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McVeigh TP, Monahan KJ, Christopher J, West N, Scott M, Murray J, Hanson H. Extent of investigation and management of cases of 'unexplained' mismatch repair deficiency (u-dMMR): a UK Cancer Genetics Group consensus. J Med Genet 2024; 61:707-715. [PMID: 38531626 PMCID: PMC11228216 DOI: 10.1136/jmg-2024-109886] [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: 01/17/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Mismatch repair deficiency (dMMR) is a characteristic feature of cancers linked to Lynch syndrome. However, in most cases, it results from sporadic somatic events rather than hereditary factors. The term 'Lynch-like syndrome' (LLS) has been used to guide colorectal cancer surveillance for relatives of individuals with a dMMR tumour when somatic and germline genomic testing is uninformative. As the assessment of mismatch repair through immunohistochemistry and/or microsatellite instability is increasingly applied across various tumour types for treatment planning, dMMR is increasingly detected in tumours where suspicion of hereditary aetiology is low. Our objective was to establish current practices and develop national guidance for investigating, and managing relatives of, patients with cancers demonstrating unexplained dMMR. METHODS This was achieved through a virtual consensus meeting involving key stakeholders from the UK, through premeeting surveys, structured discussions and in-meeting polling to formulate best practice guidance. RESULTS We identified variability in the availability of diagnostic technologies across specialist centres. It was agreed that equitable access to baseline testing is required, acknowledging the need for a pragmatic approach to investigating dMMR cancers not traditionally associated with Lynch syndrome. Factors such as family history, age, tumour type, protein loss pattern and extent of the investigation were deemed crucial in guiding family management. The term 'unexplained dMMR' was recommended over LLS. CONCLUSION Decisions regarding investigations and future cancer risk management in patients and relatives should be nuanced, considering factors like clinical suspicion of hereditary predisposition to allocate limited resources efficiently and avoid unnecessary investigations in low-suspicion families.
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Affiliation(s)
- Terri Patricia McVeigh
- Cancer Genetics Unit, Royal Marsden Hospital NHS Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Kevin J Monahan
- St Mark's Academic Institute Polyposis Registry, Harrow, UK
- Imperial College London, London, UK
| | - Joseph Christopher
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Nick West
- University of Leeds, Leeds, UK
- Department of Histopathology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Malcolm Scott
- Familial Cancer Clinic, Department of Gynaecology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Jennie Murray
- Southeast Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - Helen Hanson
- Peninsula Regional Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Faculty of Health and Life Sciences, University of Exeter Medical School, Exeter, UK
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2
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Zhang X, Li P, Gan Y, Xiang S, Gu L, Zhou J, Zhou X, Wu P, Zhang B, Deng D. Driving effect of P16 methylation on telomerase reverse transcriptase-mediated immortalization and transformation of normal human fibroblasts. Chin Med J (Engl) 2024:00029330-990000000-00975. [PMID: 38420748 DOI: 10.1097/cm9.0000000000003004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND P16 inactivation is frequently accompanied by telomerase reverse transcriptase (TERT) amplification in human cancer genomes. P16 inactivation by DNA methylation often occurs automatically during immortalization of normal cells by TERT. However, direct evidence remains to be obtained to support the causal effect of epigenetic changes, such as P16 methylation, on cancer development. This study aimed to provide experimental evidence that P16 methylation directly drives cancer development. METHODS A zinc finger protein-based P16-specific DNA methyltransferase (P16-Dnmt) vector containing a "Tet-On" switch was used to induce extensive methylation of P16 CpG islands in normal human fibroblast CCD-18Co cells. Battery assays were used to evaluate cell immortalization and transformation throughout their lifespan. Cell subcloning and DNA barcoding were used to track the diversity of cell evolution. RESULTS Leaking P16-Dnmt expression (without doxycycline-induction) could specifically inactivate P16 expression by DNA methylation. P16 methylation only promoted proliferation and prolonged lifespan but did not induce immortalization of CCD-18Co cells. Notably, cell immortalization, loss of contact inhibition, and anchorage-independent growth were always prevalent in P16-Dnmt&TERT cells, indicating cell transformation. In contrast, almost all TERT cells died in the replicative crisis. Only a few TERT cells recovered from the crisis, in which spontaneous P16 inactivation by DNA methylation occurred. Furthermore, the subclone formation capacity of P16-Dnmt&TERT cells was two-fold that of TERT cells. DNA barcoding analysis showed that the diversity of the P16-Dnmt&TERT cell population was much greater than that of the TERT cell population. CONCLUSION P16 methylation drives TERT-mediated immortalization and transformation of normal human cells that may contribute to cancer development.
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Affiliation(s)
- Xuehong Zhang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Paiyun Li
- Division of Etiology, Beijing Cancer Hospital, Beijing 100142, China
- Radiation Oncology Department, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ying Gan
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Shengyan Xiang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaorui Zhou
- Department of Biomedical Engineering, Peking University Cancer Hospital and Institute, Beijing 100871, China
| | - Peihuang Wu
- Department of Biomedical Engineering, Peking University Cancer Hospital and Institute, Beijing 100871, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
- Division of Etiology, Beijing Cancer Hospital, Beijing 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
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Nakamura W, Hirata M, Oda S, Chiba K, Okada A, Mateos RN, Sugawa M, Iida N, Ushiama M, Tanabe N, Sakamoto H, Sekine S, Hirasawa A, Kawai Y, Tokunaga K, Tsujimoto SI, Shiba N, Ito S, Yoshida T, Shiraishi Y. Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. NPJ Genom Med 2024; 9:11. [PMID: 38368425 PMCID: PMC10874402 DOI: 10.1038/s41525-024-00394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers adaptive sampling and computationally driven target enrichment technology. This enables more affordable intensive analysis of target gene regions compared to standard non-selective long-read sequencing. In this study, we developed an efficient computational workflow for target adaptive sampling long-read sequencing (TAS-LRS) and evaluated it through application to 33 genomes collected from suspected hereditary cancer patients. Our workflow can identify single nucleotide variants with nearly the same accuracy as the short-read platform and elucidate complex forms of structural variations. We also newly identified several SINE-R/VNTR/Alu (SVA) elements affecting the APC gene in two patients with familial adenomatous polyposis, as well as their sites of origin. In addition, we demonstrated that off-target reads from adaptive sampling, which is typically discarded, can be effectively used to accurately genotype common single-nucleotide polymorphisms (SNPs) across the entire genome, enabling the calculation of a polygenic risk score. Furthermore, we identified allele-specific MLH1 promoter hypermethylation in a Lynch syndrome patient. In summary, our workflow with TAS-LRS can simultaneously capture monogenic risk variants including complex structural variations, polygenic background as well as epigenetic alterations, and will be an efficient platform for genetic disease research and diagnosis.
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Affiliation(s)
- Wataru Nakamura
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Makoto Hirata
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoyo Oda
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Division of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Sugawa
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Mineko Ushiama
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Noriko Tanabe
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Hirasawa
- Department of Clinical Genetics and Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Tokyo, Japan
| | - Shin-Ichi Tsujimoto
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Shuichi Ito
- Department of Pediatrics, Yokohama City University Hospital, Kanagawa, Japan
| | - Teruhiko Yoshida
- Division of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
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Joder C, Gmür A, Solass W, Christe L, Rabaglio M, Fluri M, Rau TT, Saner FAM, Knabben L, Imboden S, Mueller MD, Siegenthaler F. Real-World Data on Institutional Implementation of Screening for Mismatch Repair Deficiency and Lynch Syndrome in Endometrial Cancer Patients. Cancers (Basel) 2024; 16:671. [PMID: 38339422 PMCID: PMC10854690 DOI: 10.3390/cancers16030671] [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: 12/31/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Lynch syndrome is an inherited tumor syndrome caused by a pathogenic germline variant in DNA mismatch repair genes. As the leading cause of hereditary endometrial cancer, international guidelines recommend universal screening in women with endometrial cancer. However, testing for Lynch syndrome is not yet well established in clinical practice. The aim of this study was to evaluate adherence to our Lynch syndrome screening algorithm. A retrospective, single-center cohort study was conducted of all endometrial cancer patients undergoing surgical treatment at the Bern University Hospital, Switzerland, between 2017 and 2022. Adherence to immunohistochemical analysis of mismatch repair status, and, if indicated, to MLH1 promoter hypermethylation and to genetic counseling and testing was assessed. Of all 331 endometrial cancer patients, 102 (30.8%) were mismatch repair-deficient and 3 (0.9%) patients were diagnosed with Lynch syndrome. Overall screening adherence was 78.2%, with a notable improvement over the six years from 61.4% to 90.6%. A major reason for non-adherence was lack of provider recommendation for testing, with advanced patient age as a potential patient risk factor. Simplification of the algorithm through standardized reflex screening was recommended to provide optimal medical care for those affected and to allow for cascading testing of at-risk relatives.
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Affiliation(s)
- Carmen Joder
- Faculty of Medicine, University of Bern, 3010 Bern, Switzerland;
| | - Andrea Gmür
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
| | - Wiebke Solass
- Institute of Tissue Medicine and Pathology, University of Bern, 3010 Bern, Switzerland
| | - Lucine Christe
- Institute of Tissue Medicine and Pathology, University of Bern, 3010 Bern, Switzerland
| | - Manuela Rabaglio
- Department of Medical Oncology, Bern University Hospital, 3010 Bern, Switzerland
| | - Muriel Fluri
- Department of Medical Oncology, Bern University Hospital, 3010 Bern, Switzerland
| | - Tilman T. Rau
- Institute of Pathology, Universitätsklinikum Düsseldorf, 40225 Düsseldorf, Germany
| | - Flurina A. M. Saner
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
| | - Laura Knabben
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
| | - Sara Imboden
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
| | - Michael D. Mueller
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
| | - Franziska Siegenthaler
- Department of Obstetrics and Gynecology, Bern University Hospital, 3010 Bern, Switzerland
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Helderman NC, Andini KD, van Leerdam ME, van Hest LP, Hoekman DR, Ahadova A, Bajwa-Ten Broeke SW, Bosse T, van der Logt EMJ, Imhann F, Kloor M, Langers AMJ, Smit VTHBM, Terlouw D, van Wezel T, Morreau H, Nielsen M. MLH1 Promotor Hypermethylation in Colorectal and Endometrial Carcinomas from Patients with Lynch Syndrome. J Mol Diagn 2024; 26:106-114. [PMID: 38061582 DOI: 10.1016/j.jmoldx.2023.10.005] [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: 04/25/2023] [Revised: 07/19/2023] [Accepted: 10/17/2023] [Indexed: 01/26/2024] Open
Abstract
Screening for Lynch syndrome (LS) in colorectal cancer (CRC) and endometrial cancer patients generally involves immunohistochemical staining of the mismatch repair (MMR) proteins. In case of MLH1 protein loss, MLH1 promotor hypermethylation (MLH1-PM) testing is performed to indirectly distinguish the constitutional MLH1 variants from somatic epimutations. Recently, multiple studies have reported that MLH1-PM and pathogenic constitutional MMR variants are not mutually exclusive. This study describes 6 new and 86 previously reported MLH1-PM CRCs or endometrial cancers in LS patients. Of these, methylation of the MLH1 gene promotor C region was reported in 30 MLH1, 6 MSH2, 6 MSH6, and 3 PMS2 variant carriers at a median age at diagnosis of 48.5 years [interquartile range (IQR), 39-56.75 years], 39 years (IQR, 29-51 years), 58 years (IQR, 53.5-67 years), and 68 years (IQR, 65.6-68.5 years), respectively. For 31 MLH1-PM CRCs in LS patients from the literature, only the B region of the MLH1 gene promotor was tested, whereas for 13 cases in the literature the tested region was not specified. Collectively, these data indicate that a diagnosis of LS should not be excluded when MLH1-PM is detected. Clinicians should carefully consider whether follow-up genetic MMR gene testing should be offered, with age <60 to 70 years and/or a positive family history among other factors being suggestive for a potential constitutional MMR gene defect.
