Somatic Nonepigenetic Mismatch Repair Gene Aberrations Underly Most Mismatch Repair–Deficient Lynch-Like Tumors

Individuals with Lynch syndrome have a pathogenic germline variant in one of the mismatch repair (MMR) genes (MLH1, MSH2/EPCAM, MSH6, or PMS2) and are often recognized based on MMR-deficient (dMMR) colorectal cancers (CRCs) endometrial (ECs).1Lynch H.T. et al.Clin Genet. 2009; 76: 1-18Crossref PubMed Scopus (555) Google Scholar,2Kunitomi H. al.Oncol Lett. 2017; 14: 3297-3301Crossref (17) Scholar Approximately 15% CRCs 20%–30% ECs dMMR, mostly due to MLH1-promoter hypermethylation. dMMR tumors without hypermethylation (Lynch-like) may 2 somatic nonepigenetic MMR aberrations (somatic dMMRs).3Herman J.G. al.Proc Natl Acad Sci U S A. 1998; 95: 6870-6875Crossref (1628) Scholar, 4Mensenkamp A.R. Vogelaar I.P. al.Gastroenterology. 2014; 146: 643-646Abstract Full Text PDF (211) 5Haraldsdottir S. 147: 1308-1316Abstract (233) 6Geurts-Giele W.R. Leenen C.H. al.J Pathol. 234: 548-559Crossref (96) 7Pearlman R. Haraldsdottir Med 2019; 56: 462-470Crossref (19) Knowledge contribution syndrome–associated variants as cause for different age groups is important tumor surveillance strategies. However, percentage that missed by current methods unclear. Here, we show an unprecedented prevalence patients who were referred diagnostic testing after exclusion Study cohort 1 included individuals (N = 304) CRC EC counseled clinical geneticist at Radboudumc (Nijmegen, Netherlands) between 2009 2019. The (n 151) 130) 23) variant. consisted 125) 101) 28) which methylation excluded elsewhere only underwent mutation analysis (Supplementary Figure 1A). Thirty from study 8 insufficient material excluded. This (CMO-2018-4922) was approved local ethical committee Radboudumc. Genomic DNA extracted formalin-fixed, paraffin-embedded normal tissues (252 248 patients) analyzed targeted sequencing genes. Tumors no identified event subjected multiplex ligation-dependent probe amplification (MLPA) detect gene deletions duplications methylation-specific MLPA evaluate MSH2-, MSH6-, PMS2-promoter (for details, see Supplementary Methods). Pathogenic this Pearlman al7Pearlman mutational signature analysis. In total, performed analyses 205 47 ECs. Somatic 88.8% 80.9% (182/205) (38/47), respectively (total, 87.3%; 220/252 tumors) (Figure 1A Table 1). majority inactivating events (211/220 tumors; 95.9%), exon detected 3.6% (8/220 0.5% (1/220 tumors). Loss heterozygosity occurred more frequently MLH1 (78.3%) than other (<43.4%) 1B). To investigate distribution throughout groups, divided into 6 cohorts mean diagnosis significantly higher compared (52 vs 48 years; P < .01). Furthermore, fraction associated older 1B 1C–F). proportion differs per inactivated (P .01) 1C). For MLH1, larger (50.5% 34.7%, respectively), whereas MSH2, similar (42.0% 44.4%, most MSH6 PMS2 result (76.2% 73.9%, respectively) (51.5% 53.8%) (34.6% 30.8%) independent whether not screened before referral genetic counseling > .89). Next, investigated, means analysis, general mechanism underlies collective pattern CRCs, but did identify single responsible process 1G). (87.3% Whereas inactivation can be using sequencing, harbor sequencing. Unexpectedly, presented methylation, which, best our knowledge, has been described before. minority tumors, might missing stay undetected techniques used. general, diagnosed tumors. Their likely underestimated, because Netherlands, 69 years irrespective status. 70 years, shown occur 4.5 times dMMR.8Vos J.R. al.International Journal Cancer. 2020; 2150-2158Crossref (8) Especially young it remains interest determine these mutations. common investigated. conclude, absence caused aberrations. These findings indicate yield high reduces number remain uncertain about their susceptibility testing. Therefore, combined testing, potentially including promoter-methylation -exon deletions, should considered eligible authors thank all participants. would like Evelien Hoenselaar, Neeltje Arts, Hanneke Volleberg-Gorissen, Monique Goossens. Sandra Hendriks-Cornelissen, Mandy Hermsen, contributions project. Dutch LS-like group (alphabetical order): Fonnet E. Bleeker, Antoni van Leeuwenhoek Hospital; Charlotte J. Dommering, Amsterdam University Medical Centers; Mirjam M. de Jong, Center Groningen; Nicoline Hoogerbrugge, Rachel der Post, Brigit Wapstra, Radboud university medical center; Edward Leter, Maastricht Center+; Tom G.W. Letteboer, Utrecht; Maartje Nielsen, Leiden Center. Lisa Elze, MSc (Data curation: Equal; Formal analysis: Investigation: Validation: Writing – original draft: review & editing: Equal); Arjen Mensenkamp, PhD Iris D. Nagtegaal, MD, Wendy Zelst-Stams, Resources: Richarda M, Voer, (Conceptualization: Supervision: Marjolijn J.L. Ligtenberg, Equal). Immunohistochemistry detection MLH1-deficient (MS-MLPA) (MRC-Holland) standard procedures during routine procedures. categorized immunohistochemical deficient (loss staining), MSH2 staining). white blood cells tissue. (NM_000249.3), (NM_000251.2), (NM_000179.2), (NM_000535.5) sequenced Sanger- AmpliSeq-based (Life Technologies, Bleiswijk, according manufacturer’s instructions and/or single-molecule molecular inversion probe–based next-generation previously.1Eijkelenboom Mol Diagn. 2016; 18: 851-863Abstract (64) 2Mensenkamp (218) 3de Voer Diets I. Post Gastroenterol Hepatol.2021Google Sanger ion semiconductor resequenced Sequence primers probes available upon request. matched tissue EPCAM, MS-MLPA reveal promoter MRC-Holland SALSA mix assays instructions. when following type combinations tissue: (1) (likely) mutations gene, (2) loss (LOH) same (3) unknown significance either LOH (4) needed fulfill criteria defined event: event, LOH, least presumed subclonal event. pathogenic-variant benign variants, variants. distributions 4 2. Only first each patient included. One comparison. nature second hit analyzed. Sequencing changes variant, complete compared. Six built compare diagnosis. microsatellite instable specific status unknown. ascertained Clinical Genetic screening. Over used refer changed less stringent criteria. found Additionally, al4Pearlman (22) third cohort. Mutational R package DeconstructSigs tool.5Rosenthal al.Genome Biol. 17: 31Crossref (440) characteristics mutated summarized mean. 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