Lynch Syndrome Genetics and Clinical Implications

Lynch syndrome (LS) is one of the most prevalent hereditary cancer syndromes in humans and accounts for some 3% of unselected patients with colorectal or endometrial cancer and 10%–15% of those with DNA mismatch repair–deficient tumors. Previous studies have established the genetic basis of LS predisposition, but there have been significant advances recently in the understanding of the molecular pathogenesis of LS tumors, which has important implications in clinical management. At the same time, immunotherapy has revolutionized the treatment of advanced cancers with DNA mismatch repair defects. We aim to review the recent progress in the LS field and discuss how the accumulating epidemiologic, clinical, and molecular information has contributed to a more accurate and complete picture of LS, resulting in genotype- and immunologic subtype–specific strategies for surveillance, cancer prevention, and treatment. Lynch syndrome (LS) is one of the most prevalent hereditary cancer syndromes in humans and accounts for some 3% of unselected patients with colorectal or endometrial cancer and 10%–15% of those with DNA mismatch repair–deficient tumors. Previous studies have established the genetic basis of LS predisposition, but there have been significant advances recently in the understanding of the molecular pathogenesis of LS tumors, which has important implications in clinical management. At the same time, immunotherapy has revolutionized the treatment of advanced cancers with DNA mismatch repair defects. We aim to review the recent progress in the LS field and discuss how the accumulating epidemiologic, clinical, and molecular information has contributed to a more accurate and complete picture of LS, resulting in genotype- and immunologic subtype–specific strategies for surveillance, cancer prevention, and treatment. Minna NyströmView Large Image Figure ViewerDownload Hi-res image Download (PPT)Jukka-Pekka MecklinView Large Image Figure ViewerDownload Hi-res image Download (PPT)Toni T. SeppäläView Large Image Figure ViewerDownload Hi-res image Download (PPT) Lynch syndrome (LS) represents an autosomal dominant predisposition to colorectal carcinoma (CRC), endometrial carcinoma (EC), and other cancers because of defective DNA mismatch repair (dMMR). The history of the syndrome dates back to 1895, when Dr Warthin started to collect information on the first LS family later, designated Family G.1Lynch H.T. Snyder C.L. Shaw T.G. et al.The history of Lynch syndrome.Nat Rev Cancer. 2015; 15: 181-194Crossref PubMed Google Scholar The stringent Amsterdam criteria,2Vasen H.F. Mecklin J.P. Khan P.M. Lynch H.T. The International Collaborative Group on Hereditary Non-Polyposis Colorectal Cancer (ICG-HNPCC).Dis Colon Rectum. 1991; 34: 424-425Crossref PubMed Google Scholar,3Vasen H.F. Watson P. Mecklin J.P. Lynch H.T. New clinical criteria for hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) proposed by the international collaborative group on HNPCC.Gastroenterology. 1999; 116: 1453-1456Abstract Full Text Full Text PDF PubMed Scopus (2089) Google Scholar which require 3 or more family members diagnosed with an LS-associated cancer at an early age, were formulated to guide the selection of families for molecular studies. These and the less stringent Bethesda criteria4Umar A. Boland C.R. Terdiman J.P. et al.Revised Bethesda guidelines for hereditary non-polyposis colorectal cancer (Lynch syndrome) and microsatellite instability.J Natl Cancer Inst. 2004; 96: 261-268Crossref PubMed Google Scholar facilitate recognition of LS in the clinical setting. The discovery of the 4 LS-associated DNA mismatch repair (MMR) genes—MSH2, MLH1, MSH6, and PMS2—in 1993–1995 marks the beginning of the molecular era of LS.5Peltomäki P. Lynch syndrome genes.Fam Cancer. 