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Xie M, Li F. Incidental diagnosis of primary appendiceal signet-ring cell adenocarcinoma after appendectomy for acute appendicitis: a case report. Ann Med Surg (Lond) 2024; 86:3117-3122. [PMID: 38694365 PMCID: PMC11060291 DOI: 10.1097/ms9.0000000000001973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/06/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Appendiceal signet-ring cell adenocarcinoma (ASCA) is rare and more aggressive in malignant appendiceal neoplasms. The presentation can be appendicitis, which is lack of specific symptom and makes early diagnosis difficult. There is no effective surveillance. Prognosis largely relies on timely detection. We report a case of ASCA incidentally diagnosed through pathological examination after appendectomy for appendicitis. Case presentation The patient presented to our department with a progressive right lower quadrant abdominal pain lasting for 3 days. Physical examination revealed rigidity, tenderness, and rebound tenderness on the right lower quadrant. A computed tomography scan showed a thickened, inflamed appendix with peri-appendiceal fat stranding without noticeable appendiceal mass at initial evaluation. The diagnosis was considered acute appendicitis, and an appendectomy was performed. The appendix was inflamed, gangrenous and perforated, and no mass was found during the surgery. Surgical specimen was sent for physiological examination, which incidentally detected signet-ring cell in H&E staining. And immunohistochemistry confirmed the diagnosis of ASCA with small amount of neuroendocrine neoplasms. Conclusion Early diagnosis of ASCA can incidentally be made on pathological specimen following appendectomy for appendicitis. A routine pathological examination should be emphasized, and appendectomy may not be the endpoint of the treatment. Hemicolectomy and adjuvant therapy might ensue upon the diagnosis of appendiceal neoplasm. The poor prognosis of ASCA makes a timely diagnosis significant. Basic research is promising to unravel the molecular mechanisms of pathogenesis, finding typical tumor markers for screening and novel effective therapies for advanced cases.
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Affiliation(s)
- Miao Xie
- Department of Gastrointestinal Surgery
| | - Fei Li
- Department of Gastrointestinal Surgery
- Department of Hepatobiliary and Pancreatic Surgery, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, People’s Republic of China
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2
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Li M, Yan X, Liu H, Miao W, Wu W, Zhao Y, Wang C, Liu H. Novel MSH2 and TSC2 variants in a Chinese family with Lynch syndrome and their synergistic impact in urothelial carcinoma. Transl Res 2024; 265:26-35. [PMID: 37914149 DOI: 10.1016/j.trsl.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/24/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
Lynch syndrome, an autosomal dominant hereditary disease arising from mutations in mismatch repair genes, is linked to the development of multiple tumor types, notably colorectal cancer, endometrial carcinoma and upper urinary tract urothelial carcinoma. In this study, we present the case of a young patient diagnosed with upper urinary tract urothelial carcinoma, notable for a familial history of diverse malignancies. By employing genetic analysis, we verified the presence of Lynch syndrome within the family and detected novel variants, MSH2 p.A604D and TSC2 p.C738Y, utilizing NGS technology. Subsequently, we conducted validation experiments to assess the pathogenicity of the MSH2 and TSC2 variants. We illustrated that the MSH2 variant can result in diminished MSH2 expression, compromised mismatch repair function, and induce resistance to cisplatin in urothelial carcinoma. Furthermore, we substantiated the promotional impact of the identified TSC2 variant on urothelial carcinoma, encompassing proliferation, invasion, and migration. Significantly, we found that the MSH2 p.A604D variant and TSC2 p.C738Y variant synergistically enhance the promotion of urothelial carcinoma.
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Affiliation(s)
- Mingyang Li
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Xingjian Yan
- Department of Urology, The First Hospital of Jilin University, Changchun, Jilin 130021, Chin
| | - He Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Wenhao Miao
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Wenbo Wu
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Yuyang Zhao
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China.
| | - Chungang Wang
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China.
| | - Haitao Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China.
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3
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Andjelkovic B, Stojanovic B, Stojanovic MD, Milosevic B, Cvetkovic A, Spasic M, Jakovljevic S, Cvetkovic D, Stojanovic BS, Milosev D, Mitrovic M, Stankovic V. Appendiceal Signet Ring Cell Carcinoma: An Atypical Cause of Acute Appendicitis-A Case Study and Review of Current Knowledge. Diagnostics (Basel) 2023; 13:2359. [PMID: 37510102 PMCID: PMC10378069 DOI: 10.3390/diagnostics13142359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Appendiceal signet ring cell carcinoma (ASRCC) is a rare and aggressive form of appendiceal cancer, often presenting with nonspecific symptoms that overlap with acute appendicitis. Early diagnosis and appropriate management are crucial for improving patient outcomes in these rare malignancies. This case report and literature review aims to raise awareness among clinicians about ASRCC of the appendix as a cause of acute appendicitis and highlight the importance of considering this diagnosis in patients with atypical presentations or unexpected histopathological findings. We present a 65-year-old female patient with ASRCC who underwent successful surgical treatment and remains disease-free at the one-year follow-up. It also highlights the necessity of early detection and appropriate treatment in order to improve patient outcomes. In addition, a comprehensive literature review is provided, discussing the clinical presentation, histopathological characteristics, potential pathogenesis, treatment options, and prognosis of ASRCC.
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Affiliation(s)
- Branko Andjelkovic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
| | - Bojan Stojanovic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
- Department of Surgery, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | | | - Bojan Milosevic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
- Department of Surgery, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Aleksandar Cvetkovic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
- Department of Surgery, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Marko Spasic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
- Department of Surgery, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Stefan Jakovljevic
- Department of General Surgery, University Clinical Center Kragujevac, 34000 Kragujevac, Serbia
- Department of Surgery, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Danijela Cvetkovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Bojana S Stojanovic
- Department of Pathophysiology, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Danijela Milosev
- Department of Pathology, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Minja Mitrovic
- Department of Neurology, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Vesna Stankovic
- Department of Pathology, Faculty of Medical Sciences, University of Kragujevac, 34000 Kragujevac, Serbia
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4
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Plavskin Y, de Biase MS, Schwarz RF, Siegal ML. The rate of spontaneous mutations in yeast deficient for MutSβ function. G3 (BETHESDA, MD.) 2023; 13:6931805. [PMID: 36529906 PMCID: PMC9997558 DOI: 10.1093/g3journal/jkac330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 08/25/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Mutations in simple sequence repeat loci underlie many inherited disorders in humans, and are increasingly recognized as important determinants of natural phenotypic variation. In eukaryotes, mutations in these sequences are primarily repaired by the MutSβ mismatch repair complex. To better understand the role of this complex in mismatch repair and the determinants of simple sequence repeat mutation predisposition, we performed mutation accumulation in yeast strains with abrogated MutSβ function. We demonstrate that mutations in simple sequence repeat loci in the absence of mismatch repair are primarily deletions. We also show that mutations accumulate at drastically different rates in short (<8 bp) and longer repeat loci. These data lend support to a model in which the mismatch repair complex is responsible for repair primarily in longer simple sequence repeats.
