@article{730f79c746c24805b29827c3aee1084a,
title = "Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation",
abstract = "Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation. Stemness features extracted from transcriptomic and epigenetic data from TCGA tumors reveal novel biological and clinical insight, as well as potential drug targets for anti-cancer therapies.",
keywords = "The Cancer Genome Atlas, cancer stem cells, dedifferentiation, epigenomic, genomic, machine learning, pan-cancer, stemness",
author = "{The Cancer Genome Atlas Research Network} and Malta, {Tathiane M.} and Artem Sokolov and Gentles, {Andrew J.} and Tomasz Burzykowski and Laila Poisson and Weinstein, {John N.} and Bo{\.z}ena Kami{\'n}ska and Joerg Huelsken and Larsson Omberg and Olivier Gevaert and Antonio Colaprico and Patrycja Czerwi{\'n}ska and Sylwia Mazurek and Lopa Mishra and Holger Heyn and Alex Krasnitz and Godwin, {Andrew K.} and Lazar, {Alexander J.} and Caesar-Johnson, {Samantha J.} and Demchok, {John A.} and Ina Felau and Melpomeni Kasapi and Ferguson, {Martin L.} and Hutter, {Carolyn M.} and Sofia, {Heidi J.} and Roy Tarnuzzer and Zhining Wang and Liming Yang and Zenklusen, {Jean C.} and Zhang, {Jiashan (Julia)} and Sudha Chudamani and Jia Liu and Laxmi Lolla and Rashi Naresh and Todd Pihl and Qiang Sun and Yunhu Wan and Ye Wu and Juok Cho and Timothy DeFreitas and Li Ding and Fulton, {Lucinda A.} and Fulton, {Robert S.} and John DiPersio and Bettina Drake and Ramaswamy Govindan and Timothy Ley and {Van Tine}, Brian and Peter Westervelt",
note = "Funding Information: We thank Marcin Cie{\'s}lik from Michigan Center for Translational Pathology at University of Michigan for providing the MTE500 dataset. This work was supported by the following grants: NIH grants U54 HG003273, U54 HG003067, U54 HG003079, U24 CA143799, U24 CA143835, U24 CA143840, U24 CA143843, U24 CA143845, U24 CA143848, U24 CA143858, U24 CA143866, U24 CA143867, U24 CA143882, U24 CA143883, U24 CA144025, and P30 CA016672; NCI grants 5R01CA180778, 3U24CA143858, 1U24CA210990, 5U54HG006097, 1U24CA210949, and 1U24CA210950; NIGMS grant 5R01GM109031; the Henry Ford Cancer Institute's Early Career Investigator Award grant A20054 to T.M.M; Sao Paulo Research Foundation (FAPESP) grants 2014/02245-3 and 2016/01975-3 to T.M.M. and H.N.; FAPESP grants 2014/08321-3, 2015/07925-5, 2016/01389-7, 2016/10436-9, 2016/06488-3, 2016/12329-5, and 2016/15485-8, and Henry Ford Hospital grant A30935 to H.N.; Spanish Institute of Health Carlos III grant CP14/00229; Mary K. Chapman Foundation gift “Chapman Foundation Fund for Bioinformatics,” CPRIT grant RP13039, and the Michael & Susan Dell Foundation grant “The Lorraine Dell Program in Bioinformatics” to J.N.W.; and the Polish Science Foundation Welcome grant 2010/3-3 to M.W. Funding Information: We thank Marcin Cie{\'s}lik from Michigan Center for Translational Pathology at University of Michigan for providing the MTE500 dataset. This work was supported by the following grants: NIH grants U54 HG003273 , U54 HG003067 , U54 HG003079 , U24 CA143799 , U24 CA143835 , U24 CA143840 , U24 CA143843 , U24 CA143845 , U24 CA143848 , U24 CA143858 , U24 CA143866 , U24 CA143867 , U24 CA143882 , U24 CA143883 , U24 CA144025 , and P30 CA016672 ; NCI grants 5R01CA180778 , 3U24CA143858 , 1U24CA210990 , 5U54HG006097 , 1U24CA210949 , and 1U24CA210950 ; NIGMS grant 5R01GM109031 ; the Henry Ford Cancer Institute{\textquoteright}s Early Career Investigator Award grant A20054 to T.M.M; Sao Paulo Research Foundation (FAPESP) grants 2014/02245-3 and 2016/01975-3 to T.M.M. and H.N.; FAPESP grants 2014/08321-3 , 2015/07925-5 , 2016/01389-7 , 2016/10436-9 , 2016/06488-3 , 2016/12329-5 , and 2016/15485-8 , and Henry Ford Hospital grant A30935 to H.N.; Spanish Institute of Health Carlos III grant