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Affiliation(s)
- Noah C Helderman
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Katarina D Andini
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Liselotte P van Hest
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Daniël R Hoekman
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Heidelberg University Hospital, Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Centre, Heidelberg, Germany
| | - Sanne W Bajwa-Ten Broeke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Floris Imhann
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Matthias Kloor
- Department of Applied Tumor Biology, Heidelberg University Hospital, Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Centre, Heidelberg, Germany
| | - Alexandra M J Langers
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Diantha Terlouw
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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Geissler F, Nesic K, Kondrashova O, Dobrovic A, Swisher EM, Scott CL, J. Wakefield M. The role of aberrant DNA methylation in cancer initiation and clinical impacts. Ther Adv Med Oncol 2024; 16:17588359231220511. [PMID: 38293277 PMCID: PMC10826407 DOI: 10.1177/17588359231220511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024] Open
Abstract
Epigenetic alterations, including aberrant DNA methylation, are now recognized as bone fide hallmarks of cancer, which can contribute to cancer initiation, progression, therapy responses and therapy resistance. Methylation of gene promoters can have a range of impacts on cancer risk, clinical stratification and therapeutic outcomes. We provide several important examples of genes, which can be silenced or activated by promoter methylation and highlight their clinical implications. These include the mismatch DNA repair genes MLH1 and MSH2, homologous recombination DNA repair genes BRCA1 and RAD51C, the TERT oncogene and genes within the P15/P16/RB1/E2F tumour suppressor axis. We also discuss how these methylation changes might occur in the first place - whether in the context of the CpG island methylator phenotype or constitutional DNA methylation. The choice of assay used to measure methylation can have a significant impact on interpretation of methylation states, and some examples where this can influence clinical decision-making are presented. Aberrant DNA methylation patterns in circulating tumour DNA (ctDNA) are also showing great promise in the context of non-invasive cancer detection and monitoring using liquid biopsies; however, caution must be taken in interpreting these results in cases where constitutional methylation may be present. Thus, this review aims to provide researchers and clinicians with a comprehensive summary of this broad, but important subject, illustrating the potentials and pitfalls of assessing aberrant DNA methylation in cancer.
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Affiliation(s)
- Franziska Geissler
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, VIC, Australia
| | | | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Matthew J. Wakefield
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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Chao AS, Chao A, Lai CH, Lin CY, Yang LY, Chang SC, Wu RC. Comparison of immediate germline sequencing and multi-step screening for Lynch syndrome detection in high-risk endometrial and colorectal cancer patients. J Gynecol Oncol 2024; 35:e5. [PMID: 37743058 PMCID: PMC10792205 DOI: 10.3802/jgo.2024.35.e5] [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: 05/13/2023] [Revised: 07/08/2023] [Accepted: 08/13/2023] [Indexed: 09/26/2023] Open
Abstract
OBJECTIVE Lynch syndrome (LS) is a hereditary cancer predisposition syndrome with a significantly increased risk of colorectal and endometrial cancers. Current standard practice involves universal screening for LS in patients with newly diagnosed colorectal or endometrial cancer using a multi-step screening protocol (MSP). However, MSP may not always accurately identify LS cases. To address this limitation, we compared the diagnostic performance of immediate germline sequencing (IGS) with MSP in a high-risk group. METHODS A total of 31 Taiwanese women with synchronous or metachronous endometrial and colorectal malignancies underwent MSP which included immunohistochemical staining of DNA mismatch repair (MMR) proteins, MLH1 promoter hypermethylation analysis, and germline sequencing to identify pathogenic variants. All patients who were excluded during MSP received germline sequencing for MMR genes to simulate IGS for the detection of LS. RESULTS Our findings indicate that IGS surpassed MSP in terms of diagnostic yield (29.0% vs. 19.4%, respectively) and sensitivity (90% vs. 60%, respectively). Specifically, IGS successfully identified nine LS cases, which is 50% more than the number detected through MSP. Additionally, germline methylation analysis revealed one more LS case with constitutional MLH1 promoter hypermethylation, bringing the total LS cases to ten (32.3%). Intriguingly, we observed no significant differences in clinical characteristics or overall survival between patients with and without LS in our cohort. CONCLUSION Our study suggests that IGS may potentially offer a more effective approach compared to MSP in identifying LS among high-risk patients. This advantage is evident when patients have been pre-selected utilizing specific clinical criteria.
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Affiliation(s)
- An-Shine Chao
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Angel Chao
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lan-Yan Yang
- Biostatistics Unit, Clinical Trial Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ren-Chin Wu
- Gynecologic Cancer Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Pathology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University College of Medicine, Taoyuan, Taiwan.
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8
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Carnevali IW, Cini G, Libera L, Sahnane N, Facchi S, Viel A, Sessa F, Tibiletti MG. MLH1 Promoter Methylation Could Be the Second Hit in Lynch Syndrome Carcinogenesis. Genes (Basel) 2023; 14:2060. [PMID: 38003003 PMCID: PMC10670941 DOI: 10.3390/genes14112060] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
(1) Background: MLH1 hypermethylation is an epigenetic alteration in the tumorigenesis of colorectal cancer (CRC) and endometrial cancer (EC), causing gene silencing, and, as a consequence, microsatellite instability. Commonly, MLH1 hypermethylation is considered a somatic and sporadic event in cancer, and its detection is recognized as a useful tool to distinguish sporadic from inherited conditions (such as, Lynch syndrome (LS)). However, MLH1 hypermethylation has been described in rare cases of CRC and EC in LS patients. (2) Methods: A total of 61 cancers (31 CRCs, 27 ECs, 2 ovarian cancers, and 1 stomach cancer) from 56 patients referred to cancer genetic counselling were selected for loss of MLH1 protein expression and microsatellite instability. All cases were investigated for MLH1 promoter methylation and MLH1/PMS2 germline variants. (3) Results: Somatic MLH1 promoter hypermethylation was identified in 16.7% of CRC and in 40% of EC carriers of MLH1 germline pathogenic variants. In two families, primary and secondary MLH1 epimutations were demonstrated. (4) Conclusions: MLH1 hypermethylation should not be exclusively considered as a sporadic cancer mechanism, as a non-negligible number of LS-related cancers are MLH1 hypermethylated. Current flow charts for universal LS screening, which include MLH1 methylation, should be applied, paying attention to a patient's family and personal history.
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Affiliation(s)
- Ileana Wanda Carnevali
- UO Anatomia Patologica Ospedale di Circolo ASST-Settelaghi, 21100 Varese, Italy; (N.S.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
| | - Giulia Cini
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (G.C.); (A.V.)
| | - Laura Libera
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
- Department of Medicine and Thecnological Innovation, Università dell’Insubria, 21100 Varese, Italy
| | - Nora Sahnane
- UO Anatomia Patologica Ospedale di Circolo ASST-Settelaghi, 21100 Varese, Italy; (N.S.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
| | - Sofia Facchi
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
- Department of Medicine and Thecnological Innovation, Università dell’Insubria, 21100 Varese, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (G.C.); (A.V.)
| | - Fausto Sessa
- UO Anatomia Patologica Ospedale di Circolo ASST-Settelaghi, 21100 Varese, Italy; (N.S.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
- Department of Medicine and Thecnological Innovation, Università dell’Insubria, 21100 Varese, Italy
| | - Maria Grazia Tibiletti
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università dell’Insubria, 21100 Varese, Italy; (L.L.); (S.F.); (M.G.T.)
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9
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Joo JE, Mahmood K, Walker R, Georgeson P, Candiloro I, Clendenning M, Como J, Joseland S, Preston S, Graversen L, Wilding M, Field M, Lemon M, Wakeling J, Marfan H, Susman R, Isbister J, Edwards E, Bowman M, Kirk J, Ip E, McKay L, Antill Y, Hopper JL, Boussioutas A, Macrae FA, Dobrovic A, Jenkins MA, Rosty C, Winship IM, Buchanan DD. Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. Clin Epigenetics 2023; 15:95. [PMID: 37270516 PMCID: PMC10239107 DOI: 10.1186/s13148-023-01511-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND MLH1 epimutation is characterised by constitutional monoallelic MLH1 promoter hypermethylation, which can cause colorectal cancer (CRC). Tumour molecular profiles of MLH1 epimutation CRCs were used to classify germline MLH1 promoter variants of uncertain significance and MLH1 methylated early-onset CRCs (EOCRCs). Genome-wide DNA methylation and somatic mutational profiles of tumours from two germline MLH1: c.-11C > T and one MLH1: c.-[28A > G; 7C > T] carriers and three MLH1 methylated EOCRCs (< 45 years) were compared with 38 reference CRCs. Methylation-sensitive droplet digital PCR (ddPCR) was used to detect mosaic MLH1 methylation in blood, normal mucosa and buccal DNA. RESULTS Genome-wide methylation-based Consensus Clustering identified four clusters where the tumour methylation profiles of germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs clustered with the constitutional MLH1 epimutation CRCs but not with the sporadic MLH1 methylated CRCs. Furthermore, monoallelic MLH1 methylation and APC promoter hypermethylation in tumour were observed in both MLH1 epimutation and germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs. Mosaic constitutional MLH1 methylation in MLH1: c.-11C > T carriers and 1 of 3 MLH1 methylated EOCRCs was identified by methylation-sensitive ddPCR. CONCLUSIONS Mosaic MLH1 epimutation underlies the CRC aetiology in MLH1: c.-11C > T germline carriers and a subset of MLH1 methylated EOCRCs. Tumour profiling and ultra-sensitive ddPCR methylation testing can be used to identify mosaic MLH1 epimutation carriers.
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Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia.
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Ida Candiloro
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Lise Graversen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mathilda Wilding
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michael Field
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michelle Lemon
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Janette Wakeling
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Tasman Health Care, Southport, QLD, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanne Isbister
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
| | - Emma Edwards
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Michelle Bowman
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Emilia Ip
- Department of Cancer Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Lynne McKay
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - Yoland Antill
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Alex Boussioutas
- Department of Gastroenterology, The Alfred Hospital, Melbourne, Parkville, VIC, 3010, Australia
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Finlay A Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Alexander Dobrovic
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Envoi Specialist Pathologists, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
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10
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Parente P, Grillo F, Vanoli A, Macciomei MC, Ambrosio MR, Scibetta N, Filippi E, Cataldo I, Baron L, Ingravallo G, Cazzato G, Melocchi L, Liserre B, Giordano C, Arborea G, Pilozzi E, Scapinello A, Aquilano MC, Gafà R, Battista S, Dal Santo L, Campora M, Carbone FG, Sartori C, Lazzi S, Hanspeter E, Angerilli V, Mastracci L, Fassan M. The Day-To-Day Practice of MMR and MSI Assessment in Colorectal Adenocarcinoma: What We Know and What We Still Need to Explore. Dig Dis 2023; 41:746-756. [PMID: 37231848 DOI: 10.1159/000531003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND The DNA mismatch repair (MMR) system is a highly preserved protein complex recognizing short insertions, short deletions, and single base mismatches during DNA replication and recombination. MMR protein status is identified using immunohistochemistry. Deficit in one or more MMR proteins, configuring deficient MMR status (dMMR), leads to frameshift mutations particularly clustered in microsatellite repeats. Thus, microsatellite instability (MSI) is the epiphenomenon of dMMR. In colorectal cancer (CRC), MMR/MSI status is a biomarker with prognostic and predictive value of resistance to 5-fluorouracil and response to immune checkpoint inhibitor therapy. SUMMARY In this Review, we describe the challenges the practicing pathologist may face in relation to the assessment of MMR/MSI status and any open issues which still need to be addressed, focusing on pre-analytic issues, pitfalls in the interpretation, and technical aspects of the different assays. KEY MESSAGES The current methods of detecting dMMR/MSI status have been optimized for CRCs, and whether these techniques can be applied to all tumor and specimen types is still not fully understood. Following the Food and Drug Administration (FDA), tissue/site agnostic drug approval of pembrolizumab for advanced/metastatic MSI tumors, MMR/MSI status in gastrointestinal tract is a common request from the oncologist. In this setting, several issues still need to be addressed, including criteria for sample adequacy.