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Affiliation(s)
- Yevgeniy Plavskin
- Center for Genomics and Systems Biology, New York University, New York 10003, USA.,Department of Biology, New York University, New York 10003, USA
| | - Maria Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany.,Department of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany.,Institute for Computational Cancer Biology, Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50937, Germany.,Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin 10623, Germany
| | - Mark L Siegal
- Center for Genomics and Systems Biology, New York University, New York 10003, USA.,Department of Biology, New York University, New York 10003, USA
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5
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Sun M, Moquet J, Ellender M, Bouffler S, Badie C, Baldwin-Cleland R, Monahan K, Latchford A, Lloyd D, Clark S, Anyamene NA, Ainsbury E, Burling D. Potential risks associated with the use of ionizing radiation for imaging and treatment of colorectal cancer in Lynch syndrome patients. Fam Cancer 2023; 22:61-70. [PMID: 35718836 PMCID: PMC9829596 DOI: 10.1007/s10689-022-00299-9] [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: 02/08/2022] [Accepted: 05/29/2022] [Indexed: 01/13/2023]
Abstract
The aim of this review is to investigate the literature pertaining to the potential risks of low-dose ionizing radiation to Lynch syndrome patients by use of computed tomography (CT), either diagnostic CT colonography (CTC), standard staging CT or CT surveillance. Furthermore, this review explores the potential risks of using radiotherapy for treatment of rectal cancer in these patients. No data or longitudinal observational studies of the impact of radiation exposure on humans with Lynch syndrome were identified. Limited experimental studies utilizing cell lines and primary cells exposed to both low and high radiation doses have been carried out to help determine radio-sensitivity associated with DNA mismatch repair gene deficiency, the defining feature of Lynch syndrome. On balance, these studies suggest that mismatch repair deficient cells may be relatively radio-resistant (particularly for low dose rate exposures) with higher mutation rates, albeit no firm conclusions can be drawn. Mouse model studies, though, showed an increased risk of developing colorectal tumors in mismatch repair deficient mice exposed to radiation doses around 2 Gy. With appropriate ethical approval, further studies investigating radiation risks associated with CT imaging and radiotherapy relevant doses using cells/tissues derived from confirmed Lynch patients or genetically modified animal models are urgently required for future clinical guidance.
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Affiliation(s)
- Mingzhu Sun
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ, UK.
| | - Jayne Moquet
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Michele Ellender
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Simon Bouffler
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Christophe Badie
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK ,Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London, W12 0BZ UK
| | - Rachel Baldwin-Cleland
- Intestinal Imaging Centre, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Kevin Monahan
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Andrew Latchford
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - David Lloyd
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK
| | - Susan Clark
- Lynch Syndrome Clinic, Centre for Familial Intestinal Cancer, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
| | - Nicola A. Anyamene
- East and North Hertfordshire NHS Trust, Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, HA6 2RN Middlesex UK
| | - Elizabeth Ainsbury
- UK Health Security Agency, Department of Radiation Effects, RCEHD, Chilton, Didcot, OX11 0RQ UK ,Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London, W12 0BZ UK
| | - David Burling
- Intestinal Imaging Centre, St Mark’s Hospital, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ UK
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6
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Meulemans L, Baert Desurmont S, Waill MC, Castelain G, Killian A, Hauchard J, Frebourg T, Coulet F, Martins A, Muleris M, Gaildrat P. Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in-frame splicing alterations. J Med Genet 2022; 60:450-459. [PMID: 36113988 DOI: 10.1136/jmg-2022-108576] [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: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
BackgroundSpliceogenic variants in disease-causing genes are often presumed pathogenic since most induce frameshifts resulting in loss of function. However, it was recently shown in cancer predisposition genes that some may trigger in-frame anomalies that preserve function. Here, we addressed this question by using MSH2, a DNA mismatch repair gene implicated in Lynch syndrome, as a model system.MethodsEighteen MSH2 variants, mostly localised within canonical splice sites, were analysed by using minigene splicing assays. The impact of the resulting protein alterations was assessed in a methylation tolerance-based assay. Clinicopathological characteristics of variant carriers were collected.ResultsThree in-frame RNA biotypes were identified based on variant-induced spliceogenic outcomes: exon skipping (E3, E4, E5 and E12), segmental exonic deletions (E7 and E15) and intronic retentions (I3, I6, I12 and I13). The 10 corresponding protein isoforms exhibit either large deletions (49–93 amino acids (aa)), small deletions (12 or 16 aa) or insertions (3–10 aa) within different functional domains. We showed that all these modifications abrogate MSH2 function, in agreement with the clinicopathological features of variant carriers.ConclusionAltogether, these data demonstrate that MSH2 function is intolerant to in-frame indels caused by the spliceogenic variants analysed in this study, supporting their pathogenic nature. This work stresses the importance of combining complementary RNA and protein approaches to ensure accurate clinical interpretation of in-frame spliceogenic variants.
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Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Stéphanie Baert Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Marie-Christine Waill
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Gaia Castelain
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Audrey Killian
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Julie Hauchard
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, and CHU Rouen, Department of Genetics, F-76000 Rouen, France
| | - Florence Coulet
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
| | - Martine Muleris
- Department of Genetics, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMR-S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, F-76000 Rouen, France
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7
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Scott RJ. Modifier genes and Lynch syndrome: some considerations. Hered Cancer Clin Pract 2022; 20:35. [PMID: 36088367 PMCID: PMC9463843 DOI: 10.1186/s13053-022-00240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractLynch Syndrome (LS) is a highly variable entity with some patients presenting at very young ages with malignancy whereas others may never develop a malignancy yet carry an unequivocal genetic predisposition to disease. The most frequent LS malignancy remains colorectal cancer, a disease that is thought to involve genetic as well as environmental factors in its aetiology. Environmental insults are undeniably associated with cancer risk, especially those imparted by such activities as smoking and excessive alcohol consumption. Notwithstanding, in an inherited predisposition the expected exposures to an environmental insult are considered to be complex and require knowledge about the respective exposure and how it might interact with a genetic predisposition. Typically, smoking is one of the major confounders when considering environmental factors that can influence disease expression on a background of significant genetic risk. In addition to environmental triggers, the risk of developing a malignancy for people carrying an inherited predisposition to disease can be influenced by additional genetic factors that do not necessarily segregate with a disease predisposition allele. The purpose of this review is to examine the current state of modifier gene detection in people with a genetic predisposition to develop LS and present some data that supports the notion that modifier genes are gene specific thus explaining why some modifier gene studies have failed to identify associations when this is not taken into account.
