Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer

Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding...

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Veröffentlicht in:PloS one 2015-05, Vol.10 (5), p.e0122143-e0122143
Hauptverfasser: Bawa, Pushpinder, Zackaria, Sajna, Verma, Mohit, Gupta, Saurabh, Srivatsan, R, Chaudhary, Bibha, Srinivasan, Subhashini
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container_title PloS one
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Zackaria, Sajna
Verma, Mohit
Gupta, Saurabh
Srivatsan, R
Chaudhary, Bibha
Srinivasan, Subhashini
description Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant.
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The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25933431</pmid><doi>10.1371/journal.pone.0122143</doi><oa>free_for_read</oa></addata></record>
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subjects Androgens
Bias
Bioinformatics
Biotechnology
Breast cancer
Cancer
Chromosome 8
Chromosomes, Human, Pair 17 - genetics
Databases, Genetic
Datasets
Demography
Epigenetics
EZH2 gene
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene regulation
Gene Regulatory Networks
Genes
Genes, Neoplasm
Genetic Loci
Genomes
Genomics
Human tissues
Humans
Liver
Loci
Lung cancer
Male
Multigene Family
Principal Component Analysis
Prostate cancer
Prostatic Neoplasms - genetics
Proteins
Reproducibility of Results
Ribonucleic acid
RNA
RNA, Long Noncoding - genetics
RNA, Long Noncoding - metabolism
Sequence Analysis, RNA
Suppressor factor
Thyroid
Tissues
Tumor suppressor genes
title Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer
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