Epimutations and Cancer Susceptibility

Abstract

Germline genetic testing often fails to detect a mutation in the coding region of the relevant predisposition gene despite a strong clinical suspicion of a hereditary cancer syndrome. In some cases, cancer predisposition is caused by a constitutional epimutation. Epimutations are epigenetic aberrations, typically defined by deoxyribonucleic acid (DNA) methylation, that predispose individuals to cancer through soma‐wide changes in the expression of the afflicted gene. They have been documented in patients with colorectal cancer, chronic lymphocytic leukaemias and some imprinting disorders. The molecular cause of most epimutations is unknown but it is hypothesised that they could be driven by hitherto unidentified genetic alterations in long‐range cis‐regulatory elements that manifest as DNA methylation or repressive histone modifications at a gene promoter. An understanding of the molecular origin of epimutations may help elucidate the basis of predisposition to cancer.

Key Concepts:

  • Constitutional epimutations predispose carriers to early‐onset cancer.

  • A constitutional epimutation inactivates expression from one allele of a gene throughout normal tissues.

  • Primary constitutional epimutations are not inherited in a Mendelian fashion. They are absent in the germline but are present in tissues derived from all three germ layers.

  • Secondary constitutional epimutations cosegregate with an in cis genetic change.

  • In cis DNA elements such as enhancers and insulators regulate gene expression and are potential sites of genetic alterations that give rise to epimutations.

  • Identifying the cause of epimutations will help explain the origin of some cases of familial cancer without a germline DNA mutation.

Keywords: antisense transcription; cancer predisposition; constitutional; DNA methylation; epigenetics; epimutation; histone modification; nucleosome

Figure 1.

Types of constitutional epimutation. Constitutional epimutations are classified as primary, secondary or nonclassical. (a) Primary constitutional epimutations are not associated with any known genetic changes and display a non‐Mendelian pattern of inheritance. (b) Secondary constitutional epimutations are inherited in a Mendelian fashion due to their physical linkage to an in cis genetic alteration such as transcriptional readthrough and promoter single‐nucleotide variation (SNV). (c) Nonclassical constitutional epimutations have low or no DNA methylation with no identified DNA sequence change. Green, normal allele; blue, epimutation allele; boxes, exons; black line, intron or intergenic region; arrow, direction of transcription; lollipops, CpG islands (white, unmethylated and black, methylated); dashed line, deletion; and *, SNV.

Figure 2.

The establishment of constitutional epimutations. A constitutional epimutation refers to an epigenetic aberration that is present on one parental allele throughout normal tissues, and which represses or activates expression from the affected allele. (a) Primary epimutations are erased in the germline but their soma‐wide distribution indicates that they are established at an early stage of development before differentiation of the three germ layers (endoderm, ectoderm and mesoderm). (b) Secondary mutations are facilitated by an in cis genetic alteration (*) that is also present in the germline. DNA methylation at CpG island promoters (black lollipops) is the most extensively described epimutation. Epimutations at the MLH1 locus preferentially arise on the maternal allele and constitute the first ‘hit’ in Knudson's two‐hit hypothesis that predisposes carriers to cancer.

Figure 3.

The effect of promoter SNV on MLH1 expression in Lynch syndrome. MLH1 and EPM2AP1 share a bidirectional CpG island promoter (green bar) on human chromosome 3. The position of common SNPs (c.‐269C>G and c.‐93G>A) and SNVs whose effect on MLH1 expression has been tested in human tissues (c.‐27C>A and c.85G>T) or luciferase promoter reporter assays in HCT116 and HEK293 cells (all others) are shown below the CpG island. *, DNA methylation cosegregates with the designated allele; blue, expression lost from the methylated allele in the germline of carriers; black, no effect on gene expression; grey, common SNP with reduced expression in one cell line; red, SNV with reduced expression in two cell lines. The c.‐27C>A and c.85G>T SNVs form a haplotype in families with Lynch syndrome (Hitchins et al., ; Ward et al., ).

Figure 4.

