@article{a7b7f7e433394274b9b4fa491e7863e7,
title = "Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression",
abstract = "Deep proteogenomic landscape of early stage lung adenocarcinoma in a cohort of mostly non-smokers reveals unique drivers and biomarkers, as well as gender-associated mutagenesis.",
keywords = "APOBEC signature, carcinogen signature, genomics, lung cancer, MMP, non-smoker, phosphoproteomics, proteogenomics, proteomics, subtyping",
author = "Chen, {Yi Ju} and Roumeliotis, {Theodoros I.} and Chang, {Ya Hsuan} and Chen, {Ching Tai} and Han, {Chia Li} and Lin, {Miao Hsia} and Chen, {Huei Wen} and Chang, {Gee Chen} and Chang, {Yih Leong} and Wu, {Chen Tu} and Lin, {Mong Wei} and Hsieh, {Min Shu} and Wang, {Yu Tai} and Chen, {Yet Ran} and Inge Jonassen and Ghavidel, {Fatemeh Zamanzad} and Lin, {Ze Shiang} and Lin, {Kuen Tyng} and Chen, {Ching Wen} and Sheu, {Pei Yuan} and Hung, {Chen Ting} and Huang, {Ke Chieh} and Yang, {Hao Chin} and Lin, {Pei Yi} and Yen, {Ta Chi} and Lin, {Yi Wei} and Wang, {Jen Hung} and Lovely Raghav and Lin, {Chien Yu} and Chen, {Yan Si} and Wu, {Pei Shan} and Lai, {Chi Ting} and Weng, {Shao Hsing} and Su, {Kang Yi} and Chang, {Wei Hung} and Tsai, {Pang Yan} and Robles, {Ana I.} and Henry Rodriguez and Hsiao, {Yi Jing} and Chang, {Wen Hsin} and Sung, {Ting Yi} and Chen, {Jin Shing} and Yu, {Sung Liang} and Choudhary, {Jyoti S.} and Chen, {Hsuan Yu} and Yang, {Pan Chyr} and Chen, {Yu Ju}",
note = "Funding Information: This research was supported by the Next-Generation Pathway of Taiwan Cancer Precision Medicine Program ( AS-KPQ-107-TCPMP ), the Taiwan Protein Project ( AS-KPQ-105-TPP ) at Academia Sinica, Ministry of Science and Technology ( MOST-106-3114-Y-043F-014 , MOST108-2319-B-002-001 ), and National Taiwan University ( NTU-CDP-106R7891 ) in Taiwan. We thank Drs. Fu-Tong Liu, Karin D. Rodland, and Tzu-Ching Meng for advice on the project and Drs. Chia-Feng Tsai, Chuan-Chih Hsu, and Yasushi Ishihama for comments on phosphoproteomic workflow. We thank the Academia Sinica Common Mass Spectrometry Facilities ( AS-CFII-108-107 ) at the Institute of Chemistry and Institute of Biological Chemistry for mass spectrometry analysis, National Core Facility for Biopharmaceuticals Pharmacogenomics Lab TR6 ( MOST108-2319-B-002-001 ) for NGS technical support, National Center for High-Performance Computing of National Applied Research Laboratories in Taiwan for providing computational and storage resources ( MOST108-2319-B-492-001 ), and Mathematics in Biology Group at the Institute of Statistical Science, Academia Sinica for bioinformatics work. P.-C.Y. acknowledges support from Ministry of Science and Technology ( MOST 107-0210-01-19-01 , MOST 108-3114-Y-001-002 ). S.-L.Y. acknowledges support of the Center of Precision Medicine from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), Taiwan. T.I.R. and J.S.C. are funded by CRUK Centre ( C309/A25144 ), UK. We thank Dr. Serena Nik Zainal for comments on data analysis. We thank Dr. Anguraj Sadanandam and Dr. Gift Nyamundanda for discussions about data analysis. This work was done under the auspices of a memorandum of understanding between the Academia Sinica and the U.S. National Cancer Institute{\textquoteright}s International Cancer Proteogenome Consortium ( ICPC ). ICPC encourages international cooperation among institutions and nations in proteogenomic cancer research in which proteogenomic datasets are made available to the public. This work was also done in collaboration with the U.S. National Cancer Institute{\textquoteright}s Clinical Proteomic Tumor Analysis Consortium ( CPTAC ). Funding Information: This research was supported by the Next-Generation Pathway of Taiwan Cancer Precision Medicine Program (AS-KPQ-107-TCPMP), the Taiwan Protein Project (AS-KPQ-105-TPP) at