TY - JOUR
T1 - A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition
AU - Mak, Milena P.
AU - Tong, Pan
AU - Diao, Lixia
AU - Cardnell, Robert J.
AU - Gibbons, Don L.
AU - William, William N.
AU - Skoulidis, Ferdinandos
AU - Parra, Edwin R.
AU - Rodriguez-Canales, Jaime
AU - Wistuba, Ignacio I.
AU - Heymach, John V.
AU - Weinstein, John N.
AU - Coombes, Kevin R.
AU - Wang, Jing
AU - Byers, Lauren Averett
N1 - Funding Information:
This project was partially supported by the NIH through the TCGA (5-U24- CA143883-05), the Lung SPORE (P50 CA070907), DoD PROSPECT grant W81XWH-07-1-0306, and the Cancer Center Support Grant (CCSG -CA016672), by the Mary K. Chapman Foundation, and through generous philanthropic contributions to The University of Texas MD Anderson Lung Cancer Moon Shot Program. D.L. Gibbons was supported by Rexanna''s Foundation for Fighting Lung Cancer, The Stading Lung Cancer Research Fund, the National Institutes of Health (K08-CA151651), and the Cancer Prevention & Research Institute of Texas (RP150405); W.N. William was supported by a Conquer Cancer Foundation Career Development Award (4546); I.I. Wistuba was supported by MD Anderson''s Institutional Tissue Bank (ITB), Award Number 2P30CA016672 from theNIH National Cancer Institute. J.V. Heymach was supported by NIH/NCI (1 R01 CA168484-04) the LUNGevity foundation, The V Foundation for Cancer Research, the David Bruton, Jr. Endowed Chair and the Rexana Foundation for Fighting Lung Cancer; J.N.Weinstein was supported by NIH/NCI (5, 2P50 CA100632-11, 2 UL1RR00037106-A1, and 2 P30 CA016672 38), the Cancer Prevention & Research Institute of Texas (RP130397), and The Michael and Susan Dell Foundation; L.A. Byers was supported by an NCI Cancer Clinical Investigator Team leadership Award (P30 CA016672), The Sidney Kimmel Foundation for Cancer Research, and the Sheikh Khalifa Bin Zayed Al Nahyan Institute for the Personalized Cancer Therapy''s (IPCT''s) Center for Professional Education and Training; D.L. Gibbons and L.A. Byers are supported by MD Anderson Cancer Center Physician Scientist Awards, R. Lee Clark Fellowships of The University of Texas MD Anderson Cancer Center, supported by the Jeane F. Shelby Scholarship Fund, and the LUNGvevity Foundation. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
Publisher Copyright:
© 2015 American Association for Cancer Research.
PY - 2016/2/1
Y1 - 2016/2/1
N2 - Purpose: We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature. Experimental Design: Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated. Results: Compared with the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets, such as PD1, PD-L1, CTLA4, OX40L, and PD-L2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by IHC in an independent lung cancer cohort. Conclusions: This new signature provides a novel, patientbased, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints.
AB - Purpose: We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature. Experimental Design: Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated. Results: Compared with the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets, such as PD1, PD-L1, CTLA4, OX40L, and PD-L2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by IHC in an independent lung cancer cohort. Conclusions: This new signature provides a novel, patientbased, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints.
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U2 - 10.1158/1078-0432.CCR-15-0876
DO - 10.1158/1078-0432.CCR-15-0876
M3 - Article
C2 - 26420858
AN - SCOPUS:84958954805
SN - 1078-0432
VL - 22
SP - 609
EP - 620
JO - Clinical Cancer Research
JF - Clinical Cancer Research
IS - 3
ER -