Genetic variants in ultraconserved regions associate with prostate cancer recurrence and survival

Bao, Bo-Ying; Lin, Victor C.; Yu, Chia‐Cheng; Yin, Hsin‐Ling; Chang, Ta-Yuan; Lu, Te‐Ling; Lee, Hong‐Zin; Pao, Jiunn-Bey; Huang, Chao-Yuan; Huang, Shu‐Pin

doi:10.1038/srep22124

Cited by 21 publications

(12 citation statements)

References 38 publications

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“…They might also be good candidates for targeted sequencing projects and association studies (Silla et al, 2014) and might present valuable and easily detectable disease biomarkers. Bao et al (2016) for example found association between rs8004379 and prostate cancer-specific mortality. SNPs within UCEs may also be valuable prognostic biomarkers for patients with locally advanced colorectal cancer who receive 5-fluorouracil-based chemotherapy (Lin et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Genetic Variations of Ultraconserved Elements in the Human Genome

Habic

Mattick

Calin

et al. 2019

OMICS: A Journal of Integrative Biology

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Ultraconserved elements (UCEs) are among the most popular DNA markers for phylogenomic analysis. In at least three of five placental mammalian genomes (human, dog, cow, mouse, and rat), 2189 UCEs of at least 200 bp in length that are identical have been identified. Most of these regions have not yet been functionally annotated, and their associations with diseases remain largely unknown. This is an important knowledge gap in human genomics with regard to UCE roles in physiologically critical functions, and by extension, their relevance for shared susceptibilities to common complex diseases across several mammalian organisms in the event of their polymorphic variations. In the present study, we remapped the genomic locations of these UCEs to the latest human genome assembly, and examined them for documented polymorphisms in sequenced human genomes. We identified 29,983 polymorphisms within analyzed UCEs, but revealed that a vast majority exhibits very low minor allele frequencies. Notably, only 112 of the identified polymorphisms are associated with a phenotype in the Ensembl genome browser. Through literature analyses, we confirmed associations of 37 (i.e., out of the 112) polymorphisms within 23 UCEs with 25 diseases and phenotypic traits, including, muscular dystrophies, eye diseases, and cancers (e.g., familial adenomatous polyposis). Most reports of UCE polymorphism-disease associations appeared to be not cognizant that their candidate polymorphisms were actually within UCEs. The present study offers strategic directions and knowledge gaps for future computational and experimental work so as to better understand the thus far intriguing and puzzling role(s) of UCEs in mammalian genomes.

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Section: Discussionmentioning

confidence: 99%

Genetic Variations of Ultraconserved Elements in the Human Genome

Habic

Mattick

Calin

et al. 2019

OMICS: A Journal of Integrative Biology

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“…It has been suggested that lncRNA PRNCR1 promotes prostate carcinogenesis via activating AR (26). SNPs, a class of genetic variations, are commonly used in the prediction of cancer risk (38,44,45), prognosis (46) and clinical outcome (47). Cumulative evidence indicates that non-coding genes may be involved in gene expression complexity in humans (48,49).…”

Section: Discussionmentioning

confidence: 99%

Association between genetic polymorphisms of long non‑coding RNA PRNCR1 and prostate cancer risk in a sample of the Iranian population

et al. 2017

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Abstract. The aim of the present study was to determine whether there is an association between the long non-coding RNA (lncRNA) prostate cancer-associated non-coding RNA 1 (PRNCR1) polymorphisms and prostate cancer (PCa) risk in a sample of the Iranian population. This case-control study was performed on 178 patients with PCa and 180 subjects with benign prostatic hyperplasia (BPH). Genotyping assay was performed by polymerase chain reaction-restriction fragment length polymorphism. The findings indicated that the GG genotype of the rs13252298 A>G variant significantly increased the risk of PCa (odds ratio=3.49, 95% confidence interval: 1.79-6.81, P=0.0001) compared with AA+AG. As regards the rs1456315 G>A polymorphism, the AG genotype and G allele significantly increased the risk of PCa. As regards the rs7841060 T>G variant, the findings demonstrated that this TG genotype and the G allele significantly increased the risk of PCa. The rs7007694 T>C variant was not found to be associated with the risk of PCa. Haplotype analysis indicated that GTGA and GTGG significantly increased the risk of PCa compared with rs1456315A/rs7007694T/rs7841060T/rs13252298G (ATTG). The PRNCR1 variants were not found to be significantly associated with the clinicopathological characteristics of PCa patients. In conclusion, our findings support an association between PRNCR1 variants and the risk of PCa in a sample of the Iranian population.

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“…Bao et al () demonstrated that rs8004379 (A>C) in uc.368 exhibits a significant association in recurrence localized PC. The protective C allele was associated with a decreased risk of mortality in advanced PC patients.…”

Section: Single Nucleotide Variation In T‐ucrsmentioning

confidence: 99%

“…The protective C allele was associated with a decreased risk of mortality in advanced PC patients. By bioinformatic approaches, rs8004379 probably affects NPAS3, a PC prognostic marker (Bao et al, 2016). Wojcik et al (2010)genotyped 35 patients diagnosed with CRC to 28 SNPs located in T-UCRs.…”

Section: Single Nucleotide Variation In T-ucrsmentioning

confidence: 99%

Highlighting transcribed ultraconserved regions in human diseases

et al. 2019

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Ultraconserved regions (UCRs) are 481 DNA segments longer than 200 bp in length that are completely conserved among human, mouse, and rat and, extremely conserved across disparate taxa. More than 90% of UCRs are transcribed (T‐UCRs) in normal tissues, but most of them remain uncharacterized. In addition, it was demonstrated that T‐UCRs have a tissue‐specific expression, and a differential expression profile between tumors and other diseases, which suggests that most of T‐UCRs may have an important role in cell processes. However, there is little information about T‐UCR characterization or about their molecular mechanisms of action. Taking this into account, in this study, we aim to summarize deregulated T‐UCRs in human diseases, emphasizing the ones with stronger functional evidences that are associated with important cell pathways and have a detailed molecular characterization. This article is characterized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

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Genetic variants in ultraconserved regions associate with prostate cancer recurrence and survival

Cited by 21 publications

References 38 publications

Genetic Variations of Ultraconserved Elements in the Human Genome

Genetic Variations of Ultraconserved Elements in the Human Genome

Association between genetic polymorphisms of long non‑coding RNA PRNCR1 and prostate cancer risk in a sample of the Iranian population

Highlighting transcribed ultraconserved regions in human diseases

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