Academia Sinica, Ministry of Science and Technology (MOST-106-3114-Y-043F-014, MOST108-2319-B-002-001), and National Taiwan University (NTU-CDP-106R7891) in Taiwan. We thank Drs. Fu-Tong Liu, Karin D. Rodland, and Tzu-Ching Meng for advice on the project and Drs. Chia-Feng Tsai, Chuan-Chih Hsu, and Yasushi Ishihama for comments on phosphoproteomic workflow. We thank the Academia Sinica Common Mass Spectrometry Facilities (AS-CFII-108-107) at the Institute of Chemistry and Institute of Biological Chemistry for mass spectrometry analysis, National Core Facility for Biopharmaceuticals Pharmacogenomics Lab TR6 (MOST108-2319-B-002-001) for NGS technical support, National Center for High-Performance Computing of National Applied Research Laboratories in Taiwan for providing computational and storage resources (MOST108-2319-B-492-001), and Mathematics in Biology Group at the Institute of Statistical Science, Academia Sinica for bioinformatics work. P.-C.Y. acknowledges support from Ministry of Science and Technology (MOST 107-0210-01-19-01, MOST 108-3114-Y-001-002). S.-L.Y. acknowledges support of the Center of Precision Medicine from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE), Taiwan. T.I.R. and J.S.C. are funded by CRUK Centre (C309/A25144), UK. We thank Dr. Serena Nik Zainal for comments on data analysis. We thank Dr. Anguraj Sadanandam and Dr. Gift Nyamundanda for discussions about data analysis. This work was done under the auspices of a memorandum of understanding between the Academia Sinica and the U.S. National Cancer Institute's International Cancer Proteogenome Consortium (ICPC). ICPC encourages international cooperation among institutions and nations in proteogenomic cancer research in which proteogenomic datasets are made available to the public. This work was also done in collaboration with the U.S. National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC). Conceptualization, T.I.R. J.-S.C. S.-L.Y. J.S.C. H.-Y.C. P.-C.Y. and Yu-Ju Chen; Methodology, Yi-Ju Chen, Y.-H.C. M.-H.L. P.-Y.L. Y.-S.C. P.-S.W. C.-T.L. S.-H.W. K.-Y.S. S.-L.Y. H.-Y.C. and Yu-Ju Chen; Software, Y.-H.C. C.-T.C. T.-C.Y. J.-H.W. P.-Y.T. and H.-Y.C.; Validation, G.-C.C. Y.-L.C. C.-T.W. and H.-Y.C.; Formal Analysis, Yi-Ju Chen, T.I.R. Y.-H.C. C.-T.C. C.-L.H. M.-H.L. Y.-R.C. I.J. F.Z.G. T.-C.Y. J.-H.W. L.R. C.-Y.L. Wei-Hung Chang, P.-Y.T. T.-Y.S. H.-Y.C. and Yu-Ju Chen; Investigation, Yi-Ju Chen, T.I.R. Y.-H.C. M.-H.L. Z.-S.L. K.-T.L. C.-W.C. P.Y.S. C.-T.H. K.-C.H. H.-C.Y. P.-Y.L. Y.-W.L. L.R. Wen-Hsin Chang, Y.-J.H. C.-Y.L. P.-S.W. C.-T.L. J.S.C. and H.-Y.C.; Computation & Statistical Analysis, Yi-Ju Chen, T.I.R. Y.-H.C. C.-T.C. M.-H.L. I.J. F.Z.G. T.-C.Y. J.-H.W. T.-Y.S. and H.-Y.C.; Resources, M.-W.L. M.-S.H. Y.-T.W. T.-Y.S. J.-S.C. S.-L.Y. and Yu-Ju Chen; Data Curation, Yi-Ju Chen, Y.-H.C. C.-L.H. M.-H.L. Y.-T.W. C.-T.L. H.-Y.C. and Yu-Ju Chen; Writing – Original Draft, Yi-Ju Chen, T.I.R. Y.-H.C. C.-L.H. M.-H.L. G.-C.C. Y.-L.C. C.-T.W. M.-W.L. K.-T.L. S.-L.Y. J.S.C. H.-Y.C. and Yu-Ju Chen; Writing – Review & Editing, Yi-Ju Chen, T.I.R. C.-L.H. H.-W.C. I.J. F.Z.G. A.I.R. H.R. J.S.C. H.-Y.C. P.-C.Y. and Yu-Ju Chen; Visualization, Yi-Ju Chen, T.I.R. Y.-H.C. C.-T.C. C.-L.H. M.-H.L. I.J. F.Z.G. K.-T.L. L.R. C.-Y.L. H.-Y.C. P.-C.Y. and Yu-Ju Chen; Supervision, C.-L.H. H.-W.C. Y.-R.C. I.J. T.-Y.S. J.-S.C. S.-L.Y. J.S.C. H.-Y.C. P.-C.Y. and Yu-Ju Chen; Project Administration, Yi-Ju Chen, Y.-H.C. C.-T.C. C.-L.H. H.R. S.-L.Y. J.S.C. H.-Y.C. and Yu-Ju Chen; Funding Acquisition, S.-L.Y. J.S.C. H.-Y.C. and Yu-Ju Chen. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",
year = "2020",
month = jul,
day = "9",
doi = "10.1016/j.cell.2020.06.012",
language = "English",
volume = "182",
pages = "226--244.e17",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "1",
}