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8
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Detection of MSH2 Gene Methylation in Extramammary Paget's Disease by Methylation-Sensitive High-Resolution Melting Analysis. JOURNAL OF ONCOLOGY 2021; 2021:5514426. [PMID: 34759969 PMCID: PMC8575627 DOI: 10.1155/2021/5514426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 08/18/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Background Extramammary Paget's disease (EMPD) is a rare skin tumor. Hypermethylation in the MSH2 promoter resulting in the downregulation of its protein expression shows a high detection rate in EMPD tumor tissue, which indicates that the methylation of MSH2 may play an important role in the pathogenesis of EMPD. Objective This study aims to establish a rapid analysis strategy based on the methylation-sensitive high-resolution melting curve (MS-HRM) to detect the methylation level of the MSH2 promoter. Methods With the use of universal methylated human DNA products, we established the MS-HRM standard curve to quantitatively detect the methylation level of the MSH2 promoter. Then, all 57 EMPD tumor DNA samples were analyzed. Pyrosequencing assay was also carried out to test the accuracy and efficacy of MS-HRM. Besides, a total of 54 human normal and other cancerous tissues were included in this study to test the reliability and versatility of the MS-HRM standard curve. Results In this study, by using the established MS-HRM, we found that 96.5% (55/57) EMPD tumor samples had varying methylation levels in the MSH2 promoter ranging from 0% to 30%. Then, the methylation data were compared to the results obtained from pyrosequencing, which showed a high correlation between these two techniques by Pearson's correlation (r = 0.9425) and Bland–Altman plots (mean difference = −0.1069) indicating that the methylation levels analyzed by MS-HRM were consistent with DNA pyrosequencing. Furthermore, in 23 normal and 31 other cancerous tissue samples, there were two colorectal cancer (CRC) tissues that tested MSH2 methylation positive (1% and 5%) which confirmed that our established MS-HRM can be widely applied to various types of samples. Conclusion MS-HRM standard curve can be used for the detection of the methylation level of MSH2 in EMPD tumor samples and other cancerous tissues potentially, which presents a promising candidate as a quantitative assay to analyze MSH2 promoter methylation in routine pathological procedure.
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9
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Norouzi M, Shafiei M, Abdollahi Z, Miar P, Galehdari H, Emami MH, Zeinalian M, Tabatabaiefar MA. WRN Germline Mutation Is the Likely Inherited Etiology of Various Cancer Types in One Iranian Family. Front Oncol 2021; 11:648649. [PMID: 34164337 PMCID: PMC8215443 DOI: 10.3389/fonc.2021.648649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Background Familial cancers comprise a considerable distribution of colorectal cancers (CRCs), of which only about 5% occurs through well-established hereditary syndromes. It has been demonstrated that deleterious variants at the newly identified cancer-predisposing genes could describe the etiology of undefined familial cancers. Methods The present study aimed to identify the genetic etiology in a 32-year-old man with early onset familial CRC employing several molecular diagnostic techniques. DNA was extracted from tumoral and normal formalin-fixed-paraffin-embedded (FFPE) blocks, and microsatellite instability (MSI) was evaluated. Immunohistochemistry staining of MMR proteins was performed on tumoral FFPE blocks. Next-generation sequencing (NGS), multiplex ligation-dependent amplification (MLPA) assay, and Sanger sequencing were applied on the genomic DNA extracted from peripheral blood. Data analysis was performed using bioinformatics tools. Genetic variants interpretation was based on ACMG. Results MSI analysis indicated MSI-H phenotype, and IHC staining proved no expressions of MSH2 and MSH6 proteins. MLPA and NGS data showed no pathogenic variants in MMR genes. Further analysis of NGS data revealed a candidate WRN frameshift variant (p.R389Efs*3), which was validated with Sanger sequencing. The variant was interpreted as pathogenic since it met the criteria based on the ACMG guideline including very strong (PVS1), strong (PS3), and moderate (PM2). Conclusion WRN is a DNA helicase participating in DNA repair pathways to sustain genomic stability. WRN deficient function may contribute to CRC development that is valuable for further investigation as a candidate gene in hereditary cancer syndrome diagnosis.
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Affiliation(s)
- Mahnaz Norouzi
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Zeinab Abdollahi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Paniz Miar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Hasan Emami
- Department of Gastroenterology, Poursina Hakim Digestive Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Zeinalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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10
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Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C, Momen S, Young J, Amarante TD, Side L, Brice G, Perez-Alonso V, Rueda D, Gomez C, Bushell W, Harris R, Choudhary JS, Jiricny J, Skarnes WC, Nik-Zainal S. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. NATURE CANCER 2021; 2:643-657. [PMID: 34164627 PMCID: PMC7611045 DOI: 10.1038/s43018-021-00200-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023]
Abstract
Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts (Δ) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage, and performed whole-genome sequencing of 173 subclones. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 produced marked mutational signatures indicative of being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-dG elimination is sequence-context-specific while uracil clearance is sequence-context-independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C>A transversions), differential misincorporation by replicative polymerases (T>C and C>T transitions), and we propose a 'reverse template slippage' model for T>A transversions. ΔMLH1, ΔMSH6, and ΔMSH2 signatures were similar to each other but distinct from ΔPMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 WGS cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.
