Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility

Abstract

Glioma is the most common malignant primary brain tumor and is associated with poor prognosis. Genetic factors contributing to glioma risk have recently been investigated through genome-wide association studies (GWAS), implicating seven independent glioma risk loci in six chromosomal regions. Here, we performed an in-depth functional analysis of the risk locus proximal to the PHLDB1 gene on 11q23.3. We retrieved all SNPs in linkage disequilibrium (r2 ≥ 0.2) with the glioma-associated SNP (rs498872) and performed a comprehensive bioinformatics and experimental functional analysis for the region. After testing candidate SNPs for allele-specific activity in a luciferase-based enhancer scanning assay, we established a subset of 10 functional SNPs in the promoters of PHLDB1 and DDX6, and in a putative enhancer element. Chromatin conformation capture (3C) identified a physical interaction between the enhancer element containing a functional SNP (rs73001406) and the promoter of the DDX6 gene. Knockdown experiments in cell culture and 3D assays to evaluate the role of PHLDB1 and DDX6 suggest that both genes may contribute to the phenotype. These studies reveal the functional landscape of the 11q23.3 glioma susceptibility locus and identify a network of functional SNPs in regulatory elements and two target genes as a possible mechanism driving glioma risk association.

The Updated World Health Organization Glioma Classification: Cellular and Molecular Origins of Adult Infiltrating Gliomas

“…111,112 Inherited Factors Genome-wide association studies have identified several genetic loci associated with increased risk of glioma, including TERT, CDKN2A/2B, RTEL1, PHLDB1, EGFR, TP53, TERC, DDX6, and PIWI-interacting RNAs. [113][114][115] Of these genes, TERT, CDKN2A/2B, EGFR, and TP53 are wellcharacterized recurrently altered genes in sporadic IGs. In addition to well-known inherited tumor syndromes, such as Li Fraumeni, the study of familial cases of IG remains an important avenue toward identifying genetic candidates that drive glioma formation.…”

Pleckstrin homology domain-containing protein PHLDB3 supports cancer growth via a negative feedback loop involving p53

“…In addition, PHLDB1 can bind PI (3, 4, 5) P3 through its PH domain in adipocytes and function as a positive regulator of Akt activation by insulin16. More recent studies171819 have shown the correlation between PHLDB1 SNPs and glioma risk, implicating that PHLDB1 may play a potential role in the development of glioma. Noteworthily, PHLDA3, one of the pleckstrin homology-like domain family A proteins, was previously reported as a direct target gene of p53 (ref.…”

Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

“…Nuclear extracts were obtained from iOSE4 CMYC cells at 70%-90% confluence and electrophoretic mobility shift assays (EMSA) were run as described previously (18).…”