Oncogenic splicing abnormalities induced by DEAD-Box Helicase 56 amplification in colorectal cancer

Cancer Science
Yuta KouyamaKoshi Mimori

Abstract

Alternative splicing, regulated by DEAD-Box Helicase (DDX) families, plays an important role in cancer. However, the relationship between the DDX family and cancer has not been fully elucidated. In the present study, we identified a candidate oncogene DDX56 on Ch.7p by a bioinformatics approach using The Cancer Genome Atlas (TCGA) dataset of colorectal cancer (CRC). DDX56 expression was measured by RT-qPCR and immunochemical staining in 108 CRC patients. Clinicopathological and survival analyses were carried out using three CRC datasets. Biological roles of DDX56 were explored by gene set enrichment analysis (GSEA), and cell proliferation in vitro and in vivo, cell cycle assays, and using DDX56-knockdown or overexpressed CRC cells. RNA sequencing was carried out to elucidate the effect of DDX56 on mRNA splicing. We found that DDX56 expression was positively correlated with the amplification of DDX56 and was upregulated in CRC cells. High DDX56 expression was associated with lymphatic invasion and distant metastasis and was an independent poor prognostic factor. In vitro analysis, in vivo analysis and GSEA showed that DDX56 promoted proliferation ability through regulating the cell cycle. DDX56 knockdown reduced intron retention...Continue Reading

References

Jun 1, 1996·Genes, Chromosomes & Cancer·J HerbergsA H Hopman
Aug 14, 1999·International Journal of Cancer. Journal International Du Cancer·S BackertC Hanski
Feb 5, 2004·Annals of Oncology : Official Journal of the European Society for Medical Oncology·T YoshidaH Kuwano
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jun 22, 2006·Journal of Cell Science·Anabella Srebrow, Alberto R Kornblihtt
Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rameen BeroukhimWilliam R Sellers
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Apr 28, 2009·BMC Medical Genomics·Hideaki MizunoAkinori Sarai
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Jul 23, 2011·Nature Reviews. Molecular Cell Biology·Patrick Linder, Eckhard Jankowsky
Sep 13, 2011·Nature·Kenichi YoshidaSeishi Ogawa
Oct 18, 2011·International Journal of Clinical Oncology·Toshiaki WatanabeUNKNOWN Japanese Society for Cancer of the Colon and Rectum
Oct 2, 2012·Nature Structural & Molecular Biology·Etienne DardenneDidier Auboeuf
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Sep 21, 2013·Nature·Philippe L BedardLillian L Siu
Nov 6, 2013·Molecular Oncology·Andrea BisogninSusanna Mandruzzato
Feb 14, 2014·Wiley Interdisciplinary Reviews. RNA·Kenichi Yoshida, Seishi Ogawa
Sep 27, 2014·Genome Research·Ulrich BraunschweigBenjamin J Blencowe
May 8, 2015·Journal of Molecular Cell Biology·Marco SilipoAlison Tyson-Capper
Aug 12, 2015·Proceedings of the National Academy of Sciences of the United States of America·Jian ZhangJames L Manley
Sep 4, 2015·Current Protocols in Bioinformatics·Alexander Dobin, Thomas R Gingeras
Oct 6, 2015·Nature Genetics·Hyunchul JungEunjung Lee
Jun 3, 2016·Nature Reviews. Molecular Cell Biology·Cyril F BourgeoisDidier Auboeuf
Nov 9, 2016·Virology·Colleen R Reid, Tom C Hobman
Jul 4, 2018·PLoS Genetics·Juan Pablo FernandezAntonio J Giraldez

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Citations

Jun 6, 2020·Cancer Science·Kuniaki SatoTakashi Nakagawa
Nov 5, 2019·Frontiers in Bioengineering and Biotechnology·Tong MengLiming Cheng
Sep 29, 2020·Frontiers in Cell and Developmental Biology·Runzhi HuangZongqiang Huang
Jan 14, 2021·Cell Death & Disease·Chengcheng HeQingyuan Li
Feb 20, 2021·Cancer Science·Atsushi FujiiKoshi Mimori
Apr 4, 2021·International Journal of Molecular Sciences·Olga Sergeeva, Timofei Zatsepin
Feb 16, 2020·Molecular Therapy : the Journal of the American Society of Gene Therapy·Jiwei ZhangYongsheng Li
May 20, 2021·Cancer Science·Yuta KobayashiKoshi Mimori
Jun 18, 2021·World Journal of Gastroenterology : WJG·Zai-Sheng YeLu-Chuan Chen
Oct 7, 2021·Cell Death and Differentiation·Pavel MoudryJiri Bartek

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Datasets Mentioned

BETA
GSE21815

Methods Mentioned

BETA
surgical resection
xenograft
FACS

Software Mentioned

R
TopHat2
GSEA
SAS
Intron
JMP Pro
‐ retention ‐ utils
DAVID
Integrative Genomics Viewer ( IGV )

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