Previous genome-wide association studies (GWAS) have identified linkages about 40 PCA loci, including between PCA genetic alterations detected in the 8q24 region, β-microseminoprotein (MSMB), and allele -8 of the microsatellite DG8S737 . These studies have limited their scope to individual SNPs across the entire genome. Such assessments tend to ignore the genetic architecture of PCA that potentially involves complex interactions along key regulatory pathways. For the first time, the current study evaluates complex interactions among 172 apoptosis-related SNPs in relation to PCA risk and disease aggressiveness among 2,286 European-American men using SEN-guided MDR. Specifically, SEN was used to build a topographically significant aggressive PCA epistasis network, prior to evaluating complex interactions. This inferred epistasis network consisted of 24 SNPs and 34 pairwise interactions, and reduced MDR analysis from > 36 million to < 13,000 SNP interactions. Consequently, we observed a non-linear and modest interaction between AKT3 rs2125230-PRKCQ rs571715 in relation to aggressive PCA. This state-of-the-art bioinformatics technique facilitates the logical prioritization of SNPs for gene-gene interaction analyses in relation to complex diseases.
Unfortunately, there are no published reports on the functional consequence of these two intronic SNPs in AKT3 and PRKCQ in relation to mRNA stability/expression protein expression/structure/function or PCA outcomes. However, we speculate that the AKT3 rs2125230 and PRKCQ rs571715 sequence variants, with minor allele frequencies ranging from 14.4-22.9 among men of European descent, may alter transcription regulation, leading to increased mRNA expression. Increased mRNA/protein expression AKT3 rs2125230 and PRKCQ rs571715 may cause: decreased apoptosis, an escape of transformed cells from programmed cell death, increased accumulation of genetic alterations, genomic instability, and ultimately an invasive PCA phenotype. Thus, in vitro and in vivo assays using (short hairpin RNAs) shRNAs or small interfering RNAs (siRNAs) are needed to elucidate the impact of AKT3-PRKCQ genetic alterations on protein expression, apoptosis capacity, and prostate tumorigenesis.
The impact of a non-linear interaction along the AKT3 rs2125230-PRKCQ rs571715 axis in relation to aggressive PCA may be attributed to markers involved in the apoptosis signaling pathway. Overexpression of PRKCQ and AKT3 are associated with invasive cancer phenotypes [6–19]. In fact, AKT3 is responds to insulin and growth factors, transduces signals including cell death, and is upregulated in androgen-independent PCA cell lines . PRKCQ is also associated with apoptosis. In particular PRKCQ, a protein kinase C (PRKC) family member, promotes cell survival by inactivating BAD (BCL2-associated agonist of cell death), which subsequently results in NFκB activation.
Although AKT3 and PRKCQ are involved in pro-survival pathways, their interaction is not fully understood. However, their interactions with other related protein kinases may offer biological clues on the mechanism by which AKT3 and PRKCQ synergistically influence aggressive PCA. For example, PRKCQ interacts with another AKT family member, AKT1, to activate NFκB . If the AKT3-PRKCQ axis has a similar function as other protein kinases, namely AKT1 and PRKCQ, then these pro-survival markers may synergistically activate NFκB. As a result, activated NFκB may enable the tumor to escape programmed cell death and progress toward an aggressive PCA phenotype.
Numerous observational studies evaluated the impact of one or more apoptosis-related SNPs in relation to cancer outcomes [20–37]. Among 15 case-control studies, less than 10% of the sequence variants evaluated in the current study were significantly associated with various tumors, including of the colon, rectal, ovarian, breast, pancreatic, and non-small cell lung cancers [20–37]. In particular, modest cancer risk estimates were observed among 8 apoptosis-related SNPs detected in CASP3, CASP8, CASP9, TP53, NFKB2, and NFKBIA. However, some of these studies were limited by a small sample size, small number of analyzed SNPs, or failure to consider the impact of multiple SNPs on disease susceptibility. In the current study, there were 24 SNPs detected in 10 apoptosis-related genes [i.e., AKT3, BIK, BNIP3L, CARD8, CASP9, IKBKE, PRKCE, TNFSF10, and TNFRSF10 (B, D)]. These apoptosis-related SNPs, after adjusting for confounders, were modestly associated with PCA risk and/or aggressive disease. Yet, these findings lost statistical significance after adjusting for multiple hypothesis testing. Main effects were not observed for AKT3 rs2125230 and PRKCQ rs571715 in relation to PCA risk or disease progression in our study set. Wang and co-workers (2009) evaluated interactions among 5 apoptosis-related SNPs, including death receptor 4 (DR4), and pack-years of smoking in relation to bladder cancer using entropy-based MDR . MDR analysis revealed a significant additive interaction between DR4 -397 G > T and smoking on bladder cancer. Unfortunately, this study analyzed a relatively small number of sequence variants in the DR4 apoptosis-related gene; hence, making it difficult to compare study findings. In a post-hoc analysis, we did not observe any interactions among the selected apoptosis-related markers and sources of reactive oxygen species, antioxidants, and anti-inflammatory agents, including cigarette smoking, dietary supplements, aspirin, ibuprofen, and meat-derived carcinogens (data not shown).
We considered the strengths, limitations and future directions of the current study. Although SEN-guided MDR only identified a nominally significant network for disease aggressiveness in the current study, this approach overcomes the computational challenge of detecting all possible two-, three- and four-way SNP combinations involved in PCA progression. SEN, in the current study, was used to prioritize > 10 million possible interactions by focusing on a "sub-network" of informative SNPs in relation to aggressive PCA. Reduction of our genetic data set to the most informative markers improved the feasibility to detect interactions that may have otherwise remained undetected. Unfortunately, the genome-wide association studies (GWAS) database used for the current study did not include apoptosis-related sequence variants (e.g., TNF-308 rs1800629, TNFSF10 rs1131532, BCL2 -936 rs2279115) previously reported in published cancer epidemiology studies [52–54]. Future studies in our laboratory will focus on high-throughput targeted sequencing to evaluate the impact of novel and commonly reported sequence variants on PCA susceptibility and disease prognosis. In light of recent GWAS reports, it is tempting to assume that extremely large case-control study sets, involving tens of thousands subjects are required to evaluate millions of SNP interactions in relation to PCA outcomes. However, the current study had adequate statistical power to evaluate individual and SNP combination effects in relation to prostate cancer. In particular, MDR has 80% statistical power to evaluate all possible two-, three-, and four-way gene-gene interactions with as low as 200 cases and 200 controls . MDR remains effective even in the presence of 5% genotyping errors and/or 5% missing data . It is anticipated that 5% of the about 13,000 possible interactions among 24 apoptosis-related SNPs will result in approximately 650 significant relationships due to chance alone. However, MDR coupled with permutation testing adjust for multiple comparison bias. Given the low prediction accuracy affiliated with the interaction between AKT3 and PRKCQ, our study findings require replication within independent study sets. However, recent simulation studies demonstrate that even modest disparities in genotype allele frequencies among study participants of independent study sets may interfere with the capacity to replicate complex interactions . Thus, to ensure reproducibility within future studies, we plan to select study sets with similar genetic architecture (i.e., ancestry identification markers and SNP genotypes) as CGEMS PCA case-control subjects.