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Affiliation(s)
- Paola Parente
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Federica Grillo
- Anatomic Pathology, Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
- Pathology Unit, Ospedale Policlinico San Martino IRCCS, Genoa, Italy
| | - Alessandro Vanoli
- Anatomic Pathology Unit, Department of Molecular Medicine, University of Pavia and Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | | | | | - Nunzia Scibetta
- UOC Anatomia Patologica ARNAS Ospedali Civico e G. Di Gristina, Palermo, Italy
| | | | - Ivana Cataldo
- Surgical Pathology Section University and Hospital Trust of Treviso, Treviso, Italy
| | - Luigi Baron
- Surgical Pathology Unit ASL Napoli 3 Sud, Ospedale S. Leonardo, Naples, Italy
| | - Giuseppe Ingravallo
- Section of Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari "Aldo Moro", Bari, Italy
| | - Gerardo Cazzato
- Section of Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari "Aldo Moro", Bari, Italy
| | - Laura Melocchi
- Unit of Pathology, Department of Oncology, Fondazione Poliambulanza Hospital Institute, Brescia, Italy
| | - Barbara Liserre
- Unit of Pathology, Department of Oncology, Fondazione Poliambulanza Hospital Institute, Brescia, Italy
| | - Carla Giordano
- Pathology Unit, Università La Sapienza; Policlinico Umberto I, Rome, Italy
| | - Graziana Arborea
- Department of Pathology, National Institute of Gastroenterology IRCCS "S. de Bellis", Castellana Grotte, Italy
| | - Emanuela Pilozzi
- Department of Clinical and Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Maria Costanza Aquilano
- Department of Hematology, Oncology and Molecular Medicine, ASST Grande Ospedale Metropolitano/Niguarda, Milan, Italy
| | - Roberta Gafà
- Anatomic Pathology Unit, University Hospital of Ferrara, Ferrara, Italy
| | - Serena Battista
- Pathology Department, S. Maria della Misericordia Hospital, Udine, Italy
| | - Luca Dal Santo
- Department of Pathology, Ospedale dell'Angelo, Venice, Italy
| | - Michela Campora
- U.O.M. Anatomia e Istologia Patologica e Citodiagnostica Ospedale S. Chiara, Trento, Italy
| | | | - Chiara Sartori
- U.O.M. Anatomia e Istologia Patologica e Citodiagnostica Ospedale S. Chiara, Trento, Italy
| | - Stefano Lazzi
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Ester Hanspeter
- Department of Pathology, Provincial Hospital of Bolzano (SABES-ASDAA), Bolzano-Bozen, Italy
| | - Valentina Angerilli
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Luca Mastracci
- Anatomic Pathology, Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
- Pathology Unit, Ospedale Policlinico San Martino IRCCS, Genoa, Italy
| | - Matteo Fassan
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
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11
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Walker R, Mahmood K, Joo JE, Clendenning M, Georgeson P, Como J, Joseland S, Preston SG, Antill Y, Austin R, Boussioutas A, Bowman M, Burke J, Campbell A, Daneshvar S, Edwards E, Gleeson M, Goodwin A, Harris MT, Henderson A, Higgins M, Hopper JL, Hutchinson RA, Ip E, Isbister J, Kasem K, Marfan H, Milnes D, Ng A, Nichols C, O'Connell S, Pachter N, Pope BJ, Poplawski N, Ragunathan A, Smyth C, Spigelman A, Storey K, Susman R, Taylor JA, Warwick L, Wilding M, Williams R, Win AK, Walsh MD, Macrae FA, Jenkins MA, Rosty C, Winship IM, Buchanan DD. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome. J Transl Med 2023; 21:282. [PMID: 37101184 PMCID: PMC10134620 DOI: 10.1186/s12967-023-04143-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023] Open
Abstract
Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n = 135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n = 137; 80×CRCs, 33×ECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3051, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Susan G Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Yoland Antill
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
- Familial Cancer Centre, Cabrini Health, Malvern, VIC, 3144, Australia
- Familial Cancer Centre, Monash Health, Clayton, VIC, 3168, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Alex Boussioutas
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Gastroenterology, The Alfred Hospital, Melbourne, VIC, 3004, Australia
- Department of Medicine, The Royal Melbourne Hospital, Melbourne, VIC, 3010, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Parkville, VIC, 3000, Australia
| | - Michelle Bowman
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, 7000, Australia
- School of Medicine, University of Tasmania, Sandy Bay, TAS, 7005, Australia
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC, 3084, Australia
| | - Simin Daneshvar
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | | | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
- University of Sydney, Sydney, NSW, 2050, Australia
| | - Marion T Harris
- Monash Health Familial Cancer Centre, Clayton, VIC, 3168, Australia
| | - Alex Henderson
- Genetic Health Service, Wellington, Greater Wellington, 6242, New Zealand
- Wellington Hospital, Newtown, Greater Wellington, 6021, New Zealand
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- University of Queensland, St Lucia, QLD, 4067, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Ryan A Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
| | - Emilia Ip
- Cancer Genetics Service, Liverpool Hospital, Liverpool, NSW, 2170, Australia
| | - Joanne Isbister
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Kais Kasem
- Department of Clinical Pathology, Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Annabelle Ng
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Shona O'Connell
- Monash Health Familial Cancer Centre, Clayton, VIC, 3168, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
- School of Medicine, Curtin University, Perth, WA, 6845, Australia
| | - Bernard J Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3051, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Abiramy Ragunathan
- Familial Cancer Service, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Courtney Smyth
- Familial Cancer Centre, Monash Health, Clayton, VIC, 3168, Australia
| | - Allan Spigelman
- Hunter Family Cancer Service, Newcastle, NSW, 2298, Australia
- St Vincent's Cancer Genetics Unit, Sydney, NSW, 2290, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW, 2052, Australia
| | - Kirsty Storey
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Jessica A Taylor
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
| | - Linda Warwick
- ACT Genetic Service, The Canberra Hospital, Woden, ACT, 2606, Australia
| | - Mathilda Wilding
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, NSW, 2065, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Aung K Win
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
| | - Michael D Walsh
- Sullivan Nicolaides Pathology, Bowen Hills, QLD, 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4072, Australia
| | - Finlay A Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Mark A Jenkins
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, 4059, Australia
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ingrid M Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, 3010, Australia.
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC, 3000, Australia.
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12
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Hitchins MP, Alvarez R, Zhou L, Aguirre F, Dámaso E, Pineda M, Capella G, Wong JJL, Yuan X, Ryan SR, Sathe DS, Baxter MD, Cannon T, Biswas R, DeMarco T, Grzelak D, Hampel H, Pearlman R. MLH1-methylated endometrial cancer under 60 years of age as the "sentinel" cancer in female carriers of high-risk constitutional MLH1 epimutation. Gynecol Oncol 2023; 171:129-140. [PMID: 36893489 PMCID: PMC10153467 DOI: 10.1016/j.ygyno.2023.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/11/2023]
Abstract
OBJECTIVE Universal screening of endometrial carcinoma (EC) for mismatch repair deficiency (MMRd) and Lynch syndrome uses presence of MLH1 methylation to omit common sporadic cases from follow-up germline testing. However, this overlooks rare cases with high-risk constitutional MLH1 methylation (epimutation), a poorly-recognized mechanism that predisposes to Lynch-type cancers with MLH1 methylation. We aimed to determine the role and frequency of constitutional MLH1 methylation among EC cases with MMRd, MLH1-methylated tumors. METHODS We screened blood for constitutional MLH1 methylation using pyrosequencing and real-time methylation-specific PCR in patients with MMRd, MLH1-methylated EC ascertained from (i) cancer clinics (n = 4, <60 years), and (ii) two population-based cohorts; "Columbus-area" (n = 68, all ages) and "Ohio Colorectal Cancer Prevention Initiative (OCCPI)" (n = 24, <60 years). RESULTS Constitutional MLH1 methylation was identified in three out of four patients diagnosed between 36 and 59 years from cancer clinics. Two had mono-/hemiallelic epimutation (∼50% alleles methylated). One with multiple primaries had low-level mosaicism in normal tissues and somatic "second-hits" affecting the unmethylated allele in all tumors, demonstrating causation. In the population-based cohorts, all 68 cases from the Columbus-area cohort were negative and low-level mosaic constitutional MLH1 methylation was identified in one patient aged 36 years out of 24 from the OCCPI cohort, representing one of six (∼17%) patients <50 years and one of 45 patients (∼2%) <60 years in the combined cohorts. EC was the first/dual-first cancer in three patients with underlying constitutional MLH1 methylation. CONCLUSIONS A correct diagnosis at first presentation of cancer is important as it will significantly alter clinical management. Screening for constitutional MLH1 methylation is warranted in patients with early-onset EC or synchronous/metachronous tumors (any age) displaying MLH1 methylation.
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Affiliation(s)
- Megan P Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine (Oncology), Stanford University, Stanford, CA, USA.
