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Tompkins JD. Transgenerational Epigenetic DNA Methylation Editing and Human Disease. Biomolecules 2023; 13:1684. [PMID: 38136557 PMCID: PMC10742326 DOI: 10.3390/biom13121684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
During gestation, maternal (F0), embryonic (F1), and migrating primordial germ cell (F2) genomes can be simultaneously exposed to environmental influences. Accumulating evidence suggests that operating epi- or above the genetic DNA sequence, covalent DNA methylation (DNAme) can be recorded onto DNA in response to environmental insults, some sites which escape normal germline erasure. These appear to intrinsically regulate future disease propensity, even transgenerationally. Thus, an organism's genome can undergo epigenetic adjustment based on environmental influences experienced by prior generations. During the earliest stages of mammalian development, the three-dimensional presentation of the genome is dramatically changed, and DNAme is removed genome wide. Why, then, do some pathological DNAme patterns appear to be heritable? Are these correctable? In the following sections, I review concepts of transgenerational epigenetics and recent work towards programming transgenerational DNAme. A framework for editing heritable DNAme and challenges are discussed, and ethics in human research is introduced.
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Affiliation(s)
- Joshua D Tompkins
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
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2
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Hitchins MP, Alvarez R, Zhou L, Aguirre F, Dámaso E, Pineda M, Capella G, Wong JJL, Yuan X, Ryan SR, Sathe DS, Baxter MD, Cannon T, Biswas R, DeMarco T, Grzelak D, Hampel H, Pearlman R. MLH1-methylated endometrial cancer under 60 years of age as the "sentinel" cancer in female carriers of high-risk constitutional MLH1 epimutation. Gynecol Oncol 2023; 171:129-140. [PMID: 36893489 PMCID: PMC10153467 DOI: 10.1016/j.ygyno.2023.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/11/2023]
Abstract
OBJECTIVE Universal screening of endometrial carcinoma (EC) for mismatch repair deficiency (MMRd) and Lynch syndrome uses presence of MLH1 methylation to omit common sporadic cases from follow-up germline testing. However, this overlooks rare cases with high-risk constitutional MLH1 methylation (epimutation), a poorly-recognized mechanism that predisposes to Lynch-type cancers with MLH1 methylation. We aimed to determine the role and frequency of constitutional MLH1 methylation among EC cases with MMRd, MLH1-methylated tumors. METHODS We screened blood for constitutional MLH1 methylation using pyrosequencing and real-time methylation-specific PCR in patients with MMRd, MLH1-methylated EC ascertained from (i) cancer clinics (n = 4, <60 years), and (ii) two population-based cohorts; "Columbus-area" (n = 68, all ages) and "Ohio Colorectal Cancer Prevention Initiative (OCCPI)" (n = 24, <60 years). RESULTS Constitutional MLH1 methylation was identified in three out of four patients diagnosed between 36 and 59 years from cancer clinics. Two had mono-/hemiallelic epimutation (∼50% alleles methylated). One with multiple primaries had low-level mosaicism in normal tissues and somatic "second-hits" affecting the unmethylated allele in all tumors, demonstrating causation. In the population-based cohorts, all 68 cases from the Columbus-area cohort were negative and low-level mosaic constitutional MLH1 methylation was identified in one patient aged 36 years out of 24 from the OCCPI cohort, representing one of six (∼17%) patients <50 years and one of 45 patients (∼2%) <60 years in the combined cohorts. EC was the first/dual-first cancer in three patients with underlying constitutional MLH1 methylation. CONCLUSIONS A correct diagnosis at first presentation of cancer is important as it will significantly alter clinical management. Screening for constitutional MLH1 methylation is warranted in patients with early-onset EC or synchronous/metachronous tumors (any age) displaying MLH1 methylation.
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Affiliation(s)
- Megan P Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine (Oncology), Stanford University, Stanford, CA, USA.
| | - Rocio Alvarez
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Zhou
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesca Aguirre
- Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Estela Dámaso
- Department of Medicine (Oncology), Stanford University, Stanford, CA, USA; Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain; Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain
| | - Marta Pineda
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Gabriel Capella
- Molecular Genetics Unit, Elche University Hospital, Elche, Alicante. Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), FISABIO- Elche Health Department, Spain; Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Av. De Monforte de Lemos 5, 28029 Madrid, Spain
| | - Justin J-L Wong
- Epigenetics and RNA Biology Program Centenary Institute, and Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Xiaopu Yuan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shawnia R Ryan
- Hereditary Cancer Assessment Program, University of New Mexico Comprehensive Cancer Center, NM, USA
| | - Devika S Sathe
- Precision Medicine and Genetics, Frederick Health, MD, USA
| | | | - Timothy Cannon
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Rakesh Biswas
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | - Tiffani DeMarco
- Cancer Genetics Program, Inova Schar Cancer Institute, Inova Fairfax Hospital, VA, USA
| | | | - Heather Hampel
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA; Division of Clinical Cancer Genomics, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Rachel Pearlman
- Department of Internal Medicine and the Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Takahashi Y, Morales Valencia M, Yu Y, Ouchi Y, Takahashi K, Shokhirev MN, Lande K, Williams AE, Fresia C, Kurita M, Hishida T, Shojima K, Hatanaka F, Nuñez-Delicado E, Esteban CR, Izpisua Belmonte JC. Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice. Cell 2023; 186:715-731.e19. [PMID: 36754048 DOI: 10.1016/j.cell.2022.12.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/19/2022] [Accepted: 12/29/2022] [Indexed: 02/10/2023]
Abstract
Transgenerational epigenetic inheritance in mammals remains a debated subject. Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to their offspring in mice. We generated DNA methylation-edited mouse embryonic stem cells (ESCs), in which CGIs of two metabolism-related genes, the Ankyrin repeat domain 26 and the low-density lipoprotein receptor, were specifically methylated and silenced. DNA methylation-edited mice generated by microinjection of the methylated ESCs exhibited abnormal metabolic phenotypes. Acquired methylation of the targeted CGI and the phenotypic traits were maintained and transmitted across multiple generations. The heritable CGI methylation was subjected to reprogramming in parental PGCs and subsequently reestablished in the next generation at post-implantation stages. These observations provide a concrete step toward demonstrating transgenerational epigenetic inheritance in mammals, which may have implications in our understanding of evolutionary biology as well as the etiology, diagnosis, and prevention of non-genetically inherited human diseases.
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Affiliation(s)
- Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Mariana Morales Valencia
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Yang Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yasuo Ouchi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuou-ku, Chiba 260-8670, Japan
| | - Kazuki Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Maxim Nikolaievich Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kathryn Lande
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - April E Williams
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chiara Fresia
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Masakazu Kurita
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Plastic, Reconstructive and Aesthetic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shitibancho, Wakayama, Wakayama, Japan
| | - Kensaku Shojima
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Estrella Nuñez-Delicado
- Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, no. 135 Guadalupe 30107, Murcia, Spain
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Altos Labs, 5510 Morehouse Drive, Suite 300, San Diego, CA 92121, USA.
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Lynch-like Syndrome: Potential Mechanisms and Management. Cancers (Basel) 2022; 14:cancers14051115. [PMID: 35267422 PMCID: PMC8909420 DOI: 10.3390/cancers14051115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Lynch-like syndrome (LLS) is defined as colorectal cancer cases with microsatellite instability (MSI) and loss of expression of MLH1, MSH2, MSH6, or PMS2 by immunohistochemistry (IHC) in the absence of a germline mutation in these genes that cannot be explained by BRAF mutation or MLH1 hypermethylation. The application of the universal strategy for the diagnosis of Lynch syndrome (LS) in all CRCs is leading to an increase in the incidence of cases of LLS. It has been described that risk of cancer in relatives of LLS patients is in between of that found in Lynch syndrome families and sporadic cases. That makes LLS patients and their families a challenging group for which the origin of CRC is unknown, being a mixture between unidentified hereditary CRC and sporadic cases. The potential causes of LLS are discussed in this review, as well as methods for identification of truly hereditary cases. Abstract Lynch syndrome is an autosomal dominant disorder caused by germline mutations in DNA mismatch repair (MMR) system genes, such as MLH1, MSH2, MSH6, or PMS2. It is the most common hereditary colorectal cancer syndrome. Screening is regularly performed by using microsatellite instability (MSI) or immunohistochemistry for the MMR proteins in tumor samples. However, in a proportion of cases, MSI is found or MMR immunohistochemistry is impaired in the absence of a germline mutation in MMR genes, BRAF mutation, or MLH1 hypermethylation. These cases are defined as Lynch-like syndrome. Patients with Lynch-like syndrome represent a mixture of truly hereditary and sporadic cases, with a risk of colorectal cancer in first-degree relatives that is between the risk of Lynch syndrome in families and relatives of sporadic colon cancer cases. Although multiple approaches have been suggested to distinguish between hereditary and sporadic cases, a homogeneous testing protocol and consensus on the adequate classification of these patients is still lacking. For this reason, management of Lynch-like syndrome and prevention of cancer in these families is clinically challenging. This review explains the concept of Lynch-like syndrome, potential mechanisms for its development, and methods for adequately distinguishing between sporadic and hereditary cases of this entity.