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Affiliation(s)
- Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Gene Ching Chiek Koh
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Arjun Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Cherif Badja
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Sophie Momen
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Jamie Young
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Tauanne Dias Amarante
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Lucy Side
- UCL Institute for Women's Health, Great Ormond Street Hospital, London, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Glen Brice
- Southwest Thames Regional Genetics Service, St George's University of London, London, UK
| | - Vanesa Perez-Alonso
- Pediatrics Department, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | - Daniel Rueda
- Hereditary Cancer Laboratory, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | | | | | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Jyoti S Choudhary
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Josef Jiricny
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - William C Skarnes
- Wellcome Sanger Institute, Hinxton, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
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11
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Khan FH, Dervan E, Bhattacharyya DD, McAuliffe JD, Miranda KM, Glynn SA. The Role of Nitric Oxide in Cancer: Master Regulator or NOt? Int J Mol Sci 2020; 21:ijms21249393. [PMID: 33321789 PMCID: PMC7763974 DOI: 10.3390/ijms21249393] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Nitric oxide (NO) is a key player in both the development and suppression of tumourigenesis depending on the source and concentration of NO. In this review, we discuss the mechanisms by which NO induces DNA damage, influences the DNA damage repair response, and subsequently modulates cell cycle arrest. In some circumstances, NO induces cell cycle arrest and apoptosis protecting against tumourigenesis. NO in other scenarios can cause a delay in cell cycle progression, allowing for aberrant DNA repair that promotes the accumulation of mutations and tumour heterogeneity. Within the tumour microenvironment, low to moderate levels of NO derived from tumour and endothelial cells can activate angiogenesis and epithelial-to-mesenchymal transition, promoting an aggressive phenotype. In contrast, high levels of NO derived from inducible nitric oxide synthase (iNOS) expressing M1 and Th1 polarised macrophages and lymphocytes may exert an anti-tumour effect protecting against cancer. It is important to note that the existing evidence on immunomodulation is mainly based on murine iNOS studies which produce higher fluxes of NO than human iNOS. Finally, we discuss different strategies to target NO related pathways therapeutically. Collectively, we present a picture of NO as a master regulator of cancer development and progression.
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Affiliation(s)
- Faizan H. Khan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), H91 YR71 Galway, Ireland; (F.H.K.); (E.D.); (D.D.B.); (J.D.M.)
| | - Eoin Dervan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), H91 YR71 Galway, Ireland; (F.H.K.); (E.D.); (D.D.B.); (J.D.M.)
| | - Dibyangana D. Bhattacharyya
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), H91 YR71 Galway, Ireland; (F.H.K.); (E.D.); (D.D.B.); (J.D.M.)
| | - Jake D. McAuliffe
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), H91 YR71 Galway, Ireland; (F.H.K.); (E.D.); (D.D.B.); (J.D.M.)
| | - Katrina M. Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA;
| | - Sharon A. Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), H91 YR71 Galway, Ireland; (F.H.K.); (E.D.); (D.D.B.); (J.D.M.)
- Correspondence:
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12
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Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby. Proc Natl Acad Sci U S A 2020; 117:17775-17784. [PMID: 32669440 DOI: 10.1073/pnas.1918517117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA resynthesis. Dominant MMR models posit that after mismatch recognition, ATP converts MutS to a hydrolysis-independent, diffusive mobile clamp that no longer recognizes the mismatch. Little is known about the postrecognition MutS mobile clamp and its interactions with MutL. Two disparate frameworks have been proposed: One in which MutS-MutL complexes remain mobile on the DNA, and one in which MutL stops MutS movement. Here we use single-molecule FRET to follow the postrecognition states of MutS and the impact of MutL on its properties. In contrast to current thinking, we find that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA. Notably, ATP hydrolysis is required to alter the conformation of MutS such that it can recognize the mismatch again instead of bypassing it; thus, ATP hydrolysis licenses the MutS mobile clamp to rebind the mismatch. Moreover, interaction with MutL can both trap MutS at the mismatch en route to mobile clamp formation and stop movement of the mobile clamp on DNA. MutS's frequent rebinding of the mismatch, which increases its residence time in the vicinity of the mismatch, coupled with MutL's ability to trap MutS, should increase the probability that MutS-MutL MMR initiation complexes localize near the mismatch.
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13
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Dynamic human MutSα-MutLα complexes compact mismatched DNA. Proc Natl Acad Sci U S A 2020; 117:16302-16312. [PMID: 32586954 DOI: 10.1073/pnas.1918519117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA mismatch repair (MMR) corrects errors that occur during DNA replication. In humans, mutations in the proteins MutSα and MutLα that initiate MMR cause Lynch syndrome, the most common hereditary cancer. MutSα surveilles the DNA, and upon recognition of a replication error it undergoes adenosine triphosphate-dependent conformational changes and recruits MutLα. Subsequently, proliferating cell nuclear antigen (PCNA) activates MutLα to nick the error-containing strand to allow excision and resynthesis. The structure-function properties of these obligate MutSα-MutLα complexes remain mostly unexplored in higher eukaryotes, and models are predominately based on studies of prokaryotic proteins. Here, we utilize atomic force microscopy (AFM) coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα-MutLα-DNA complexes. We find that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. On the timescale of a few minutes, these complexes rearrange, folding and compacting the DNA. These observations contrast with dominant models of MMR initiation that envision diffusive MutS-MutL complexes that move away from the mismatch. Our results suggest MutSα localizes MutLα near the mismatch and promotes DNA configurations that could enhance MMR efficiency by facilitating MutLα nicking the DNA at multiple sites around the mismatch. In addition, such complexes may also protect the mismatch region from nucleosome reassembly until repair occurs, and they could potentially remodel adjacent nucleosomes.
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14
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Bádon ES, Mokánszki A, Mónus A, András C, Damjanovich L, Méhes G. Quadruplicate Synchronous Adenocarcinoma of the Colon with Distant Metastases-Long-Term Molecular Follow-Up by KRAS and TP53 Mutational Profiling. Diagnostics (Basel) 2020; 10:diagnostics10060407. [PMID: 32560038 PMCID: PMC7345140 DOI: 10.3390/diagnostics10060407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Anatomically independent tumor foci represent biologically distinct neoplasias, potentially featured by different progressivity and treatment responsiveness. To demonstrate the biological complexity, a metastatic colon adenocarcinoma patient originally presenting with four independent primary tumors of the right colon half and altogether eight distant metastases was followed by molecular testing. Next-generation sequencing results highlighted the mutational profile of the individual primaries and the dynamics of the different gene variants observed during follow-up. The four primary colon tumors presented with four different KRAS genotypes, one of them with a wild-type and three with pathogenic variants, without overlap. These were the following: c.35G > A; p.Gly12Asp with 40.6% variant allele frequency (VAF); c.34G > T; p.Gly12Cys with 16.2% VAF and c.35G > T; p.Gly12Val with 15.1% VAF. In metastatic tumors, with one exception where no mutation was detected, only the KRAS c.34G > T; p.Gly12Cys mutation could be detected. TP53 gene variants were variable in the primary tumors, with a single dominant variant evolving in the follow-up metastases (c.820G > T; p.Val274Phe). Genetic profiling of individually developing synchronous malignancies uncovers the clonal relations of metastatic tumors. NGS gene panels provide a solution to follow the dynamics of key oncogene variants during the course of the disease and greatly contribute to therapy optimization.
