Chein Lai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Road, Taichung, 402, Taiwan, Republic of China.
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DNA Methylation Identifies Loci Distinguishing Hereditary Nonpolyposis Colorectal Cancer Without Germ-Line MLH1/MSH2 Mutation from Sporadic Colorectal Cancer. Clin Transl Gastroenterol 2016; 7:e208. [PMID: 27977020 PMCID: PMC5288582 DOI: 10.1038/ctg.2016.59] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 10/26/2016] [Indexed: 12/26/2022] Open
Abstract
Objectives: Roughly half of hereditary nonpolyposis colorectal cancer (HNPCC) cases are Lynch syndrome and exhibit germ-line mutations in DNA mismatch repair (MMR) genes; the other half are familial colorectal cancer (CRC) type X (FCCTX) and are MMR proficient. About 70% of Lynch syndrome tumors have germ-line MLH1 or MSH2 mutations. The clinical presentation, histopathological features, and carcinogenesis of FCCTX resemble those of sporadic MMR-proficient colorectal tumors. It is of interest to obtain biomarkers that distinguish FCCTX from sporadic microsatellite stable (MSS) CRC, to develop preventive strategies. Methods: The tumors and adjacent normal tissues of 40 patients with HNPCC were assayed using the Illumina Infinium HumanMethylation27 (HM27) BeadChip to assess the DNA methylation level at about 27,000 loci. The germ-line mutation status of MLH1 and MSH2 and the microsatellite instability status in these patients were obtained. Genome-wide DNA methylation measurements of three groups of patients with general CRC were downloaded from public domain databases. Probes with DNA methylation levels that differed significantly between patients with sporadic MSS CRC and FCCTX were examined, to explore their potential as biomarkers. Results: We found that MSS HNPCC tumors were overwhelmingly hypomethylated compared with those from patient groups with other types of CRC, including germ-line MLH1/MSH2-mutated HNPCC and sporadic MSS CRC. Five gene-marker panels that exhibited a sensitivity of 100% and a specificity higher than 90% in both discovery and validation cohorts were proposed to distinguish MSS HNPCC tumors from sporadic MSS CRC. Conclusions: Our results warrant further investigation and validation. The loci identified here may become useful biomarkers for distinguishing between FCCTX and sporadic MSS CRC tumors.
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Ponti G, Manfredini M, Tomasi A, Pellacani G. Muir–Torre Syndrome and founder mismatch repair gene mutations: A long gone historical genetic challenge. Gene 2016; 589:127-32. [DOI: 10.1016/j.gene.2015.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/18/2015] [Accepted: 06/29/2015] [Indexed: 12/11/2022]
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Li J, Dai H, Feng Y, Tang J, Chen S, Tian X, Gorman E, Schmitt ES, Hansen TAA, Wang J, Plon SE, Zhang VW, Wong LJC. A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2. J Mol Diagn 2016; 17:545-53. [PMID: 26320870 DOI: 10.1016/j.jmoldx.2015.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/07/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022] Open
Abstract
Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome.
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Affiliation(s)
- Jianli Li
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | - Yanming Feng
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Jia Tang
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Stella Chen
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Xia Tian
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | | | - Terah A A Hansen
- Central Washington Genetics Program, Yakima Valley Memorial Hospital, Yakima, Washington
| | - Jing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Victor Wei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
| | - Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
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Functional role of DNA mismatch repair gene PMS2 in prostate cancer cells. Oncotarget 2016; 6:16341-51. [PMID: 26036629 PMCID: PMC4599273 DOI: 10.18632/oncotarget.3854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/24/2015] [Indexed: 11/25/2022] Open
Abstract
DNA mismatch repair (MMR) enzymes act as proofreading complexes that maintains genomic integrity and MMR-deficient cells show an increased mutation rate. MMR has also been shown to influence cell signaling and the regulation of tumor development. MMR consists of various genes and includes post-meiotic segregation (PMS) 2 which is a vital component of mutL-alpha. In prostate, the functional role of this gene has never been reported and in this study, our aim was to investigate the effect of PMS2 on growth properties of prostate cancer (PCa) cells. Previous studies have shown PMS2 to be deficient in DU145 cells and this lack of expression was confirmed by Western blotting whereas normal prostatic PWR-1E and RWPE-1 cells expressed this gene. PMS2 effects on various growth properties of DU145 were then determined by creating stable gene transfectants. Interestingly, PMS2 caused decreased cell proliferation, migration, invasion, and in vivo growth; and increased apoptosis as compared to vector control. We further analyzed genes affected by PMS2 expression and observe the apoptosis-related TMS1 gene to be significantly upregulated whereas anti-apoptotic BCL2A1 was downregulated. These results demonstrate a functional role for PMS2 to protect against PCa progression by enhancing apoptosis of PCa cells.