CP14/00229 ; Mary K. Chapman Foundation gift “Chapman Foundation Fund for Bioinformatics,” CPRIT grant RP13039 , and the Michael & Susan Dell Foundation grant “The Lorraine Dell Program in Bioinformatics” to J.N.W.; and the Polish Science Foundation Welcome grant 2010/3-3 to M.W. Funding Information: Michael Seiler, Peter G. Smith, Ping Zhu, Silvia Buonamici, and Lihua Yu are employees of H3 Biomedicine, Inc. Parts of this work are the subject of a patent application: WO2017040526 titled “Splice variants associated with neomorphic sf3b1 mutants.” Shouyoung Peng, Anant A. Agrawal, James Palacino, and Teng Teng are employees of H3 Biomedicine, Inc. Andrew D. Cherniack, Ashton C. Berger, and Galen F. Gao receive research support from Bayer Pharmaceuticals. Gordon B. Mills serves on the External Scientific Review Board of Astrazeneca. Anil Sood is on the Scientific Advisory Board for Kiyatec and is a shareholder in BioPath. Jonathan S. Serody receives funding from Merck, Inc. Kyle R. Covington is an employee of Castle Biosciences, Inc. Preethi H. Gunaratne is founder, CSO, and shareholder of NextmiRNA Therapeutics. Christina Yau is a part-time employee/consultant at NantOmics. Franz X. Schaub is an employee and shareholder of SEngine Precision Medicine, Inc. Carla Grandori is an employee, founder, and shareholder of SEngine Precision Medicine, Inc. Robert N. Eisenman is a member of the Scientific Advisory Boards and shareholder of Shenogen Pharma and Kronos Bio. Daniel J. Weisenberger is a consultant for Zymo Research Corporation. Joshua M. Stuart is the founder of Five3 Genomics and shareholder of NantOmics. Marc T. Goodman receives research support from Merck, Inc. Andrew J. Gentles is a consultant for Cibermed. Charles M. Perou is an equity stock holder, consultant, and Board of Directors member of BioClassifier and GeneCentric Diagnostics and is also listed as an inventor on patent applications on the Breast PAM50 and Lung Cancer Subtyping assays. Matthew Meyerson receives research support from Bayer Pharmaceuticals; is an equity holder in, consultant for, and Scientific Advisory Board chair for OrigiMed; and is an inventor of a patent for EGFR mutation diagnosis in lung cancer, licensed to LabCorp. Eduard Porta-Pardo is an inventor of a patent for domainXplorer. Han Liang is a shareholder and scientific advisor of Precision Scientific and Eagle Nebula. Da Yang is an inventor on a pending patent application describing the use of antisense oligonucleotides against specific lncRNA sequence as diagnostic and therapeutic tools. Yonghong Xiao was an employee and shareholder of TESARO, Inc. Bin Feng is an employee and shareholder of TESARO, Inc. Carter Van Waes received research funding for the study of IAP inhibitor ASTX660 through a Cooperative Agreement between NIDCD, NIH, and Astex Pharmaceuticals. Raunaq Malhotra is an employee and shareholder of Seven Bridges, Inc. Peter W. Laird serves on the Scientific Advisory Board for AnchorDx. Joel Tepper is a consultant at EMD Serono. Kenneth Wang serves on the Advisory Board for Boston Scientific, Microtech, and Olympus. Andrea Califano is a founder, shareholder, and advisory board member of DarwinHealth, Inc. and a shareholder and advisory board member of Tempus, Inc. Toni K. Choueiri serves as needed on advisory boards for Bristol-Myers Squibb, Merck, and Roche. Lawrence Kwong receives research support from Array BioPharma. Sharon E. Plon is a member of the Scientific Advisory Board for Baylor Genetics Laboratory. Beth Y. Karlan serves on the Advisory Board of Invitae. Publisher Copyright: {\textcopyright} 2018 The Authors",
year = "2018",
month = apr,
day = "5",
doi = "10.1016/j.cell.2018.03.034",
language = "English",
volume = "173",
pages = "338--354.e15",
journal = "Cell",
issn = "0092-8674",
number = "2",
}