Suhas V Vasaikar1, Abhijeet P Deshmukh1, Petra den Hollander1, Sridevi Addanki1, Nick Allen Kuburich1, Sriya Kudaravalli1, Robiya Joseph1, Jeffrey T Chang2, Rama Soundararajan1, Sendurai A Mani3. 1. Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. 2. Department of Integrative Biology & Pharmacology, Institute of Molecular Medicine, School of Biomedical Informatics University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. 3. Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. smani@mdanderson.org.
Abstract
BACKGROUND: The epithelial-mesenchymal transition (EMT) enables dissociation of tumour cells from the primary tumour mass, invasion through the extracellular matrix, intravasation into blood vessels and colonisation of distant organs. Cells that revert to the epithelial state via the mesenchymal-epithelial transition cause metastases, the primary cause of death in cancer patients. EMT also empowers cancer cells with stem-cell properties and induces resistance to chemotherapeutic drugs. Understanding the driving factors of EMT is critical for the development of effective therapeutic interventions. METHODS: This manuscript describes the generation of a database containing EMT gene signatures derived from cell lines, patient-derived xenografts and patient studies across cancer types and multiomics data and the creation of a web-based portal to provide a comprehensive analysis resource. RESULTS: EMTome incorporates (i) EMT gene signatures; (ii) EMT-related genes with multiomics features across different cancer types; (iii) interactomes of EMT-related genes (miRNAs, transcription factors, and proteins); (iv) immune profiles identified from The Cancer Genome Atlas (TCGA) cohorts by exploring transcriptomics, epigenomics, and proteomics, and drug sensitivity and (iv) clinical outcomes of cancer cohorts linked to EMT gene signatures. CONCLUSION: The web-based EMTome portal is a resource for primary and metastatic tumour research publicly available at www.emtome.org .
BACKGROUND: The epithelial-mesenchymal transition (EMT) enables dissociation of tumour cells from the primary tumour mass, invasion through the extracellular matrix, intravasation into blood vessels and colonisation of distant organs. Cells that revert to the epithelial state via the mesenchymal-epithelial transition cause metastases, the primary cause of death in cancerpatients. EMT also empowers cancer cells with stem-cell properties and induces resistance to chemotherapeutic drugs. Understanding the driving factors of EMT is critical for the development of effective therapeutic interventions. METHODS: This manuscript describes the generation of a database containing EMT gene signatures derived from cell lines, patient-derived xenografts and patient studies across cancer types and multiomics data and the creation of a web-based portal to provide a comprehensive analysis resource. RESULTS: EMTome incorporates (i) EMT gene signatures; (ii) EMT-related genes with multiomics features across different cancer types; (iii) interactomes of EMT-related genes (miRNAs, transcription factors, and proteins); (iv) immune profiles identified from The Cancer Genome Atlas (TCGA) cohorts by exploring transcriptomics, epigenomics, and proteomics, and drug sensitivity and (iv) clinical outcomes of cancer cohorts linked to EMT gene signatures. CONCLUSION: The web-based EMTome portal is a resource for primary and metastatic tumour research publicly available at www.emtome.org .