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31
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Kadyrova LY, Kadyrov FA. Endonuclease activities of MutLα and its homologs in DNA mismatch repair. DNA Repair (Amst) 2016; 38:42-49. [PMID: 26719141 PMCID: PMC4820397 DOI: 10.1016/j.dnarep.2015.11.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/26/2015] [Accepted: 11/30/2015] [Indexed: 12/28/2022]
Abstract
MutLα is a key component of the DNA mismatch repair system in eukaryotes. The DNA mismatch repair system has several genetic stabilization functions. Of these functions, DNA mismatch repair is the major one. The loss of MutLα abolishes DNA mismatch repair, thereby predisposing humans to cancer. MutLα has an endonuclease activity that is required for DNA mismatch repair. The endonuclease activity of MutLα depends on the DQHA(X)2E(X)4E motif which is a part of the active site of the nuclease. This motif is also present in many bacterial MutL and eukaryotic MutLγ proteins, DNA mismatch repair system factors that are homologous to MutLα. Recent studies have shown that yeast MutLγ and several MutL proteins containing the DQHA(X)2E(X)4E motif possess endonuclease activities. Here, we review the endonuclease activities of MutLα and its homologs in the context of DNA mismatch repair.
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Affiliation(s)
- Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Farid A Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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32
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Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte AJ, Ding K. Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome. Oncol Rep 2015; 35:1519-28. [PMID: 26707089 DOI: 10.3892/or.2015.4501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/29/2015] [Indexed: 11/05/2022] Open
Abstract
To identify rare mutations and retrospectively estimate the cancer risk of a 45-year old female patient diagnosed with Li-Fraumeni syndrome (LFS), who developed nine primary malignant neoplasms in a period of 38 years, we conducted next-generation sequencing in this patient. Whole-genome and whole-exome sequencing were performed in DNA of whole blood obtained a year prior to the diagnosis of acute myeloid leukemia (AML) and at the time of diagnosis of AML, respectively. We analyzed rare mutations in cancer susceptibility genes using a candidate strategy and estimated cancer risk using the Risk-O-Gram algorithm. We found rare mutations in cancer susceptibility genes associated with an increased hereditary cancer risk in the patient. Notably, the number of mutated genes in p53 signaling pathway was significantly higher than expected (p=0.02). However, the phenotype of multiple malignant neoplasms of the studied patient was unlikely to be caused by accumulation of common cancer risk alleles. In conclusion, we established the mutation profile in a rare case of Li-Fraumeni syndrome, illustrating that the rare mutations rather than the cumulative of common risk alleles leading to an increased cancer risk in the patient.
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Affiliation(s)
- Xiaoyuan Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Juan Kang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Qi Pan
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | | | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Changting Meng
- Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | | | | | - Hong Ren
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Atul J Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University, CA, USA
| | - Keyue Ding
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education of China; Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
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Yurgelun MB, Allen B, Kaldate RR, Bowles KR, Judkins T, Kaushik P, Roa BB, Wenstrup RJ, Hartman AR, Syngal S. Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Gastroenterology 2015; 149:604-13.e20. [PMID: 25980754 PMCID: PMC4550537 DOI: 10.1053/j.gastro.2015.05.006] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Multigene panels are commercially available tools for hereditary cancer risk assessment that allow for next-generation sequencing of numerous genes in parallel. However, it is not clear if these panels offer advantages over traditional genetic testing. We investigated the number of cancer predisposition gene mutations identified by parallel sequencing in individuals with suspected Lynch syndrome. METHODS We performed germline analysis with a 25-gene, next-generation sequencing panel using DNA from 1260 individuals who underwent clinical genetic testing for Lynch syndrome from 2012 through 2013. All patients had a history of Lynch syndrome-associated cancer and/or polyps. We classified all identified germline alterations for pathogenicity and calculated the frequencies of pathogenic mutations and variants of uncertain clinical significance (VUS). We also analyzed data on patients' personal and family history of cancer, including fulfillment of clinical guidelines for genetic testing. RESULTS Of the 1260 patients, 1112 met National Comprehensive Cancer Network (NCCN) criteria for Lynch syndrome testing (88%; 95% confidence interval [CI], 86%-90%). Multigene panel testing identified 114 probands with Lynch syndrome mutations (9.0%; 95% CI, 7.6%-10.8%) and 71 with mutations in other cancer predisposition genes (5.6%; 95% CI, 4.4%-7.1%). Fifteen individuals had mutations in BRCA1 or BRCA2; 93% of these met the NCCN criteria for Lynch syndrome testing and 33% met NCCN criteria for BRCA1 and BRCA2 analysis (P = .0017). An additional 9 individuals carried mutations in other genes linked to high lifetime risks of cancer (5 had mutations in APC, 3 had bi-allelic mutations in MUTYH, and 1 had a mutation in STK11); all of these patients met NCCN criteria for Lynch syndrome testing. A total of 479 individuals had 1 or more VUS (38%; 95% CI, 35%-41%). CONCLUSIONS In individuals with suspected Lynch syndrome, multigene panel testing identified high-penetrance mutations in cancer predisposition genes, many of which were unexpected based on patients' histories. Parallel sequencing also detected a high number of potentially uninformative germline findings, including VUS.