| | - Rocio Alvarez
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Zhou
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesca Aguirre
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Estela Dámaso
- Department of Medicine (Oncology), Stanford University, Stanford, CA, USA; Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain; Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain
| | - Marta Pineda
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Gabriel Capella
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, and Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Xiaopu Yuan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shawnia R Ryan
- Hereditary Cancer Assessment Program, University of New Mexico Comprehensive Cancer Center, NM, USA
| | - Devika S Sathe
- Precision Medicine and Genetics, Frederick Health, MD, USA
| | | | - Timothy Cannon
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Rakesh Biswas
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Tiffani DeMarco
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | | | - Heather Hampel
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA; Division of Clinical Cancer Genomics, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Rachel Pearlman
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
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13
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Walker R, Mahmood K, Joo JE, Clendenning M, Georgeson P, Como J, Joseland S, Preston SG, Antill Y, Austin R, Boussioutas A, Bowman M, Burke J, Campbell A, Daneshvar S, Edwards E, Gleeson M, Goodwin A, Harris MT, Henderson A, Higgins M, Hopper JL, Hutchinson RA, Ip E, Isbister J, Kasem K, Marfan H, Milnes D, Ng A, Nichols C, O’Connell S, Pachter N, Pope BJ, Poplawski N, Ragunathan A, Smyth C, Spigelman A, Storey K, Susman R, Taylor JA, Warwick L, Wilding M, Williams R, Win AK, Walsh MD, Macrae FA, Jenkins MA, Rosty C, Winship IM, Buchanan DD. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23285541. [PMID: 36909643 PMCID: PMC10002795 DOI: 10.1101/2023.02.27.23285541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). SLS cases (n=135) were recruited from Family Cancer Clinics across Australia and New Zealand. Targeted panel sequencing was performed on tumor (n=137; 80xCRCs, 33xECs and 24xSSTs) and matched blood-derived DNA to assess for microsatellite instability status, tumor mutation burden, COSMIC tumor mutational signatures and to identify germline and somatic MMR gene variants. MMR immunohistochemistry (IHC) and MLH1 promoter methylation were repeated. In total, 86.9% of the 137 SLS tumors could be resolved into established subtypes. For 22.6% of these resolved SLS cases, primary MLH1 epimutations (2.2%) as well as previously undetected germline MMR pathogenic variants (1.5%), tumor MLH1 methylation (13.1%) or false positive dMMR IHC (5.8%) results were identified. Double somatic MMR gene mutations were the major cause of dMMR identified across each tumor type (73.9% of resolved cases, 64.2% overall, 70% of CRC, 45.5% of ECs and 70.8% of SSTs). The unresolved SLS tumors (13.1%) comprised tumors with only a single somatic (7.3%) or no somatic (5.8%) MMR gene mutations. A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3051, Australia
| | - Jihoon E. Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Susan G. Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Yoland Antill
- Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3050, Australia
- Familial Cancer Centre, Cabrini Health, Malvern, VIC 3144, Australia
- Familial Cancer Centre, Monash Health, Clayton, VIC 3168, Australia
- Faculty of Medicine, Dentistry and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Rachel Austin
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Alex Boussioutas
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Gastroenterology, The Alfred Hospital, Melbourne, VIC 3004, Australia
- Department of Medicine, The Royal Melbourne Hospital, Melbourne, VIC 3010, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
| | - Michelle Bowman
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
- School of Medicine, University of Tasmania, Sandy Bay, TAS 7005 Australia
| | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC 3084, Australia
| | - Simin Daneshvar
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Emma Edwards
- Familial Cancer Service, Westmead Hospital, Sydney, NSW 2145, Australia
| | | | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- University of Sydney, Sydney, NSW 2050, Australia
| | - Marion T. Harris
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia
| | - Alex Henderson
- Genetic Health Service, Wellington, Greater Wellington, 6242, New Zealand
- Wellington Hospital, Newtown, Greater Wellington 6021, New Zealand
| | - Megan Higgins
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- University of Queensland, St Lucia, QLD 4067, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
| | - Ryan A. Hutchinson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Emilia Ip
- Cancer Genetics service, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Joanne Isbister
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Department of Medicine, The University of Melbourne, VIC 3000, Australia
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Kais Kasem
- Department of Clinical Pathology, Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Royal Brisbane and Women’s Hospital, Herston, QLD 4029, Australia
| | - Annabelle Ng
- Cancer Genetics Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Cassandra Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia
| | - Shona O’Connell
- Monash Health Familial Cancer Centre, Clayton, VIC 3168, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia
- Medical School, University of Western Australia, Perth, WA 6009, Australia
- School of Medicine, Curtin University, Perth, WA 6845, Australia
| | - Bernard J. Pope
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3051, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Courtney Smyth
- Familial Cancer Centre, Monash Health, Clayton, VIC 3168, Australia
| | - Allan Spigelman
- Hunter Family Cancer Service, Newcastle, NSW 2298, Australia
- St Vincent’s Cancer Genetics Unit, Sydney, NSW 2290, Australia
- Surgical Professorial Unit, UNSW Clinical School of Clinical Medicine, Sydney, NSW 2052, Australia
| | - Kirsty Storey
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Jessica A. Taylor
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
| | - Linda Warwick
- ACT Genetic Service, The Canberra Hospital, Woden, ACT 2606, Australia
| | - Mathilda Wilding
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Kensington, NSW 2052, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Aung K. Win
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
| | - Michael D. Walsh
- Sullivan Nicolaides Pathology, Bowen Hills, QLD 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4072, Australia
| | - Finlay A. Macrae
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A. Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, Melbourne, Victoria, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD 4059, Australia
- University of Queensland, Brisbane, QLD 4072, Australia
| | - Ingrid M. Winship
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
- Department of Medicine, The University of Melbourne, VIC 3000, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, VIC 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
- Genomic Medicine and Familial Cancer Centre, Royal Melbourne Hospital, Parkville, VIC 3000, Australia
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14
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Abildgaard AB, Nielsen SV, Bernstein I, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Lynch syndrome, molecular mechanisms and variant classification. Br J Cancer 2023; 128:726-734. [PMID: 36434153 PMCID: PMC9978028 DOI: 10.1038/s41416-022-02059-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.
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Affiliation(s)
- Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Inge Bernstein
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Institute of Clinical Medicine, Aalborg University Hospital, Aalborg University, Aalborg, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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15
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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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16
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Peltomäki P, Nyström M, Mecklin JP, Seppälä TT. Lynch Syndrome Genetics and Clinical Implications. Gastroenterology 2023; 164:783-799. [PMID: 36706841 DOI: 10.1053/j.gastro.2022.08.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/29/2023]
Abstract
Lynch syndrome (LS) is one of the most prevalent hereditary cancer syndromes in humans and accounts for some 3% of unselected patients with colorectal or endometrial cancer and 10%-15% of those with DNA mismatch repair-deficient tumors. Previous studies have established the genetic basis of LS predisposition, but there have been significant advances recently in the understanding of the molecular pathogenesis of LS tumors, which has important implications in clinical management. At the same time, immunotherapy has revolutionized the treatment of advanced cancers with DNA mismatch repair defects. We aim to review the recent progress in the LS field and discuss how the accumulating epidemiologic, clinical, and molecular information has contributed to a more accurate and complete picture of LS, resulting in genotype- and immunologic subtype-specific strategies for surveillance, cancer prevention, and treatment.
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Affiliation(s)
- Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
| | - Minna Nyström
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland; Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Toni T Seppälä
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland; Applied Tumor Genomics Research Programs Unit, University of Helsinki, Helsinki, Finland; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
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17
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Te Paske IBAW, Mensenkamp AR, Neveling K, Hoogerbrugge N, Ligtenberg MJL, De Voer RM. Noncoding Aberrations in Mismatch Repair Genes Underlie a Substantial Part of the Missing Heritability in Lynch Syndrome. Gastroenterology 2022; 163:1691-1694.e7. [PMID: 36037994 DOI: 10.1053/j.gastro.2022.08.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Iris B A W Te Paske
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | | | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Department of Pathology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Richarda M De Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.
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18
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DNA Methylation Biomarkers for Prediction of Response to Platinum-Based Chemotherapy: Where Do We Stand? Cancers (Basel) 2022; 14:cancers14122918. [PMID: 35740584 PMCID: PMC9221086 DOI: 10.3390/cancers14122918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Platinum-based agents are one of the most widely used chemotherapy drugs for various types of cancer. However, one of the main challenges in the application of platinum drugs is resistance, which is currently being widely investigated. Epigenetic DNA methylation-based biomarkers are promising to aid in the selection of patients, helping to foresee their platinum therapy response in advance. These biomarkers enable minimally invasive patient sample collection, short analysis, and good sensitivity. Hence, improved methodologies for the detection and quantification of DNA methylation biomarkers will facilitate their use in the choice of an optimal treatment strategy. Abstract Platinum-based chemotherapy is routinely used for the treatment of several cancers. Despite all the advances made in cancer research regarding this therapy and its mechanisms of action, tumor resistance remains a major concern, limiting its effectiveness. DNA methylation-based biomarkers may assist in the selection of patients that may benefit (or not) from this type of treatment and provide new targets to circumvent platinum chemoresistance, namely, through demethylating agents. We performed a systematic search of studies on biomarkers that might be predictive of platinum-based chemotherapy resistance, including in vitro and in vivo pre-clinical models and clinical studies using patient samples. DNA methylation biomarkers predictive of response to platinum remain mostly unexplored but seem promising in assisting clinicians in the generation of more personalized follow-up and treatment strategies. Improved methodologies for their detection and quantification, including non-invasively in liquid biopsies, are additional attractive features that can bring these biomarkers into clinical practice, fostering precision medicine.
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19
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Wallander K, Thonberg H, Nilsson D, Tham E. Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis. Hered Cancer Clin Pract 2021; 19:46. [PMID: 34711244 PMCID: PMC8555269 DOI: 10.1186/s13053-021-00203-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
Multiple primary cancers, defined as three or more primary tumours, are rare, and there are few genetic studies concerning them. There is a need for increased knowledge on the heritability of multiple primary cancers and genotype-phenotype correlations. We have performed whole-genome/exome sequencing (WGS/WES) in ten individuals with three or more primary tumours, with no previous findings on standard clinical genetic investigations. In one individual with a clinical diagnosis of MEN1, a likely pathogenic cryptic splice site variant was detected in the MEN1 gene. The variant (c.654C > A) is synonymous but we showed in a cDNA analysis that it affects splicing and leads to a frameshift, with the theoretical new amino acid sequence p.(Gly219Glufs*13). In one individual with metachronous colorectal cancers, ovarian cancer, endometrial cancer and chronic lymphocytic leukaemia, we found a likely pathogenic variant in the MLH1 gene (c.27G > A), and two risk factor variants in the genes CHEK2 and HOXB13. The MLH1 variant is synonymous but has previously been shown to be associated to constitutional low-grade hypermethylation of the MLH1 promoter, and segregates with disease in families with colorectal and endometrial cancer. No pathogenic single nucleotide or structural variants were detected in the remaining eight individuals in the study. The pathogenic variants found by WGS/WES were in genes already sequenced by Sanger sequencing and WES in the clinic, without any findings. We conclude that, in individuals with an unequivocal clinical diagnosis of a specific hereditary cancer syndrome, where standard clinical testing failed to detect a causative variant, re-analysis may lead to a diagnosis.
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Affiliation(s)
- Karin Wallander
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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20
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Ottaiano A, Santorsola M, Caraglia M, Circelli L, Gigantino V, Botti G, Nasti G. Genetic regressive trajectories in colorectal cancer: A new hallmark of oligo-metastatic disease? Transl Oncol 2021; 14:101131. [PMID: 34034007 PMCID: PMC8144733 DOI: 10.1016/j.tranon.2021.101131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) originates as consequence of multiple genetic alterations. Some of the involved genes have been extensively studied (APC, TP53, KRAS, SMAD4, PIK3CA, MMR genes) in highly heterogeneous and poly-metastatic cohorts. However, about 10% of metastatic CRC patients presents with an indolent oligo-metastatic disease differently from other patients with poly-metastatic and aggressive clinical course. Which are the genetic dynamics underlying the differences between oligo- and poly-metastatic CRC? The understanding of the genetic trajectories (primary→metastatic) of CRC, in patients selected to represent homogenous clinical models, is crucial to make genotype/phenotype correlations and to identify the molecular events pushing the disease towards an increasing malignant phenotype. This information is crucial to plan innovative therapeutic strategies aimed to reverse or inhibit these phenomena. In the present study, we review the genetic evolution of CRC with the intent to give a developmental perspective on the border line between oligo- and poly-metastatic diseases.
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Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy.
