Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer

Abstract

Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.

Figure 1

Design and workflow for integrative analysis combining germline with somatic mutation information using gene expression data. RNA-seq read count data and somatic information were downloaded from The Cancer Genome Atlas (TCGA) via the Genomics Data Commons. Germline mutation information was manually curated from GWAS studies. Limma (R) package was used for the discovery of differentially expressed (DE) mutated and nonmutated genes. Ingenuity Pathway Analysis (IPA) was used for functional analysis and discovery of molecular networks and biological pathways enriched for germline and somatic mutations.

Figure 2

Venn diagram showing differentially and nondifferentially expressed germline and somatic mutated and nonmutated genes. Middle intersections show 61 genes containing both germline and somatic mutations and are also significantly expressed with RNA-seq dataset. Germline indicates genes with germline genetic susceptibility variants from GWAS. Somatic indicates genes with somatic mutations from TCGA. RNA-seq indicates differentially expressed genes evaluated using TCGA gene expression data.

Figure 3

Patterns of expression profiles for the 61 genes containing both germline and somatic mutations distinguishing patients with aggressive tumors and controls generated using hierarchical clustering.

Figure 4

Molecular networks showing interactions among genes containing both germline and somatic mutations. Gene names (symbols) are presented in the nodes. Gene names in purple color font contain both germline and somatic mutations. Gene names in blue color fonts indicate genes with more >5 somatic mutations whereas gene names in red font indicate genes containing germline mutations directly associated with aggressive prostate cancer. Note that the networks were filtered to remove spurious connections.

Figure 5

Molecular networks showing interactions among genes containing both germline and somatic mutations. Gene names (symbols) are presented in the nodes. Gene names in purple color font contain both germline and somatic mutations. Gene names in blue color fonts indicate genes with more >5 somatic mutations, gene names in green font indicate genes containing germline mutations only, and gene names in red font indicate genes containing germline mutations directly associated with aggressive prostate cancer. Note that the networks were filtered to remove spurious connections. The colors red and black represent overlap in functional relations among genes in merged networks.