Cis‐regulatory regions in cancer predisposition genes. UCSC genome browser screenshots of the cancer predisposition genes: (a) MLH1, (b) APC and (c) BRCA2 showing the location of putative regulatory regions. DNase HS sites (DNase), transcription factor binding sites (TF), regions with enhancer signatures (H3K4me1 and H3K27Ac) (arrows) and CTCF binding sites (*) are shown for three cell lines derived from the ectoderm (HeLa), endoderm (A549) and the mesoderm (K562) (Encode Project Consortium et al., ). Curved lines below the MLH1 tracks represent potential interactions between the MLH1 promoter and distal regulatory elements.

Figure 5.

Novel potential mechanisms of epimutations. (a) An enhancer fails to engage with the promoter of a cancer predisposition gene because of a genetic mutation that prevents the binding of transcriptional activators. An unoccupied promoter results in DNA methylation and the recruitment of repressive histone modifications such as H3K27me3 to the promoter on the epimutation allele. (b) A genetic mutation in an insulator prevents binding of an insulator protein such as CTCF. The insulator is unable to defend the promoter of a cancer predisposition gene from the encroachment of repressive histone modifications or DNA methylation on the epimutation allele. (c) Antisense transcription induces the formation of DNA methylation and/or repressive histone modifications at an overlapping gene promoter. For clarity, other active (e.g., H3K4me2, H3K4me3, H3Ac and H4Ac) and repressive histone modifications (e.g. H3K9me3 and H4K20me3) that exist at gene promoters are not shown. In each model, genetic recombination between the promoter and the enhancer could explain the non‐Mendelian pattern of inheritance of primary and nonclassical constitutional epimutations.

close

References

Beckedorff FC, Ayupe AC, Crocci‐Souza R et al. (2013) The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation. PLoS Genetics 9(8): e1003705.

Bennett KL, Mester J and Eng C (2010) Germline epigenetic regulation of KILLIN in Cowden and Cowden‐like syndrome. Journal of the American Medical Association 304(24): 2724–2731.

Bird A (2007) Perceptions of epigenetics. Nature 447(7143): 396–398.

Cooper DN, Chen JM, Ball EV et al. (2010) Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Human Mutation 31(6): 631–655.

Creyghton MP, Cheng AW, Welstead GG et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proceedings of the National Academy of Sciences of the USA 107(50): 21931–21936.

Dickson J, Gowher H, Strogantsev R et al. (2010) VEZF1 elements mediate protection from DNA methylation. PLoS Genetics 6(1): e1000804.

Encode Project Consortium, Bernstein BE, Birney E et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414): 57–74.

Fackenthal JD and Olopade OI (2007) Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations. Nature Reviews Cancer 7(12): 937–948.

Galetzka D, Hansmann T, El Hajj N et al. (2012) Monozygotic twins discordant for constitutive BRCA1 promoter methylation, childhood cancer and secondary cancer. Epigenetics 7(1): 47–54.

Giardiello FM, Brensinger JD, Petersen GM et al. (1997) The use and interpretation of commercial APC gene testing for familial adenomatous polyposis. New England Journal of Medicine 336(12): 823–827.

Gylling A, Ridanpaa M, Vierimaa O et al. (2009) Large genomic rearrangements and germline epimutations in Lynch syndrome. International Journal of Cancer Journal 124(10): 2333–2340.

Hansmann T, Pliushch G, Leubner M et al. (2012) Constitutive promoter methylation of BRCA1 and RAD51C in patients with familial ovarian cancer and early‐onset sporadic breast cancer. Human Molecular Genetics 21(21): 4669–4679.

Hark AT, Schoenherr CJ, Katz DJ et al. (2000) CTCF mediates methylation‐sensitive enhancer‐blocking activity at the H19/Igf2 locus. Nature 405(6785): 486–489.

Heintzman ND and Ren B (2009) Finding distal regulatory elements in the human genome. Current Opinion in Genetics and Development 19(6): 541–549.

Heintzman ND, Stuart RK, Hon G et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics 39(3): 311–318.

Hesson LB, Hitchins MP and Ward RL (2010) Epimutations and cancer predisposition: importance and mechanisms. Current Opinion in Genetics and Development 20(3): 290–298.