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Dörk T, Hillemanns P, Tempfer C, Breu J, Fleisch MC. Genetic Susceptibility to Endometrial Cancer: Risk Factors and Clinical Management. Cancers (Basel) 2020; 12:cancers12092407. [PMID: 32854222 PMCID: PMC7565375 DOI: 10.3390/cancers12092407] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Endometrial cancer (EC) is the most common cancer affecting the female reproductive organs in higher-income states. Apart from reproductive factors and excess weight, genetic predisposition is increasingly recognized as a major factor in endometrial cancer risk. Endometrial cancer is genetically heterogeneous: while a subgroup of patients belongs to cancer predisposition syndromes (most notably the Lynch Syndrome) with high to intermediate lifetime risks, there are also several common genomic polymorphisms contributing to the spectrum of germline predispositions. Germline variants and somatic events may act in concert to modulate the molecular evolution of the tumor, where mismatch-repair deficiency is common in endometrioid endometrial tumors whereas homologous recombinational repair deficiency has been described for non-endometrioid endometrial tumors. In this review, we will survey the currently known genomic predispositions for endometrial cancer and discuss their relevance for clinical management in terms of counseling, screening and novel treatments.
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Affiliation(s)
- Thilo Dörk
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
- Correspondence:
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
| | - Clemens Tempfer
- Department of Gynaecology, Marien-Hospital, Ruhr University of Bochum, 44625 Herne, Germany;
| | - Julius Breu
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
| | - Markus C. Fleisch
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
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Kientz C, Prieur F, Clemenson A, Joly MO, Stachowicz ML, Auclair J, Attignon V, Schiappa R, Wang Q. MLH1 promoter hypermethylation: are you absolutely sure about the absence of MLH1 germline mutation? About a new case. Fam Cancer 2019; 19:11-14. [PMID: 31745674 DOI: 10.1007/s10689-019-00151-7] [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: 05/31/2019] [Accepted: 11/12/2019] [Indexed: 11/30/2022]
Abstract
Lynch syndrome accounts for 3-5% of colorectal cancers and is due to a germline mutation in one of the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. Somatic hypermethylation of the MLH1 promoter is commonly associated to sporadic cases. Strategies have been developed to identify patients with Lynch Syndrome based on clinical findings, tumoral phenotype, family history and immunohistochemistry analysis. However, there still are some pitfalls in this strategy, possibly responsible for an underdiagnosis of Lynch syndrome. Here we report the case of a 37 years-old man presenting with two concomitant tumors located in the rectosigmoid and in the ileocecal angle. Both tumors were microsatellites instability-high (MSI-H) and showed a loss of MLH1 and PMS2 protein expression, but only one had MLH1 promoter hypermethylation. Constitutional analysis of mismatch repair genes could not be performed from a blood sample, because of the early death of the patient. However, tumoral tissue analyses revealed in both tumors a pathogenic variant in the MLH1 gene. Further analysis of the surrounding tumor-free tissue also showed the presence of this alteration of the MHL1 gene. Finally, the same pathogenic variant was present constitutionally in one of the siblings of the patient, confirming its hereditary nature. This new case of concomitant presence of MLH1 promoter hypermethylation and MLH1 germline mutation demonstrates that the presence of MLH1 promoter hypermethylation should not rule out the diagnosis of Lynch Syndrome.
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Affiliation(s)
- Caroline Kientz
- Department of Genetics, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne Cedex 2, France.
| | - Fabienne Prieur
- Department of Genetics, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne Cedex 2, France
| | - Alix Clemenson
- Department of Pathology, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne cedex 2, France
| | - Marie-Odile Joly
- Hospices Civils de Lyon, Molecular Biopathology, Centre of Pathology, GHE Hospital, Bron, France.,Claude Bernard University Lyon 1, University of Lyon, 69622, Villeurbanne cedex, France
| | - Marie-Laure Stachowicz
- Department of Pathology, Hôpital Nord, CHU Saint Etienne, 42055, Saint-Etienne cedex 2, France
| | - Jessie Auclair
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France
| | - Valéry Attignon
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France
| | - Renaud Schiappa
- Epidemiology and Biostatistics Unit, Centre Antoine Lacassagne, University of Cote d'Azur, 33 avenue de valombrose, 06189, Nice, France
| | - Qing Wang
- Centre Léon Bérard, Cancer Genomics Platform, 69272, Lyon cedex 08, France.,Centre Léon Bérard, Joint laboratory for constitutional genetics HCL-CLB, 69272, Lyon cedex 08, France
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Evrard C, Tachon G, Randrian V, Karayan-Tapon L, Tougeron D. Microsatellite Instability: Diagnosis, Heterogeneity, Discordance, and Clinical Impact in Colorectal Cancer. Cancers (Basel) 2019; 11:E1567. [PMID: 31618962 PMCID: PMC6826728 DOI: 10.3390/cancers11101567] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/17/2022] Open
Abstract
Tumor DNA mismatch repair (MMR) deficiency testing is important to the identification of Lynch syndrome and decision making regarding adjuvant chemotherapy in stage II colorectal cancer (CRC) and has become an indispensable test in metastatic tumors due to the high efficacy of immune checkpoint inhibitor (ICI) in deficient MMR (dMMR) tumors. CRCs greatly benefit from this testing as approximately 15% of them are dMMR but only 3% to 5% are at a metastatic stage. MMR status can be determined by two different methods, microsatellite instability (MSI) testing on tumor DNA, and immunohistochemistry of the MMR proteins on tumor tissue. Recent studies have reported a rate of 3% to 10% of discordance between these two tests. Moreover, some reports suggest possible intra- and inter-tumoral heterogeneity of MMR and MSI status. These issues are important to know and to clarify in order to define therapeutic strategy in CRC. This review aims to detail the standard techniques used for the determination of MMR and MSI status, along with their advantages and limits. We review the discordances that may arise between these two tests, tumor heterogeneity of MMR and MSI status, and possible explanations. We also discuss the strategies designed to distinguish sporadic versus germline dMMR/MSI CRC. Finally, we present new and accurate methods aimed at determining MMR/MSI status.
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Affiliation(s)
- Camille Evrard
- Department of Medical Oncology, Poitiers University Hospital, 86021 Poitiers, France.
| | - Gaëlle Tachon
- Department of Cancer biology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Laboratory of Experimental and Clinical Neuroscience, Institut national de la santé et de la recherche médicale (INSERM) 1084, F-86073 Poitiers, France.
| | - Violaine Randrian
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Department of Gastroenterology, Poitiers University Hospital, 86021 Poitiers, France.
| | - Lucie Karayan-Tapon
- Department of Cancer biology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Laboratory of Experimental and Clinical Neuroscience, Institut national de la santé et de la recherche médicale (INSERM) 1084, F-86073 Poitiers, France.
| | - David Tougeron
- Department of Medical Oncology, Poitiers University Hospital, 86021 Poitiers, France.
- Faculty of medicine, University of Poitiers, 86000 Poitiers, France.
- Department of Gastroenterology, Poitiers University Hospital, 86021 Poitiers, France.
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Abstract
The idea that epigenetic determinants such as DNA methylation, histone modifications or RNA can be passed to the next generation through meiotic products (gametes) is long standing. Such meiotic epigenetic inheritance (MEI) is fairly common in yeast, plants and nematodes, but its extent in mammals has been much debated. Advances in genomics techniques are now driving the profiling of germline and zygotic epigenomes, thereby improving our understanding of MEI in diverse species. Whereas the role of DNA methylation in MEI remains unclear, insights from genome-wide studies suggest that a previously underappreciated fraction of mammalian genomes bypass epigenetic reprogramming during development. Notably, intergenerational inheritance of histone modifications, tRNA fragments and microRNAs can affect gene regulation in the offspring. It is important to note that MEI in mammals rarely constitutes transgenerational epigenetic inheritance (TEI), which spans multiple generations. In this Review, we discuss the examples of MEI in mammals, including mammalian epigenome reprogramming, and the molecular mechanisms of MEI in vertebrates in general. We also discuss the implications of the inheritance of histone modifications and small RNA for embryogenesis in metazoans, with a particular focus on insights gained from genome-wide studies.