Authors: E Batlle; E Sancho; C Francí; D Domínguez; M Monfar; J Baulida; A García De Herreros Journal: Nat Cell Biol Date: 2000-02 Impact factor: 28.824
Authors: Tathiane M Malta; Artem Sokolov; Andrew J Gentles; Tomasz Burzykowski; Laila Poisson; John N Weinstein; Bożena Kamińska; Joerg Huelsken; Larsson Omberg; Olivier Gevaert; Antonio Colaprico; Patrycja Czerwińska; Sylwia Mazurek; Lopa Mishra; Holger Heyn; Alex Krasnitz; Andrew K Godwin; Alexander J Lazar; Joshua M Stuart; Katherine A Hoadley; Peter W Laird; Houtan Noushmehr; Maciej Wiznerowicz Journal: Cell Date: 2018-04-05 Impact factor: 41.582
Authors: Achilleas D Theocharis; Spyros S Skandalis; Thomas Neill; Hinke A B Multhaupt; Mario Hubo; Helena Frey; Sandeep Gopal; Angélica Gomes; Nikos Afratis; Hooi Ching Lim; John R Couchman; Jorge Filmus; Ralph D Sanderson; Liliana Schaefer; Renato V Iozzo; Nikos K Karamanos Journal: Biochim Biophys Acta Date: 2015-03-28
Authors: Milena P Mak; Pan Tong; Lixia Diao; Robert J Cardnell; Don L Gibbons; William N William; Ferdinandos Skoulidis; Edwin R Parra; Jaime Rodriguez-Canales; Ignacio I Wistuba; John V Heymach; John N Weinstein; Kevin R Coombes; Jing Wang; Lauren Averett Byers Journal: Clin Cancer Res Date: 2015-09-29 Impact factor: 12.531
Authors: Chun-Liang Chen; Devalingam Mahalingam; Pawel Osmulski; Rohit R Jadhav; Chiou-Miin Wang; Robin J Leach; Tien-Cheng Chang; Steven D Weitman; Addanki Pratap Kumar; Luzhe Sun; Maria E Gaczynska; Ian M Thompson; Tim Hui-Ming Huang Journal: Prostate Date: 2012-12-31 Impact factor: 4.104
Authors: Dan R Robinson; Yi-Mi Wu; Robert J Lonigro; Pankaj Vats; Erin Cobain; Jessica Everett; Xuhong Cao; Erica Rabban; Chandan Kumar-Sinha; Victoria Raymond; Scott Schuetze; Ajjai Alva; Javed Siddiqui; Rashmi Chugh; Francis Worden; Mark M Zalupski; Jeffrey Innis; Rajen J Mody; Scott A Tomlins; David Lucas; Laurence H Baker; Nithya Ramnath; Ann F Schott; Daniel F Hayes; Joseph Vijai; Kenneth Offit; Elena M Stoffel; J Scott Roberts; David C Smith; Lakshmi P Kunju; Moshe Talpaz; Marcin Cieślik; Arul M Chinnaiyan Journal: Nature Date: 2017-08-02 Impact factor: 49.962
Authors: O I Brovkina; I V Pronina; A M Burdennyy; L A Uroshlev; E A Filippova; M V Fridman; T P Kazubskaya; K I Zhordania; V I Loginov; N E Kushlinskii; E A Braga Journal: Bull Exp Biol Med Date: 2022-05-02 Impact factor: 0.804
Authors: Hannah Weisser; Tamara Göbel; G Melissa Krishnathas; Marius Kreiß; Carlo Angioni; Duran Sürün; Dominique Thomas; Tobias Schmid; Ann-Kathrin Häfner; Astrid S Kahnt Journal: Cancer Gene Ther Date: 2022-09-16 Impact factor: 5.854
Authors: Meng Lin; Amy T Ku; Jie Dong; Fei Yue; Weiyu Jiang; Ahmed Atef Ibrahim; Fanglue Peng; Chad J Creighton; Chandandeep Nagi; Carolina Gutierrez; Jeffrey M Rosen; Xiang H-F Zhang; Susan G Hilsenbeck; Xi Chen; Yi-Chieh Nancy Du; Shixia Huang; Aiping Shi; Zhimin Fan; Yi Li Journal: Oncogene Date: 2022-10-19 Impact factor: 8.756
Authors: Abhijeet P Deshmukh; Suhas V Vasaikar; Katarzyna Tomczak; Shubham Tripathi; Petra den Hollander; Emre Arslan; Priyanka Chakraborty; Rama Soundararajan; Mohit Kumar Jolly; Kunal Rai; Herbert Levine; Sendurai A Mani Journal: Proc Natl Acad Sci U S A Date: 2021-05-11 Impact factor: 11.205
Authors: Seo Rin Kim; Amrutesh S Puranik; Kai Jiang; Xiaojun Chen; Xiang-Yang Zhu; Ian Taylor; Alireza Khodadadi-Jamayran; Amir Lerman; LaTonya J Hickson; Bennett G Childs; Stephen C Textor; Tamara Tchkonia; Timothy B Niewold; James L Kirkland; Lilach O Lerman Journal: J Am Soc Nephrol Date: 2021-06-16 Impact factor: 14.978