Premium
Non‐coding and coding genomic variants distinguish prostate cancer, castration‐resistant prostate cancer, familial prostate cancer, and metastatic castration‐resistant prostate cancer from each other
Author(s) -
Alanazi Ibrahim O.,
Al Shehri Zafer S.,
Ebrahimie Esmaeil,
Giahi Hassan,
MohammadiDehcheshmeh Manijeh
Publication year - 2019
Publication title -
molecular carcinogenesis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.254
H-Index - 97
eISSN - 1098-2744
pISSN - 0899-1987
DOI - 10.1002/mc.22975
Subject(s) - prostate cancer , biology , cancer research , cancer , prostate , chromoplexy , pten , metastasis , oncology , single nucleotide polymorphism , gene , genetics , pca3 , medicine , genotype , apoptosis , pi3k/akt/mtor pathway
A considerable number of deposited variants has provided new possibilities for knowledge discovery in different types of prostate cancer. Here, we analyzed variants located on 3′UTR, 5′UTR, CDs, Intergenic, and Intronic regions in castration‐resistant prostate cancer (8496 variants), familial prostate cancer (3241 variants), metastatic castration‐resistant prostate cancer (3693 variants), and prostate cancer (16599 variants). Chromosome regions 10p15‐p14 and 2p13 were highly enriched ( P < 0.00001) for variants located in 3′UTR, 5′UTR, CDs, intergenic, and intronic regions in castration‐resistant prostate cancer. In contrast, 10p15‐p14, 10q23.3, 12q13.11, 13q12.3, 1q25, and 8p22 regions were enriched ( P < 0.001) in familial prostate cancer. In metastatic castration‐resistant prostate cancer, 10p15‐p14, 10q23.3, 11q22‐q23, 14q21.1, and 14q32.13 were highly variant regions ( P < 0.001). Chromosome 2 and chromosome 1 hosted many enriched variant regions. AKR1C3 , BRCA1 , BRCA2 , CHGA , CYP19A1 , HOXB13 , KLK3 , and PTEN contained the highest number of 3′UTR, 5′UTR, CDs, Intergenic, and Intronic variants. Network analysis showed that these genes are upstream of important functions including prostate gland development, tumor recurrence, prostate cancer‐specific survival, tumor progression, cancer mortality, long‐term survival, cancer recurrence, angiogenesis, and AR. Interestingly, all of EGFR , JAK2 , NR3C1 , PDZD2 , and SEMA3C genes had single nucleotide polymorphisms (SNP) in castration‐resistant prostate cancer, consistent with high selection pressure on these genes during drug treatment and consequent resistance. High occurrence of variants in 3′UTRs suggests the importance of regulatory variants in different types of prostate cancer; an area that has been neglected compared with coding variants. This study provides a comprehensive overview of genomic regions contributing to different types of prostate cancer.