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Affiliation(s)
- Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Csilla András
- Department of Oncology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - László Damjanovich
- Department of Surgery, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
- Correspondence:
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15
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Mardenborough YSN, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada-Vial A, Winterwerp HHK, Sixma TK, Kanaar R, Friedhoff P, Strick TR, Lebbink JHG. The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair. Nucleic Acids Res 2020; 47:11667-11680. [PMID: 31598722 PMCID: PMC6902014 DOI: 10.1093/nar/gkz834] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
DNA mismatch repair (MMR) maintains genome stability through repair of DNA replication errors. In Escherichia coli, initiation of MMR involves recognition of the mismatch by MutS, recruitment of MutL, activation of endonuclease MutH and DNA strand incision at a hemimethylated GATC site. Here, we studied the mechanism of communication that couples mismatch recognition to daughter strand incision. We investigated the effect of catalytically-deficient Cas9 as well as stalled RNA polymerase as roadblocks placed on DNA in between the mismatch and GATC site in ensemble and single molecule nanomanipulation incision assays. The MMR proteins were observed to incise GATC sites beyond a roadblock, albeit with reduced efficiency. This residual incision is completely abolished upon shortening the disordered linker regions of MutL. These results indicate that roadblock bypass can be fully attributed to the long, disordered linker regions in MutL and establish that communication during MMR initiation occurs along the DNA backbone.
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Affiliation(s)
| | - Katerina Nitsenko
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Charlie Laffeber
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Camille Duboc
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Enes Sahin
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Audrey Quessada-Vial
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | | | - Titia K Sixma
- Oncode Institute, the Netherlands.,Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Terence R Strick
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.,Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Superieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,Programme "Equipe Labellisée", Ligue Nationale contre le Cancer
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, the Netherlands
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16
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Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics. Int J Mol Sci 2019; 20:ijms20174271. [PMID: 31480444 PMCID: PMC6747400 DOI: 10.3390/ijms20174271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
The mismatch repair (MMR) pathway maintains genome integrity by correcting errors such as mismatched base pairs formed during DNA replication. In MMR, Msh2–Msh6, a heterodimeric protein, targets single base mismatches and small insertion/deletion loops for repair. By incorporating the fluorescent nucleoside base analog 6-methylisoxanthopterin (6-MI) at or adjacent to a mismatch site to probe the structural and dynamic elements of the mismatch, we address how Msh2–Msh6 recognizes these mismatches for repair within the context of matched DNA. Fluorescence quantum yield and rotational correlation time measurements indicate that local base dynamics linearly correlate with Saccharomyces cerevisiae Msh2–Msh6 binding affinity where the protein exhibits a higher affinity (KD ≤ 25 nM) for mismatches that have a significant amount of dynamic motion. Energy transfer measurements measuring global DNA bending find that mismatches that are both well and poorly recognized by Msh2–Msh6 experience the same amount of protein-induced bending. Finally, base-specific dynamics coupled with protein-induced blue shifts in peak emission strongly support the crystallographic model of directional binding, in which Phe 432 of Msh6 intercalates 3′ of the mismatch. These results imply an important role for local base dynamics in the initial recognition step of MMR.
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17
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Rath A, Mishra A, Ferreira VD, Hu C, Omerza G, Kelly K, Hesse A, Reddi HV, Grady JP, Heinen CD. Functional interrogation of Lynch syndrome-associated MSH2 missense variants via CRISPR-Cas9 gene editing in human embryonic stem cells. Hum Mutat 2019; 40:2044-2056. [PMID: 31237724 DOI: 10.1002/humu.23848] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) predisposes patients to cancer and is caused by germline mutations in the DNA mismatch repair (MMR) genes. Identifying the deleterious mutation, such as a frameshift or nonsense mutation, is important for confirming an LS diagnosis. However, discovery of a missense variant is often inconclusive. The effects of these variants of uncertain significance (VUS) on disease pathogenesis are unclear, though understanding their impact on protein function can help determine their significance. Laboratory functional studies performed to date have been limited by their artificial nature. We report here an in-cellulo functional assay in which we engineered site-specific MSH2 VUS using clustered regularly interspaced short palindromic repeats-Cas9 gene editing in human embryonic stem cells. This approach introduces the variant into the endogenous MSH2 loci, while simultaneously eliminating the wild-type gene. We characterized the impact of the variants on cellular MMR functions including DNA damage response signaling and the repair of DNA microsatellites. We classified the MMR functional capability of eight of 10 VUS providing valuable information for determining their likelihood of being bona fide pathogenic LS variants. This human cell-based assay system for functional testing of MMR gene VUS will facilitate the identification of high-risk LS patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
| | - Akriti Mishra
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | | | - Chaoran Hu
- Department of Statistics, University of Connecticut, Storrs, Connecticut.,Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Gregory Omerza
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Kevin Kelly
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Andrew Hesse
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Honey V Reddi
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - James P Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Christopher D Heinen
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
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18
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Kang Z, Zhu Y, Zhang QA, Dong L, Xu F, Zhang X, Guan M. Methylation and expression analysis of mismatch repair genes in extramammary Paget's disease. J Eur Acad Dermatol Venereol 2019; 33:874-879. [PMID: 30784122 DOI: 10.1111/jdv.15404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Extramammary Paget's disease (EMPD) is a rare skin cancer with relative high frequencies of germline and somatic mismatch repair (MMR) genes mutations. However, the methylation and expression of these genes have not been validated in EMPD. OBJECTIVE This study aims to confirm the methylation and expression of MMR genes in EMPD. METHODS Immunohistochemical (IHC) staining detection and Methylation-specific PCR (MSP) were used to analyse MLH1, MSH2, MSH6 and PMS2 proteins' expression and promoters' methylation in 57 EMMD samples, and pyro-sequence was used to find highly methylated CpG sites in MSH2 promoter. RESULTS Immunohistochemical detection displayed reduced expression of MSH2 in 38.6% EMPD cases but normal expression of MLH1, MSH6 and PMS2 in all tumour tissues. Hypermethylation also was found in the promoter of MSH2 but not in other MMR genes. Pyrosequencing of MSH2 promoter showed CpG6 (-87) and CpG3 (-98) were the most common two methylated CpG dinucleotides. There is a significant correlation between reduced MSH2 expression and MSH2 methylation. CONCLUSION Reduced MSH2 expression and hypermethylation in this gene promoter were common genetic changes in EMPD, which expands our understanding of the role of MMR function in this skin cancer.