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10
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Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
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Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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11
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Pellat A, Netter J, Perkins G, Cohen R, Coulet F, Parc Y, Svrcek M, Duval A, André T. [Lynch syndrome: What is new?]. Bull Cancer 2018; 106:647-655. [PMID: 30527816 DOI: 10.1016/j.bulcan.2018.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Lynch syndrome is a genetic condition defined by a germline mutation of an MMR (MisMatch Repair) gene leading to a defective DNA MMR system. Therefore, it is characterized by the predisposition to a spectrum of cancers, primarily colorectal cancer (CRC) and endometrial cancer (EC). Lynch syndrome-related CRC accounts for 3% of all CRC. Lynch syndrome also accounts for 2% of all EC. In case of Lynch syndrome, there is usually a familial history of cancer defined by the Amsterdam and Bethesda criteria. Diagnosis is made by tumor testing with (i) MMR immunohistochemistry and (ii) PCR for MSI (microsatellite instability), a genetic phenotype that characterizes these tumors. MSI can also be detected in sporadic tumors, through epigenetic events inactivating the MMR system. Progress in diagnosis and molecular biology has allowed for better identification of Lynch patients but also other rare genetic syndromes. MSI tumors can now benefit from new treatments such as immunotherapy which underlines the importance of their diagnosis. Finally, patients with Lynch syndrome as well as their relatives, undergo specific surveillance in order to prevent development of other cancers. This review will summarize the different aspects of Lynch syndrome and also focus on recent progress on the topic.
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Affiliation(s)
- Anna Pellat
- AP-HP, Sorbonne université, hôpital Saint-Antoine, et service d'oncologie médicale, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France.
| | - Jeanne Netter
- AP-HP, hôpital Tenon, service de gastro entérologie, 4, rue de la Chine, 75020 Paris, France
| | - Géraldine Perkins
- AP-HP, hôpital européen Georges Pompidou, unité d'oncogénétique, 20, rue Leblanc, 75015 Paris, France
| | - Romain Cohen
- AP-HP, Sorbonne université, hôpital Saint-Antoine, et service d'oncologie médicale, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France; Sorbonne université, unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de recherche Saint-Antoine, équipe instabilité des microsatellites et cancer, équipe labellisée par la Ligue Nationale contre le cancer, Inserm, 75012 Paris, France
| | - Florence Coulet
- AP-HP, hôpitaux universitaire Pitié Salpêtrière-Charles, département de génétique, 47-83, boulevard de l'Hôpital, 75013 Paris, France
| | - Yann Parc
- AP-HP, Sorbonne université, hôpital Saint-Antoine, service de chirurgie générale et digestive, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France
| | - Magali Svrcek
- Sorbonne université, unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de recherche Saint-Antoine, équipe instabilité des microsatellites et cancer, équipe labellisée par la Ligue Nationale contre le cancer, Inserm, 75012 Paris, France; AP-HP, hôpital Saint-Antoine, Sorbonne université et service d'anatomopathologie, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France
| | - Alex Duval
- Sorbonne université, unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de recherche Saint-Antoine, équipe instabilité des microsatellites et cancer, équipe labellisée par la Ligue Nationale contre le cancer, Inserm, 75012 Paris, France
| | - Thierry André
- AP-HP, Sorbonne université, hôpital Saint-Antoine, et service d'oncologie médicale, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France; Sorbonne université, unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de recherche Saint-Antoine, équipe instabilité des microsatellites et cancer, équipe labellisée par la Ligue Nationale contre le cancer, Inserm, 75012 Paris, France
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12
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Dámaso E, Castillejo A, Arias MDM, Canet-Hermida J, Navarro M, Del Valle J, Campos O, Fernández A, Marín F, Turchetti D, García-Díaz JDD, Lázaro C, Genuardi M, Rueda D, Alonso Á, Soto JL, Hitchins M, Pineda M, Capellá G. Primary constitutional MLH1 epimutations: a focal epigenetic event. Br J Cancer 2018; 119:978-987. [PMID: 30283143 PMCID: PMC6203851 DOI: 10.1038/s41416-018-0019-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Background Constitutional MLH1 epimutations are characterised by monoallelic methylation of the MLH1 promoter throughout normal tissues, accompanied by allele-specific silencing. The mechanism underlying primary MLH1 epimutations is currently unknown. The aim of this study was to perform an in-depth characterisation of constitutional MLH1 epimutations targeting the aberrantly methylated region around MLH1 and other genomic loci. Methods Twelve MLH1 epimutation carriers, 61 Lynch syndrome patients, and 41 healthy controls, were analysed by Infinium 450 K array. Targeted molecular techniques were used to characterise the MLH1 epimutation carriers and their inheritance pattern. Results No nucleotide or structural variants were identified in-cis on the epimutated allele in 10 carriers, in which inter-generational methylation erasure was demonstrated in two, suggesting primary type of epimutation. CNVs outside the MLH1 locus were found in two cases. EPM2AIP1-MLH1 CpG island was identified as the sole differentially methylated region in MLH1 epimutation carriers compared to controls. Conclusion Primary constitutional MLH1 epimutations arise as a focal epigenetic event at the EPM2AIP1-MLH1 CpG island in the absence of cis-acting genetic variants. Further molecular characterisation is needed to elucidate the mechanistic basis of MLH1 epimutations and their heritability/reversibility.
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Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Adela Castillejo
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Camino de la Almazara 11, Elche, 03203, Alicante, Spain
| | - María Del Mar Arias
- Genetics Service, Complejo Hospitalario de Navarra, Calle de Irunlarrea 3, Pamplona, 31008, Navarra, Spain
| | - Julia Canet-Hermida
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Daniela Turchetti
- Dipartimento di Scienze Mediche e Chirurgiche, Alma Mater Studiorum - Università di Bologna, Via Massarenti 11, Bologna, 40138, Italy
| | - Juan de Dios García-Díaz
- Unidad de Genética Clínica, Servicio de Medicina Interna, Hospital Universitario Príncipe de Asturias, Carretera Alcalá-Meco, Alcalá de Henares, 28805, Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Maurizio Genuardi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Agostino Gemelli, Largo Agostino Gemelli 8, Rome, 00168, Italy
| | - Daniel Rueda
- Hereditary Cancer Genetic Diagnostic Laboratory, Doce de Octubre University Hospital, Avenida de Córdoba, Madrid, Madrid, 28041, Spain
| | - Ángel Alonso
- Genetics Service, Complejo Hospitalario de Navarra, Calle de Irunlarrea 3, Pamplona, 31008, Navarra, Spain
| | - Jose Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Camino de la Almazara 11, Elche, 03203, Alicante, Spain.,Alicante Institute for Health and Biomedical Research (ISABIAL-FISABIO Foundation), Alicante, Spain
| | - Megan Hitchins
- Department of Medicine, Division of Oncology, Stanford University, 1291 Welch Road, Stanford, 94305, California, USA
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-Bellvitge Biomedical Research Institute (ICO-IDIBELL),ONCOBELL, CIBERONC, Av.Gran Via de l'Hospitalet 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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13
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Al-Moghrabi N, Al-Showimi M, Al-Yousef N, Al-Shahrani B, Karakas B, Alghofaili L, Almubarak H, Madkhali S, Al Humaidan H. Methylation of BRCA1 and MGMT genes in white blood cells are transmitted from mothers to daughters. Clin Epigenetics 2018; 10:99. [PMID: 30049288 PMCID: PMC6062990 DOI: 10.1186/s13148-018-0529-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/08/2018] [Indexed: 12/31/2022] Open
Abstract
Background Constitutive methylation of tumor suppressor genes are associated with increased cancer risk. However, to date, the question of epimutational transmission of these genes remains unresolved. Here, we studied the potential transmission of BRCA1 and MGMT promoter methylations in mother-newborn pairs. Methods A total of 1014 female subjects (cancer-free women, n = 268; delivering women, n = 295; newborn females, n = 302; breast cancer patients, n = 67; ovarian cancer patients, n = 82) were screened for methylation status in white blood cells (WBC) using methylation-specific PCR and bisulfite pyrosequencing assays. In addition, BRCA1 gene expression levels were analyzed by quantitative real-time PCR. Results We found similar methylation frequencies in newborn and adults for both BRCA1 (9.9 and 9.3%) and MGMT (12.3 and 13.1%). Of the 290 mother-newborn pairs analyzed for promoter methylation, 20 mothers were found to be positive for BRCA1 and 29 for MGMT. Four mother-newborn pairs were positive for methylated BRCA1 (20%) and nine pairs were positive for methylated MGMT (31%). Intriguingly, the delivering women had 26% lower BRCA1 and MGMT methylation frequencies than those of the cancer-free female subjects. BRCA1 was downregulated in both cancer-free woman carriers and breast cancer patients but not in newborn carriers. There was a statistically significant association between the MGMT promoter methylation and late-onset breast cancers. Conclusions Our study demonstrates that BRCA1and MGMT epimutations are present from the early life of the carriers. We show the transmission of BRCA1 and MGMT epimutations from mother to daughter. Our data also point at the possible demethylation of BRCA1and MGMT during pregnancy.