2005; 4: 227-232Crossref PubMed Scopus (197) Google Scholar Definitive diagnosis of LS requires the identification of a pathogenic or likely pathogenic constitutional variant affecting one of the MMR genes (or EPCAM), and the term LS is currently restricted to cases fulfilling this molecular definition. dMMR often results in absent MMR protein(s) and microsatellite instability (MSI) in tumor tissue, providing valuable shortcuts to the identification of LS among consecutive patients with CRC or EC. This so-called universal tumor screening followed by constitutional testing has led to an estimate of some 3% of CRCs6Moreira L. Balaguer F. Lindor N. et al.Identification of Lynch syndrome among patients with colorectal cancer.JAMA. 2012; 308: 1555-1565Crossref PubMed Scopus (376) Google Scholar and a roughly similar proportion of ECs7Hampel H. Frankel W. Panescu J. et al.Screening for Lynch syndrome (hereditary nonpolyposis colorectal cancer) among endometrial cancer patients.Cancer Res. 2006; 66: 7810-7817Crossref PubMed Scopus (495) Google Scholar being attributable to LS. Recent studies applying hereditary cancer panel testing to patients with unselected CRC8Yurgelun M.B. Kulke M.H. Fuchs C.S. et al.Cancer susceptibility gene mutations in individuals with colorectal cancer.J Clin Oncol. 2017; 35: 1086-1095Crossref PubMed Scopus (269) Google Scholar or EC9Ring K.L. Bruegl A.S. Allen B.A. et al.Germline multi-gene hereditary cancer panel testing in an unselected endometrial cancer cohort.Mod Pathol. 2016; 29: 1381-1389Abstract Full Text Full Text PDF PubMed Scopus (68) Google Scholar without prior tumor-based screening arrived at estimates of 3% and 6% of LS among all CRCs and ECs, respectively. Using nuclear families of nearly 6000 incident CRC cases recruited irrespective of family history from population-based cancer registries, Win et al10Win A.K. Jenkins M.A. Dowty J.G. et al.Prevalence and penetrance of major genes and polygenes for colorectal cancer.Cancer Epidemiol Biomarkers Prev. 2017; 26: 404-412Crossref PubMed Scopus (227) Google Scholar estimated that 1 in 279 individuals (0.359%) could be carriers of pathogenic variants of any MMR gene in the US, Canadian, and Australian populations. In a gene-specific analysis, PMS2 and MSH6 were associated with the highest population prevalences, 1 in 714 (0.140%) and 1 in 758 (0.132%), respectively, compared with MLH1 (1 in 1946 [0.051%]) and MSH2 (1 in 2841 [0.035%]).10Win A.K. Jenkins M.A. Dowty J.G. et al.Prevalence and penetrance of major genes and polygenes for colorectal cancer.Cancer Epidemiol Biomarkers Prev. 2017; 26: 404-412Crossref PubMed Scopus (227) Google Scholar The finding reflects lower penetrance of PMS2 and MSH6 compared to MLH1 and MSH2. Accordingly, enrichment of founder variants in PMS2 and MSH6 resulted in a high LS carrier frequency (1 in 226 [0.442%]) in the Icelandic population.11Haraldsdottir S. Rafnar T. Frankel W.L. et al.Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2.Nat Commun. 2017; 814755Crossref PubMed Scopus (67) Google Scholar Population frequencies of even up to 1 in 100 have been suggested.12Frankel W.L. Arends M.J. Frayling I.M. et al.Lynch syndrome.in: Arends M.J. Carniero F. Lax S.F. Digestive system tumours. 5th ed. International Agency for Research on Cancer, Lyon, France2019: 515-521Google Scholar These figures make LS the most common form of hereditary CRC and probably the most prevalent single-gene cause of cancer predisposition overall. Phenotypes associated with constitutional variants of MMR genes depend on heterozygosity vs homozygosity for the predisposing defects (Table 1). Heterozygous variants of MLH1, MSH2, MSH6, and PMS2 underlie LS predisposition.13Thompson B.A. Spurdle A.B. Plazzer J.P. et al.Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.Nat Genet. 2014; 46: 107-115Crossref PubMed Scopus (351) Google Scholar,14Mendelian Inheritance in Man. Available at.https://omim.orgDate accessed: June 20, 2022Google Scholar Rarely, genomic deletions of the 3′ end of EPCAM may cause LS predisposition through epigenetic inactivation of a structurally intact MSH2.15Ligtenberg M.J.L. Kuiper R.P. Chan T.L. et al.Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1.Nat Genet. 2009; 41: 112-117Crossref PubMed Scopus (587) Google Scholar Muir–Torre syndrome may accompany LS.16South C.D. Hampel H. Comeras I. et al.The frequency of Muir-Torre syndrome among Lynch syndrome families.J Natl Cancer Inst. 2008; 100: 277-281Crossref PubMed Scopus (132) Google Scholar LS also covers part of Turcot syndrome17Therkildsen C. Ladelunda S. Rambech E. et al.Glioblastomas, astrocytomas and oligodendrogliomas linked to Lynch syndrome.Eur J Neurol. 2015; 22: 717-724Crossref PubMed Scopus (44) Google Scholar as a phenotypic variant (Table 1). In rare instances (∼200 cases reported), pathogenic constitutional variants in any 1 of the 4 LS-associated MMR genes (or 3′ untranslated region deletions of EPCAM) may occur at a homozygous or compound heterozygous state. This results in a distinct syndrome called constitutional mismatch repair deficiency (CMMRD).18Wimmer K. Etzler J. Constitutional mismatch repair-deficiency syndrome: have we so far seen only the tip of an iceberg?.Hum Genet. 2008; 124: 105-122Crossref PubMed Scopus (214) Google Scholar, 19Bodo S. Colas C. Buhard O. et al.Diagnosis of constitutional mismatch repair-deficiency syndrome based on microsatellite instability and lymphocyte tolerance to methylating agents.Gastroenterology. 2015; 149: 1017-1029Abstract Full Text Full Text PDF PubMed Google Scholar, 20Aronson M. Colas C. Shuen A. et al.Diagnostic criteria for constitutional mismatch repair deficiency (CMMRD): recommendations from the international consensus working group.J Med Genet. 2022; 59: 318-327Crossref PubMed Scopus (0) Google Scholar The predominant genes underlying CMMRD are PMS2 and MSH6, possibly reflecting higher population prevalence and lower penetrance (better tolerability) of their variants compared to MLH1 and MSH2.18Wimmer K. Etzler J. Constitutional mismatch repair-deficiency syndrome: have we so far seen only the tip of an iceberg?.Hum Genet. 2008; 124: 105-122Crossref PubMed Scopus (214) Google ScholarTable 1LS and Related PhenotypesSyndromeMIM numberaPhenotype number in MIM.14Susceptibility genesMode of inheritanceClinical featuresLSbShares of MLH1, MSH2, MSH6, and PMS2 variants are based on a total of 2105 variants of classes 3–5 reported in Thompson et al.13609310MLH1 (41%)ADColonic and extracolonic cancers of a defined spectrum3Vasen H.F. Watson P. Mecklin J.P. Lynch H.T. New clinical criteria for hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) proposed by the international collaborative group on HNPCC.Gastroenterology. 1999; 116: 1453-1456Abstract Full Text Full Text PDF PubMed Scopus (2089) Google Scholar and occurring earlier than in the average population (at ∼40–60 years of age)120435MSH2 (36%)614350MSH6 (18%)614337PMS2 (5%)185535EPCAM (rare)Muir–Torre syndrome158320Mostly MSH2 and MLH1ADMultiple sebaceous gland adenomas co-occurring with visceral malignancies, such as colorectal carcinomaTurcot syndrome—See LS and CMMRDAD or ARcTurcot syndrome may arise as a variant of LS (dominant) or CMMRD (recessive). It may also arise from constitutional defects of APC (MIM no. 175100), in which case the transmission pattern is dominant.Primary brain tumors co-occurring with multiple colorectal adenomasCMMRD276300Mostly PMS2 and MSH6ARChildhood cancers, mainly hematologic malignancies and/or brain tumors, signs of neurofibromatosis type 1 (café-au-lait spots), combined with early-onset colorectal cancers and polyposisAD, autosomal dominant; AR, autosomal recessive; MIM, Mendelian Inheritance in Man.a Phenotype number in MIM.14Mendelian Inheritance in Man. Available at.https://omim.orgDate accessed: June 20, 2022Google Scholarb Shares of MLH1, MSH2, MSH6, and PMS2 variants are based on a total of 2105 variants of classes 3–5 reported in Thompson et al.13Thompson B.A. Spurdle A.B. Plazzer J.P. et al.Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.Nat Genet. 