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Affiliation(s)
- Z Kang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
| | - Y Zhu
- Department of Pathology, Huashan Hospital North, Fudan University, Shanghai, P. R. China
| | - Q-A Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, P. R. China
| | - L Dong
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China
| | - F Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, P. R. China
| | - X Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, P. R. China
| | - M Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, P. R. China.,Central Laboratory, Huashan Hospital, Fudan University, Shanghai, P. R. China
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19
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D'Arcy BM, Blount J, Prakash A. Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene. Hum Mutat 2019; 40:458-471. [PMID: 30653781 DOI: 10.1002/humu.23708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/28/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited disorder that is associated with an increased predisposition to certain cancers caused by loss-of-function mutations in one of four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, or PMS2). The diagnosis of LS is often challenged by the identification of missense mutations where the functional effects are not known. These are termed variants of uncertain significance (VUSs) and account for 20%-30% of noncoding and missense mutations. VUSs cause ambiguity during clinical diagnosis and hinder implementation of appropriate medical management. In the current study, we focus on the functional and biological consequences of two nonsynonymous VUSs in PMS2. These variants, c.620G>A and c.123_131delGTTAGTAGA, result in the alteration of glycine 207 to glutamate (p.Gly207Glu) and the deletion of amino acid residues 42-44 (p.Leu42_Glu44del), respectively. While the PMS2 p.Gly207Glu variant retains in vitro MMR and ATPase activities, PMS2 p.Leu42_Glu44del appears to lack such capabilities. Structural and biophysical characterization using circular dichroism, small-angle X-ray scattering, and X-ray crystallography of the N-terminal domain of the PMS2 variants indicate that the p.Gly207Glu variant is properly folded similar to the wild-type enzyme, whereas p.Leu42_Glu44del is disordered and prone to aggregation.
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Affiliation(s)
- Brandon M D'Arcy
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama
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20
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Blount J, Prakash A. The changing landscape of Lynch syndrome due to PMS2 mutations. Clin Genet 2018; 94:61-69. [PMID: 29286535 PMCID: PMC5995637 DOI: 10.1111/cge.13205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/12/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
Abstract
DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations.
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Affiliation(s)
- Jessa Blount
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
| | - Aishwarya Prakash
- Mitchell Cancer Institute, The University of South Alabama, 1660 Springhill Avenue, Mobile, AL - 36604
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21
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Abstract
Growing knowledge of inherited colorectal cancer syndromes has led to better surveillance and better care of this subset of patients. The most well-known entities, including Lynch syndrome and familial adenomatous polyposis, are continually being studied and with the advent of more sophisticated genetic testing, additional genetic discoveries have been made in the field of inherited cancer. This article will summarize many of the updates to both the familiar and perhaps less familiar syndromes that can lead to inherited or early-onset colorectal cancer.
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Affiliation(s)
- Molly M Ford
- Division of Colon and Rectal Surgery, Department of General Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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22
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Hereditary Nonpolyposis Colorectal Cancer and Cancer Syndromes: Recent Basic and Clinical Discoveries. JOURNAL OF ONCOLOGY 2018; 2018:3979135. [PMID: 29849630 PMCID: PMC5937448 DOI: 10.1155/2018/3979135] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 12/14/2022]
Abstract
Approximately one-third of individuals diagnosed with colorectal cancer have a family history of cancer, suggesting that CRCs may result from a heritable component. Despite the availability of current gene-identification techniques, only 5% of all CRCs emerge from well-identifiable inherited causes for predisposition, including polyposis and nonpolyposis syndromes. Hereditary nonpolyposis colorectal cancer represents a large proportion of cases, and robustly affected patients are at increased risk for early onset, synchronous, and metachronous colorectal malignancies and extracolonic malignancies. HNPCC encompasses several cancer syndromes, such as Lynch syndrome, Lynch-like syndrome, and familial colorectal cancer type X, which have remarkable clinical presentations and overlapping genetic profiles that make clinical diagnosis a challenging task. Therefore, distinguishing between the HNPCC disorders is crucial for physicians as an approach to tailor different recommendations for patients and their at-risk family members according to the risks for colonic and extracolonic cancer associated with each syndrome. Identification of these potential patients through epidemiological characteristics and new genetic testing can estimate the individual risk, which informs appropriate cancer screening, surveillance, and/or treatment strategies. In the past three years, many appealing and important advances have been made in our understanding of the relationship between HNPCC and CRC-associated syndromes. The knowledge from the genetic profile of cancer syndromes and unique genotype-phenotype profiles in the different syndromes has changed our cognition. Therefore, this review presents and discusses HNPCC and several common nonpolyposis syndromes with respect to molecular phenotype, histopathologic features, and clinical presentation.
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23
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Kessler E, Liu J, Awad H, Hingorani M. Investigating the Link Between Mutations in MutS DNA Repair Protein and Lynch Cancer Syndrome. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.786.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Emily Kessler
- Molecular Biology and BiochemistryWesleyan UniversityMiddletownCT
| | - Juan Liu
- Molecular Biology and BiochemistryWesleyan UniversityMiddletownCT
| | - Helena Awad
- Molecular Biology and BiochemistryWesleyan UniversityMiddletownCT
| | - Manju Hingorani
- Molecular Biology and BiochemistryWesleyan UniversityMiddletownCT
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24
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Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics 2017; 206:1187-1225. [PMID: 28684602 PMCID: PMC5500125 DOI: 10.1534/genetics.112.145805] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements result in mutations that underlie many human diseases, and ongoing genome instability likely contributes to the development of many cancers. The tools for studying genome instability in mammalian cells are limited, whereas model organisms such as Saccharomyces cerevisiae are more amenable to these studies. Here, we discuss the many genetic assays developed to measure the rate of occurrence of Gross Chromosomal Rearrangements (called GCRs) in S. cerevisiae. These genetic assays have been used to identify many types of GCRs, including translocations, interstitial deletions, and broken chromosomes healed by de novo telomere addition, and have identified genes that act in the suppression and formation of GCRs. Insights from these studies have contributed to the understanding of pathways and mechanisms that suppress genome instability and how these pathways cooperate with each other. Integrated models for the formation and suppression of GCRs are discussed.