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio, 7 80138, Naples, Italy; Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031, Ariano Irpino, Italy
| | - Luisa Circelli
- AMES-Centro Polidiagnostico Strumentale, 80013, Casalnuovo di Napoli, Italy
| | - Valerio Gigantino
- Innovalab scarl, Molecular Biology, Centro Direzionale, isola A2, 80143, Naples, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
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21
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Zyla R, Graham T, Aronson M, Velsher L, Mrkonjic M, Turashvili G. MLH1 epimutation is a rare mechanism for Lynch syndrome: A case report and review of the literature. Genes Chromosomes Cancer 2021; 60:635-639. [PMID: 33934415 DOI: 10.1002/gcc.22957] [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: 03/24/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/10/2022] Open
Abstract
Endometrial carcinoma is one of the prototypical malignancies associated with Lynch syndrome, an inherited cancer syndrome most commonly caused by germline mutations in DNA mismatch repair (MMR) genes, although rare alternative mechanisms also exist. In this report, we describe a patient first diagnosed with colorectal cancer at age 33, then vulvar squamous cell carcinoma, facial sebaceous adenoma/sebaceoma, and finally endometrial carcinoma at age 52. All tumors were MLH1/PMS2-deficient by immunohistochemistry, and MLH1 promoter methylation was identified in the endometrial cancer. Germline MLH1 testing was negative for pathogenic variants, but she was subsequently diagnosed with Lynch syndrome secondary to a germline monoallelic constitutional epimutation of the MLH1 promoter. Identification of patients displaying a Lynch syndrome phenotype but lacking germline MMR mutations is important to avoid delays in the diagnosis of Lynch syndrome as well as the initiation of appropriate cancer screening and genetic counseling.
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Affiliation(s)
- Roman Zyla
- Department of Pathology and Laboratory Medicine, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Tracy Graham
- Cancer Genetics and High Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Lea Velsher
- Cancer Genetics and High Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Miralem Mrkonjic
- Department of Pathology and Laboratory Medicine, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
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22
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Peltomäki P, Olkinuora A, Nieminen TT. Updates in the field of hereditary nonpolyposis colorectal cancer. Expert Rev Gastroenterol Hepatol 2020; 14:707-720. [PMID: 32755332 DOI: 10.1080/17474124.2020.1782187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Up to one third of colorectal cancers show familial clustering and 5% are hereditary single-gene disorders. Hereditary non-polyposis colorectal cancer comprises DNA mismatch repair-deficient and -proficient subsets, represented by Lynch syndrome (LS) and familial colorectal cancer type X (FCCTX), respectively. Accurate knowledge of molecular etiology and genotype-phenotype correlations are critical for tailored cancer prevention and treatment. AREAS COVERED The authors highlight advances in the molecular dissection of hereditary non-polyposis colorectal cancer, based on recent literature retrieved from PubMed. Future possibilities for novel gene discoveries are discussed. EXPERT COMMENTARY LS is molecularly well established, but new information is accumulating of the associated clinical and tumor phenotypes. FCCTX remains poorly defined, but several promising candidate genes have been discovered and share some preferential biological pathways. Multi-level characterization of specimens from large patient cohorts representing multiple populations, combined with proper bioinformatic and functional analyses, will be necessary to resolve the outstanding questions.
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Affiliation(s)
- Paivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki , Helsinki, Finland
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23
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Jansen AML, Goel A. Mosaicism in Patients With Colorectal Cancer or Polyposis Syndromes: A Systematic Review. Clin Gastroenterol Hepatol 2020; 18:1949-1960. [PMID: 32147591 PMCID: PMC7725418 DOI: 10.1016/j.cgh.2020.02.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Somatic mosaicism, in which variants arise post-zygotically and are therefore not present in all cells in the body, may be an underestimated cause of colorectal cancer (CRC) and polyposis syndromes. We performed a systematic review to provide a comprehensive overview of somatic mosaicism in patients with CRC and polyposis syndromes. METHODS We searched PubMed through March 2018 to identify reports of mosaicism in patients with CRC or polyposis syndromes. We divided the final set of studies into 3 subgroups describing APC mosaicism, mosaicism in other CRC susceptibility genes, and epigenetic mosaicism. RESULTS Of the 232 articles identified in our systematic search, 46 met the criteria for further analysis. Of these, 35 studies described mosaic variants or epimutations in patients with CRC or polyposis syndromes. Nineteen studies described APC mosaicism, comprising a total of 57 patients. Six described mosaicism in genes associated with familial CRC syndromes, such as Lynch and Cowden syndromes. Ten studies described epigenetic mosaicism, sometimes resulting from a germline variant (such as deletion of EPCAM). CONCLUSIONS We found that somatic mosaicism is underdiagnosed but critical for determining the clinical management of patients with de novo polyposis who possibly carry mosaic APC variants, and present a decision tree for the clinical management of these patients. Mosaicism in genes associated with susceptibility to CRC contributes to development of other familial CRC syndromes. Heritable epigenetic mosaicism is likely underestimated and could have a dominant pattern of inheritance. However, the inheritance of primary mosaic epimutations, without an underlying genetic cause, is complex and not fully understood.
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Affiliation(s)
- Anne Maria Lucia Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California.
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24
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Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
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25
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Wong EM, Southey MC, Terry MB. Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer. Br J Cancer 2020; 122:1133-1140. [PMID: 32066913 PMCID: PMC7156506 DOI: 10.1038/s41416-019-0720-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.
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Affiliation(s)
- Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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26
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Dámaso E, Canet-Hermida J, Vargas-Parra G, Velasco À, Marín F, Darder E, Del Valle J, Fernández A, Izquierdo À, Mateu G, Oliveras G, Escribano C, Piñol V, Uchima HI, Soto JL, Hitchins M, Farrés R, Lázaro C, Queralt B, Brunet J, Capellá G, Pineda M. Highly sensitive MLH1 methylation analysis in blood identifies a cancer patient with low-level mosaic MLH1 epimutation. Clin Epigenetics 2019; 11:171. [PMID: 31779681 PMCID: PMC6883525 DOI: 10.1186/s13148-019-0762-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
Constitutional MLH1 methylation (epimutation) is a rare cause of Lynch syndrome. Low-level methylation (≤ 10%) has occasionally been described. This study aimed to identify low-level constitutional MLH1 epimutations and determine its causal role in patients with MLH1-hypermethylated colorectal cancer. Eighteen patients with MLH1-hypermethylated colorectal tumors in whom MLH1 methylation was previously undetected in blood by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were screened for MLH1 methylation using highly sensitive MS-melting curve analysis (MS-MCA). Constitutional methylation was characterized by different approaches. MS-MCA identified one patient (5.6%) with low-level MLH1 methylation (~ 1%) in blood and other normal tissues, which was confirmed by clonal bisulfite sequencing in blood. The patient had developed three clonally related gastrointestinal MLH1-methylated tumor lesions at 22, 24, and 25 years of age. The methylated region in normal tissues overlapped with that reported for other carriers of constitutional MLH1 epimutations. Low-level MLH1 methylation and reduced allelic expression were linked to the same genetic haplotype, whereas the opposite allele was lost in patient’s tumors. Mutation screening of MLH1 and other hereditary cancer genes was negative. Herein, a highly sensitive MS-MCA-based approach has demonstrated its utility for the identification of low-level constitutional MLH1 epigenetic mosaicism. The eventual identification and characterization of additional cases will be critical to ascertain the cancer risks associated with constitutional MLH1 epigenetic mosaicism.
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Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Júlia Canet-Hermida
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Àngela Velasco
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Esther Darder
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Àngel Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Gemma Mateu
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | - Glòria Oliveras
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | | | - Virgínia Piñol
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - Hugo-Ikuo Uchima
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - José Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Elche, Alicante, Spain
| | - Megan Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, CA, Los Angeles, USA
| | - Ramon Farrés
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Bernat Queralt
- Department of Medical Oncology, Catalan Institute of Oncology, Girona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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27
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Evrard C, Tachon G, Randrian V, Karayan-Tapon L, Tougeron D. Microsatellite Instability: Diagnosis, Heterogeneity, Discordance, and Clinical Impact in Colorectal Cancer. Cancers (Basel) 2019; 11:E1567. [PMID: 31618962 PMCID: PMC6826728 DOI: 10.3390/cancers11101567] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/17/2022] Open
Abstract
Tumor DNA mismatch repair (MMR) deficiency testing is important to the identification of Lynch syndrome and decision making regarding adjuvant chemotherapy in stage II colorectal cancer (CRC) and has become an indispensable test in metastatic tumors due to the high efficacy of immune checkpoint inhibitor (ICI) in deficient MMR (dMMR) tumors. CRCs greatly benefit from this testing as approximately 15% of them are dMMR but only 3% to 5% are at a metastatic stage. MMR status can be determined by two different methods, microsatellite instability (MSI) testing on tumor DNA, and immunohistochemistry of the MMR proteins on tumor tissue. Recent studies have reported a rate of 3% to 10% of discordance between these two tests. Moreover, some reports suggest possible intra- and inter-tumoral heterogeneity of MMR and MSI status. These issues are important to know and to clarify in order to define therapeutic strategy in CRC. This review aims to detail the standard techniques used for the determination of MMR and MSI status, along with their advantages and limits. We review the discordances that may arise between these two tests, tumor heterogeneity of MMR and MSI status, and possible explanations. We also discuss the strategies designed to distinguish sporadic versus germline dMMR/MSI CRC. Finally, we present new and accurate methods aimed at determining MMR/MSI status.
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Affiliation(s)
- Camille Evrard
- Department of Medical Oncology, Poitiers University Hospital, 86021 Poitiers, France.
| | - Gaëlle Tachon
- Department of Cancer biology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Laboratory of Experimental and Clinical Neuroscience, Institut national de la santé et de la recherche médicale (INSERM) 1084, F-86073 Poitiers, France.
| | - Violaine Randrian
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Department of Gastroenterology, Poitiers University Hospital, 86021 Poitiers, France.
| | - Lucie Karayan-Tapon
- Department of Cancer biology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Laboratory of Experimental and Clinical Neuroscience, Institut national de la santé et de la recherche médicale (INSERM) 1084, F-86073 Poitiers, France.
| | - David Tougeron
- Department of Medical Oncology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Department of Gastroenterology, Poitiers University Hospital, 86021 Poitiers, France.
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28
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Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
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Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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Non-Coding Variants in BRCA1 and BRCA2 Genes: Potential Impact on Breast and Ovarian Cancer Predisposition. Cancers (Basel) 2018; 10:cancers10110453. [PMID: 30453575 PMCID: PMC6266896 DOI: 10.3390/cancers10110453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
BRCA1 and BRCA2 are major breast cancer susceptibility genes whose pathogenic variants are associated with a significant increase in the risk of breast and ovarian cancers. Current genetic screening is generally limited to BRCA1/2 exons and intron/exon boundaries. Most identified pathogenic variants cause the partial or complete loss of function of the protein. However, it is becoming increasingly clear that variants in these regions only account for a small proportion of cancer risk. The role of variants in non-coding regions beyond splice donor and acceptor sites, including those that have no qualitative effect on the protein, has not been thoroughly investigated. The key transcriptional regulatory elements of BRCA1 and BRCA2 are housed in gene promoters, untranslated regions, introns, and long-range elements. Within these sequences, germline and somatic variants have been described, but the clinical significance of the majority is currently unknown and it remains a significant clinical challenge. This review summarizes the available data on the impact of variants on non-coding regions of BRCA1/2 genes and their role on breast and ovarian cancer predisposition.