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Affiliation(s)
- Matthew B. Yurgelun
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA,Harvard Medical School, Boston, Massachusetts, USA,Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Brian Allen
- Myriad Genetic Laboratories, Salt Lake City, Utah, USA
| | | | | | | | | | | | | | | | - Sapna Syngal
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA,Harvard Medical School, Boston, Massachusetts, USA,Brigham and Women’s Hospital, Boston, Massachusetts, USA
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Millson A, Lewis T, Pesaran T, Salvador D, Gillespie K, Gau CL, Pont-Kingdon G, Lyon E, Bayrak-Toydemir P. Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4. J Mol Diagn 2015; 17:576-82. [DOI: 10.1016/j.jmoldx.2015.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/23/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
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Germline MLH1 Mutations Are Frequently Identified in Lynch Syndrome Patients With Colorectal and Endometrial Carcinoma Demonstrating Isolated Loss of PMS2 Immunohistochemical Expression. Am J Surg Pathol 2015; 39:1114-20. [DOI: 10.1097/pas.0000000000000425] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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36
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PMS2 monoallelic mutation carriers: the known unknown. Genet Med 2015; 18:13-9. [PMID: 25856668 DOI: 10.1038/gim.2015.27] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/23/2015] [Indexed: 12/17/2022] Open
Abstract
Germ-line mutations in MLH1, MSH2, MSH6, and PMS2 have been shown to cause Lynch syndrome. The penetrance of the cancer and tumor spectrum has been repeatedly studied, and multiple professional societies have proposed clinical management guidelines for affected individuals. Several studies have demonstrated a reduced penetrance for monoallelic carriers of PMS2 mutations compared with the other mismatch repair (MMR) genes, but clinical management guidelines have largely proposed the same screening recommendations for all MMR gene carriers. The authors considered whether enough evidence existed to propose new screening guidelines specific to PMS2 mutation carriers with regard to age at onset and frequency of colonic screening. Published reports of PMS2 germ-line mutations were combined with unpublished cases from the authors' research registries and clinical practices, and a discussion of potential modification of cancer screening guidelines was pursued. A total of 234 monoallelic PMS2 mutation carriers from 170 families were included. Approximately 8% of those with colorectal cancer (CRC) were diagnosed before age 30, and each of these tumors presented on the left side of the colon. As it is currently unknown what causes the early onset of CRC in some families with monoallelic PMS2 germline mutations, the authors recommend against reducing cancer surveillance guidelines in families found having monoallelic PMS2 mutations in spite of the reduced penetrance.Genet Med 18 1, 13-19.
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37
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Abstract
Lynch syndrome, which is now recognized as the most common hereditary colorectal cancer condition, is characterized by the predisposition to a spectrum of cancers, primarily colorectal cancer and endometrial cancer. We chronicle over a century of discoveries that revolutionized the diagnosis and clinical management of Lynch syndrome, beginning in 1895 with Warthin's observations of familial cancer clusters, through the clinical era led by Lynch and the genetic era heralded by the discovery of causative mutations in mismatch repair (MMR) genes, to ongoing challenges.