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25
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Abstract
The instability of microsatellite DNA repeats is responsible for at least 40 neurodegenerative diseases. Recently, Mirkin and co-workers presented a novel mechanism for microsatellite expansions based on break-induced replication (BIR) at sites of microsatellite-induced replication stalling and fork collapse. The BIR model aims to explain single-step, large expansions of CAG/CTG trinucleotide repeats in dividing cells. BIR has been characterized extensively in Saccharomyces cerevisiae as a mechanism to repair broken DNA replication forks (single-ended DSBs) and degraded telomeric DNA. However, the structural footprints of BIR-like DSB repair have been recognized in human genomic instability and tied to the etiology of diverse developmental diseases; thus, the implications of the paper by Kim et al. (Kim JC, Harris ST, Dinter T, Shah KA, et al., Nat Struct Mol Biol 24: 55-60) extend beyond trinucleotide repeat expansion in yeast and microsatellite instability in human neurological disorders. Significantly, insight into BIR-like repair can explain certain pathways of complex genome rearrangements (CGRs) initiated at non-B form microsatellite DNA in human cancers.
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Affiliation(s)
- Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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26
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González-Acosta M, Del Valle J, Navarro M, Thompson BA, Iglesias S, Sanjuan X, Paúles MJ, Padilla N, Fernández A, Cuesta R, Teulé À, Plotz G, Cadiñanos J, de la Cruz X, Balaguer F, Lázaro C, Pineda M, Capellá G. Elucidating the clinical significance of two PMS2 missense variants coexisting in a family fulfilling hereditary cancer criteria. Fam Cancer 2017; 16:501-507. [PMID: 28365877 DOI: 10.1007/s10689-017-9981-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The clinical spectrum of germline mismatch repair (MMR) gene variants continues increasing, encompassing Lynch syndrome, Constitutional MMR Deficiency (CMMRD), and the recently reported MSH3-associated polyposis. Genetic diagnosis of these hereditary cancer syndromes is often hampered by the presence of variants of unknown significance (VUS) and overlapping phenotypes. Two PMS2 VUS, c.2149G>A (p.V717M) and c.2444C>T (p.S815L), were identified in trans in one individual diagnosed with early-onset colorectal cancer (CRC) who belonged to a family fulfilling clinical criteria for hereditary cancer. Clinico-pathological data, multifactorial likelihood calculations and functional analyses were used to refine their clinical significance. Likelihood analysis based on cosegregation and tumor data classified the c.2444C>T variant as pathogenic, which was supported by impaired MMR activity associated with diminished protein expression in functional assays. Conversely, the c.2149G>A variant displayed MMR proficiency and protein stability. These results, in addition to the conserved PMS2 expression in normal tissues and the absence of germline microsatellite instability (gMSI) in the biallelic carrier ruled out a CMMRD diagnosis. The use of comprehensive strategies, including functional and clinico-pathological information, is mandatory to improve the clinical interpretation of naturally occurring MMR variants. This is critical for appropriate clinical management of cancer syndromes associated to MMR gene mutations.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - María José Paúles
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Raquel Cuesta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Guido Plotz
- Medical Clinic 1, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain.
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27
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28
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Lakhani B, Thayer KM, Hingorani MM, Beveridge DL. Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein. J Phys Chem B 2017; 121:2049-2061. [PMID: 28135092 PMCID: PMC5346969 DOI: 10.1021/acs.jpcb.6b11976] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Mismatch
repair (MMR) is an essential, evolutionarily conserved
pathway that maintains genome stability by correcting base-pairing
errors in DNA. Here we examine the sequence and structure of MutS
MMR protein to decipher the amino acid framework underlying its two
key activities—recognizing mismatches in DNA and using ATP
to initiate repair. Statistical coupling analysis (SCA) identified
a network (sector) of coevolved amino acids in the MutS protein family.
The potential functional significance of this SCA sector was assessed
by performing molecular dynamics (MD) simulations for alanine mutants
of the top 5% of 160 residues in the distribution, and control nonsector
residues. The effects on three independent metrics were monitored:
(i) MutS domain conformational dynamics, (ii) hydrogen bonding between
MutS and DNA/ATP, and (iii) relative ATP binding free energy. Each
measure revealed that sector residues contribute more substantively
to MutS structure–function than nonsector residues. Notably,
sector mutations disrupted MutS contacts with DNA and/or ATP from
a distance via contiguous pathways and correlated motions, supporting
the idea that SCA can identify amino acid networks underlying allosteric
communication. The combined SCA/MD approach yielded novel, experimentally
testable hypotheses for unknown roles of many residues distributed
across MutS, including some implicated in Lynch cancer syndrome.
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Affiliation(s)
- Bharat Lakhani
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Kelly M Thayer
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - David L Beveridge
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
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29
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Hingorani MM. Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair. DNA Repair (Amst) 2016; 38:24-31. [PMID: 26704427 PMCID: PMC4740199 DOI: 10.1016/j.dnarep.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS-our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation.
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30
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Kadyrova LY, Kadyrov FA. Endonuclease activities of MutLα and its homologs in DNA mismatch repair. DNA Repair (Amst) 2016; 38:42-49. [PMID: 26719141 PMCID: PMC4820397 DOI: 10.1016/j.dnarep.2015.11.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/26/2015] [Accepted: 11/30/2015] [Indexed: 12/28/2022]
Abstract
MutLα is a key component of the DNA mismatch repair system in eukaryotes. The DNA mismatch repair system has several genetic stabilization functions. Of these functions, DNA mismatch repair is the major one. The loss of MutLα abolishes DNA mismatch repair, thereby predisposing humans to cancer. MutLα has an endonuclease activity that is required for DNA mismatch repair. The endonuclease activity of MutLα depends on the DQHA(X)2E(X)4E motif which is a part of the active site of the nuclease. This motif is also present in many bacterial MutL and eukaryotic MutLγ proteins, DNA mismatch repair system factors that are homologous to MutLα. Recent studies have shown that yeast MutLγ and several MutL proteins containing the DQHA(X)2E(X)4E motif possess endonuclease activities. Here, we review the endonuclease activities of MutLα and its homologs in the context of DNA mismatch repair.
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Affiliation(s)
- Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Farid A Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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31
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Li Z, Pearlman AH, Hsieh P. DNA mismatch repair and the DNA damage response. DNA Repair (Amst) 2016; 38:94-101. [PMID: 26704428 PMCID: PMC4740233 DOI: 10.1016/j.dnarep.2015.11.019] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/17/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
This review discusses the role of DNA mismatch repair (MMR) in the DNA damage response (DDR) that triggers cell cycle arrest and, in some cases, apoptosis. Although the focus is on findings from mammalian cells, much has been learned from studies in other organisms including bacteria and yeast [1,2]. MMR promotes a DDR mediated by a key signaling kinase, ATM and Rad3-related (ATR), in response to various types of DNA damage including some encountered in widely used chemotherapy regimes. An introduction to the DDR mediated by ATR reveals its immense complexity and highlights the many biological and mechanistic questions that remain. Recent findings and future directions are highlighted.
