There are currently 14 known germline variants that are associated with risk of RCC; however, it remains unclear how germline genetics modify the risk of developing RCC or their association with tumor aggressiveness. To date, associations between germlines genetics and tumor genetics is largely unknown for RCC. With respect to tumor aggressiveness, previous investigators did not observe significant associations between a polygenic risk model that was derived from these 14 germline variants and age at onset or tumor stage [5]. However, the analyses were performed on overall RCC and not within relevant RCC subtypes. Herein, we not only evaluated ccRCC specifically, but also the association of these 14 variants with specific molecular (BAP1, PBRM1, SETD2 and VHL) and clinically-aggressive subtypes of ccRCC. Using a case-case analysis, we observed that the 8q24 germline variant rs35252396 was significantly associated with tumor VHL mutation status as well as with the Mayo SSIGN score. Notably, the Mayo SSIGN score has been reproducibly shown to be associated with clinical outcome [13–16]. The 8q24 germline variant is located within PVT1, a candidate oncogene that is thought to regulate MYC to promote tumor formation. Of note, the 8q24 variant also overlaps a DNase I hypersensitive site and H3K4me1 peak from fetal kidney [23], indicating its location within a regulatory region. Through functional laboratory studies, investigators recently demonstrated that the 8q24 germline variant affects HIF binding to a MYC enhancer [24]. While the EPAS1 (rs7579899) and CCND1 (rs7105934) variants are also linked to the HIF pathway, we did not observe a statistically-significant association between these two variants and VHL mutation. Additionally, while it did not pass our multiple testing significance threshold, we also observed a candidate association between the EPAS1 germline variant rs57579899 and SETD2 tumor mutation (p = 0.012). We previously reported that loss of SETD2 activity was associated with greater risk of ccRCC death [25].
While previous investigators did not observe a significant association between a RCC-derived polygenic risk model and tumor stage [5], we observed a significant association between the 8q24 germline variant and the Mayo SSIGN score. The difference could be due to the fact that the original analysis [5] was performed for overall RCC whereas our analyses were performed within a more homogeneous subtype of RCC, particularly, ccRCC. The Mayo SSIGN score is derived from an additive model that contains tumor stage, tumor size, tumor grade and presence of necrosis and the model has reproducibly been shown to be associated with outcome in ccRCC, with higher SSIGN score being associated with poorer prognosis [13–16]. While we observed a significant association of the 8q24 germline variant and the Mayo SSIGN score, we did not observe a significant association between any of the 14 variants and the molecularly-defined ccA/ccB expression subtype that has been linked to ccRCC aggressiveness [11, 12, 17].
Previous studies have performed expression quantitative trait loci (eQTL) analyses to evaluate function of the 14 RCC germline variants [2, 5]. Herein, we used Hi-C data to identify candidate target genes underlying the association of each of the 14 germline variants with ccRCC risk. While some variants demonstrated interactions with nearby genes, we observed additional long-range interactions. Laboratory studies are necessary to further understand these observations.