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Affiliation(s)
- Henry T Lynch
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Carrie L Snyder
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Trudy G Shaw
- Department of Preventive Medicine and Public Health, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3101, USA
| | - Megan P Hitchins
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Grant Building S169, 1291 Welch Road, Stanford, California 94305, USA
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38
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Clendenning M, Walsh MD, Gelpi JB, Thibodeau SN, Lindor N, Potter JD, Newcomb P, LeMarchand L, Haile R, Gallinger S, Hopper JL, Jenkins MA, Rosty C, Young JP, Buchanan DD. Detection of large scale 3' deletions in the PMS2 gene amongst Colon-CFR participants: have we been missing anything? Fam Cancer 2014; 12:563-6. [PMID: 23288611 DOI: 10.1007/s10689-012-9597-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Current screening practices have been able to identify PMS2 mutations in 78 % of cases of colorectal cancer from the Colorectal Cancer Family Registry (Colon CFR) which showed solitary loss of the PMS2 protein. However the detection of large-scale deletions in the 3' end of the PMS2 gene has not been possible due to technical difficulties associated with pseudogene sequences. Here, we utilised a recently described MLPA/long-range PCR-based approach to screen the remaining 22 % (n = 16) of CRC-affected probands for mutations in the 3' end of the PMS2 gene. No deletions encompassing any or all of exons 12 through 15 were identified; therefore, our results suggest that 3' deletions in PMS2 are not a frequent occurrence in such families.
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Affiliation(s)
- Mark Clendenning
- Cancer and Population Studies, Queensland Institute of Medical Research, 300 Herston Road, Herston, QLD, 4006, Australia,
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Hansen MF, Neckmann U, Lavik LAS, Vold T, Gilde B, Toft RK, Sjursen W. A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes. Mol Genet Genomic Med 2014; 2:186-200. [PMID: 24689082 PMCID: PMC3960061 DOI: 10.1002/mgg3.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/21/2013] [Accepted: 12/02/2013] [Indexed: 11/11/2022] Open
Abstract
The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
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Affiliation(s)
- Maren F Hansen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Ulrike Neckmann
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Liss A S Lavik
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Trine Vold
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Bodil Gilde
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Ragnhild K Toft
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Wenche Sjursen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway ; Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
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Drost M, Koppejan H, de Wind N. Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene. Hum Mutat 2013; 34:1477-80. [PMID: 24027009 DOI: 10.1002/humu.22426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/05/2013] [Indexed: 01/14/2023]
Abstract
Lynch syndrome (LS) is a common cancer predisposition caused by an inactivating mutation in one of four DNA mismatch repair (MMR) genes. Frequently a variant of uncertain significance (VUS), rather than an obviously pathogenic mutation, is identified in one of these genes. The inability to define pathogenicity of such variants precludes targeted healthcare. Here, we have modified a cell-free assay to test VUS in the MMR gene PMS2 for functional activity. We have analyzed nearly all VUS in PMS2 found thus far and describe loss of MMR activity for five, suggesting the applicability of the assay for diagnosis of LS.
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Affiliation(s)
- Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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Brea-Fernández A, Cameselle-Teijeiro J, Alenda C, Fernández-Rozadilla C, Cubiella J, Clofent J, Reñé J, Anido U, Milá M, Balaguer F, Castells A, Castellvi-Bel S, Jover R, Carracedo A, Ruiz-Ponte C. High incidence of large deletions in thePMS2gene in Spanish Lynch syndrome families. Clin Genet 2013; 85:583-8. [DOI: 10.1111/cge.12232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 12/24/2022]
Affiliation(s)
- A.J. Brea-Fernández
- Grupo de Medicina Xenómica-USC; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Santiago de Compostela Spain
- Unidad de Investigación; Hospital General Universitario; Alicante Spain
| | - J.M. Cameselle-Teijeiro
- Servicio de Anatomía Patológica, Hospital Clínico Universitario, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS); Universidad de Santiago de Compostela; Santiago de Compostela Spain
| | - C. Alenda
- Servicio de Anatomía Patológica; Hospital General Universitario; Alicante Spain
| | - C. Fernández-Rozadilla
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Santiago de Compostela Spain
| | - J. Cubiella
- Servicio de Gastroenterología; Complexo Hospitalario Universitario de Ourense; Ourense Spain
| | - J. Clofent
- Sección Aparato Digestivo, Servicio de Medicina Interna; Hospital de Sagunto; Sagunto Spain
- Servicio de Gastroenterología; Complexo Hospitalario Universitario de Vigo; Spain
| | - J.M. Reñé