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Affiliation(s)
- Zhongdao Li
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Alexander H Pearlman
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA.
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32
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Targeting Mismatch Repair defects: A novel strategy for personalized cancer treatment. DNA Repair (Amst) 2016; 38:135-139. [DOI: 10.1016/j.dnarep.2015.11.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 11/21/2022]
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33
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Manhart CM, Alani E. Roles for mismatch repair family proteins in promoting meiotic crossing over. DNA Repair (Amst) 2016; 38:84-93. [PMID: 26686657 PMCID: PMC4740264 DOI: 10.1016/j.dnarep.2015.11.024] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/14/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
The mismatch repair (MMR) family complexes Msh4-Msh5 and Mlh1-Mlh3 act with Exo1 and Sgs1-Top3-Rmi1 in a meiotic double strand break repair pathway that results in the asymmetric cleavage of double Holliday junctions (dHJ) to form crossovers. This review discusses how meiotic roles for Msh4-Msh5 and Mlh1-Mlh3 do not fit paradigms established for post-replicative MMR. We also outline models used to explain how these factors promote the formation of meiotic crossovers required for the accurate segregation of chromosome homologs during the Meiosis I division.
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Affiliation(s)
- Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA.
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34
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Gauer J, LeBlanc S, Hao P, Qiu R, Case B, Sakato M, Hingorani M, Erie D, Weninger K. Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins. Methods Enzymol 2016; 581:285-315. [PMID: 27793283 PMCID: PMC5423442 DOI: 10.1016/bs.mie.2016.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Single-molecule FRET measurements have a unique sensitivity to protein conformational dynamics. The FRET signals can either be interpreted quantitatively to provide estimates of absolute distance in a molecule configuration or can be qualitatively interpreted as distinct states, from which quantitative kinetic schemes for conformational transitions can be deduced. Here we describe methods utilizing single-molecule FRET to reveal the conformational dynamics of the proteins responsible for DNA mismatch repair. Experimental details about the proteins, DNA substrates, fluorescent labeling, and data analysis are included. The complementarity of single molecule and ensemble kinetic methods is discussed as well.
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Affiliation(s)
- J.W. Gauer
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - S. LeBlanc
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - P. Hao
- North Carolina State University, Raleigh, NC, United States
| | - R. Qiu
- North Carolina State University, Raleigh, NC, United States
| | - B.C. Case
- Wesleyan University, Middletown, CT, United States
| | - M. Sakato
- Wesleyan University, Middletown, CT, United States
| | | | - D.A. Erie
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Corresponding authors: ;
| | - K.R. Weninger
- North Carolina State University, Raleigh, NC, United States,Corresponding authors: ;
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35
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Sijmons RH, Hofstra RMW. Review: Clinical aspects of hereditary DNA Mismatch repair gene mutations. DNA Repair (Amst) 2015; 38:155-162. [PMID: 26746812 DOI: 10.1016/j.dnarep.2015.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 09/28/2015] [Accepted: 11/30/2015] [Indexed: 12/15/2022]
Abstract
Inherited mutations of the DNA Mismatch repair genes MLH1, MSH2, MSH6 and PMS2 can result in two hereditary tumor syndromes: the adult-onset autosomal dominant Lynch syndrome, previously referred to as Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and the childhood-onset autosomal recessive Constitutional Mismatch Repair Deficiency syndrome. Both conditions are important to recognize clinically as their identification has direct consequences for clinical management and allows targeted preventive actions in mutation carriers. Lynch syndrome is one of the more common adult-onset hereditary tumor syndromes, with thousands of patients reported to date. Its tumor spectrum is well established and includes colorectal cancer, endometrial cancer and a range of other cancer types. However, surveillance for cancers other than colorectal cancer is still of uncertain value. Prophylactic surgery, especially for the uterus and its adnexa is an option in female mutation carriers. Chemoprevention of colorectal cancer with aspirin is actively being investigated in this syndrome and shows promising results. In contrast, the Constitutional Mismatch Repair Deficiency syndrome is rare, features a wide spectrum of childhood onset cancers, many of which are brain tumors with high mortality rates. Future studies are very much needed to improve the care for patients with this severe disorder.
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Affiliation(s)
- Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB, Groningen, The Netherlands.
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, P.O. Box 2040, 3000CA Rotterdam, The Netherlands.
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36
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Friedhoff P, Li P, Gotthardt J. Protein-protein interactions in DNA mismatch repair. DNA Repair (Amst) 2015; 38:50-57. [PMID: 26725162 DOI: 10.1016/j.dnarep.2015.11.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022]
Abstract
The principal DNA mismatch repair proteins MutS and MutL are versatile enzymes that couple DNA mismatch or damage recognition to other cellular processes. Besides interaction with their DNA substrates this involves transient interactions with other proteins which is triggered by the DNA mismatch or damage and controlled by conformational changes. Both MutS and MutL proteins have ATPase activity, which adds another level to control their activity and interactions with DNA substrates and other proteins. Here we focus on the protein-protein interactions, protein interaction sites and the different levels of structural knowledge about the protein complexes formed with MutS and MutL during the mismatch repair reaction.
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Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
| | - Pingping Li
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Julia Gotthardt
- Institute for Biochemistry FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
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37
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Regulation of mismatch repair by histone code and posttranslational modifications in eukaryotic cells. DNA Repair (Amst) 2015; 38:68-74. [PMID: 26719139 DOI: 10.1016/j.dnarep.2015.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 09/09/2015] [Accepted: 11/30/2015] [Indexed: 12/15/2022]
Abstract
DNA mismatch repair (MMR) protects genome integrity by correcting DNA replication-associated mispairs, modulating DNA damage-induced cell cycle checkpoints and regulating homeologous recombination. Loss of MMR function leads to cancer development. This review describes progress in understanding how MMR is carried out in the context of chromatin and how chromatin organization/compaction, epigenetic mechanisms and posttranslational modifications of MMR proteins influence and regulate MMR in eukaryotic cells.
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38
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Abstract
Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.
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Affiliation(s)
- Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina 27709;
| | - Dorothy A Erie
- Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599-3290;
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