2014; 46: 107-115Crossref PubMed Scopus (351) Google Scholarc Turcot syndrome may arise as a variant of LS (dominant) or CMMRD (recessive). It may also arise from constitutional defects of APC (MIM no. 175100), in which case the transmission pattern is dominant. Open table in a new tab AD, autosomal dominant; AR, autosomal recessive; MIM, Mendelian Inheritance in Man. The primary responsibility of the MMR system is to correct errors that arise during DNA replication and recombination—a function critical for cancer avoidance.21Jiricny J. Postreplicative mismatch repair.Cold Spring Harb Perspect Biol. 2013; 5: a012633Crossref PubMed Scopus (0) Google Scholar In humans, 5 MutS homologues (MSH2, MSH6, MSH3, MSH4, and MSH5) and 4 MutL homologues (MLH1, PMS2, PMS1, and MLH3) exist, 6 of which function in MMR (Figure 1). The main mismatch-binding factor in humans (h) is hMuSα, a heterodimer of MSH2 and MSH6. Another mismatch-recognition complex is hMutSβ formed by MSH2 and MSH3. MSH6 is required for the correction of single base mispairs and 1–2 nucleotide insertion–deletion loops, and both MSH3 and MSH6 may participate in the correction of insertion–deletion loops larger than 2 nucleotides. The MSH proteins are in the resting state in the adenosine diphosphate–bound form. Adenosine triphosphate–bound hMutSα or hMutSβ undergoes a conformational change into a clamp that moves along the DNA to signal to the additional components of the MMR machinery.22Fishel R. Mismatch repair.J Biol Chem. 2015; 290: 26395-26403Abstract Full Text Full Text PDF PubMed Scopus (141) Google Scholar MLH1 and PMS2 (the latter is a homologue of yeast PMS1) form hMutLα, which coordinates the interplay between the mismatch-recognition complex and other proteins necessary for MMR (Figure 1). Although hMutLα is the main hMutL heterodimer, MLH1 can also complex with MLH3 (hMutLγ) and PMS1 (hMutLβ). PMS2 is primarily required for the correction of single base mispairs, whereas MLH3 may contribute to the repair of insertion–deletion loops and, additionally, the correction of mismatches if PMS2 is absent.23Cannavo E. Marra G. Sabates-Bellver J. et al.Expression of the MutL homologue hMLH3 in human cells and its role in DNA mismatch repair.Cancer Res. 2005; 65: 10759-10766Crossref PubMed Scopus (94) Google Scholar The hMutLβ complex does not seem to participate in MMR. Unlike Escherichia coli, whose MMR is methyl directed (a transient lack of methylation identifies the nascent strand), DNA replication-associated daughter strand nicks that direct asymmetric loading of proliferating cell nuclear antigen likely mediate strand discrimination in eukaryotes.24Putnam C.D. Strand discrimination in DNA mismatch repair.DNA Repair (Amst). 2021; 105103161Crossref PubMed Scopus (9) Google Scholar Upon encountering a strand discontinuity, the hMutS–hMutL complex recruits excision machinery, and degradation of the error-containing fragment and synthesis of a new strand follow. Defective MMR results in length variation of short tandem nucleotide repeats, microsatellites (MSI). MSI is a hallmark of LS and up to 30% of sporadic cancers of various organs.25Hause R.J. Pritchard C.C. Shendure J. Salipante S.J. Classification and characterization of microsatellite instability across 18 cancer types.Nat Med. 2016; 22: 1342-1350Crossref PubMed Scopus (499) Google Scholar Different substrate preferences of individual MMR proteins may explain different MSI phenotypes resulting from MMR gene defects.26Carethers J.M. Hereditary, sporadic and metastatic colorectal cancer are commonly driven by specific spectrums of defective DNA mismatch repair components.Trans Am Clin Climatol Assoc. 2016; 127: 81-94PubMed Google Scholar MSH2, MLH1, or PMS2 inactivation is associated with high-degree MSI (MSI-H) with mononucleotide, dinucleotide, and other short tandem repeats affected. MSH6 inactivation mainly results in mononucleotide repeat instability. MSH3 (hMutSβ) dysfunction may lead to a distinct form of MSI called elevated microsatellite alterations at selected tetranucleotide repeats, also seen in tumors from carriers of biallelic MSH3 constitutional defects.27Adam R. Spier I. Zhao B. et al.Exome sequencing identifies biallelic MSH3 germline mutations as a recessive subtype of colorectal adenomatous polyposis.Am J Hum Genet. 