TY - JOUR
T1 - Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers
AU - Kaczkowski, Bogumil
AU - Tanaka, Yuji
AU - Kawaji, Hideya
AU - Sandelin, Albin Gustav
AU - Andersson, Robin
AU - Itoh, Masayoshi
AU - Lassmann, Timo
AU - the FANTOM5 consortium, null
AU - Hayashizaki, Yoshihide
AU - Carninci, Piero
AU - Forrest, Alistair R. R.
N1 - Copyright © 2015, American Association for Cancer Research.
PY - 2016/1/15
Y1 - 2016/1/15
N2 - Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genomewide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression.
AB - Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genomewide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression.
U2 - 10.1158/0008-5472.can-15-0484
DO - 10.1158/0008-5472.can-15-0484
M3 - Journal article
C2 - 26552699
SN - 0008-5472
VL - 76
SP - 216
EP - 226
JO - Cancer Research
JF - Cancer Research
IS - 2
ER -