- Servicio de Gastroenterología; Hospital Arnau de Vilanova; Lleida Spain
| | - U. Anido
- Servicio de Oncología Clínica; Complexo Hospitalario Universitario de Santiago; Santiago de Compostela Spain
| | - M. Milá
- Servicio de Bioquímica y Genética Molecular, Hospital Clínic, IDIBAPS; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Barcelona Spain
| | - F. Balaguer
- Servicio de Gastroenterología, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, IDIBAPS; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona; Barcelona Spain
| | - A. Castells
- Servicio de Gastroenterología, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, IDIBAPS; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona; Barcelona Spain
| | - S. Castellvi-Bel
- Servicio de Gastroenterología, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, IDIBAPS; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universitat de Barcelona; Barcelona Spain
| | - R. Jover
- Unidad de Investigación; Hospital General Universitario; Alicante Spain
| | - A. Carracedo
- Grupo de Medicina Xenómica-USC; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Santiago de Compostela Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Santiago de Compostela Spain
| | - C. Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Santiago de Compostela Spain
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Raymond VM, Everett JN, Furtado LV, Gustafson SL, Jungbluth CR, Gruber SB, Hammer GD, Stoffel EM, Greenson JK, Giordano TJ, Else T. Adrenocortical carcinoma is a lynch syndrome-associated cancer. J Clin Oncol 2013; 31:3012-8. [PMID: 23752102 DOI: 10.1200/jco.2012.48.0988] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Adrenocortical carcinoma (ACC) is an endocrine malignancy with a poor prognosis. The association of adult-onset ACC with inherited cancer predisposition syndromes is poorly understood. Our study sought to define the prevalence of Lynch syndrome (LS) among patients with ACC. PATIENTS AND METHODS One hundred fourteen patients with ACC were evaluated in a specialized endocrine oncology clinic and were prospectively offered genetic counseling and clinical genetics risk assessment (group 1). In addition, families with known mismatch repair (MMR) gene mutations that were recorded in the University of Michigan Cancer Genetics Registry were retrospectively reviewed for the presence of ACC (group 2). ACC tumors from patients with LS were tested for microsatellite instability and immunohistochemistry (IHC) to evaluate for MMR deficiency. RESULTS Ninety-four (82.5%) of 114 patients with ACC underwent genetic counseling (group 1). Three individuals (3.2%) had family histories suggestive of LS. All three families were found to have MMR gene mutations. Retrospective review of an additional 135 MMR gene-positive probands identified two with ACC (group 2). Four ACC tumors were available (group 1, 3; group 2, 1). All four tumors were microsatellite stable; three had IHC staining patterns consistent with germline mutation status. CONCLUSION The prevalence of LS among patients with ACC is 3.2%, which is comparable to the prevalence of LS in colorectal and endometrial cancer. Patients with ACC and a personal or family history of LS tumors should be strongly considered for genetic risk assessment. IHC screening of all ACC tumors may be an effective strategy for identifying patients with LS.
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43
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Borràs E, Pineda M, Cadiñanos J, Del Valle J, Brieger A, Hinrichsen I, Cabanillas R, Navarro M, Brunet J, Sanjuan X, Musulen E, van der Klift H, Lázaro C, Plotz G, Blanco I, Capellá G. Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants. J Med Genet 2013; 50:552-63. [PMID: 23709753 DOI: 10.1136/jmedgenet-2012-101511] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM The majority of mismatch repair (MMR) gene mutations causing Lynch syndrome (LS) occur either in MLH1 or MSH2. However, the relative contribution of PMS2 is less well defined. The aim of this study was to evaluate the role of PMS2 in LS by assessing the pathogenicity of variants of unknown significance (VUS) detected in the mutational analysis of PMS2 in a series of Spanish patients. METHODS From a cohort of 202 LS suspected patients, 13 patients showing loss of PMS2 expression in tumours were screened for germline mutations in PMS2, using a long range PCR based strategy and multiplex ligation dependent probe amplification (MLPA). Pathogenicity assessment of PMS2 VUS was performed evaluating clinicopathological data, frequency in control population and in silico and in vitro analyses at the RNA and protein level. RESULTS Overall 25 different PMS2 DNA variants were detected. Fourteen were classified as polymorphisms. Nine variants were classified as pathogenic: seven alterations based on their molecular nature and two after demonstrating a functional defect (c.538-3C>G affected mRNA processing and c.137G>T impaired MMR activity). The c.1569C>G variant was classified as likely neutral while the c.384G>A remained as a VUS. We have also shown that the polymorphic variant c.59G>A is MMR proficient. CONCLUSIONS Pathogenic PMS2 mutations were detected in 69% of patients harbouring LS associated tumours with loss of PMS2 expression. In all, PMS2 mutations account for 6% of the LS cases identified. The comprehensive functional analysis shown here has been useful in the classification of PMS2 VUS and contributes to refining the role of PMS2 in LS.