Hesson LB, Packham D, Pontzer E et al. (2012) A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines. Biological Procedures Online 14(1): 5.

Hesson LB, Patil V, Sloane MA et al. (2013) Reassembly of nucleosomes at the MLH1 promoter initiates resilencing following decitabine exposure. PLoS Genetics 9(7): e1003636.

Hitchins M, Suter C, Wong J et al. (2006) Germline epimutations of APC are not associated with inherited colorectal polyposis. Gut 55(4): 586–587.

Hitchins M, Williams R, Cheong K et al. (2005) MLH1 germline epimutations as a factor in hereditary nonpolyposis colorectal cancer. Gastroenterology 129(5): 1392–1399.

Hitchins MP (2013) The role of epigenetics in Lynch syndrome. Familial Cancer 12(2): 189–205.

Hitchins MP, Rapkins RW, Kwok CT et al. (2011) Dominantly inherited constitutional epigenetic silencing of MLH1 in a cancer‐affected family is linked to a single nucleotide variant within the 5′UTR. Cancer Cell 20(2): 200–213.

Hitchins MP, Wong JJ, Suthers G et al. (2007) Inheritance of a cancer‐associated MLH1 germ‐line epimutation. New England Journal of Medicine 356(7): 697–705.

Hnisz D, Abraham BJ, Lee TI et al. (2013) Super‐enhancers in the control of cell identity and disease. Cell 155(4): 934–947.

Hon GC, Rajagopal N, Shen Y et al. (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics 45(10): 1198–1207.

Huang S, Li X, Yusufzai TM, Qiu Y and Felsenfeld G (2007) USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Molecular and Cellular Biology 27(22): 7991–8002.

Jin F, Li Y, Dixon JR et al. (2013) A high‐resolution map of the three‐dimensional chromatin interactome in human cells. Nature 503(7475): 290–294.

Katayama S, Tomaru Y, Kasukawa T et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740): 1564–1566.

Kelly TK, Miranda TB, Liang G et al. (2010) H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Molecular Cell 39(6): 901–911.

Kempers MJ, Kuiper RP, Ockeloen CW et al. (2011) Risk of colorectal and endometrial cancers in EPCAM deletion‐positive Lynch syndrome: a cohort study. Lancet Oncology 12(1): 49–55.

van der Klift H, Wijnen J, Wagner A et al. (2005) 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, Chromosomes and Cancer 44(2): 123–138.

Kong A, Gudbjartsson DF, Sainz J et al. (2002) A high‐resolution recombination map of the human genome. Nature Genetics 31(3): 241–247.

Kulis M and Esteller M (2010) DNA methylation and cancer. Advances in Genetics 70: 27–56.

Kwok CT, Vogelaar IP, van Zelst‐Stams WA et al. (in press) The MLH1 c.‐27C>A and c.85G>T variants are linked to dominantly inherited MLH1 epimutation and are borne on a European ancestral haplotype. European Journal of Human Genetics.

Latos PA, Pauler FM, Koerner MV et al. (2012) Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338(6113): 1469–1472.

Li G, Ruan X, Auerbach RK et al. (2012) Extensive promoter‐centered chromatin interactions provide a topological basis for transcription regulation. Cell 148(1–2): 84–98.

Ligtenberg MJ, Kuiper RP, Chan TL et al. (2009) Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3′ exons of TACSTD1. Nature Genetics 41(1): 112–117.

Morak M, Koehler U, Schackert HK et al. (2011) Biallelic MLH1 SNP cDNA expression or constitutional promoter methylation can hide genomic rearrangements causing Lynch syndrome. Journal of Medical Genetics 48(8): 513–519.

Oberle I, Rousseau F, Heitz D et al. (1991) Instability of a 550‐base pair DNA segment and abnormal methylation in fragile X syndrome. Science 252(5009): 1097–1102.

Raval A, Tanner SM, Byrd JC et al. (2007) Downregulation of death‐associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell 129(5): 879–890.

Regha K, Sloane MA, Huang R et al. (2007) Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome. Molecular Cell 27(3): 353–366.