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Dámaso E, Castillejo A, Arias MDM, Canet-Hermida J, Navarro M, Del Valle J, Campos O, Fernández A, Marín F, Turchetti D, García-Díaz JDD, Lázaro C, Genuardi M, Rueda D, Alonso Á, Soto JL, Hitchins M, Pineda M, Capellá G. Primary constitutional MLH1 epimutations: a focal epigenetic event. Br J Cancer 2018; 119:978-987. [PMID: 30283143 PMCID: PMC6203851 DOI: 10.1038/s41416-018-0019-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Background Constitutional MLH1 epimutations are characterised by monoallelic methylation of the MLH1 promoter throughout normal tissues, accompanied by allele-specific silencing. The mechanism underlying primary MLH1 epimutations is currently unknown. The aim of this study was to perform an in-depth characterisation of constitutional MLH1 epimutations targeting the aberrantly methylated region around MLH1 and other genomic loci. Methods Twelve MLH1 epimutation carriers, 61 Lynch syndrome patients, and 41 healthy controls, were analysed by Infinium 450 K array. Targeted molecular techniques were used to characterise the MLH1 epimutation carriers and their inheritance pattern. Results No nucleotide or structural variants were identified in-cis on the epimutated allele in 10 carriers, in which inter-generational methylation erasure was demonstrated in two, suggesting primary type of epimutation. CNVs outside the MLH1 locus were found in two cases. EPM2AIP1-MLH1 CpG island was identified as the sole differentially methylated region in MLH1 epimutation carriers compared to controls. Conclusion Primary constitutional MLH1 epimutations arise as a focal epigenetic event at the EPM2AIP1-MLH1 CpG island in the absence of cis-acting genetic variants. Further molecular characterisation is needed to elucidate the mechanistic basis of MLH1 epimutations and their heritability/reversibility.
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Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Adela Castillejo
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Camino de la Almazara 11, Elche, 03203, Alicante, Spain
| | - María Del Mar Arias
- Genetics Service, Complejo Hospitalario de Navarra, Calle de Irunlarrea 3, Pamplona, 31008, Navarra, Spain
| | - Julia Canet-Hermida
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Daniela Turchetti
- Dipartimento di Scienze Mediche e Chirurgiche, Alma Mater Studiorum - Università di Bologna, Via Massarenti 11, Bologna, 40138, Italy
| | - Juan de Dios García-Díaz
- Unidad de Genética Clínica, Servicio de Medicina Interna, Hospital Universitario Príncipe de Asturias, Carretera Alcalá-Meco, Alcalá de Henares, 28805, Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Maurizio Genuardi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Agostino Gemelli, Largo Agostino Gemelli 8, Rome, 00168, Italy
| | - Daniel Rueda
- Hereditary Cancer Genetic Diagnostic Laboratory, Doce de Octubre University Hospital, Avenida de Córdoba, Madrid, Madrid, 28041, Spain
| | - Ángel Alonso
- Genetics Service, Complejo Hospitalario de Navarra, Calle de Irunlarrea 3, Pamplona, 31008, Navarra, Spain
| | - Jose Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Camino de la Almazara 11, Elche, 03203, Alicante, Spain.,Alicante Institute for Health and Biomedical Research (ISABIAL-FISABIO Foundation), Alicante, Spain
| | - Megan Hitchins
- Department of Medicine, Division of Oncology, Stanford University, 1291 Welch Road, Stanford, 94305, California, USA
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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Snowsill T, Coelho H, Huxley N, Jones-Hughes T, Briscoe S, Frayling IM, Hyde C. Molecular testing for Lynch syndrome in people with colorectal cancer: systematic reviews and economic evaluation. Health Technol Assess 2018; 21:1-238. [PMID: 28895526 DOI: 10.3310/hta21510] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Inherited mutations in deoxyribonucleic acid (DNA) mismatch repair (MMR) genes lead to an increased risk of colorectal cancer (CRC), gynaecological cancers and other cancers, known as Lynch syndrome (LS). Risk-reducing interventions can be offered to individuals with known LS-causing mutations. The mutations can be identified by comprehensive testing of the MMR genes, but this would be prohibitively expensive in the general population. Tumour-based tests - microsatellite instability (MSI) and MMR immunohistochemistry (IHC) - are used in CRC patients to identify individuals at high risk of LS for genetic testing. MLH1 (MutL homologue 1) promoter methylation and BRAF V600E testing can be conducted on tumour material to rule out certain sporadic cancers. OBJECTIVES To investigate whether testing for LS in CRC patients using MSI or IHC (with or without MLH1 promoter methylation testing and BRAF V600E testing) is clinically effective (in terms of identifying Lynch syndrome and improving outcomes for patients) and represents a cost-effective use of NHS resources. REVIEW METHODS Systematic reviews were conducted of the published literature on diagnostic test accuracy studies of MSI and/or IHC testing for LS, end-to-end studies of screening for LS in CRC patients and economic evaluations of screening for LS in CRC patients. A model-based economic evaluation was conducted to extrapolate long-term outcomes from the results of the diagnostic test accuracy review. The model was extended from a model previously developed by the authors. RESULTS Ten studies were identified that evaluated the diagnostic test accuracy of MSI and/or IHC testing for identifying LS in CRC patients. For MSI testing, sensitivity ranged from 66.7% to 100.0% and specificity ranged from 61.1% to 92.5%. For IHC, sensitivity ranged from 80.8% to 100.0% and specificity ranged from 80.5% to 91.9%. When tumours showing low levels of MSI were treated as a positive result, the sensitivity of MSI testing increased but specificity fell. No end-to-end studies of screening for LS in CRC patients were identified. Nine economic evaluations of screening for LS in CRC were identified. None of the included studies fully matched the decision problem and hence a new economic evaluation was required. The base-case results in the economic evaluation suggest that screening for LS in CRC patients using IHC, BRAF V600E and MLH1 promoter methylation testing would be cost-effective at a threshold of £20,000 per quality-adjusted life-year (QALY). The incremental cost-effectiveness ratio for this strategy was £11,008 per QALY compared with no screening. Screening without tumour tests is not predicted to be cost-effective. LIMITATIONS Most of the diagnostic test accuracy studies identified were rated as having a risk of bias or were conducted in unrepresentative samples. There was no direct evidence that screening improves long-term outcomes. No probabilistic sensitivity analysis was conducted. CONCLUSIONS Systematic review evidence suggests that MSI- and IHC-based testing can be used to identify LS in CRC patients, although there was heterogeneity in the methods used in the studies identified and the results of the studies. There was no high-quality empirical evidence that screening improves long-term outcomes and so an evidence linkage approach using modelling was necessary. Key determinants of whether or not screening is cost-effective are the accuracy of tumour-based tests, CRC risk without surveillance, the number of relatives identified for cascade testing, colonoscopic surveillance effectiveness and the acceptance of genetic testing. Future work should investigate screening for more causes of hereditary CRC and screening for LS in endometrial cancer patients. STUDY REGISTRATION This study is registered as PROSPERO CRD42016033879. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Tristan Snowsill
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
| | - Helen Coelho
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
| | - Nicola Huxley
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
| | - Tracey Jones-Hughes
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
| | - Simon Briscoe
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
| | - Ian M Frayling
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | - Chris Hyde
- Peninsula Technology Assessment Group (PenTAG), University of Exeter, Exeter, UK
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Boland PM, Yurgelun MB, Boland CR. Recent progress in Lynch syndrome and other familial colorectal cancer syndromes. CA Cancer J Clin 2018; 68:217-231. [PMID: 29485237 PMCID: PMC5980692 DOI: 10.3322/caac.21448] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/08/2018] [Accepted: 01/31/2018] [Indexed: 12/16/2022] Open
Abstract
The current understanding of familial colorectal cancer was limited to descriptions of affected pedigrees until the early 1990s. A series of landscape-altering discoveries revealed that there were distinct forms of familial cancer, and most were related to genes previously not known to be involved in human disease. This review largely focuses on advances in our understanding of Lynch syndrome because of the unique relationship of this disease to defective DNA mismatch repair and the clinical implications this has for diagnostics, prevention, and therapy. Recent advances have occurred in our understanding of the epidemiology of this disease, and the advent of broad genetic panels has altered the approach to germline and somatic diagnoses for all of the familial colorectal cancer syndromes. Important advances have been made toward a more complete mechanistic understanding of the pathogenesis of neoplasia in the setting of Lynch syndrome, and these advances have important implications for prevention. Finally, paradigm-shifting approaches to treatment of Lynch-syndrome and related tumors have occurred through the development of immune checkpoint therapies for hypermutated cancers. CA Cancer J Clin 2018;68:217-231. © 2018 American Cancer Society.
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Affiliation(s)
- Patrick M Boland
- Assistant Professor, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY
| | - Matthew B Yurgelun
- Assistant Professor of Medicine, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - C Richard Boland
- Professor, Department of Medicine, University of California at San Diego School of Medicine, San Diego, CA
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Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation. Genet Med 2018; 20:1589-1599. [DOI: 10.1038/gim.2018.47] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
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Morak M, Ibisler A, Keller G, Jessen E, Laner A, Gonzales-Fassrainer D, Locher M, Massdorf T, Nissen AM, Benet-Pagès A, Holinski-Feder E. Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional MLH1 epimutation. J Med Genet 2018; 55:240-248. [PMID: 29472279 DOI: 10.1136/jmedgenet-2017-104744] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 01/28/2023]
Abstract
BACKGROUND Germline defects in MLH1, MSH2, MSH6 and PMS2 predisposing for Lynch syndrome (LS) are mainly based on sequence changes, whereas a constitutional epimutation of MLH1(CEM) is exceptionally rare. This abnormal MLH1 promoter methylation is not hereditary when arising de novo, whereas a stably heritable and variant-induced CEM was described for one single allele. We searched for MLH1 promoter variants causing a germline or somatic methylation induction or transcriptional repression. METHODS We analysed the MLH1 promoter sequence in five different patient groups with colorectal cancer (CRC) (n=480) composed of patients with i) CEM (n=16), ii) unsolved loss of MLH1 expression in CRC (n=37), iii) CpG-island methylator-phenotype CRC (n=102), iv) patients with LS (n=83) and v) MLH1-proficient CRC (n=242) as controls. 1150 patients with non-LS tumours also served as controls to correctly judge the results. RESULTS We detected 10 rare MLH1 promoter variants. One novel, complex MLH1 variant c.-63_-58delins18 is present in a patient with CRC with CEM and his sister, both showing a complete allele-specific promoter methylation and transcriptional silencing. The other nine promoter variants detected in 17 individuals were not associated with methylation. For four of these, a normal, biallelic MLH1 expression was found in the patients' cDNA. CONCLUSION We report the second promoter variant stably inducing a hereditary CEM. Concerning the classification of promoter variants, we discuss contradictory results from the literature for two variants, describe classification discrepancies between existing rules for five variants, suggest the (re-)classification of five promoter variants to (likely) benign and regard four variants as functionally unclear.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany.,Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Ayseguel Ibisler
- Department of Human Genetics, Ruhr University Bochum, Bochum, North Rhine-Westphalia, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University Munich, Munich, Bavaria, Germany
| | - Ellen Jessen
- Praxis für Humangenetik, Praxis für Humangenetik, Hamburg, Hamburg, Germany
| | - Andreas Laner
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | | | - Melanie Locher
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Trisari Massdorf
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany
| | - Anke M Nissen
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Anna Benet-Pagès
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany.,Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
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Somatic Testing on Gynecological Cancers Improve the Identification of Lynch Syndrome. Int J Gynecol Cancer 2018; 27:1543-1549. [PMID: 28471861 DOI: 10.1097/igc.0000000000001010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE Recent data from the literature indicate gynecological cancers (GCs) as sentinel cancers for a diagnosis of Lynch syndrome (LS). Clinical approaches to identifying LS have low sensitivity, whereas somatic tests on GCs may be a more sensitive and cost-effective strategy. METHODS A series of 78 GCs belonging to 74 patients sent to the Genetic Counselling Service were investigated using microsatellite instability, immunohistochemical expression of mismatch repair (MMR) genes, and MLH1 promoter methylation. RESULTS The presence of microsatellite instability was observed in 67.5% of GCs, and the absence of immunohistochemical expression of at least 1 of the 4 MMR proteins was observed in 71.4% of GCs, showing 96.1% concordance between the methods. Methylation analysis using methylation specific multiplex ligation-dependent probe amplification performed on 35 samples revealed MLH1 promoter hypermethylation in 18 cases (54%). Molecular analysis identified 36 LS carriers of MMR variants (27 pathogenetic and 9 variants of uncertain significance), and, interestingly, 3 LS patients had MLH1 methylated GC.With regard to histological features, LS-related GCs included endocervical cancers and also histological types different from the endometrioid cancers. The presence of peritumoral lymphocytes in GCs was statistically associated with LS tumors. CONCLUSIONS Somatic analysis is a useful strategy to distinguish sporadic from LS GC. Our data allow the identification of a subset of LS patients otherwise unrecognized on the basis of clinical or family history alone. In addition, our results indicate that some clinicopathological features including age of GC diagnosis; presence of peritumoral lymphocytes; isthmic, endocervical sites, and body mass index value could be useful criteria to select patients for genetic counseling.