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Affiliation(s)
- Nisreen Al-Moghrabi
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia.
| | - Maram Al-Showimi
- Cancer Epigenetic section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Nujoud Al-Yousef
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Bushra Al-Shahrani
- Cancer Epigenetic section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Bedri Karakas
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Lamyaa Alghofaili
- Al Faisal University College of Medicine, PO BOX 50927, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Hannah Almubarak
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Safia Madkhali
- King Saud bin Abdulaziz University for Health Sciences, PO BOX 22490, Riyadh, 3130, Kingdom of Saudi Arabia
| | - Hind Al Humaidan
- Department of pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
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14
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Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation. Genet Med 2018; 20:1589-1599. [DOI: 10.1038/gim.2018.47] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
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15
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Morak M, Ibisler A, Keller G, Jessen E, Laner A, Gonzales-Fassrainer D, Locher M, Massdorf T, Nissen AM, Benet-Pagès A, Holinski-Feder E. Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new variants including one with a heritable constitutional MLH1 epimutation. J Med Genet 2018; 55:240-248. [PMID: 29472279 DOI: 10.1136/jmedgenet-2017-104744] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 01/28/2023]
Abstract
BACKGROUND Germline defects in MLH1, MSH2, MSH6 and PMS2 predisposing for Lynch syndrome (LS) are mainly based on sequence changes, whereas a constitutional epimutation of MLH1(CEM) is exceptionally rare. This abnormal MLH1 promoter methylation is not hereditary when arising de novo, whereas a stably heritable and variant-induced CEM was described for one single allele. We searched for MLH1 promoter variants causing a germline or somatic methylation induction or transcriptional repression. METHODS We analysed the MLH1 promoter sequence in five different patient groups with colorectal cancer (CRC) (n=480) composed of patients with i) CEM (n=16), ii) unsolved loss of MLH1 expression in CRC (n=37), iii) CpG-island methylator-phenotype CRC (n=102), iv) patients with LS (n=83) and v) MLH1-proficient CRC (n=242) as controls. 1150 patients with non-LS tumours also served as controls to correctly judge the results. RESULTS We detected 10 rare MLH1 promoter variants. One novel, complex MLH1 variant c.-63_-58delins18 is present in a patient with CRC with CEM and his sister, both showing a complete allele-specific promoter methylation and transcriptional silencing. The other nine promoter variants detected in 17 individuals were not associated with methylation. For four of these, a normal, biallelic MLH1 expression was found in the patients' cDNA. CONCLUSION We report the second promoter variant stably inducing a hereditary CEM. Concerning the classification of promoter variants, we discuss contradictory results from the literature for two variants, describe classification discrepancies between existing rules for five variants, suggest the (re-)classification of five promoter variants to (likely) benign and regard four variants as functionally unclear.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany.,Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Ayseguel Ibisler
- Department of Human Genetics, Ruhr University Bochum, Bochum, North Rhine-Westphalia, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University Munich, Munich, Bavaria, Germany
| | - Ellen Jessen
- Praxis für Humangenetik, Praxis für Humangenetik, Hamburg, Hamburg, Germany
| | - Andreas Laner
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | | | - Melanie Locher
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Trisari Massdorf
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany
| | - Anke M Nissen
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Anna Benet-Pagès
- Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Bavaria, Germany.,Center of Medical Genetics, Medizinisch Genetisches Zentrum, Munich, Bavaria, Germany
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16
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Pinto D, Pinto C, Guerra J, Pinheiro M, Santos R, Vedeld HM, Yohannes Z, Peixoto A, Santos C, Pinto P, Lopes P, Lothe R, Lind GE, Henrique R, Teixeira MR. Contribution of MLH1 constitutional methylation for Lynch syndrome diagnosis in patients with tumor MLH1 downregulation. Cancer Med 2018; 7:433-444. [PMID: 29341452 PMCID: PMC6193414 DOI: 10.1002/cam4.1285] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/23/2022] Open
Abstract
Constitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, has been identified as an alternative mechanism that predisposes to the development of Lynch syndrome. In the present work, we aimed to investigate the prevalence of MLH1 constitutional methylation in colorectal cancer (CRC) patients with abnormal expression of the MLH1 protein in their tumors. In a series of 38 patients who met clinical criteria for Lynch syndrome genetic testing, with loss of MLH1 expression in the tumor and with no germline mutations in the MLH1 gene (35/38) or with tumors presenting the BRAF p.Val600Glu mutation (3/38), we screened for constitutional methylation of the MLH1 gene promoter using methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) in various biological samples. We found four (4/38; 10.5%) patients with constitutional methylation in the MLH1 gene promoter. RNA studies demonstrated decreased MLH1 expression in the cases with constitutional methylation when compared with controls. We could infer the mosaic nature of MLH1 constitutional hypermethylation in tissues originated from different embryonic germ layers, and in one family we could show that it occurred de novo. We conclude that constitutional MLH1 methylation occurs in a significant proportion of patients who have loss of MLH1 protein expression in their tumors and no MLH1 pathogenic germline mutation. Furthermore, we provide evidence that MLH1 constitutional hypermethylation is the molecular mechanism behind about 3% of Lynch syndrome families diagnosed in our institution, especially in patients with early onset or multiple primary tumors without significant family history.
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Affiliation(s)
- Diana Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Rui Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Zeremariam Yohannes
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Ana Peixoto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Paula Lopes
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Ragnhild Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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van Otterdijk SD, Binder AM, Szarc vel Szic K, Schwald J, Michels KB. DNA methylation of candidate genes in peripheral blood from patients with type 2 diabetes or the metabolic syndrome. PLoS One 2017; 12:e0180955. [PMID: 28727822 PMCID: PMC5519053 DOI: 10.1371/journal.pone.0180955] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/23/2017] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION The prevalence of type 2 diabetes (T2D) and the metabolic syndrome (MetS) is increasing and several studies suggested an involvement of DNA methylation in the development of these metabolic diseases. This study was designed to investigate if differential DNA methylation in blood can function as a biomarker for T2D and/or MetS. METHODS Pyrosequencing analyses were performed for the candidate genes KCNJ11, PPARγ, PDK4, KCNQ1, SCD1, PDX1, FTO and PEG3 in peripheral blood leukocytes (PBLs) from 25 patients diagnosed with only T2D, 9 patients diagnosed with T2D and MetS and 11 control subjects without any metabolic disorders. RESULTS No significant differences in gene-specific methylation between patients and controls were observed, although a trend towards significance was observed for PEG3. Differential methylation was observed between the groups in 4 out of the 42 single CpG loci located in the promoters regions of the genes FTO, KCNJ11, PPARγ and PDK4. A trend towards a positive correlation was observed for PEG3 methylation with HDL cholesterol levels. DISCUSSION Altered levels of DNA methylation in PBLs of specific loci might serve as a biomarker for T2D or MetS, although further investigation is required.
