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
AU - Andersson, Robin
AU - Itoh, Masayoshi
AU - Lassmann, Timo
AU - Hayashizaki, Yoshihide
AU - Carninci, Piero
AU - Forrest, Alistair R.R.
N1 - Funding Information:
B. Kaczkowski was supported by Postdoctoral Fellowship Program from Japan Society for the Promotion of Science (JSPS) and Foreign Postdoctoral Researcher (FPR) program from RIKEN, Japan. Y. Tanaka was supported by Grants-in-Aid for Scientific Research (KAKENHI) from the Ministry of Education, Culture, Sports, Science, and Technology. R. Andersson was supported by funding from the European Research Council (ERC) under the European Union''s Horizon 2020 Research and Innovation Programme (grant agreement No. 638273). A. Sandelin was supported by the Novo Nordisk Foundation and the Lundbeck Foundation. FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y. Hayashizaki and a Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y. Hayashizaki. This study is also supported by Research Grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology through RIKEN Preventive Medicine and Diagnosis Innovation Program to Y. Hayashizaki and RIKEN Centre for Life Science, Division of Genomic Technologies to P. Carninci. A.R.R. Forrest is supported by a Senior Cancer Research Fellowship from the Cancer Research Trust and funds raised by the MACA Ride to Conquer Cancer.
Publisher 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.
UR - http://www.scopus.com/inward/record.url?scp=84958975245&partnerID=8YFLogxK
U2 - 10.1158/0008-5472.CAN-15-0484
DO - 10.1158/0008-5472.CAN-15-0484
M3 - Article
C2 - 26552699
SN - 0008-5472
VL - 76
SP - 216
EP - 226
JO - Cancer Research
JF - Cancer Research
IS - 2
ER -