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Pinto D, Pinto C, Guerra J, Pinheiro M, Santos R, Vedeld HM, Yohannes Z, Peixoto A, Santos C, Pinto P, Lopes P, Lothe R, Lind GE, Henrique R, Teixeira MR. Contribution of MLH1 constitutional methylation for Lynch syndrome diagnosis in patients with tumor MLH1 downregulation. Cancer Med 2018; 7:433-444. [PMID: 29341452 PMCID: PMC6193414 DOI: 10.1002/cam4.1285] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/23/2022] Open
Abstract
Constitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, has been identified as an alternative mechanism that predisposes to the development of Lynch syndrome. In the present work, we aimed to investigate the prevalence of MLH1 constitutional methylation in colorectal cancer (CRC) patients with abnormal expression of the MLH1 protein in their tumors. In a series of 38 patients who met clinical criteria for Lynch syndrome genetic testing, with loss of MLH1 expression in the tumor and with no germline mutations in the MLH1 gene (35/38) or with tumors presenting the BRAF p.Val600Glu mutation (3/38), we screened for constitutional methylation of the MLH1 gene promoter using methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) in various biological samples. We found four (4/38; 10.5%) patients with constitutional methylation in the MLH1 gene promoter. RNA studies demonstrated decreased MLH1 expression in the cases with constitutional methylation when compared with controls. We could infer the mosaic nature of MLH1 constitutional hypermethylation in tissues originated from different embryonic germ layers, and in one family we could show that it occurred de novo. We conclude that constitutional MLH1 methylation occurs in a significant proportion of patients who have loss of MLH1 protein expression in their tumors and no MLH1 pathogenic germline mutation. Furthermore, we provide evidence that MLH1 constitutional hypermethylation is the molecular mechanism behind about 3% of Lynch syndrome families diagnosed in our institution, especially in patients with early onset or multiple primary tumors without significant family history.
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Affiliation(s)
- Diana Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Rui Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Zeremariam Yohannes
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Ana Peixoto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Paula Lopes
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Ragnhild Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, Krieger S, Rogan PK, Mucaki EJ, Burke LJ, Bièche I, Houdayer C, Vaur D, Stoppa-Lyonnet D, Brown MA, Lallemand F, Rouleau E. Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition. Breast Cancer Res Treat 2017; 168:311-325. [PMID: 29236234 DOI: 10.1007/s10549-017-4602-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2). The impact of a set of variants on BRCA1/2 gene regulation was evaluated by site-directed mutagenesis, transfection, followed by Luciferase gene reporter assay. RESULTS We identified a total of 117 variants and tested twelve BRCA1 and 8 BRCA2 variants mapping to promoter and intronic regions. We highlighted two neighboring BRCA1 promoter variants (c.-130del; c.-125C > T) and one BRCA2 promoter variants (c.-296C > T) inhibiting significantly the promoter activity. In the functional assays, a regulating region within the intron 12 was found with the same enhancing impact as within the intron 2. Furthermore, the variants c.81-3980A > G and c.4186-2022C > T suppress the positive effect of the introns 2 and 12, respectively, on the BRCA1 promoter activity. We also found some variants inducing the promoter activities. CONCLUSION In this study, we highlighted some variants among many, modulating negatively the promoter activity of BRCA1 or 2 and thus having a potential impact on the risk of developing cancer. This selection makes it possible to conduct future validation studies on a limited number of variants.
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Affiliation(s)
- E Santana Dos Santos
- Department of Oncology, Center for Translational Oncology, Cancer Institute of the State of São Paulo - ICESP, São Paulo, Brazil
- Service de Génétique, Institut Curie, Paris, France
- A.C.Camargo Cancer Center, São Paulo, Brazil
| | - S M Caputo
- Service de Génétique, Institut Curie, Paris, France
| | - L Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - M Gendrot
- Service de Génétique, Institut Curie, Paris, France
| | - A Briaux
- Service de Génétique, Institut Curie, Paris, France
| | - M Breault
- Service de Génétique, Institut Curie, Paris, France
| | - S Krieger
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - P K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - E J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - L J Burke
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - I Bièche
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - C Houdayer
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - D Vaur
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - D Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - M A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - F Lallemand
- Service de Génétique, Institut Curie, Paris, France.
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Markow M, Chen W, Frankel WL. Immunohistochemical Pitfalls: Common Mistakes in the Evaluation of Lynch Syndrome. Surg Pathol Clin 2017; 10:977-1007. [PMID: 29103543 DOI: 10.1016/j.path.2017.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
At least 15% of colorectal cancers diagnosed in the United States are deficient in mismatch repair mechanisms. Most of these are sporadic, but approximately 3% of colorectal cancers result from germline alterations in mismatch repair genes and represent Lynch syndrome. It is critical to identify patients with Lynch syndrome to institute appropriate screening and surveillance for patients and their families. Exclusion of Lynch syndrome in sporadic cases is equally important because it reduces anxiety for patients and prevents excessive spending on unnecessary surveillance. Immunohistochemistry is one of the most widely used screening tools for identifying patients with Lynch syndrome.
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Affiliation(s)
- Michael Markow
- Department of Pathology, The Ohio State University Wexner Medical Center, 129 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA
| | - Wei Chen
- Department of Pathology, The Ohio State University Wexner Medical Center, 129 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA
| | - Wendy L Frankel
- Department of Pathology, The Ohio State University Wexner Medical Center, 129 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA.
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Abstract
Four main DNA mismatch repair (MMR) genes have been identified, MLH1, MSH2, MSH6, and PMS2, which when mutated cause susceptibility to Lynch syndrome (LS). LS is one of the most prevalent hereditary cancer syndromes in man and accounts for 1–3 % of unselected colorectal carcinomas and some 15 % of those with microsatellite instability and/or absent MMR protein. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) maintains a database for LS-associated mutations since 1996. The database was recently reorganized to efficiently gather published and unpublished data and to classify the variants according to a five-tiered scheme linked to clinical recommendations. This review provides an update of germline mutations causing susceptibility to LS based on information available in the InSiGHT database and the latest literature. MMR gene mutation profiles, correlations between genotype and phenotype, and possible mechanisms leading to the characteristic spectrum of tumors in LS are discussed in light of the different functions of MMR proteins, many of which directly serve cancer avoidance.
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Yanokura M, Banno K, Adachi M, Aoki D, Abe K. Genome-wide DNA methylation sequencing reveals miR-663a is a novel epimutation candidate in CIMP-high endometrial cancer. Int J Oncol 2017; 50:1934-1946. [PMID: 28440489 PMCID: PMC5435325 DOI: 10.3892/ijo.2017.3966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/26/2017] [Indexed: 12/26/2022] Open
Abstract
Aberrant DNA methylation is widely observed in many cancers. Concurrent DNA methylation of multiple genes occurs in endometrial cancer and is referred to as the CpG island methylator phenotype (CIMP). However, the features and causes of CIMP-positive endometrial cancer are not well understood. To investigate DNA methylation features characteristic to CIMP-positive endometrial cancer, we first classified samples from 25 patients with endometrial cancer based on the methylation status of three genes, i.e. MLH1, CDH1 (E-cadherin) and APC: CIMP-high (CIMP-H, 2/25, 8.0%), CIMP-low (CIMP-L, 7/25, 28.0%) and CIMP-negative (CIMP(-), 16/25, 64.0%). We then selected two samples each from CIMP-H and CIMP(-) classes, and analyzed DNA methylation status of both normal (peripheral blood cells: PBCs) and cancer tissues by genome-wide, targeted bisulfite sequencing. Genomes of the CIMP-H cancer tissues were significantly hypermethylated compared to those of the CIMP(-). Surprisingly, in normal tissues of the CIMP-H patients, promoter region of the miR-663a locus is hypermethylated relative to CIMP(-) samples. Consistent with this finding, miR-663a expression was lower in the CIMP-H PBCs than in the CIMP(-) PBCs. The same region of the miR663a locus is found to be highly methylated in cancer tissues of both CIMP-H and CIMP(-) cases. This is the first report showing that aberrant DNA methylation of the miR-663a promoter can occur in normal tissue of the cancer patients, suggesting a possible link between this epigenetic abnormality and endometrial cancer. This raises the possibility that the hypermethylation of the miR-663a promoter represents an epimutation associated with the CIMP-H endometrial cancers. Based on these findings, relationship of the aberrant DNA methylation and CIMP-H phenotype is discussed.
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Affiliation(s)
- Megumi Yanokura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Cente, Tsukuba, Ibaraki 305-0074
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kouji Banno
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masataka Adachi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kuniya Abe
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Cente, Tsukuba, Ibaraki 305-0074
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Chen W, Swanson BJ, Frankel WL. Molecular genetics of microsatellite-unstable colorectal cancer for pathologists. Diagn Pathol 2017; 12:24. [PMID: 28259170 PMCID: PMC5336657 DOI: 10.1186/s13000-017-0613-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
Background Microsatellite-unstable colorectal cancers (CRC) that are due to deficient DNA mismatch repair (dMMR) represent approximately 15% of all CRCs in the United States. These microsatellite-unstable CRCs represent a heterogenous group of diseases with distinct oncogenesis pathways. There are overlapping clinicopathologic features between some of these groups, but many important differences are present. Therefore, determination of the etiology for the dMMR is vital for proper patient management and follow-up. Main body Epigenetic inactivation of MLH1 MMR gene (sporadic microsatellite-unstable CRC) and germline mutation in an MMR gene (Lynch syndrome, LS) are the two most common mechanisms in the pathogenesis of microsatellite instability in CRC. However, in a subset of dMMR CRC cases that are identified by screening tests, no known LS-associated genetic alterations are appreciated by current genetic analysis. When the etiology for dMMR is unclear, it leads to patient anxiety and creates challenges for clinical management. Conclusion It is critical to distinguish LS patients from other patients with tumors due to dMMR, so that the proper screening protocol can be employed for the patients and their families, with the goal to save lives while avoiding unnecessary anxiety and costs. This review summarizes the major pathogenesis pathways of dMMR CRCs, their clinicopathologic features, and practical screening suggestions. In addition, we include frequently asked questions for MMR immunohistochemistry interpretation.
