Genetic variants of the autophagy pathway as prognostic indicators for prostate cancer

Abstract

Autophagy is a complex process of autodigestion in conditions of cellular stress, and it might play an important role in the pathophysiology during carcinogenesis. We hypothesize that genetic variants of the autophagy pathway may influence clinical outcomes in prostate cancer patients. We genotyped 40 tagging single-nucleotide polymorphisms (SNPs) from 7 core autophagy pathway genes in 458 localized prostate cancer patients. Multivariate Cox regression was performed to evaluate the independent association of each SNP with disease progression. Positive findings were then replicated in an independent cohort of 504 advanced prostate cancer patients. After adjusting for known clinicopathologic factors, the association between ATG16L1 rs78835907 and recurrence in localized disease [hazard ratio (HR) 0.70, 95% confidence interval (CI) 0.54-0.90, P = 0.006] was replicated in more advanced disease (HR 0.78, 95% CI 0.64-0.95, P = 0.014). Additional integrated in silico analysis suggests that rs78835907 tends to affect ATG16L1 expression, which in turn is correlated with tumor aggressiveness and patient prognosis. In conclusion, genetic variants of the autophagy pathway contribute to the variable outcomes in prostate cancer, and discovery of these novel biomarkers might help stratify patients according to their risk of disease progression.

Figure 1. Impact of ATG16L1 rs78835907 on prostate cancer progression.

Kaplan-Meier estimates of (A) BCR-free survival in localized prostate cancer patients who underwent RP, and (B) progression-free survival in advanced prostate cancer patients who received ADT, by ATG16L1 rs78835907 genotypes. Numbers in parentheses indicate the number of patients.

Figure 2. Summary of the functional analyses for the linkage disequilibrium (LD) block containing ATG16L1 rs78835907.

(A) Expanded view of the ENCODE data for the LD block containing the ATG16L1 rs78835907. The H3K4Me1, H3K4Me3, and H3K27Ac tracks show the genome-wide levels of enrichment of the mono-methylation of lysine 4, tri-methylation of lysine 4, and acetylation of lysine 27 of the H3 histone protein, as determined by the ChIP-seq assays. These levels are thought to be associated with promoter and enhancer regions. Chromatin State Segmentation track displays chromatin state segmentations by integrating ChIP-seq data using a Hidden Markov Model for H1 embryonic stem cells, HepG2 hepatocellular carcinoma cells, HUVEC umbilical vein endothelial cells, HMEC mammary epithelial cells, HSMM, skeletal muscle myoblasts, NHEK epidermal keratinocytes, and NHLF lung fibroblasts. The chromatin state regions predicted for promoters and enhancers are highlighted. DNase clusters track shows DNase hypersensitivity areas. Tnx Factor track shows regions of transcription factor binding of DNA, as assayed by ChIP-seq experiments. (B) Regulatory annotation of variants within the LD block containing ATG16L1 rs78835907. In the LD block with the lead SNP rs78835907, ENCODE data showed evidence of promoter and enhancer elements coinciding with the variants in many different cell types. In addition, HDAC2 and AP-2 motifs are predicted to be affected. (C) Expression quantitative trait locus association between rs78835907 genotype and ATG16L1 expression in prostate tissues (GTEx data set). Numbers in parentheses indicate the number of cases.

Figure 3. Correlation of ATG16L1 mRNA expression with prostate cancer progression.

The associations between ATG16L1 expression and prostate cancer aggressiveness were analyzed using MSKCC Prostate Oncogenome data. More advanced prostate cancers with metastasis (A) and high pathologic Gleason score (B) display a tendency toward lower ATG16L1 mRNA expression. Numbers in parentheses indicate the number of patients. (C) ATG16L1 shows higher levels of gene expression in tumors with increased DNA copy number at 2q37. (D) Kaplan-Meier curves of recurrence-free survival according to the downregulation of ATG16L1 expression. Patients were dichotomized with or without ATG16L1 mRNA downregulation (z-scores < −2).