Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors

Abstract

Background Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals’ risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown. Methods We hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. We assessed their potential regulatory role via in-silico TF binding sequence perturbations, convolutional neural network trained on TF binding data, and simulated-annealing-based interpretation methods. Results We built an interactive website (http://education.knoweng.org/alg3/) summarizing the functional footprinting of 280 variants in 25 LGG GWAS regions, providing rich information for further computational and experimental scrutiny. As case studies, we identified PHLDB1 and SLC25A26 as candidate target genes of rs12803321 and rs11706832, respectively, and also predicted the GWAS variant rs648044 to be the causal SNP modulating ZBTB16, a known tumor suppressor in multiple cancers. We showed that rs648044 likely perturbed the binding affinity of the TF MAFF, as supported by RNA interference and in-vitro MAFF binding experiments. Conclusions The identified candidate (causal SNP, target gene, TF) triplets and the accompanying resource will help accelerate our understanding of the molecular mechanisms underlying genetic risk factors for gliomas.

Association of RNA m7G Modification Gene Polymorphisms with Pediatric Glioma Risk

“…Besides, polymorphisms of other important genes also contribute to glioma risk. For instance, a functional SNP rs12803321 with Solute Carrier Family 25 Member 26 as the target gene was found to be a causal locus of LGG [ 12 ]. Recently, our group investigated the impacts of SNPs in the RNA m6A modification core genes on pediatric glioma susceptibility.…”

“…(2) Some well-recognized genetic syndromes confer glioma risk, including the Turcot and Li-Fraumeni syndromes, neurofibromatosis type 1, and multiple enchondromatosis [8]. Moreover, numerous candidate gene association studies provide evidence of a link between genetic variation and glioma predisposition [8][9][10][11][12]. For instance, glioma susceptibility loci have been comprehensively explored in DNA repair, cell cycle, metabolism, and inflammation (including allergies and infections) pathways [8].…”

A Functional Polymorphism in Accessible Chromatin Region Confers Risk of Non-Small Cell Lung Cancer in Chinese Population

“…For example, with the combination of ATAC-seq and whole genome sequencing (WGS) data, three TERT promoter mutations were found to generate ETF motif sites, leading to an increase in TERT gene expression ( 25 ). Furthermore, an integrative analysis of ATAC-seq and gene expression data from public repositories has identified low-grade glioma GWAS variant rs648044 as a causative SNP, which perturbed the binding affinity of the TF MAFF and thus regulated the expression of ZBTB16 ( 26 ). In the present study, by integrating the ATAC-seq and ChIP-seq data, we discovered and validated a functional polymorphism rs13064999 in TP63 , which associated with NSCLC susceptibility.…”

Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines

“…Although the location of rs11706832 in intron 2 of LRIG1 could indicate a role in the regulation of LRIG1 itself, the SNP is not a documented expression quantitative trait locus (eQTL) for LRIG1 , but rs11706832 affect the expression of the adjacent solute carrier family 25 member 26 gene SLC25A26 according to the GTEx database ( https://gtexportal.org/home/snp/rs11706832 ). It has previously been suggested that the rs11706832 A-C conversion would create a possible perturbation of the binding motif for the transcriptional repressor LEF1 12 13 . Public data from DNase hypersensitivity sequencing from ENCODE reveals rs11706832 lies in an open chromatin region, indicating a regulatory mechanism of the SNP.…”