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Affiliation(s)
- Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Cranmer LD, Chen CC, Morgan S, Martino G, Ray J. Pleomorphic Rhabdomyosarcoma in a Patient With Hereditary Nonpolyposis Colorectal Cancer. J Clin Oncol 2013; 31:e108-10. [DOI: 10.1200/jco.2012.43.4910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Jessica Ray
- University of Arizona Cancer Center, Tucson, AZ
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Putative circulating markers of the early and advanced stages of breast cancer identified by high-resolution label-free proteomics. Cancer Lett 2013. [DOI: 10.1016/j.canlet.2012.11.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Chen J, Pande M, Huang YJ, Wei C, Amos CI, Talseth-Palmer BA, Meldrum CJ, Chen WV, Gorlov IP, Lynch PM, Scott RJ, Frazier ML. Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. Carcinogenesis 2012; 34:299-306. [PMID: 23125224 DOI: 10.1093/carcin/bgs344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Heterogeneity in age of onset of colorectal cancer in individuals with mutations in DNA mismatch repair genes (Lynch syndrome) suggests the influence of other lifestyle and genetic modifiers. We hypothesized that genes regulating the cell cycle influence the observed heterogeneity as cell cycle-related genes respond to DNA damage by arresting the cell cycle to provide time for repair and induce transcription of genes that facilitate repair. We examined the association of 1456 single nucleotide polymorphisms (SNPs) in 128 cell cycle-related genes and 31 DNA repair-related genes in 485 non-Hispanic white participants with Lynch syndrome to determine whether there are SNPs associated with age of onset of colorectal cancer. Genotyping was performed on an Illumina GoldenGate platform, and data were analyzed using Kaplan-Meier survival analysis, Cox regression analysis and classification and regression tree (CART) methods. Ten SNPs were independently significant in a multivariable Cox proportional hazards regression model after correcting for multiple comparisons (P < 5 × 10(-4)). Furthermore, risk modeling using CART analysis defined combinations of genotypes for these SNPs with which subjects could be classified into low-risk, moderate-risk and high-risk groups that had median ages of colorectal cancer onset of 63, 50 and 42 years, respectively. The age-associated risk of colorectal cancer in the high-risk group was more than four times the risk in the low-risk group (hazard ratio = 4.67, 95% CI = 3.16-6.92). The additional genetic markers identified may help in refining risk groups for more tailored screening and follow-up of non-Hispanic white patients with Lynch syndrome.
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Affiliation(s)
- Jinyun Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Vaughn CP, Baker CL, Samowitz WS, Swensen JJ. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene. Genes Chromosomes Cancer 2012; 52:107-12. [PMID: 23012243 DOI: 10.1002/gcc.22011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 07/11/2012] [Accepted: 08/16/2012] [Indexed: 12/30/2022] Open
Abstract
Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology.