2016; 99: 337-351Abstract Full Text Full Text PDF PubMed Scopus (148) Google Scholar Whether MLH3 inactivation results in a specific type of MSI or not is unclear. Tumors from biallelic MLH3 variant carriers showed no instability at mono-, di-, tri-, or tetranucleotide repeats.28Olkinuora A. Nieminen T.T. Mårtensson E. et al.Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition.Genet Med. 2019; 21: 1868-1873Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar If correction of replication errors is not possible, MMR proteins signal DNA damage to cell cycle arrest or apoptosis.29Li Z. Pearlman A.H. Hsieh P. DNA mismatch repair and the DNA damage response.DNA Repair (Amst). 2016; 38: 94-101Crossref PubMed Scopus (0) Google Scholar The MMR system also blocks recombination between related but nonidentical (homeologous) sequences, acting as a barrier to chromosomal rearrangements.30George C.M. Alani E. Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA.Crit Rev Biochem Mol Biol. 2012; 47: 297-313Crossref PubMed Scopus (0) Google Scholar Under certain circumstances, MMR proteins can promote sequence alterations. Inferred from yeast studies, the MLH1–MLH3 complex (hMutLγ) and the MSH4–MSH5 complex (hMutSγ) facilitate meiotic crossover between homologous chromosomes.31Pannafino G. Alani E. Coordinated and independent roles for MLH subunits in DNA repair.Cells. 2021; 10: 948Crossref PubMed Scopus (3) Google Scholar PMS1 (yeast MLH2), too, functions in meiosis. The MLH1–PMS1 complex (hMutLβ) limits the length of the gene conversion tract in meiotic recombination.31Pannafino G. Alani E. Coordinated and independent roles for MLH subunits in DNA repair.Cells. 2021; 10: 948Crossref PubMed Scopus (3) Google Scholar When the MMR system recognizes mismatches outside replication, strand discrimination between the old and new DNA is lost, and the MMR proteins can act mutagenically and contribute to trinucleotide repeat expansion.32Manley K. Shirley T.L. Flaherty L. Messer A. Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice.Nat Genet. 1999; 23: 471-473Crossref PubMed Scopus (316) Google Scholar,33Wheeler V.C. Dion V. Modifiers of CAG/CTG repeat instability: insights from mammalian models.J Huntingtons Dis. 2021; 10: 123-148Crossref PubMed Scopus (24) Google Scholar Counterintuitively, trinucleotide repeat expansion requires MMR proficiency (pMMR). MLH1 and MSH2 are the most important predisposing genes for LS (Table 1), which is compatible with the fact that their products are obligatory components in all types of MMR protein heterodimers, whereas MSH6 is redundant with MSH3 and PMS2 is redundant with MLH3 (Figure 1). There is no convincing evidence that heterozygous variants of MSH3 or MLH3 would underlie LS predisposition. Interestingly, homozygous variants of these genes cause susceptibility to adenomatous polyposis with possible features of CMMRD, highlighting the dosage dependency of phenotypes associated with MMR gene defects.27Adam R. Spier I. Zhao B. et al.Exome sequencing identifies biallelic MSH3 germline mutations as a recessive subtype of colorectal adenomatous polyposis.Am J Hum Genet. 2016; 99: 337-351Abstract Full Text Full Text PDF PubMed Scopus (148) Google Scholar,28Olkinuora A. Nieminen T.T. Mårtensson E. et al.Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition.Genet Med. 2019; 21: 1868-1873Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar There are no reports of LS-associated constitutional defects of PMS1, MSH4, or MSH5, which agrees with the primary role of these genes in meiotic recombination rather than MMR. A functional MMR system needs to produce MMR proteins, transport them to the nucleus, form appropriate protein complexes at the site of the DNA mismatch, and perform the actual MMR. LS-predisposing MMR gene alterations are pathogenic through the loss of any one of these functions (often several of them), which typically results from nonsense or frameshift changes. The share of missense alterations that lead to single amino acid substitutions is also significant (30%–60%) for all 4 LS-associated MMR genes.34Peltomäki P. Update on Lynch syndrome genomics.Fam Cancer. 