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Affiliation(s)
- Sanne D. van Otterdijk
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexandra M. Binder
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America
| | - Katarzyna Szarc vel Szic
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Schwald
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States of America
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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Yanokura M, Banno K, Adachi M, Aoki D, Abe K. Genome-wide DNA methylation sequencing reveals miR-663a is a novel epimutation candidate in CIMP-high endometrial cancer. Int J Oncol 2017; 50:1934-1946. [PMID: 28440489 PMCID: PMC5435325 DOI: 10.3892/ijo.2017.3966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/26/2017] [Indexed: 12/26/2022] Open
Abstract
Aberrant DNA methylation is widely observed in many cancers. Concurrent DNA methylation of multiple genes occurs in endometrial cancer and is referred to as the CpG island methylator phenotype (CIMP). However, the features and causes of CIMP-positive endometrial cancer are not well understood. To investigate DNA methylation features characteristic to CIMP-positive endometrial cancer, we first classified samples from 25 patients with endometrial cancer based on the methylation status of three genes, i.e. MLH1, CDH1 (E-cadherin) and APC: CIMP-high (CIMP-H, 2/25, 8.0%), CIMP-low (CIMP-L, 7/25, 28.0%) and CIMP-negative (CIMP(-), 16/25, 64.0%). We then selected two samples each from CIMP-H and CIMP(-) classes, and analyzed DNA methylation status of both normal (peripheral blood cells: PBCs) and cancer tissues by genome-wide, targeted bisulfite sequencing. Genomes of the CIMP-H cancer tissues were significantly hypermethylated compared to those of the CIMP(-). Surprisingly, in normal tissues of the CIMP-H patients, promoter region of the miR-663a locus is hypermethylated relative to CIMP(-) samples. Consistent with this finding, miR-663a expression was lower in the CIMP-H PBCs than in the CIMP(-) PBCs. The same region of the miR663a locus is found to be highly methylated in cancer tissues of both CIMP-H and CIMP(-) cases. This is the first report showing that aberrant DNA methylation of the miR-663a promoter can occur in normal tissue of the cancer patients, suggesting a possible link between this epigenetic abnormality and endometrial cancer. This raises the possibility that the hypermethylation of the miR-663a promoter represents an epimutation associated with the CIMP-H endometrial cancers. Based on these findings, relationship of the aberrant DNA methylation and CIMP-H phenotype is discussed.
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Affiliation(s)
- Megumi Yanokura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Kouji Banno
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masataka Adachi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kuniya Abe
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients. PLoS One 2016; 11:e0157381. [PMID: 27300758 PMCID: PMC4907507 DOI: 10.1371/journal.pone.0157381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/27/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND AIMS Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. METHODS Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. RESULTS Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). CONCLUSIONS This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.
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20
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Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
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21
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Hitchins MP. Finding the needle in a haystack: identification of cases of Lynch syndrome with MLH1 epimutation. Fam Cancer 2016; 15:413-22. [DOI: 10.1007/s10689-016-9887-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
Genetic causes for human disorders are being discovered at an unprecedented pace. A growing subclass of disease-causing mutations involves changes in the epigenome or in the abundance and activity of proteins that regulate chromatin structure. This article focuses on research that has uncovered human diseases that stem from such epigenetic deregulation. Disease may be caused by direct changes in epigenetic marks, such as DNA methylation, commonly found to affect imprinted gene regulation. Also described are disease-causing genetic mutations in epigenetic modifiers that either affect chromatin in trans or have a cis effect in altering chromatin configuration.
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Affiliation(s)
- Huda Y Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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Short E, Thomas LE, Hurley J, Jose S, Sampson JR. Inherited predisposition to colorectal cancer: towards a more complete picture. J Med Genet 2015; 52:791-6. [PMID: 26297796 DOI: 10.1136/jmedgenet-2015-103298] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/28/2015] [Indexed: 12/14/2022]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer worldwide. Hereditary factors are important in 15%-35% of affected patients. This review provides an update on the genetic basis of inherited predisposition to CRC. Currently known genetic factors include a group of highly penetrant mutant genes associated with rare mendelian cancer syndromes and a group of common low-penetrance alleles that have been identified through genetic association studies. Additional mechanisms, which may underlie a predisposition to CRC, will be outlined, for example, variants in intermediate penetrance alleles. Recent findings, including mutations in POLE, POLD1 and NTHL1, will be highlighted, and we identify gaps in present knowledge and consider how these may be addressed through current and emerging genomic approaches. It is expected that identification of the missing heritable component of CRC will be resolved through evermore comprehensive cataloguing and phenotypic annotation of CRC-associated variants identified through sequencing approaches. This will have important clinical implications, particularly in areas such as risk stratification, public health and CRC prevention.
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Affiliation(s)
- Emma Short
- Institute of Cancer and Genetics, Cardiff University, Heath Park Campus, Cardiff, UK
| | - Laura E Thomas
- Institute of Cancer and Genetics, Cardiff University, Heath Park Campus, Cardiff, UK
| | - Joanna Hurley
- Department of Gastroenterology, Cwm Taf University Health Board, Prince Charles Hospital, Merthyr Tydfil, UK
| | - Sian Jose
- Institute of Medical Genetics, Cardiff and Vale Health Board, Cardiff, UK
| | - Julian R Sampson
- Institute of Cancer and Genetics, Cardiff University, Heath Park Campus, Cardiff, UK
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Carethers JM, Stoffel EM. Lynch syndrome and Lynch syndrome mimics: The growing complex landscape of hereditary colon cancer. World J Gastroenterol 2015; 21:9253-9261. [PMID: 26309352 PMCID: PMC4541378 DOI: 10.3748/wjg.v21.i31.9253] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/13/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) was previously synonymous with Lynch syndrome; however, identification of the role of germline mutations in the DNA mismatch repair (MMR) genes has made it possible to differentiate Lynch syndrome from other conditions associated with familial colorectal cancer (CRC). Broadly, HNPCC may be dichotomized into conditions that demonstrate defective DNA MMR and microsatellite instability (MSI) vs those conditions that demonstrate intact DNA MMR. Conditions characterized by MMR deficient CRCs include Lynch syndrome (germline MMR mutation), Lynch-like syndrome (biallelic somatic MMR mutations), constitutional MMR deficiency syndrome (biallelic germline MMR mutations), and sporadic MSI CRC (somatic biallelic methylation of MLH1). HNPCC conditions with intact DNA MMR associated with familial CRC include polymerase proofreading associated polyposis and familial colorectal cancer type X. Although next generation sequencing technologies have elucidated the genetic cause for some HNPCC conditions, others remain genetically undefined. Differentiating between Lynch syndrome and the other HNPCC disorders has profound implications for cancer risk assessment and surveillance of affected patients and their at-risk relatives. Clinical suspicion coupled with molecular tumor analysis and testing for germline mutations can help differentiate the clinical mimicry within HNPCC and facilitate diagnosis and management.
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Crucianelli F, Tricarico R, Turchetti D, Gorelli G, Gensini F, Sestini R, Giunti L, Pedroni M, Ponz de Leon M, Civitelli S, Genuardi M. MLH1 constitutional and somatic methylation in patients with MLH1 negative tumors fulfilling the revised Bethesda criteria. Epigenetics 2015; 9:1431-8. [PMID: 25437057 DOI: 10.4161/15592294.2014.970080] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lynch syndrome (LS) is a tumor predisposing condition caused by constitutional defects in genes coding for components of the mismatch repair (MMR) apparatus. While hypermethylation of the promoter of the MMR gene MLH1 occurs in about 15% of colorectal cancer samples, it has also been observed as a constitutional alteration, in the absence of DNA sequence mutations, in a small number of LS patients. In order to obtain further insights on the phenotypic characteristics of MLH1 epimutation carriers, we investigated the somatic and constitutional MLH1 methylation status of 14 unrelated subjects with a suspicion of LS who were negative for MMR gene constitutional mutations and whose tumors did not express the MLH1 protein. A novel case of constitutional MLH1 epimutation was identified. This patient was affected with multiple primary tumors, including breast cancer, diagnosed starting from the age of 55 y. Investigation of her offspring by allele specific expression revealed that the epimutation was not stable across generations. We also found MLH1 hypermethylation in cancer samples from 4 additional patients who did not have evidence of constitutional defects. These patients had some characteristics of LS, namely early age at onset and/or positive family history, raising the possibility of genetic influences in the establishment of somatic MLH1 methylation.
