Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes

Abstract

More knowledge is needed regarding germline predisposition to Ewing sarcoma to inform biological investigation and clinical practice. Here, we evaluated the enrichment of pathogenic germline variants in Ewing sarcoma relative to other pediatric sarcoma subtypes, as well as patterns of inheritance of these variants. We carried out European-focused and pan-ancestry case-control analyses to screen for enrichment of pathogenic germline variants in 141 established cancer predisposition genes in 1,147 individuals with pediatric sarcoma diagnoses (226 Ewing sarcoma, 438 osteosarcoma, 180 rhabdomyosarcoma, and 303 other sarcoma) relative to identically processed cancer-free control individuals. Findings in Ewing sarcoma were validated with an additional cohort of 430 individuals, and a subset of 301 Ewing sarcoma parent-proband trios was analyzed for inheritance patterns of identified pathogenic variants. A distinct pattern of pathogenic germline variants was seen in Ewing sarcoma relative to other sarcoma subtypes. FANCC was the only gene with an enrichment signal for heterozygous pathogenic variants in the European Ewing sarcoma discovery cohort (three individuals, OR 12.6, 95% CI 3.0-43.2, p = 0.003, FDR = 0.40). This enrichment in FANCC heterozygous pathogenic variants was again observed in the European Ewing sarcoma validation cohort (three individuals, OR 7.0, 95% CI 1.7-23.6, p = 0.014), representing a broader importance of genes involved in DNA damage repair, which were also nominally enriched in individuals with Ewing sarcoma. Pathogenic variants in DNA damage repair genes were acquired through autosomal inheritance. Our study provides new insight into germline risk factors contributing to Ewing sarcoma pathogenesis.

Keywords: Ewing sarcoma, cancer predisposition, pediatric oncology, genetic risk.

Figure 1

Study overview and characteristics of discovery and validation cohorts (A) Study schematic overview. The discovery cohort comprised 1,147 individuals, and the enrichment of pathogenic germline variants across 141 established cancer predisposition genes was evaluated. Case-control analyses restricted to the European ancestry (EUR) were carried out across the pan-sarcoma cohort (879 individuals), as well as major sarcoma histologic subtypes: osteosarcoma (304 individuals), rhabdomyosarcoma (138 individuals), and Ewing sarcoma (195 individuals). The validation cohort comprised 433 individuals with Ewing sarcoma. The enrichment of pathogenic germline variants in 43 DNA damage repair genes was evaluated employing an ancestry-matched case-control analysis. Mechanisms of inheritance were evaluated for 301 individuals that were a part of parent-proband trios. (B) Discovery cohort demographics: mean age 10.8 years, 52% male. (C) Ewing sarcoma validation cohort demographics: mean age 13.3 years, 54% male.

Figure 2

Ancestry composition of discovery cohort Enrichment of pathogenic germline variants in discovery cohort, across and within major histologic subtypes (A) Ancestry composition of discovery cohort: 879 European individuals (EUR), 137 African individuals (AFR), 119 admixed American individuals (AMR), seven East Asian individuals (EAS), and five South Asian individuals (SAS). (B–D) Odds ratios and 95% confidence intervals for enrichment of pathogenic germline variants among cancer predisposition genes. Red: significant at FDR < 0.05 after Benjamini-Hochberg procedure. Gray: significant at p < 0.05 but does not meet FDR < 0.05. Genes with p > 0.05 are not displayed. (B) Pan-sarcoma cohort (879 affected individuals, 10,548 control individuals). (C) Osteosarcoma subset of cohort (304 affected individuals, 10,640 control individuals). (D) Rhabdomyosarcoma subset of cohort (138 affected individuals, 10,626 control individuals). (E) Ewing sarcoma subset of cohort (195 affected individuals, 10,530 control individuals).

Figure 3

Enrichment of pathogenic germline variants in FANCC and other DNA damage repair genes in Ewing sarcoma validation cohort (A) Enrichment of pathogenic germline variants in FANCC in the Ewing Sarcoma validation cohort versus control individuals (OR 7.0, 95% CI 1.7–23.6, p = 0.014). (B) Sensitivity analysis for enrichment of pathogenic germline FANCC variants in the Ewing sarcoma validation cohort over a range of simulated population frequencies. (C) Collective frequency of pathogenic variants in leading gene set of DNA damage repair genes in the Ewing sarcoma validation cohort. In addition to FANCC, nominal enrichment signals were also seen in CHEK2 (OR 3.6, 95% CI 1.6–7.9, p = 0.005) and FANCA (OR 3.3, 95% CI 1.1–9.1, p = 0.042). (D) Rates of pathogenic variants in TP53 in Ewing sarcoma validation cohort in comparison to Ewing sarcoma subset of discovery cohort, rhabdomyosarcoma subset of discovery cohort, osteosarcoma subset of discovery cohort, and pan-sarcoma discovery cohort (Fisher’s exact tests, n.s. denotes no significant difference, ^∗∗∗ denotes significant difference at p < 0.05).

Figure 4

Pathogenic germline variants in DNA damage repair genes are inherited in high-risk families (A) Pathogenic germline variants in DDR genes among trio probands with Ewing sarcoma. 35 pathogenic variants impacting 32 of 301 individuals with Ewing sarcoma were identified. (B) 32 of 32 probands (100%) with pathogenic germline variants in DDR genes had identical variants identified in parents. 19 of 269 probands without a pathogenic germline variant in a DDR gene had at least one parent with a germline DDR variant that was not inherited by the proband (7.1%). (C and D) Pedigrees and IGV screenshots of pathogenic variants in DDR genes. Pedigree legend: circle, female sex; square, male sex; diamond, unknown sex; gray shading, proband with Ewing sarcoma; ^∗ denotes variant 1 identified in parent-proband trio; ‡ denotes variant 2 identified in parent-proband trio. Top screenshot: carrier parent. Bottom screenshot: proband.