2016; 15: 385-393Crossref PubMed Scopus (98) Google Scholar Nonsense and frameshift alterations, canonical splice site changes, and deletions of a single exon or multiple exons generally disrupt gene function and are therefore pathogenic. Although multiple in silico tools exist to predict the pathogenicity of missense alterations,35Thompson B.A. Greenblatt M.S. Vallee M.P. et al.Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions.Hum Mutat. 2013; 34: 255-265Crossref PubMed Scopus (74) Google Scholar verification by laboratory assays,36Kansikas M. Kariola R. Nyström M. Verification of the three-step model in assessing the pathogenicity of mismatch repair gene variants.Hum Mutat. 2011; 32: 107-115Crossref PubMed Google Scholar,37Jia X. Burugula B.B. Chen V. et al.Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk.Am J Hum Genet. 2021; 108: 163-175Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar and including tests for aberrant splicing,38Thompson B.A. Martins A. Spurdle A.B. A review of mismatch repair gene transcripts: issues for interpretation of mRNA splicing assays.Clin Genet. 2015; 87: 100-108Crossref PubMed Scopus (18) Google Scholar is necessary. Characteristics of a sequence variant combined with clinical and family features have led to a 5-tiered classification13Thompson B.A. Spurdle A.B. Plazzer J.P. et al.Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.Nat Genet. 2014; 46: 107-115Crossref PubMed Scopus (351) Google Scholar,39Richards S. Aziz N. Bale S. et al.Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Genet Med. 2015; 17: 405-424Abstract Full Text Full Text PDF PubMed Scopus (15018) Google Scholar to interpret sequence variants of disease-associated genes for clinical purposes. Variants belonging to class 1 (benign) or 2 (likely benign) are considered harmless and require no special attention. Class 3 is for variants of uncertain significance, and clinical management is case by case. Class 4 (likely pathogenic) or 5 (pathogenic) indicates that the variant is deleterious, warranting surveillance according to high-risk guidelines and enabling predictive testing of at-risk relatives. LS individuals typically inherit their predisposing variants from one of their parents, and de novo alterations are rare (2.3%).40Win A.K. Jenkins M.A. Buchanan D.D. et al.Determining the frequency of de novo germline mutations in DNA mismatch repair genes.J Med Genet. 2011; 48: 530-534Crossref PubMed Scopus (34) Google Scholar Ancestral founding changes predominate in some populations and account for more than half of all LS families.41Ponti G. Castellsague E. Ruini C. et al.Mismatch repair genes founder mutations and cancer susceptibility in Lynch syndrome.Clin Genet. 2015; 87: 507-516Crossref PubMed Scopus (44) Google Scholar The extent of haplotype conservation in carriers of founding changes provides a tool to estimate the age of such alterations. Thus, a 3.5-kb genomic deletion of MLH1 exon 16 unique to Finnish LS families started to spread 400–1075 years ago.42Moisio A.-L. Sistonen P. Weissenbach J. et al.Age and origin of two common MLH1 mutations predisposing to hereditary colon cancer.Am J Hum Genet. 1996; 59: 1243-1251PubMed Google Scholar A 20-kb deletion in MSH2 exons 1–6 characteristic of North American LS families may be 500 years old.43Clendenning M. Baze M.E. Sun S. et al.Origins and prevalence of the American founder mutation of MSH2.Cancer Res. 2008; 68: 2145-2153Crossref PubMed Scopus (32) Google Scholar These 2 founder changes additionally illustrate richness of the MMR gene regions in Alu- and other repeats. Recombination events mediated by such repeats explain why some 10%–20% of all LS-associated changes are large genomic rearrangements.44van der Klift H. Wijnen J. Wagner A. et al.Molecular characterization of the spectrum of genomic deletions in the mismatch repair genes MSH2, MLH1, MSH6, and PMS2 responsible for hereditary nonpolyposis colorectal cancer (HNPCC).Genes Chrom Cancer. 