Germline MBD4 deficiency causes a multi-tumor predisposition syndrome

Abstract

We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.

Keywords: 5′-methylcytosine deamination; colorectal cancer; mutational signature; mutator phenotype; polyposis.

Figure 1

Pedigrees of individuals with MBD4 deficiency (A) Pedigree of simplex individual D:II-1 with a homozygous MBD4 loss-of-function (c.612_615del) variant. For colorectal adenomas, we show the cumulative tumor numbers from age at first presentation and screening colonoscopy to age at last contact (see also Figures S1A and S1E–S1H). (B) Pedigree of Family CRDFF-292 with a homozygous MBD4 loss-of-function (c.939dup) variant. For colorectal adenomas, we show the total tumor numbers identified from panproctocolectomy at age 53 (see also Figure S1B). (C) Pedigree of Family CRDFF-336 with a homozygous MBD4 loss-of-function (c.939dup) variant. For colorectal adenomas, we show the total tumor numbers identified from panproctocolectomy at 39 years of age (see also Figure S1C). (D) Pedigree of Family DB1 with the bi-allelic MBD4 loss-of-function c.939dup and c.1688T>A variants (see also Figure S1D). Abbreviations: Ads, colorectal adenomas; AML, acute myeloid leukemia; CRC, colorectal cancer; DCIS, ductal carcinoma in situ of the breast; OvGCT, ovarian granulosa cell tumor; PrC, prostate cancer; SADS, sudden arrhythmia death syndrome; SC, stomach cancer; UVM, uveal melanoma; upper GI TVA, upper gastrointestinal ampullary tubulovillus adenoma; question mark, age unknown; MT, mutation; WT, wild-type. Arrows indicate index individuals. Number between brackets indicate age at diagnosis.

Figure 2

Somatic mutation burden and analysis of polyps of individuals with MBD4 deficiency (A) Somatic mutation rate for each polyp, formalin-fixed and paraffin-embedded samples indicated with asterisks (^∗). The color of the bars represents mutations in different sequence contexts; red shows CG>TG mutations, blue shows CA>AA mutations (primarily detected in WEHI-2 P9), and gray represents other base contexts. The median value is presented for samples that had multi-region sequencing. Median mutation burden/Mb in fresh frozen adenomas of D:II-1 was 11.1 [range 8.5–23.3] compared to 1.8 in a set of nine fresh frozen sporadic adenomas [range 1.0–3.1] (see also Figures S1H–S1I for representative HE slides). (B) The number of somatic CG>TG mutations detected in WES data is plotted as function of age. The linear fit is shown, together with 95% confidence intervals (gray shading). (C) We assessed the contribution of deamination of 5mC to MBD4-deficient samples by comparing the number of CG>TG mutations to all other single-nucleotide mutations. The plot compares MBD4-deficient polyps and AMLs to sporadic polyps, and to colon and rectal cancers from The Cancer Genome Atlas (TCGA). MSI, microsatellite instability; MSI-H, MSI-high; MSS, microsatellite stable (“MSS” includes both MSS and MSI-low samples); TCGA NA, no MSI data available. (D) Extracted de novo signature SBS1^MBD4 C>T panel from all polyps from D:II-1(left) and polyps P1–P8 of WEHI-2 (middle) and the C>T panel from COSMIC SBS1-v3 (right). (E) Fraction of mutated CpG sites that are methylated in normal sigmoid colon (beta value > 0.5 in WGBS data from the Roadmap Epigenomics Consortium¹¹). Each point summarizes WES results from a sample and includes all sites with sufficient coverage in WGBS (n = 177–1,507 CG>TG mutations) and the median value is shown with a horizontal line. The gray line shows the fraction of methylated CG sites across all exons. (F) Oncoprint of driver gene mutation analysis of genes significantly different mutated compared to sporadic adenomas. For each polyp, the number and type of somatic mutation is shown. ^∗Polyp P10 from WEHI-2 was sequenced with a targeted panel (see also Table S5).