Identification of Novel Germline Variants in Early-Onset Familial Classical Hodgkin Lymphoma with Exome Sequencing

Hodgkin lymphoma (HL) is a malignancy of the lymphatic system that stems from germinal center B-cells. The global annual incidence of HL is 3 in 100,000, and it accounts for about 30% of all lymphomas. HL is further divided into four distinct subtypes, of which the classical Hodgkin lymphoma (cHL) constitutes 95 % of cases.

The etiology of cHL is not completely understood. There is strong evidence from epidemiological and molecular biology studies that Epstein-Barr virus infection is associated with cHL pathogenesis. Indeed, about 40% of cHL cases are Epstein-Barr virus (EBV) positive, i.e. they express EBV-encoded RNAs. The role of genetic factors is also acknowledged: familial clustering of cHL has been reported. However, to date a germline translocation affecting KLHDC8B gene is the only known candidate for a penetrant cHL predisposing mutation.

In this work, we studied a family of Middle-Eastern origin in which three out of five children were diagnosed with Epstein-Barr virus (EBV) positive cHL within a 6-year period. We exome sequenced the genomic DNA of three siblings diagnosed with cHL during childhood, and analyzed their shared germline variants using a control set of 3891 samples. In the exome data, all affected siblings displayed a relatively high degree of homozygosity, providing evidence for recessive mode of inheritance. After filtering against controls, 35 shared variants, of which only one was homozygous, remained. The candidate variants were then prioritized using computational methods and their effect to protein function was predicted. This left us with thirteen novel variants: a homozygous 57 bp in-frame deletion in ACAN, a removal of stop codon in LY75-CD302, a nonsense mutation in KIAA0140, and ten missense-type single-nucleotide variants (SNV) predicted damaging by two different computational methods. From these, homozygous deletion in ACAN (encoding for aggrecan) emerges as a candidate mutation for recessive cHL susceptibility. The deletion identified in ACAN removes part of the repeat sequence as well as 9 amino acids from the unique sequence. ACAN has not been associated with tumorigenesis or tumor predisposition thus far but recent research has, however, suggested that noncellular tumor microenvironment components may promote the oncogenic effects of EBV. Recessive pattern of inheritance would also fit the pedigree structure and the relatively high degree of homozygosity observed in affected siblings.

In this study, we identified several feasible candidate genes for cHL predisposition. The pedigree data, the overall variation data, and the homozygous ACAN mutation finding, are compatible with possible recessive inheritance, though other modes of inheritance cannot be excluded. The identified candidate genes provide a platform for validation studies in extended sets of familial cHL samples. Robust identification of additional mutations in families with this intriguing disease susceptibility phenotype would be a breakthrough in cHL risk prediction, and provide valuable clues to the molecular basis of Hodgkin lymphoma.