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Host genomics of HIV-related lymphoma
with an increased risk of NHL in the general population. We performed a series of case/control GWAS of four NHL subtypes (CLL, DLBCL, FL and MZL) as well as a com- bined GWAS with all NHL subtypes (Online Supplementary Table S4; Online Supplementary Figure S6) and assessed the association evidence at rs7919208. We found no associa- tion between rs7919208 and any of the subtypes in the general population, even at nominal significance.
Discussion
In this genome-wide analysis, including a total of 278 NHL HIV+ cases and 1,924 HIV+ controls from three independent cohorts, we identified a novel NHL suscep- tibility locus on chromosome 10 near the CXCL12 gene. The strong signal observed in the meta-analysis was driv- en by the associations detected in the SHCS and ANRS cohorts and there was no evidence of association in the MACS cohort. Notably, most NHL cases in the MACS cohort date back to the pre-ART era, while only NHL cases diagnosed after the year 2000 were included in the SHCS and ANRS analyses. Conceivably, NHL occurring in the early years of the HIV pandemic may have been primarily driven by severe immunosuppression, which could have obscured any influence of human genetic vari- ation among the cases in the MACS sample. Precise phe- notype definition is crucial in designing large-scale genet- ic studies since any environmental noise tends to decrease the likelihood of identifying potential genetic influences.
NHL is a relatively rare cancer even among HIV infect- ed individuals, making it difficult to collect the large num- bers of cases that would typically be included in contem- porary genome-wide genetic studies. Indeed, a recent study from the Data Collection on Adverse events of Anti-HIV Drugs (D:A:D) group showed an NHL inci- dence rate of 1.17/1,000 person-years of follow-up over the past 15 years (392 new cases in >40,000 HIV+ individ- uals).8 Still, we were able to obtain clinical and genetic data from a total of 278 patients with confirmed NHL diagnosis. By matching them with a larger number of controls from the same cohorts, we had enough power to identify associated variants of relatively large effects in the CXCL12 region.
Several groups have already suggested a potential role for CXCL12 variation in HIV-related NHL. A prospective study correlated increased CXCL12 expression with sub- sequent NHL development in HIV+ children but not in uninfected children.44 The number of A alleles at the CXCL12-3’ variant (rs1801157) has also previously been associated with an increased risk of developing HIV-relat- ed NHL during an 11.7 year follow-up period.45 Thus, our data further support the role of CXCL12 as a critical mod- ulator of the individual risk of developing NHL in the HIV+ population.
The role of CXCL12 and its receptor chemokine recep- tor 4 (CXCR4) in cancer in the general population is well established, with the levels of CXCL12 and CXCR4 found to be increased in multiple types of cancer and to be asso- ciated with tumor progression.46,47 Furthermore, in vivo inhibition of either CXCR4 or CXCL12 signaling is capa- ble of disrupting early lymphoma development in severe combined immunodeficient (SCID) mice transfused with EBV+ PBMC.48 These results and others have already led to the development and testing of several small molecules
targeting either CXCL12 or CXCR4 to inhibit tumor pro- gression.46
We could not identify any significant relationship between rs7919208 and the expression levels of CXCL12 in PBMC or EBV transformed lymphocytes. This could be due to the low expression levels of CXCL12 in most tis- sues, apart from stromal cells. Still, our analysis of allele- specific expression showed a significant allelic imbalance for heterozygous carriers of rs7919208 for CXCL12. This signal was only observed in fibroblasts, the GTEx tissue most closely resembling stromal cells. Furthermore, we identified a significant association between rs7919208 and CXCL12 transcript isoform usage in the visceral adi- pose tissue, which is known to also contain a minority of stromal cells.49 Combined these results underscore the potential importance of these cells in the development of HIV-related NHL and the ability of rs7919208 to modify transcription.
The new BATF and JUND binding site created by rs7919208 could act as an induced or dynamic eQTL, specifically triggered by HIV infection. Such eQTL can be found in regions deprived of regulatory annotations, since these have been mostly examined in static cell types.50 Supporting this hypothesis, HIV has been shown to induce overexpression of BATF.51 This would explain why rs7919208 is only a risk factor for HIV+ individuals and not in the general population.
Previous analyses in the general population have discov- ered both shared and distinct associations for NHL sub- types.14,21–24,43 However, similar analyses were not possible in our sample since NHL subtype information was not available for many of our cases. Furthermore, information on serostatus for relevant co-infections with EBV or other oncogenic viruses was not available and could therefore not be assessed. In particular, EBV has been largely associ- ated with the development of NHL and other lymphomas and is considered a driver of a subset of NHL in the general population.52 Variants in the HLA region have consistently been associated with all NHL subtypes in HIV uninfected populations regardless of EBV serostatus, although differ- ent HLA associations have been observed for each NHL subtype. We did not find any evidence of HLA associations in our analyses of HIV-related NHL. This might be due to a lack of power, due to our limited sample size in compar- ison to the NHL GWAS performed in the general popula- tion. However, this lack of replication of HLA variants and all other risk variants previously identified in the general population strongly suggests that distinct genes or path- ways influence susceptibility to NHL in the HIV+ popula- tion compared to the general population.53 This distinction may be due to the unique pathogenic mechanisms involved in HIV-associated NHL, such as cytokine deregu- lation, chronic antigen stimulation and impaired immune response, among others.11
In summary, we have identified variants significantly associated with the development of NHL in the HIV+ population. Fine mapping of the associated locus and sub- sequent analyses of TAD, promoter capture Hi-C data as well as deep-learning models of mutational effects on transcription factor binding, points to a causative model involving the gain of a BATF and JUND transcription binding site downstream of CXCL12 capable of physical- ly interacting with the CXCL12 promoter. These results suggest an important modulating role of CXCL12 in the development of HIV-related NHL.
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