Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prostate cancer small non-coding RNA transcriptome in Arabs.

ABSTRACT: BACKGROUND:Prostate cancer (PCa) is a complex disorder resulting from the combined effects of multiple environmental and genetic factors. Small non-coding RNAs (sRNAs), particularly microRNAs (miRNAs), regulate several cellular processes and have an important role in many human malignancies including PCa. We assessed the sRNA profiles associated with PCa in Arabs, a population that has rarely been studied. METHODS:We used next generation sequencing technology to obtain the entire sRNA transcriptome of primary prostate tumor formalin-fixed paraffin-embedded tissues, and their paired non-tumor tissues, collected from Bedouin patients (Qatari and Saudi). The miRNA and the target gene expression were evaluated by real-time quantitative PCR. miRNA KEGG pathway and miRNA target genes were subsequently analyzed by starBase and TargetScan software. RESULTS:Different expression patterns of several sRNA and miRNA editing were revealed between PCa tumor and their paired non-tumor tissues. Our study identified four miRNAs that are strongly associated with prostate cancer, which have not been reported previously. Differentially expressed miRNAs significantly affect various biological pathways, such as cell cycle, endocytosis, adherence junction and pathways involved in cancer. Prediction of potential targets for the identified miRNAs indicates the overexpression of KRAS, BCL2 and down-regulation of PTEN in PCa tumor tissues. CONCLUSION:These miRNAs, newly associated with prostate cancer, may represent not only markers for the increased risk of PCa in Arabs, but may also reflect the clinical and pathological diversity as well as the ethno-specific heterogeneity of prostate cancer.

SUBMITTER: Shan J

PROVIDER: S-EPMC5740966 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Small non-coding RNA and cancer.

Project description:The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated. In this review, focusing our attention on recent research results, we provide an overview of the four large classes of small non-coding RNAs, namely, miRNAs, piRNAs, snoRNA and the new class of tRNA-derived fragments, highlighting their fundamental role in cancer and their potential as diagnostic and prognostic biomarkers.

| S-EPMC6248440 | biostudies-literature

Long non-coding RNA in prostate cancer.

Project description:Prostate cancer is the most frequently diagnosed cancer in males and its development and progression remains an important area of study. Recently, long non-coding RNAs (lncRNAs) have been evidenced as key players in cancer pathogenesis. Specifically, dysregulation of long non-coding RNA (lncRNA) expression has shown to affect tumor proliferation and metastasis, acting as either tumor suppressors or oncogenes. However, its specific mechanisms and functions in prostate cancer remain unclear. This review provides an overview of currently available information on prostate cancer-related lncRNAs, including GAS5, GAS-007, MEG3, PCA3, PCAT14, PCAT1, PVT1, UCA1, SChLAP1, MALAT1, HOTAIR, and NEAT1. Notable tumor growth inhibitors include GAS5 and MEG3. GAS5 is evidenced to interfere with the AKT/MTOR signaling pathway through targeting microRNA mir-103. MEG3, however, is proposed to inhibit the cycle, sponge miR-9-5p, and induce gene silencing. PCAT1, PVT1, and UCA1 are important tumor growth promoters. PCAT1 is indicated to be a transcriptional repressor, a mir-145-5P sponge, and a P13K/AKT pathway activator. Studies suggest that PVT1 acts via microRNA targeting and regulating proliferating cell nuclear antigen. UCA1 may sponge miR-204 and miR-331-3p as well as regulate myosin VI. Thorough understanding of these lncRNAs may elucidate new aspects of prostate cancer pathology and serve a pivotal role in developing novel diagnostic and prognostic techniques.

| S-EPMC9301060 | biostudies-literature

Small non-coding RNA transcriptome of the NCI-60 cell line panel.

Project description:Only 3% of the transcribed human genome is translated into protein, and small non-coding RNAs from these untranslated regions have demonstrated critical roles in transcriptional and translational regulation of proteins. Here, we provide a resource that will facilitate cell line selection for gene expression studies involving sncRNAs in cancer research. As the most accessible and tractable models of tumours, cancer cell lines are widely used to study cancer development and progression. The NCI-60 panel of 59 cancer cell lines was curated to provide common models for drug screening in 9 tissue types; however, its prominence has extended to use in gene regulation, xenograft models, and beyond. Here, we present the complete small non-coding RNA (sncRNA) transcriptomes of these 59 cancer cell lines. Additionally, we examine the abundance and unique sequences of annotated microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs), and reveal novel unannotated microRNA sequences.

| S-EPMC5654365 | biostudies-literature

Transcriptome analysis reveals a long non-coding RNA signature to improve biochemical recurrence prediction in prostate cancer.