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Affiliation(s)
- Wei Chen
- Department of Pathology, The Ohio State University Wexner Medical Center, S301 Rhodes Hall, 450 W. 10th Ave, Columbus, Ohio, 43210, USA.,Department of Pathology, The Ohio State University Wexner Medical Center, 129 Hamilton Hall, Columbus, Ohio, 43210, USA
| | - Benjamin J Swanson
- Department of Pathology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wendy L Frankel
- Department of Pathology, The Ohio State University Wexner Medical Center, S301 Rhodes Hall, 450 W. 10th Ave, Columbus, Ohio, 43210, USA. .,Department of Pathology, The Ohio State University Wexner Medical Center, 129 Hamilton Hall, Columbus, Ohio, 43210, USA.
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Abstract
Colorectal cancer affects about 4.4% of the population and is a leading cause of cancer-related death in the United States. Approximately 10% to 20% of cases occur within a familial pattern, and Lynch syndrome is the most common hereditary colorectal cancer syndrome. Lynch syndrome is a hereditary predisposition to forming colorectal and extracolonic cancers, caused by a germline mutation in one of the DNA mismatch repair genes. Identifying at-risk patients and making a correct diagnosis are the keys to successful screening and interventions which will decrease formation of and death from cancers. Knowledge of the genetics and the natural history of Lynch syndrome has continued to be uncovered in recent years, leading to a better grasp on how these patients and their families should be managed. Recent developments include the approach to diagnostic testing, more precise definitions of the syndrome and risk stratification based on gene mutations, surgical decision-making, and chemoprevention.
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Affiliation(s)
- Sherief Shawki
- Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Matthew F Kalady
- Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
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43
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Zarandi A, Irani S, Savabkar S, Chaleshi V, Ghavideldarestani M, Mirfakhraie R, Khodadoostan M, Nazemalhosseini-Mojarad E, Asadzadeh Aghdaei H. Evaluation of promoter methylation status of MLH1 gene in Iranian patients with colorectal tumors and adenoma polyps. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2017; 10:S117-S121. [PMID: 29511481 PMCID: PMC5838190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
AIM The aim of this study was to evaluate the methylation status of the promoter region of MLH1 gene in colorectal cancer (CRC) and its precursor lesions as well as elucidate its association with various clinicopathological characteristics among Iranian population. BACKGROUND Epigenetic silencing of mismatch repair genes, such as MLH1, by methylation of CpG islands of their promoter region has been proved to be an important mechanism in colorectal carcinogenesis. METHODS Fifty colorectal cancer and polyp tissue samples including 13 Primary colorectal tumor and 37 Adenoma polyp samples were enrolled in this study. Methylation-specific polymerase chain reaction (MSP) was performed to find the frequency of MLH1 Promoter Methylation. RESULTS Promoter methylation of MLH1 gene was detected in 5 out of 13 tumor tissues and 4 out of 37 adenoma polyp. The frequency of MLH1 methylation in tumor samples was significantly higher compared to that in polyp tissues (P= 0.026). No significant association was observed between MLH1 promoter methylation and clinicopathological characteristics of the patients. CONCLUSION The frequency of MLH1 promoter methylation in CRC and colon polyp was 18%. Our findings indicated that methylation of MLH1 promoter region alone cannot be considered as a biomarker for early detection of CRC.
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Affiliation(s)
- Ashkan Zarandi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Sanaz Savabkar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Vahid Chaleshi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Ghavideldarestani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Mirfakhraie
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mahsa Khodadoostan
- Department of Gastroenterology and Hepatology, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Kidambi TD, Blanco A, Van Ziffle J, Terdiman JP. Constitutional MLH1 methylation presenting with colonic polyposis syndrome and not Lynch syndrome. Fam Cancer 2016; 15:275-80. [PMID: 26781822 DOI: 10.1007/s10689-016-9868-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
At least one-third of patients meeting clinical criteria for Lynch syndrome will have no germline mutation and constitutional epimutations leading to promoter methylation of MLH1 have been identified in a subset of these patients. We report the first case of constitutional MLH1 promoter methylation associated with a colonic polyposis syndrome in a 39 year-old man with a family history of colorectal cancer (CRC) and a personal history of 21 polyps identified over 8 years as well as the development of two synchronous CRCs over 16 months who was evaluated for a hereditary cancer syndrome. Immunohistochemistry (IHC) of multiple tumors showed absent MLH1 and PMS2 expression, though germline testing with Sanger sequencing and multiplex ligation-dependent probe amplification of these mismatch repair genes (MMR) genes was negative. A next generation sequencing panel of 29 genes also failed to identify a pathogenic mutation. Hypermethylation was identified in MLH1 intron 1 in tumor specimens along with buccal cells and peripheral white blood cells, confirming the diagnosis of constitutional MLH1 promoter methylation. This case highlights that constitutional MLH1 methylation should be considered in the differential diagnosis for a polyposis syndrome if IHC staining shows absent MMR gene expression.
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Affiliation(s)
- Trilokesh D Kidambi
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Amie Blanco
- Hereditary GI Cancer Prevention Program, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan P Terdiman
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA. .,Hereditary GI Cancer Prevention Program, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA. .,Clinical Medicine and Surgery, University of California, San Francisco, 1701 Divisadero, San Francisco, CA, 94115, USA.
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Takeda T, Banno K, Yanokura M, Adachi M, Iijima M, Kunitomi H, Nakamura K, Iida M, Nogami Y, Umene K, Masuda K, Kobayashi Y, Yamagami W, Hirasawa A, Tominaga E, Susumu N, Aoki D. Methylation Analysis of DNA Mismatch Repair Genes Using DNA Derived from the Peripheral Blood of Patients with Endometrial Cancer: Epimutation in Endometrial Carcinogenesis. Genes (Basel) 2016; 7:genes7100086. [PMID: 27754426 PMCID: PMC5083925 DOI: 10.3390/genes7100086] [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: 07/07/2016] [Revised: 08/28/2016] [Accepted: 10/06/2016] [Indexed: 01/28/2023] Open
Abstract
Germline mutation of DNA mismatch repair (MMR) genes is a cause of Lynch syndrome. Methylation of MutL homolog 1 (MLH1) and MutS homolog 2 (MSH2) has been detected in peripheral blood cells of patients with colorectal cancer. This methylation is referred to as epimutation. Methylation of these genes has not been studied in an unselected series of endometrial cancer cases. Therefore, we examined methylation of MLH1, MSH2, and MSH6 promoter regions of peripheral blood cells in 206 patients with endometrial cancer using a methylation-specific polymerase chain reaction (MSP). Germline mutation of MMR genes, microsatellite instability (MSI), and immunohistochemistry (IHC) were also analyzed in each case with epimutation. MLH1 epimutation was detected in a single patient out of a total of 206 (0.49%)-1 out of 58 (1.72%) with an onset age of less than 50 years. The patient with MLH1 epimutation showed high level MSI (MSI-H), loss of MLH1 expression and had developed endometrial cancer at 46 years old, complicated with colorectal cancer. No case had epimutation of MSH2 or MSH6. The MLH1 epimutation detected in a patient with endometrial cancer may be a cause of endometrial carcinogenesis. This result indicates that it is important to check epimutation in patients with endometrial cancer without a germline mutation of MMR genes.
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Affiliation(s)
- Takashi Takeda
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Kouji Banno
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Megumi Yanokura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Masataka Adachi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Moito Iijima
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Haruko Kunitomi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Kanako Nakamura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Miho Iida
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Yuya Nogami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Kiyoko Umene
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Kenta Masuda
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Yusuke Kobayashi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Wataru Yamagami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Akira Hirasawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Eiichiro Tominaga
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Nobuyuki Susumu
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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Cazaly E, Thomson R, Marthick JR, Holloway AF, Charlesworth J, Dickinson JL. Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses. Clin Epigenetics 2016; 8:75. [PMID: 27429663 PMCID: PMC4947255 DOI: 10.1186/s13148-016-0241-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/26/2016] [Indexed: 02/06/2023] Open
Abstract
Background Human methylome mapping in health and disease states has largely relied on Illumina Human Methylation 450k array (450k array) technology. Accompanying this has been the necessary evolution of analysis pipelines to facilitate data processing. The majority of these pipelines, however, cater for experimental designs where matched ‘controls’ or ‘normal’ samples are available. Experimental designs where no appropriate ‘reference’ exists remain challenging. Herein, we use data generated from our study of the inheritance of methylome profiles in families to evaluate the performance of eight normalisation pre-processing methods. Fifty individual samples representing four families were interrogated on five 450k array BeadChips. Eight normalisation methods were tested using qualitative and quantitative metrics, to assess efficacy and suitability. Results Stratified quantile normalisation combined with ComBat were consistently found to be the most appropriate when assessed using density, MDS and cluster plots. This was supported quantitatively by ANOVA on the first principal component where the effect of batch dropped from p < 0.01 to p = 0.97 after stratified QN and ComBat. Median absolute differences between replicated samples were the lowest after stratified QN and ComBat as were the standard error measures on known imprinted regions. Biological information was preserved after normalisation as indicated by the maintenance of a significant association between a known mQTL and methylation (p = 1.05e-05). Conclusions A strategy combining stratified QN with ComBat is appropriate for use in the analyses when no reference sample is available but preservation of biological variation is paramount. There is great potential for use of 450k array data to further our understanding of the methylome in a variety of similar settings. Such advances will be reliant on the determination of appropriate methodologies for processing these data such as established here. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0241-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma Cazaly
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Medical Sciences Building 2, Hobart, TAS Australia
| | - Russell Thomson
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Medical Sciences Building 2, Hobart, TAS Australia ; Centre for Research in Mathematics, School of Computing, Engineering and Mathematics, Western Sydney University, Parramatta Campus, Locked Bag 1797, Penrith, NSW 2751 Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Medical Sciences Building 2, Hobart, TAS Australia
| | - Adele F Holloway
- School of Medicine, University of Tasmania, Medical Sciences Building 2, Hobart, TAS 7001 Australia
| | - Jac Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Medical Sciences Building 2, Hobart, TAS Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Medical Sciences Building 2, Hobart, TAS Australia
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Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients. PLoS One 2016; 11:e0157381. [PMID: 27300758 PMCID: PMC4907507 DOI: 10.1371/journal.pone.0157381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/27/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND AIMS Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. METHODS Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. RESULTS Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). CONCLUSIONS This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.
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48
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Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
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Abstract
Lynch syndrome, an autosomal dominant inherited disorder, is caused by inactivating mutations involving DNA mismatch repair (MMR) genes. This leads to profound genetic instability, including microsatellite instability (MSI) and increased risk for cancer development, particularly colon and endometrial malignancies. Clinical testing of tumor tissues for the presence of MMR gene deficiency is standard practice in clinical oncology, with immunohistochemistry and PCR-based microsatellite instability analysis used as screening tests to identify potential Lynch syndrome families. The ultimate diagnosis of Lynch syndrome requires documentation of mutation within one of the four MMR genes (MLH1, PMS2, MSH2 and MSH6) or EPCAM, currently achieved by comprehensive sequencing analysis of germline DNA. In this review, the genetic basis of Lynch syndrome, methodologies of MMR deficiency testing, and current diagnostic algorithms in the clinical management of Lynch syndrome, are discussed.
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Affiliation(s)
- Natalia Buza
- a Department of Pathology, School of Medicine , Yale University , New Haven , CT , USA
| | - James Ziai
- b Genentech Inc ., San Francisco , CA , USA
| | - Pei Hui
- a Department of Pathology, School of Medicine , Yale University , New Haven , CT , USA
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Hitchins MP. Finding the needle in a haystack: identification of cases of Lynch syndrome with MLH1 epimutation. Fam Cancer 2016; 15:413-22. [DOI: 10.1007/s10689-016-9887-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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