Prevalence and spectrum of germline cancer susceptibility gene variants and somatic second hits in colorectal cancer

Abstract

Colorectal cancer (CRC) is one of the most heritable cancers, and genetic factors play an important role in the increased CRC risk. However, the well-established CRC-risk genes were limited for explaining the increased risk of CRC individuals. Germline mutations in DNA damage repair (DDR) genes have also been reported to be implicated in CRC heritability. Here, we aimed to determine the prevalence and significance of germline DDR and well-established CRC-risk gene variants in CRCs with paired somatic analyses. Next-generation sequencing (NGS) was performed on tumor tissues and paired white blood cells collected from 2160 Chinese patients with CRC using well-designed 381- or 733-cancer gene panel. Germline/somatic variations were identified and assessed for pathogenicity and likely pathogenicity. Of 2160 CRCs, 136 pathogenic germline mutations in 133 patients (133/2160, 6.1%) were identified in 21 genes, including 19 out of 32 examined DDR genes. Compared with non-carriers, individuals with germline variants were prone to a higher level of microsatellite instability (MSI) and tumor mutational burden (TMB), and an earlier age of onset. Somatic sequencing identified second hits in 24/133 (18%) patients with germline variants. Among the mismatch repair (MMR) genes with germline mutations, the second hit significantly increased MSI and TMB, particularly apparent in MSH6. All MMR germline variation carriers further with a second hit were all MSI-H and had an extraordinarily high level of TMB. Collectively, approximately 6.1% of CRC patients carried pathogenic germline variants, and additional somatic second hit increases the genomic instability in CRC, whereas the more clinical significance warrants further study.

Keywords: Colorectal cancer; DNA damage repair; germline mutation; somatic second hit.

Figure 1

The spectrum of pathogenic germline mutations and somatic second hits in our cohort. A. The identified pathogenic germline mutations and somatic second hits among 133 patients with colorectal cancer; B. Distribution of 136 pathogenic germline mutations that occurred in 21 genes; C. Location of pathogenic germline mutations (black) and somatic second hits (red) are shown by lollipop plots.

Figure 2

Effects of germline DNA damage repair (DDR) gene mutations and somatic second hits on TMB and age at diagnosis. (A, B) The effects of germline DDR gene mutations on TMB (A) and age at diagnosis (B); (C, D) The effects of DDR somatic second hits on TMB (A) and age at diagnosis (B). *P < 0.05, **P < 0.01, ****P < 0.001.

Figure 3

Effects of germline mismatch repair (MMR) gene mutations and somatic second hits on tumor mutational burden (TMB) and age at diagnosis. (A, B) The effects of germline MMR gene mutations on TMB (A) and age at diagnosis (B); (C, D) The effects of MMR somatic second hits on TMB (A) and age at diagnosis (B). **P < 0.01, ****P < 0.001.