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Affiliation(s)
- Francesca Crucianelli
- a Medical Genetics ; Department of Biomedical ; Experimental and Clinical Sciences ; University of Florence ; Florence , Italy
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Snowsill T, Huxley N, Hoyle M, Jones-Hughes T, Coelho H, Cooper C, Frayling I, Hyde C. A systematic review and economic evaluation of diagnostic strategies for Lynch syndrome. Health Technol Assess 2015; 18:1-406. [PMID: 25244061 DOI: 10.3310/hta18580] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is an inherited autosomal dominant disorder characterised by an increased risk of colorectal cancer (CRC) and other cancers, and caused by mutations in the deoxyribonucleic acid (DNA) mismatch repair genes. OBJECTIVE To evaluate the accuracy and cost-effectiveness of strategies to identify LS in newly diagnosed early-onset CRC patients (aged < 50 years). Cascade testing of relatives is employed in all strategies for individuals in whom LS is identified. DATA SOURCES AND METHODS Systematic reviews were conducted of the test accuracy of microsatellite instability (MSI) testing or immunohistochemistry (IHC) in individuals with CRC at risk of LS, and of economic evidence relating to diagnostic strategies for LS. Reviews were carried out in April 2012 (test accuracy); and in February 2012, repeated in February 2013 (economic evaluations). Databases searched included MEDLINE (1946 to April week 3, 2012), EMBASE (1980 to week 17, 2012) and Web of Science (inception to 30 April 2012), and risk of bias for test accuracy was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) quality appraisal tool. A de novo economic model of diagnostic strategies for LS was developed. RESULTS Inconsistencies in study designs precluded pooling of diagnostic test accuracy results from a previous systematic review and nine subsequent primary studies. These were of mixed quality, with significant methodological concerns identified for most. IHC and MSI can both play a part in diagnosing LS but neither is gold standard. No UK studies evaluated the cost-effectiveness of diagnosing and managing LS, although studies from other countries generally found some strategies to be cost-effective compared with no testing. The de novo model demonstrated that all strategies were cost-effective compared with no testing at a threshold of £20,000 per quality-adjusted life-year (QALY), with the most cost-effective strategy utilising MSI and BRAF testing [incremental cost-effectiveness ratio (ICER) = £5491 per QALY]. The maximum health benefit to the population of interest would be obtained using universal germline testing, but this would not be a cost-effective use of NHS resources compared with the next best strategy. When the age limit was raised from 50 to 60 and 70 years, the ICERs compared with no testing increased but remained below £20,000 per QALY (except for universal germline testing with an age limit of 70 years). The total net health benefit increased with the age limit as more individuals with LS were identified. Uncertainty was evaluated through univariate sensitivity analyses, which suggested that the parameters substantially affecting cost-effectiveness: were the risk of CRC for individuals with LS; the average number of relatives identified per index patient; the effectiveness of colonoscopy in preventing metachronous CRC; the cost of colonoscopy; the duration of the psychological impact of genetic testing on health-related quality of life (HRQoL); and the impact of prophylactic hysterectomy and bilateral salpingo-oophorectomy on HRQoL (this had the potential to make all testing strategies more expensive and less effective than no testing). LIMITATIONS The absence of high-quality data for the impact of prophylactic gynaecological surgery and the psychological impact of genetic testing on HRQoL is an acknowledged limitation. CONCLUSIONS Results suggest that reflex testing for LS in newly diagnosed CRC patients aged < 50 years is cost-effective. Such testing may also be cost-effective in newly diagnosed CRC patients aged < 60 or < 70 years. Results are subject to uncertainty due to a number of parameters, for some of which good estimates were not identified. We recommend future research to estimate the cost-effectiveness of testing for LS in individuals with newly diagnosed endometrial or ovarian cancer, and the inclusion of aspirin chemoprevention. Further research is required to accurately estimate the impact of interventions on HRQoL. STUDY REGISTRATION This study is registered as PROSPERO CRD42012002436. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Tristan Snowsill
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Nicola Huxley
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Martin Hoyle
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Tracey Jones-Hughes
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Helen Coelho
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Chris Cooper
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
| | - Ian Frayling
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Chris Hyde
- Peninsula Technology Assessment Group (PenTAG), University of Exeter Medical School, Exeter, UK
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Castillejo A, Hernández-Illán E, Rodriguez-Soler M, Pérez-Carbonell L, Egoavil C, Barberá VM, Castillejo MI, Guarinos C, Martínez-de-Dueñas E, Juan MJ, Sánchez-Heras AB, García-Casado Z, Ruiz-Ponte C, Brea-Fernández A, Juárez M, Bujanda L, Clofent J, Llor X, Andreu M, Castells A, Carracedo A, Alenda C, Payá A, Jover R, Soto JL. Prevalence of MLH1 constitutional epimutations as a cause of Lynch syndrome in unselected versus selected consecutive series of patients with colorectal cancer. J Med Genet 2015; 52:498-502. [PMID: 25908759 DOI: 10.1136/jmedgenet-2015-103076] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/12/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND The prevalence of MLH1 constitutional epimutations in the general population is unknown. We sought to analyse the prevalence of MLH1 constitutional epimutations in unselected and selected series of patients with colorectal cancer (CRC). METHODS Patients with diagnoses of CRC (n=2123) were included in the unselected group. For comparison, a group of 847 selected patients with CRC who fulfilled the revised Bethesda guidelines (rBG) were also included. Somatic and constitutional MLH1 methylation was assayed via methylation-specific multiplex ligation-dependent probe amplification of cases lacking MLH1 expression. Germline alterations in mismatch-repair (MMR) genes were assessed via Sanger sequencing and methylation-specific multiplex ligation-dependent probe amplification. RESULTS Loss of MLH1 expression occurred in 5.5% of the unselected series and 12.5% of the selected series (p<0.0001). No constitutional epimutations in MLH1 were detected in the unselected population (0/62); five cases from the selected series were positive for MLH1 epimutations (15.6%, 5/32; p=0.004). CONCLUSIONS Our results suggest a negligible prevalence of MLH1 constitutional epimutations in unselected cases of CRC. Therefore, MLH1 constitutional epimutation analysis should be conducted only for patients who fulfil the rBG and who lack MLH1 expression with methylated MLH1.
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Affiliation(s)
- Adela Castillejo
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain
| | | | - María Rodriguez-Soler
- Research Laboratory, Alicante University Hospital, Alicante, Spain Department of Gastroenterology, Alicante University Hospital, Alicante, Spain
| | | | - Cecilia Egoavil
- Department of Pathology, Alicante University Hospital, Alicante, Spain
| | - Victor M Barberá
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain
| | | | - Carla Guarinos
- Research Laboratory, Alicante University Hospital, Alicante, Spain
| | | | - María-Jose Juan
- Hereditary Cancer Unit, Valencian Institute of Oncology, Valencia, Spain
| | | | - Zaida García-Casado
- Laboratory of Molecular Biology, Valencian Institute of Oncology, Valencia, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico Santiago de Compostela, University of Santiago de Compostela Santiago de Compostela, Santiago de Compostela, Spain
| | - Alejandro Brea-Fernández
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico Santiago de Compostela, University of Santiago de Compostela Santiago de Compostela, Santiago de Compostela, Spain
| | - Miriam Juárez
- Research Laboratory, Alicante University Hospital, Alicante, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Donostia Hospital-Instituto Biodonostia, CIBERehd, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Juan Clofent
- Section of Digestive Diseases, Internal Medicine Department, Hospital Sagunto, Sagunto, Spain
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, Department of Medicine and Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Montserrat Andreu
- Department of Gastroenterology, IMIM, Hospital del Mar, Parc de Salut Mar. Pompeu Fabra University, Barcelona, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico Santiago de Compostela, University of Santiago de Compostela Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristina Alenda
- Department of Pathology, Alicante University Hospital, Alicante, Spain
| | - Artemio Payá
- Department of Pathology, Alicante University Hospital, Alicante, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Alicante University Hospital, Alicante, Spain
| | - José-Luis Soto
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain
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28
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Cini G, Carnevali I, Quaia M, Chiaravalli AM, Sala P, Giacomini E, Maestro R, Tibiletti MG, Viel A. Concomitant mutation and epimutation of the MLH1 gene in a Lynch syndrome family. Carcinogenesis 2015; 36:452-8. [DOI: 10.1093/carcin/bgv015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/24/2015] [Indexed: 12/30/2022] Open
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Newton K, Jorgensen NM, Wallace AJ, Buchanan DD, Lalloo F, McMahon RFT, Hill J, Evans DG. Tumour MLH1 promoter region methylation testing is an effective prescreen for Lynch Syndrome (HNPCC). J Med Genet 2014; 51:789-96. [PMID: 25280751 DOI: 10.1136/jmedgenet-2014-102552] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Lynch syndrome (LS) patients have DNA mismatch repair deficiency and up to 80% lifetime risk of colorectal cancer (CRC). Screening of mutation carriers reduces CRC incidence and mortality. Selection for constitutional mutation testing relies on family history (Amsterdam and Bethesda Guidelines) and tumour-derived biomarkers. Initial biomarker analysis uses mismatch repair protein immunohistochemistry and microsatellite instability. Abnormalities in either identify mismatch repair deficiency but do not differentiate sporadic epigenetic defects, due to MLH1 promoter region methylation (13% of CRCs) from LS (4% of CRCs). A diagnostic biomarker capable of making this distinction would be valuable. This study compared two biomarkers in tumours with mismatch repair deficiency; quantification of methylation of the MLH1 promoter region using a novel assay and BRAF c.1799T>A, p.(Val600Glu) mutation status in the identification of constitutional mutations. METHODS Tumour DNA was extracted (formalin fixed, paraffin embedded, FFPE tissue) and pyrosequencing used to test for MLH1 promoter methylation and presence of the BRAF c.1799T>A, p.(Val600Glu) mutation 71 CRCs from individuals with pathogenic MLH1 mutations and 73 CRCs with sporadic MLH1 loss. Specificity and sensitivity was compared. FINDINGSS Unmethylated MLH1 promoter: sensitivity 94.4% (95% CI 86.2% to 98.4%), specificity 87.7% (95% CI 77.9% to 94.2%), Wild-type BRAF (codon 600): sensitivity 65.8% (95% CI 53.7% to 76.5%), specificity 98.6% (95% CI 92.4% to 100.0%) for the identification of those with pathogenic MLH1 mutations. CONCLUSIONS Quantitative MLH1 promoter region methylation using pyrosequencing is superior to BRAF codon 600 mutation status in identifying constitutional mutations in mismatch repair deficient tumours.
