Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells

Oncotarget
Michael D WestAlex Zhavoronkov

Abstract

Here we present the application of deep neural network (DNN) ensembles trained on transcriptomic data to identify the novel markers associated with the mammalian embryonic-fetal transition (EFT). Molecular markers of this process could provide important insights into regulatory mechanisms of normal development, epimorphic tissue regeneration and cancer. Subsequent analysis of the most significant genes behind the DNNs classifier on an independent dataset of adult-derived and human embryonic stem cell (hESC)-derived progenitor cell lines led to the identification of COX7A1 gene as a potential EFT marker. COX7A1, encoding a cytochrome C oxidase subunit, was up-regulated in post-EFT murine and human cells including adult stem cells, but was not expressed in pre-EFT pluripotent embryonic stem cells or their in vitro-derived progeny. COX7A1 expression level was observed to be undetectable or low in multiple sarcoma and carcinoma cell lines as compared to normal controls. The knockout of the gene in mice led to a marked glycolytic shift reminiscent of the Warburg effect that occurs in cancer cells. The DNN approach facilitated the elucidation of a potentially new biomarker of cancer and pre-EFT cells, the embryo-onco phenotype, which...Continue Reading

References

Sep 12, 1989·Nucleic Acids Research·G M FabriziE A Schon
Sep 30, 1998·Progress in Nucleic Acid Research and Molecular Biology·N LenkaN G Avadhani
Sep 14, 2002·Science·Miguel Ramalho-SantosDouglas A Melton
Sep 16, 2003·Proteomics·Paul C HerrmannEmanuel F Petricoin
Feb 24, 1956·Science·O WARBURG
Oct 18, 2003·Science·Gretchen Vogel
Oct 19, 2006·Nature Reviews. Genetics·Alejandro Sánchez Alvarado, Panagiotis A Tsonis
Feb 17, 2007·The Journal of Biological Chemistry·Jian Li CampianJohn W Eaton
Jun 29, 2007·Nature Genetics·Joshua M AkeyJohn D Storey
May 10, 2008·Bioinformatics·Pan DuSimon M Lin
May 19, 2009·Nature Genetics·Ken K OngNicholas J Wareham
Jun 2, 2009·Nature Genetics·Srinivas R ViswanathanGeorge Q Daley
Jan 26, 2010·Biostatistics·Matthew N McCallRafael A Irizarry
Sep 15, 2010·Nature Reviews. Genetics·Jeffrey T LeekRafael A Irizarry
Mar 19, 2011·Nature Reviews. Genetics·Kathrin Plath, William E Lowry
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Nov 29, 2011·Mitochondrion·Maik HüttemannLawrence I Grossman
May 16, 2013·Nature Reviews. Molecular Cell Biology·Patrick Cahan, George Q Daley
May 30, 2013·Development·Ng Shyh-ChangLewis C Cantley
Nov 12, 2013·Cell·Ng Shyh-ChangGeorge Q Daley
Jun 17, 2014·Bioinformatics·Michael K K LeungBrendan J Frey
Aug 16, 2014·Cell·Patrick CahanJames J Collins
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Feb 27, 2015·Plastic and Reconstructive Surgery·Graham G WalmsleyMichael T Longaker
Mar 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Matt Spencer Jianlin Cheng
Jan 1, 2014·Frontiers in Molecular Biosciences·Anton A BuzdinNikolay M Borisov
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Muxuan LiangJianyang Zeng
Oct 7, 2015·Journal of Chemical Information and Modeling·Youjun XuLuhua Lai
Oct 16, 2015·Nucleic Acids Research·Sai ZhangJianyang Zeng

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Citations

Jan 9, 2019·Stem Cell Research & Therapy·Michael D WestHal Sternberg
May 5, 2020·Frontiers in Pharmacology·Rim ShayakhmetovDaniil Polykovskiy
Aug 29, 2019·Regenerative Medicine·Michael D WestDana Larocca
May 1, 2021·Genes·Dana LaroccaHal Sternberg

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Datasets Mentioned

BETA
GSE62193
GSE49996
GSE58272
GSE73003
GSE35242

Methods Mentioned

BETA
feature extractions
RNA-Seq
electrophoresis
chips

Software Mentioned

Wave desktop
iPanda
TUXEDO suite
scikit
Illumina
Affymetrix
XGBoost
CellNet
GenomeStudio
ArrayExpress

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