Singh V and Srivastava M (2008) Enhancer blocking activity of the insulator at H19‐ICR is independent of chromatin barrier establishment. Molecular and Cellular Biology 28(11): 3767–3775.

Sparago A, Cerrato F, Vernucci M et al. (2004) Microdeletions in the human H19 DMR result in loss of IGF2 imprinting and Beckwith–Wiedemann syndrome. Nature Genetics 36(9): 958–960.

Tufarelli C, Stanley JA, Garrick D et al. (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nature Genetics 34(2): 157–165.

Venkatachalam R, Ligtenberg MJ, Hoogerbrugge N et al. (2010) Germline epigenetic silencing of the tumor suppressor gene PTPRJ in early‐onset familial colorectal cancer. Gastroenterology 139(6): 2221–2224.

Ward RL, Dobbins T, Lindor NM, Rapkins RW and Hitchins MP (2013) Identification of constitutional MLH1 epimutations and promoter variants in colorectal cancer patients from the Colon Cancer Family Registry. Genetics in Medicine 15(1): 25–35.

Wei QX, Claus R, Hielscher T et al. (2013) Germline allele‐specific expression of DAPK1 in chronic lymphocytic leukemia. PloS One 8(1): e55261.

West AG, Huang S, Gaszner M, Litt MD and Felsenfeld G (2004) Recruitment of histone modifications by USF proteins at a vertebrate barrier element. Molecular Cell 16(3): 453–463.

Yan H, Dobbie Z, Gruber SB et al. (2002) Small changes in expression affect predisposition to tumorigenesis. Nature Genetics 30(1): 25–26.

Yap KL, Li S, Munoz‐Cabello AM et al. (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Molecular Cell 38(5): 662–674.

You JS, Kelly TK, DeCarvalho DD et al. (2011) OCT4 establishes and maintains nucleosome‐depleted regions that provide additional layers of epigenetic regulation of its target genes. Proceedings of the National Academy of Sciences of the USA 108(35): 14497–14502.

Yu W, Gius D, Onyango P et al. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175): 202–206.

Further Reading

Allis CD, Jenuwein T, Reinberg D and Caparros ML (2007) Epigenetics, 1st edn. New York: Cold Spring Harbor Laboratory Press.

Goel A, Nguyen TP, Leung HC et al. (2011) De novo constitutional MLH1 epimutations confer early‐onset colorectal cancer in two new sporadic Lynch syndrome cases, with derivation of the epimutation on the paternal allele in one. International Journal of Cancer 128(4): 869–878.

Hitchins MP, Owens SE, Kwok CT et al. (2011) Identification of new cases of early‐onset colorectal cancer with an MLH1 epimutation in an ethnically diverse South African cohort. Clinical Genetics 80(5): 428–434.

Kuiper RP, Vissers LE, Venkatachalam R et al. (2011) Recurrence and variability of germline EPCAM deletions in Lynch syndrome. Human Mutation 32(4): 407–414.

Lynch HT and de la Chapelle A (1999) Genetic susceptibility to non‐polyposis colorectal cancer. Journal of Medical Genetics 36(11): 801–818.

Maston GA, Landt SG, Snyder M and Green MR (2012) Characterization of enhancer function from genome‐wide analyses. Annual Review of Genomics and Human Genetics 13: 29–57.

Pauler FM, Sloane MA, Huang R et al. (2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Research 20(10): 1268–1282.

Shen H and Laird PW (2013) Interplay between the cancer genome and epigenome. Cell 153: 38–55.

Suter CM, Martin DI and Ward RL (2004) Germline epimutation of MLH1 in individuals with multiple cancers. Nature Genetics 36(5): 497–501.

Zhang Y, Wong CH, Birnbaum RY et al. (2013) Chromatin connectivity maps reveal dynamic promoter‐enhancer long‐range associations. Nature 504(7479): 306–310.

Web Link

eviQ Cancer Treatments Online. https://www.eviq.org.au/

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Sloane, Mathew Aidan, Hesson, Luke Benjamin, and Ward, Robyn Lynne(Mar 2014) Epimutations and Cancer Susceptibility. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024615]