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Affiliation(s)
- K Newton
- Department of General Surgery, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK
| | - N M Jorgensen
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - A J Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - D D Buchanan
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, Queensland, Australia Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - F Lalloo
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - R F T McMahon
- Department of Histopathology, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK Manchester Medical School, University of Manchester, Manchester, UK
| | - J Hill
- Department of General Surgery, Manchester Royal Infirmary, Central Manchester University Hospitals NHS Trust, Manchester, UK
| | - D G Evans
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
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30
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Abstract
Recognition by Warthin of the familial clustering of colorectal and gynaecological cancers a century ago laid the foundation for the recognition of familial cancer. By tracking afflicted pedigrees, Lynch defined the clinical characteristics and argued for a heritable genetic component to this autosomal dominant cancer susceptibility condition, now termed Lynch syndrome. This was proven in the 1990s, with the discovery of deleterious germline mutations of the mismatch repair genes as its cause. Yet despite the genetic revolution at the turn of the twenty-first century, no pathogenic mutation was identifiable in approximately one-third of cases with suspected Lynch syndrome. In the past decade, the alternative mechanism of constitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, was identified in a proportion of these outstanding cases. This epigenetic defect, characterized by methylation and transcriptional inactivation of a single genetic allele within normal tissues, predisposes to the development of Lynch-type cancers. MSH2 and some MLH1 epimutations have been linked to genetic alterations within their vicinity and demonstrate dominant inheritance, whilst other MLH1 epimutations are reversible between generations and demonstrate non-Mendelian inheritance. This review charts the discovery of mismatch repair epimutations, their aetiological role in Lynch syndrome and the mechanistic basis for their variable inheritance patterns.
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Affiliation(s)
- Megan P Hitchins
- Adult Cancer Program, Medical Epigenetics Laboratory, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Randwick, NSW, Australia.
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31
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Affiliation(s)
- John M Carethers
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
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32
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De Lellis L, Aceto GM, Curia MC, Catalano T, Mammarella S, Veschi S, Fantini F, Battista P, Stigliano V, Messerini L, Mareni C, Sala P, Bertario L, Radice P, Cama A. Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms. PLoS One 2013; 8:e81194. [PMID: 24278394 PMCID: PMC3835792 DOI: 10.1371/journal.pone.0081194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/09/2013] [Indexed: 01/27/2023] Open
Abstract
The identification of germline variants predisposing to hereditary nonpolyposis colorectal cancer (HNPCC) is crucial for clinical management of carriers, but several probands remain negative for such variants or bear variants of uncertain significance (VUS). Here we describe the results of integrative molecular analyses in 132 HNPCC patients providing evidences for improved genetic testing of HNPCC with traditional or next generation methods. Patients were screened for: germline allele-specific expression (ASE), nucleotide variants, rearrangements and promoter methylation of mismatch repair (MMR) genes; germline EPCAM rearrangements; tumor microsatellite instability (MSI) and immunohistochemical (IHC) MMR protein expression. Probands negative for pathogenic variants of MMR genes were screened for germline APC and MUTYH sequence variants. Most germline defects identified were sequence variants and rearrangements of MMR genes. Remarkably, altered germline ASE of MMR genes was detected in 8/22 (36.5%) probands analyzed, including 3 cases negative at other screenings. Moreover, ASE provided evidence for the pathogenic role and guided the characterization of a VUS shared by 2 additional probands. No germline MMR gene promoter methylation was observed and only one EPCAM rearrangement was detected. In several cases, tumor IHC and MSI diverged from germline screening results. Notably, APC or biallelic MUTYH germline defects were identified in 2/19 probands negative for pathogenic variants of MMR genes. Our results show that ASE complements gDNA-based analyses in the identification of MMR defects and in the characterization of VUS affecting gene expression, increasing the number of germline alterations detected. An appreciable fraction of probands negative for MMR gene variants harbors APC or MUTYH variants. These results indicate that germline ASE analysis and screening for APC and MUTYH defects should be included in HNPCC diagnostic algorithms.
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Affiliation(s)
- Laura De Lellis
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
| | - Gitana Maria Aceto
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University, Chieti, Italy
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Teresa Catalano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Serena Veschi
- Unit of Molecular Pathology and Genomics, Aging Research Center, “G. d’Annunzio” University Foundation, Chieti, Italy
| | - Fabiana Fantini
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Pasquale Battista
- Department of Experimental and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Vittoria Stigliano
- Department of Gastroenterology, Unit of Hereditary Colorectal Cancer, National Cancer Institute, Regina Elena (IRE), Rome, Italy
| | - Luca Messerini
- Section of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Cristina Mareni
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Paola Sala
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucio Bertario
- Unit of Hereditary Digestive Tract Tumors, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular bases of genetic risk and genetic testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandro Cama
- Department of Pharmacy, “G. d’Annunzio” University, Chieti, Italy
- * E-mail:
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33
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Farrell MP, Hughes DJ, Drost M, Wallace AJ, Cummins RJ, Fletcher TA, Meany MA, Kay EW, de Wind N, Power DG, Andrews EJ, Green AJ, Gallagher DJ. Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity. Fam Cancer 2013; 12:741-7. [PMID: 23712482 DOI: 10.1007/s10689-013-9652-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic testing of an Irish kindred identified an exonic nucleotide substitution c.1664T>C (p.Leu555Pro) in the MLH1 mismatch repair (MMR) gene. This previously unreported variant is classified as a "variant of uncertain significance" (VUS). Immunohistochemical (IHC) analysis and microsatellite instability (MSI) studies, genetic testing, a literature and online MMR mutation database review, in silico phenotype prediction tools, and an in vitro MMR activity assay were used to study the clinical significance of this variant. The MLH1 c.1664T>C (p.Leu555Pro) VUS co-segregated with three cases of classic Lynch syndrome-associated malignancies over two generations, with consistent loss of MLH1 and PMS2 protein expression on IHC, and evidence of the MSI-High mutator phenotype. The leucine at position 555 is well conserved across a number of species, and this novel variant has not been reported as a normal polymorphism in the general population. In silico and in vitro analyses suggest that this variant may have a deleterious effect on the MLH1 protein and abrogate MMR activity. Evidence from clinical, histological, immunohistochemical, and molecular genetic data suggests that MLH1 c.1664T>C (p.Leu555Pro) is likely to be the pathogenic cause of Lynch syndrome in this family.
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Affiliation(s)
- M P Farrell
- Cancer Genetics Department, Mater Private Hospital, 73 Eccles St, Dublin 7, Ireland,
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34
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Do age-related changes in DNA methylation play a role in the development of age-related diseases? Biochem Soc Trans 2013; 41:803-7. [DOI: 10.1042/bst20120358] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA methylation is an important epigenetic mechanism in mammalian cells. It occurs almost exclusively at CpG sites and has a key role in a number of biological processes. It plays an important part in regulating chromatin structure and has been best studied for its role in controlling gene expression. In particular, hypermethylation of gene promoters which have high levels of CpG sites, known as CpG islands, leads to gene inactivation. In healthy cells, however, it appears that only a small number of genes are controlled through promoter hypermethylation, such as genes on the inactivated X-chromosome or at imprinted loci, and most promoter-associated CpG islands remain methylation-free regardless of gene expression status. However, a large body of evidence has now shown that this protection from methylation not only breaks down in a number of pathological conditions (e.g. cancer), but also already occurs during the normal process of aging. The present review focuses on the methylation changes that occur during healthy aging and during disease development, and the potential links between them. We focus especially on the extent to which the acquisition of aberrant methylation changes during aging could underlie the development of a number of important age-related pathological conditions.
