Rare disruptive mutations in ciliary function genes contribute to testicular cancer susceptibility

Abstract

Testicular germ cell tumour (TGCT) is the most common cancer in young men. Here we sought to identify risk factors for TGCT by performing whole-exome sequencing on 328 TGCT cases from 153 families, 634 sporadic TGCT cases and 1,644 controls. We search for genes that are recurrently affected by rare variants (minor allele frequency <0.01) with potentially damaging effects and evidence of segregation in families. A total of 8.7% of TGCT families carry rare disruptive mutations in the cilia-microtubule genes (CMG) as compared with 0.5% of controls (P=2.1 × 10^-8). The most significantly mutated CMG is DNAAF1 with biallelic inactivation and loss of DNAAF1 expression shown in tumours from carriers. DNAAF1 mutation as a cause of TGCT is supported by a dnaaf1^hu255h(+/-) zebrafish model, which has a 94% risk of TGCT. Our data implicate cilia-microtubule inactivation as a cause of TGCT and provide evidence for CMGs as cancer susceptibility genes.

Figure 1. Study design.

Overview of patient samples and exome sequencing study design.

Figure 2. Disruptive germline mutations in cilia-microtubule pathway genes identified in TGCT cases.

(a) DNAAF1 and paralogue genes; (b) cilia-microtubule gene set. Red dots denote mutations identified in familial TGCT cases, blue dots denote mutations in unselected TGCT cases and white dots denote mutations in UK controls. Grey dots denote mutations catalogued by ClinVar as a cause of recessive ciliopathy. Domain abbreviations: LRR, leucine-rich repeat; LRRCT, leucine-rich repeat C-terminal; CS, CHORD-containing proteins and SGT1; NYD-SP28, NYD-SP28 sperm tail; NYD.., NYD-SP28_assoc sperm tail C-terminal domain; DHC_N1, dynein heavy chain, N-terminal region 1; DHC_N2, dynein heavy chain; N-terminal region 1, AAA.., hydrolytic ATP-binding site of dynein motor region D1; AAA_7, P-loop containing dynein motor region D3; AAA_8, P-loop containing dynein motor region D4; MT, microtubule-binding stalk of dynein motor; Dynein_heavy pfama, dynein heavy chain and region D6 of dynein motor; CEP.., coiled-coil region of centrosome protein; M1-4, Tau/MAP 1–4.

Figure 3. Segregating TGCT pedigrees of cilia-microtubule pathway gene carriers.

Circles, female; and squares, male. TGCT cases denoted by shaded symbols; ages refer to age at diagnosis of TGCT.

Figure 4. IHC staining for DNAAF1 expression in available tumour tissue from mutation carriers.

IHC showing positive DNAAF1 expression in surrounding normal tissue (left) but loss of expression within the tumour (middle and right). Data are shown for tumour from PED-2152 (p.Gly434ProfsTer4). A comparable pattern was found in PED-2331 (p.Arg636Ter) and S-1645 (c.1698+1G>A). Scale bar, 5 μm.