Project description:Despite highly successful treatments for localized prostate cancer (PCa), prognostic biomarkers are needed to improve patient management and prognosis. Accumulating evidence suggests that long noncoding RNAs (lncRNAs) are key regulators with biological and clinical significance. By transcriptome analysis, we identified a set of consistently dysregulated lncRNAs in PCa across different datasets and revealed an eight-lncRNA signature that significantly associated with the biochemical recurrence (BCR)-free survival. Based on the signature, patients could be classified into high- and low-risk groups with significantly different survival (HR = 2.19; 95% CI = 1.67-2.88; P < 0.0001). Validations in the validation cohorts and another independent cohort confirmed its prognostic value for recurrence prediction. Multivariable analysis showed that the signature was independent of common clinicopathological features and stratified analysis further revealed its role in elevating risk stratification of current prognostic models. Additionally, the eight-lncRNA signature was able to improve on the CAPRA-S score for the prediction of BCR as well as to reflect the metastatic potential of PCa. Functional characterization suggested that these lncRNAs which showed PCa-specific expression patterns may involve in critical processes in tumorigenesis. Overall, our results demonstrated potential application of lncRNAs as novel independent biomarkers. The eight-lncRNA signature may have clinical potential for facilitating further stratification of more aggressive patients who would benefit from adjuvant therapy.

| S-EPMC5982764 | biostudies-literature

[Progress of Long Non-coding RNA in Non-small Cell Lung Cancer].

Project description:Lung cancer is one of the most important malignant tumors in the world. The morbidity and mortality rank the first in all kinds of cancer. Long non-coding RNA (lncRNA) is at least 200 nt long and has no protein coding capacity. It plays an important role in the epigenetic regulation, cell cycle regulation, the regulation of cell differentiation, and many other life activities. The studies indicate that dysregulation of lncRNAs in non-small cell lung cancer (NSCLC) tissue and blood circulation is associated with the occurrence and development of cancer. The lncRNAs play an significant role in proliferation, differentiation, migration and apoptosis of the tumor cells. Explore the potential mechanism between lncRNAs and NSCLC is beneficial for the early diagnosis, target therpy and improve prognosis. Therefore, the study aims to demonstrate the latest studies on the lncRNAs related to occurence, diagnosis, therpy and prognosis of NSCLC. It can help to deeply understanding of lncRNA, and provide new ideas for the prevention of NSCLC.

| S-EPMC5972355 | biostudies-literature

Urinary exosomal small non-coding RNA expression of prostate cancer patients

Project description:Small non-coding RNA profiling of urine exosomal total RNA from patients with or without prostate cancer were performed using Affymetrix GeneChip miRNA 4.0 to identify small non-coding RNA profile that can be used for prostate cancer diagnosis.

2020-07-29 | GSE138740 | GEO

Urinary exosomal small non-coding RNA expression of prostate cancer patients

Project description:Small non-coding RNA profiling of urine exosomal total RNA from patients with or without prostate cancer were performed using Affymetrix miRNA Gene-Chip 4.0 to identify small non-coding RNA proflie that can be used for prostate cancer diagnosis.

2020-10-08 | GSE159177 | GEO

Diagnostic significance of urinary long non-coding PCA3 RNA in prostate cancer.

Project description:Prostate cancer antigen 3(PCA3) is a long non-coding RNA, which was found increased expression in CaP patients than healthy individual. In this study, the individual nucleic acid of PCA3 and PSA was recombinant expressed as a reference reagent, and a quantitative RT-PCR with TaqMan assay was developed to examine the copies of PCA3 and PSA gene in urine. The results showed that the area under the receiver operating characteristic curve (AUROC) was 0.717, 0.444 and 0.916 for the number of PCA3 copy, PSA copy and for the score of PCA3/PSA RNA, respectively. Additionally, the AUROC for serum tPSA was 0.674 with a low specificity of 12.07%. Finally, the algorithm of PCA3 RNA versus PSA RNA was evaluated and corroborated as CaP biomarker by conducting a multicentric clinical trial. This study not only validated the developed technique of qRT-PCR with TaqMan assay for examination of urinary PCA3 and PSA RNA, it also demonstrated that the score of the PCA/PSA RNA was a reliable signature for CaP diagnosis.

| S-EPMC5601676 | biostudies-literature

Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives.

Project description:Animals that lived at high altitudes have evolved distinctive physiological traits that allow them to tolerate extreme high-altitude environment, including higher hemoglobin concentration, increased oxygen saturation of blood and a high energy metabolism. Although previous investigations performed plenty of comparison between high- and low-altitude mammals at the level of morphology, physiology and genomics, mechanism underlying high-altitude adaptation remains largely unknown. Few studies provided comparative analyses in high-altitude adaptation, such as parallel analysis in multiple species. In this study, we generated high-quality small RNA sequencing data for six tissues (heart, liver, spleen, lung, kidney and muscle) from low- and high-altitude populations of four typical livestock animals, and identified comparable numbers of miRNAs in each species. This dataset will provide valuable information for understanding the molecular mechanism of high-altitude adaptation in vertebrates.

| S-EPMC6778140 | biostudies-literature

Small Non-Coding-RNA in Gynecological Malignancies.

Project description:Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.

| S-EPMC7961667 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data