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Evaluation of a new panel of six mononucleotide repeat markers for the detection of DNA mismatch repair-deficient tumours. Br J Cancer 2013; 108:2079-87. [PMID: 23652311 PMCID: PMC3670492 DOI: 10.1038/bjc.2013.213] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background: Microsatellite instability (MSI) is a molecular phenotype due to defective DNA mismatch repair (MMR) system. It is used to predict outcome of colorectal tumours and to screen tumours for Lynch syndrome (LS). A pentaplex panel composed of five mononucleotide markers has been largely recommended for determination of the MSI status. However, its sensitivity may be taken in default in occasional situations. The aim of the study was to optimise this panel for the detection of MSI. Methods: We developed an assay allowing co-amplification of six mononucleotide repeat markers (BAT25, BAT26, BAT40, NR21, NR22, NR27) and one polymorphic dinucleotide marker (D3S1260) in a single reaction. Performances of the new panel were evaluated on a cohort of patients suspected of LS. Results: We demonstrate that our assay is technically as easy to use as the pentaplex assay. The hexaplex panel shows similar performances for the identification of colorectal and non-MSH6-deficient tumours. On the other hand, the hexaplex panel has higher sensitivity for the identification of MSH6-deficient tumours (94.7% vs 84.2%) and MMR-deficient tumours other than colorectal cancer (92.9% vs 85.7%). Conclusion: The hexaplex panel could thus be an attractive alternative to the pentaplex panel for the identification of patients with LS.
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36
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Abstract
Epigenetic medicine is still in its infancy. To date, only a handful of diseases have documented epigenetic correlates upstream of gene regulation including cancer, developmental syndromes and late-onset diseases. The finding that epigenetic markers are dynamic and heterogeneous at tissue and cellular levels, combined with recent identification of a new form of functionally distinct DNA methylation has opened a wider window for investigators to pry into the epigenetic world. It is anticipated that many diseases will be elucidated through this epigenetic inquiry. In this review, we discuss the normal course of DNA methylation during development, taking alcohol as a demonstrator of the epigenetic impact of environmental factors in disease etiology, particularly the growth retardation and neurodevelopmental deficits of fetal alcohol spectrum disorders.
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Affiliation(s)
- Marisol Resendiz
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuanyuan Chen
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
| | - Nail C Öztürk
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy, Mersin University School of Medicine, Turkey
| | - Feng C Zhou
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy & Cell Biology, MS508, Indiana University School Medicine, Indianapolis, IN 46202, USA
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37
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Barrow PJ, Clancy T, Evans DG. Key genetic considerations in the management of suspected hereditary colorectal cancer. COLORECTAL CANCER 2013. [DOI: 10.2217/crc.12.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SUMMARY Hereditary bowel cancer syndromes account for up to 5% of colorectal cancer (CRC) incidence. Presentation of CRC under the age of 50 years should alert clinicians to a possible underlying genetic predisposition. This article focuses on Lynch syndrome (hereditary nonpolyposis CRC). Regular bowel screening is effective in reducing the risk of CRC and improving overall survival in Lynch syndrome families. The issues surrounding the clinical diagnostic criteria and the shortcomings of the referral process are described, and it is questioned whether a universal strategy for diagnosis should be employed. This article summarizes the evidence for the benefit of bowel screening and suggests practical steps to help ensure compliance with screening recommendations. Finally, it is discussed how collaboration between geneticists, gastroenterologists and surgeons can inform surgical decision-making for the benefit of the patient.
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Affiliation(s)
- Paul J Barrow
- Department of Genetic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Trust, Oxford Road, Manchester, M13 9WL, UK
| | - Tara Clancy
- Department of Genetic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Trust, Oxford Road, Manchester, M13 9WL, UK
| | - D Gareth Evans
- Department of Genetic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Trust, Oxford Road, Manchester, M13 9WL, UK
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Identification of constitutional MLH1 epimutations and promoter variants in colorectal cancer patients from the Colon Cancer Family Registry. Genet Med 2012; 15:25-35. [PMID: 22878509 PMCID: PMC3908650 DOI: 10.1038/gim.2012.91] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Constitutional MLH1 epimutations manifest as promoter methylation and silencing of the affected allele in normal tissues, predisposing to Lynch syndrome-associated cancers. This study investigated their frequency and inheritance. METHODS A total of 416 individuals with a colorectal cancer showing loss of MLH1 expression and without deleterious germline mutations in MLH1 were ascertained from the Colon Cancer Family Registry (C-CFR). Constitutive DNA samples were screened for MLH1 methylation in all 416 subjects and for promoter sequence changes in 357 individuals. RESULTS Constitutional MLH1 epimutations were identified in 16 subjects. Of these, seven (1.7%) had mono- or hemi-allelic methylation and eight had low-level methylation (2%). In one subject the epimutation was linked to the c.-27C>A promoter variant. Testing of 37 relatives from nine probands revealed paternal transmission of low-level methylation segregating with a c.+27G>A variant in one case. Five additional probands had a promoter variant without an MLH1 epimutation, with three showing diminished promoter activity in functional assays. CONCLUSION Although rare, sequence changes in the regulatory region of MLH1 and aberrant methylation may alone or together predispose to the development of cancer. Screening for these changes is warranted in individuals who have a negative germline sequence screen of MLH1 and loss of MLH1 expression in their tumor.Genet Med 2013:15(1):25-35.
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Relton CL, Davey Smith G. Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. Int J Epidemiol 2012; 41:161-76. [PMID: 22422451 DOI: 10.1093/ije/dyr233] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The burgeoning interest in the field of epigenetics has precipitated the need to develop approaches to strengthen causal inference when considering the role of epigenetic mediators of environmental exposures on disease risk. Epigenetic markers, like any other molecular biomarker, are vulnerable to confounding and reverse causation. Here, we present a strategy, based on the well-established framework of Mendelian randomization, to interrogate the causal relationships between exposure, DNA methylation and outcome. The two-step approach first uses a genetic proxy for the exposure of interest to assess the causal relationship between exposure and methylation. A second step then utilizes a genetic proxy for DNA methylation to interrogate the causal relationship between DNA methylation and outcome. The rationale, origins, methodology, advantages and limitations of this novel strategy are presented.
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Affiliation(s)
- Caroline L Relton
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
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40
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MLH1 methylation screening is effective in identifying epimutation carriers. Eur J Hum Genet 2012; 20:1256-64. [PMID: 22763379 DOI: 10.1038/ejhg.2012.136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Recently, constitutional MLH1 epimutations have been identified in a subset of Lynch syndrome (LS) cases. The aim of this study was the identification of patients harboring constitutional MLH1 epimutations in a set of 34 patients with a clinical suspicion of LS, MLH1-methylated tumors and non-detected germline mutations in mismatch repair (MMR) genes. MLH1 promoter methylation was analyzed in lymphocyte DNA samples by MS-MLPA (Methylation-specific multiplex ligation-dependent probe amplification). Confirmation of MLH1 constitutional methylation was performed by MS-MCA (Methylation-specific melting curve analysis), bisulfite sequencing and pyrosequencing in different biological samples. Allelic expression was determined using heterozygous polymorphisms. Vertical transmission was evaluated by MS-MLPA and haplotype analyses. MS-MLPA analysis detected constitutional MLH1 methylation in 2 of the 34 individuals whose colorectal cancers showed MLH1 methylation (5.9%). These results were confirmed by bisulfite-based methods. Both epimutation carriers had developed metachronous early-onset LS tumors, with no family history of LS-associated cancers in their first-degree relatives. In one of the cases, the identified MLH1 constitutional methylation was monoallelic and results in MLH1 and EPM2AIP1 allele-specific transcriptional silencing. It was present in normal somatic tissues and absent in spermatozoa. The methylated MLH1 allele was maternally transmitted and methylation was reversed in a daughter who inherited the same allele. MLH1 methylation screening in lymphocyte DNA from patients with early-onset MLH1-methylated LS-associated tumors allows the identification of epimutation carriers. The present study adds further evidence to the emerging entity of soma-wide MLH1 epimutation and its heritability.
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