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Affiliation(s)
- Cecily P Vaughn
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA
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Kamat N, Khidhir MA, Jaloudi M, Hussain S, Alashari MM, Al Qawasmeh KH, Rannug U. High incidence of microsatellite instability and loss of heterozygosity in three loci in breast cancer patients receiving chemotherapy: a prospective study. BMC Cancer 2012; 12:373. [PMID: 22928966 PMCID: PMC3495899 DOI: 10.1186/1471-2407-12-373] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 08/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to evaluate potential chemotherapy-induced microsatellite instability, loss of heterozygosity, loss of expression in mismatch repair proteins and associations with clinical findings in breast cancer patients, especially resistance to chemotherapy and/or development of other tumors in the four years following chemotherapy treatment. Methods A comprehensive study of chemotherapy-related effects with a follow-up period of 48 months post treatment was conducted. A total of 369 peripheral blood samples were collected from 123 de novo breast cancer patients. Microsatellite instability and loss of heterozygosity in five commonly used marker loci (including Tp53-Alu of the tumor suppressor gene TP53) were analyzed in blood samples. Sampling was conducted on three occasions; 4–5 weeks prior to the first chemotherapy session (pre-treatment), to serve as a baseline, followed by two consecutive draws at 12 weeks intervals from the first collection. Mismatch repair protein expression was evaluated in cancer tissues using immunohistochemistry for three mismatch-repair related proteins. Results A total of 70.7% of the patients showed microsatellite instability for at least one locus, including 18.6% marked as high-positive and 52.1% as low-positive; 35.8% showed loss of heterozygosity in addition to microsatellite instability, while 29.3% exhibited microsatellite stability. The following incidence rates for microsatellite instability and loss of heterozygosity were detected: 39.1% positive for Tp53-Alu, 31.1% for locus Mfd41, and 25.3% for locus Mfd28. A higher occurrence of loss of heterozygosity was noted with alleles 399 and 404 of Tp53-Alu. The mismatch repair protein expression analysis showed that the chemotherapy caused a loss of 29.3% in hMLH1 expression, and 18.7% and 25.2% loss in hMSH2 and P53 expression, respectively. A strong correlation between low or deficient hMSH2 protein expression and occurrence of mismatch repair/loss of heterozygosity events in Mfd41, Tp53-Alu, and Mfd28 was evident. A significant association between mismatch repair/loss of heterozygosity and incidence of secondary tumors was also established. Conclusion Our results suggest that microsatellite instability, loss of heterozygosity, and deficiency in mismatch repair may serve as early prognostic factors for potential chemotherapy-related side effects in breast cancer patients.
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Affiliation(s)
- Nasir Kamat
- Department of Genetics, Microbiology and Toxicology, Stockholm University, Stockholm, Sweden
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Abstract
Immunoglobulin class-switch recombination deficiencies (Ig-CSR-Ds) are rare primary immunodeficiencies characterized by defective switched isotype (IgG/IgA/IgE) production. Depending on the molecular defect in question, the Ig-CSR-D may be combined with an impairment in somatic hypermutation (SHM). Some of the mechanisms underlying Ig-CSR and SHM have been described by studying natural mutants in humans. This approach has revealed that T cell-B cell interaction (resulting in CD40-mediated signaling), intrinsic B-cell mechanisms (activation-induced cytidine deaminase-induced DNA damage), and complex DNA repair machineries (including uracil-N-glycosylase and mismatch repair pathways) are all involved in class-switch recombination and SHM. However, several of the mechanisms required for full antibody maturation have yet to be defined. Elucidation of the molecular defects underlying the diverse set of Ig-CSR-Ds is essential for understanding Ig diversification and has prompted better definition of the clinical spectrum of diseases and the development of increasingly accurate diagnostic and therapeutic approaches.
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Tomsic J, Senter L, Liyanarachchi S, Clendenning M, Vaughn CP, Jenkins MA, Hopper JL, Young J, Samowitz W, de la Chapelle A. Recurrent and founder mutations in the PMS2 gene. Clin Genet 2012; 83:238-43. [PMID: 22577899 DOI: 10.1111/j.1399-0004.2012.01898.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/04/2012] [Indexed: 12/22/2022]
Abstract
Germline mutations in PMS2 are associated with Lynch syndrome (LS), the most common known cause of hereditary colorectal cancer. Mutation detection in PMS2 has been difficult due to the presence of several pseudogenes, but a custom-designed long-range PCR strategy now allows adequate mutation detection. Many mutations are unique. However, some mutations are observed repeatedly across individuals not known to be related due to the mutation being either recurrent, arising multiple times de novo at hot spots for mutations, or of founder origin, having occurred once in an ancestor. Previously, we observed 36 distinct mutations in a sample of 61 independently ascertained Caucasian probands of mixed European background with PMS2 mutations. Eleven of these mutations were detected in more than one individual not known to be related and of these, six were detected more than twice. These six mutations accounted for 31 (51%) ostensibly unrelated probands. Here, we performed genotyping and haplotype analysis in four mutations observed in multiple probands and found two (c.137G>T and exon 10 deletion) to be founder mutations and one (c.903G>T) a probable founder. One (c.1A>G) could not be evaluated for founder mutation status. We discuss possible explanations for the frequent occurrence of founder mutations in PMS2.
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Affiliation(s)
- J Tomsic
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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