2005; 44: 123-138Crossref PubMed Scopus (0) Google Scholar All EPCAM alterations responsible for LS predisposition consist of large genomic deletions of the 3′ end of the gene leading to the removal of the stop codon, and Alu-mediated recombination plays a major role in their origin.45Kuijper R.P. Vissers L.E. Venkatachalam R. et al.Recurrence and variability of germline EPCAM deletions in Lynch syndrome.Hum Mutat. 2011; 32: 407-414Crossref PubMed Scopus (125) Google Scholar Constitutional hypermethylation at the promoter of one allele of MLH1 or MSH2 can lead to silencing of expression from that allele in all main somatic tissues, causing susceptibility to colorectal and extracolonic cancers typical of LS. Epimutation can be primary (no apparent cause for hypermethylation identifiable) or secondary (induced by genetic alteration). Primary and secondary epimutations of MLH1 may account for 1%–10% of unexplained Lynch-suspected families with silenced MLH1 expression in tumors.46Gylling A. Ridanpää M. Vierimaa O. et al.Large genomic rearrangements and germline epimutations in Lynch syndrome.Int J Cancer. 2009; 124: 2333-2340Crossref PubMed Scopus (53) Google Scholar, 47Niessen R.C. Hofstra R.M.W. Westers H. et al.Germline hypermethylation of MLH1 and EPCAM deletions are a frequent cause of Lynch syndrome.Genes Chromosomes Cancer. 2009; 48: 737-744Crossref PubMed Scopus (157) Google Scholar, 48Ward R.L. Dobbins T. Lindor N.M. et al.Identification of constitutional MLH1 epimutations and promoter variants in colorectal cancer patients from the Colon Cancer Family Registry.Genet Med. 2013; 15: 25-35Abstract Full Text Full Text PDF PubMed Scopus (63) Google Scholar, 49Morak M. Ibisler A. Keller G. et al.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: 240-248Crossref PubMed Scopus (19) Google Scholar Constitutional MLH1 epimutations are rare among unselected CRC patients.50Castillejo A. Hernández-Illán E. Rodriguez-Soler M. et al.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: 498-502Crossref PubMed Scopus (24) Google Scholar Secondary epimutation caused by deletions of the 3′ end of the upstream EPCAM gene is the only known type of constitutional epimutation for MSH2. After removal of the stop codon, transcription of EPCAM reads into the adjacent, structurally normal MSH2 gene, inducing its promoter methylation.15Ligtenberg M.J.L. Kuiper R.P. Chan T.L. et al.Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1.Nat Genet. 2009; 41: 112-117Crossref PubMed Scopus (587) Google Scholar Secondary epimutations of MSH2 may be responsible for a variable percentage of unexplained Lynch-suspected families (0%–40% depending on possible founder effects).15Ligtenberg M.J.L. Kuiper R.P. Chan T.L. et al.Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1.Nat Genet. 2009; 41: 112-117Crossref PubMed Scopus (587) Google Scholar,47Niessen R.C. Hofstra R.M.W. Westers H. et al.Germline hypermethylation of MLH1 and EPCAM deletions are a frequent cause of Lynch syndrome.Genes Chromosomes Cancer. 2009; 48: 737-744Crossref PubMed Scopus (157) Google Scholar There are no reports of LS-associated constitutional epimutations for MMR genes other than MLH1 and MSH2.51Liu Y. Chew M.H. Goh X.W. et al.Systematic study on genetic and epimutational profile of a cohort of Amsterdam criteria-defined Lynch syndrome in Singapore.PLoS One. 2014; 9e94170Google Scholar Epigenetic changes are subject to erasure when they pass through the germline. Therefore, primary constitutional epimutations segregate in a nonmendelian fashion and are seldom associated with any remarkable family history of cancer. Families of primary epimutation carriers may exhibit mosai