Constitutional MLH1 Methylation Is a Major Contributor to Mismatch Repair–Deficient, MLH1-Methylated Colorectal Cancer in Patients Aged 55 Years and Younger

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Megan P. Hitchins Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, California
Department of Medicine (Oncology), Stanford University, Stanford, California

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Estela Dámaso Department of Medicine (Oncology), Stanford University, Stanford, California
Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain

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Rocio Alvarez Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, California

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Lisa Zhou Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, California

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Yajing Hu Department of Medicine (Oncology), Stanford University, Stanford, California

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Marcio A. Diniz Biostatistics and Bioinformatics Research Center, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California

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Marta Pineda Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain
Consortium for Biomedical Research in Cancer – CIBERONC, Carlos III Institute of Health, Madrid, Spain

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Gabriel Capella Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L’Hospitalet de Llobregat, Barcelona, Spain
Consortium for Biomedical Research in Cancer – CIBERONC, Carlos III Institute of Health, Madrid, Spain

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Rachel Pearlman Department of Internal Medicine, Ohio State University, Columbus, Ohio
The Comprehensive Cancer Center, Ohio State University, Columbus, Ohio

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Heather Hampel Department of Internal Medicine, Ohio State University, Columbus, Ohio
The Comprehensive Cancer Center, Ohio State University, Columbus, Ohio
Division of Clinical Cancer Genomics, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California

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Background: Most mismatch repair–deficient (MMRd) colorectal cancer (CRC) cases arise sporadically, associated with somatic MLH1 methylation, whereas approximately 20% have germline mismatch repair pathogenic variants causing Lynch syndrome (LS). Universal screening of incident CRC uses presence of MLH1 methylation in MMRd tumors to exclude sporadic cases from germline testing for LS. However, this overlooks rare cases with constitutional MLH1 methylation (epimutation), a poorly recognized mechanism for LS. We aimed to assess the frequency and age distribution of constitutional MLH1 methylation among incident CRC cases with MMRd, MLH1-methylated tumors. Methods: In retrospective population-based studies, we selected all CRC cases with MMRd, MLH1-methylated tumors, regardless of age, prior cancer, family history, or BRAF V600E status, from the Columbus-area HNPCC study (Columbus) and Ohio Colorectal Cancer Prevention Initiative (OCCPI) cohorts. Blood DNA was tested for constitutional MLH1 methylation by pyrosequencing and real-time methylation-specific PCR, then confirmed with bisulfite-sequencing. Results: Results were achieved for 95 of 98 Columbus cases and all 281 OCCPI cases. Constitutional MLH1 methylation was identified in 4 of 95 (4%) Columbus cases, ages 34, 38, 52, and 74 years, and 4 of 281 (1.4%) OCCPI cases, ages 20, 34, 50, and 55 years, with 3 showing low-level mosaic methylation. Mosaicism in blood and normal colon, plus tumor loss of heterozygosity of the unmethylated allele, demonstrated causality in 1 case with sample availability. Age stratification showed high rates of constitutional MLH1 methylation among younger patients. In the Columbus and OCCPI cohorts, respectively, these rates were 67% (2 of 3) and 25% (2 of 8) of patients aged <50 years but with half of the cases missed, and 75% (3 of 4) and 23.5% (4 of 17) of patients aged ≤55 years with most cases detected. Conclusions: Although rare overall, a significant proportion of younger patients with MLH1-methylated CRC had underlying constitutional MLH1 methylation. Routine testing for this high-risk mechanism is warranted in patients aged ≤55 years for a timely and accurate molecular diagnosis that will significantly alter their clinical management while minimizing additional testing.

Submitted July 22, 2022; final revision received March 3, 2023; accepted for publication March 9, 2023.

Author contributions: Study design: Hitchins, Hampel. Data generation and analyses: Hitchins, Dámaso, Alvarez, Zhou, Hu, Pearlman, Hampel. Statistical analyses: Hitchins, Diniz. Results interpretation: Hitchins, Diniz, Pineda, Capella, Pearlman, Hampel. Manuscript preparation and review: All authors.

Disclosures: H. Hampel has disclosed serving on an advisory board for Invitae Genetics, Genome Medical, Natera, and Promega; serving as a consultant for 23andMe, GI OnDemand, and AIM Specialty Health; and owning stock or having an ownership interest in Genome Medical and GI OnDemand. The remaining authors have disclosed that they have not received any financial considerations from any person or organization to support the preparation, analysis, results, or discussion of this article.

Funding: Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award numbers CA218342 (M.P. Hitchins), as well as CA67941 and CA16058 (H. Hampel); the Cedars-Sinai Medical Center Precision Health Initiative (M.P. Hitchins); Ministerio de Economía y Competitividad (EEBB-I-16-11581, E. Dámaso); and the Spanish Ministry of Science (PID2019-111254RB-I00, M. Pineda; SAF2015-68016-R, G. Capella).

Disclaimer: The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Correspondence: Megan P. Hitchins, PhD, Cedars-Sinai Medical Center, 8687 Melrose Avenue, Suite 230.84 B (East), West Hollywood, CA 90069. Email: megan.hitchins@cshs.org

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