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Wong JYY, Zhang H, Hsiung CA, Shiraishi K, Yu K, Matsuo K, Wong MP, Hong YC, Wang J, Seow WJ, Wang Z, Song M, Kim HN, Chang IS, Chatterjee N, Hu W, Wu C, Mitsudomi T, Zheng W, Kim JH, Seow A, Caporaso NE, Shin MH, Chung LP, An SJ, Wang P, Yang Y, Zheng H, Yatabe Y, Zhang XC, Kim YT, Cai Q, Yin Z, Kim YC, Bassig BA, Chang J, Ho JCM, Ji BT, Daigo Y, Ito H, Momozawa Y, Ashikawa K, Kamatani Y, Honda T, Hosgood HD, Sakamoto H, Kunitoh H, Tsuta K, Watanabe SI, Kubo M, Miyagi Y, Nakayama H, Matsumoto S, Tsuboi M, Goto K, Shi J, Song L, Hua X, Takahashi A, Goto A, Minamiya Y, Shimizu K, Tanaka K, Wei F, Matsuda F, Su J, Kim YH, Oh IJ, Song F, Su WC, Chen YM, Chang GC, Chen KY, Huang MS, Chien LH, Xiang YB, Park JY, Kweon SS, Chen CJ, Lee KM, Blechter B, Li H, Gao YT, Qian B, Lu D, Liu J, Jeon HS, Hsiao CF, Sung JS, Tsai YH, Jung YJ, Guo H, Hu Z, Wang WC, Chung CC, Burdett L, Yeager M, Hutchinson A, Berndt SI, Wu W, Pang H, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Zhu M, Chen CH, Yang TY, Xu J, Guan P, Tan W, Wang CL, Hsin M, Sit KY, Ho J, Chen Y, Choi YY, Hung JY, Kim JS, Yoon HI, Lin CC, Park IK, Xu P, Wang Y, He Q, Perng RP, Chen CY, Vermeulen R, Wu J, Lim WY, Chen KC, Li YJ, Li J, Chen H, Yu CJ, Jin L, Chen TY, Jiang SS, Liu J, Yamaji T, Hicks B, Wyatt K, Li SA, Dai J, Ma H, Jin G, Song B, Wang Z, Cheng S, Li X, Ren Y, Cui P, Iwasaki M, Shimazu T, Tsugane S, Zhu J, Chen Y, Yang K, Jiang G, Fei K, Wu G, Lin HC, Chen HL, Fang YH, Tsai FY, Hsieh WS, Yu J, Stevens VL, Laird-Offringa IA, Marconett CN, Rieswijk L, Chao A, Yang PC, Shu XO, Wu T, Wu YL, Lin D, Chen K, Zhou B, Huang YC, Kohno T, Shen H, Chanock SJ, Rothman N, Lan Q. Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women. Genomics 2019; 112:1223-1232. [PMID: 31306748 DOI: 10.1016/j.ygeno.2019.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
Abstract
We investigated whether genetic susceptibility to tuberculosis (TB) influences lung adenocarcinoma development among never-smokers using TB genome-wide association study (GWAS) results within the Female Lung Cancer Consortium in Asia. Pathway analysis with the adaptive rank truncated product method was used to assess the association between a TB-related gene-set and lung adenocarcinoma using GWAS data from 5512 lung adenocarcinoma cases and 6277 controls. The gene-set consisted of 31 genes containing known/suggestive associations with genetic variants from previous TB-GWAS. Subsequently, we followed-up with Mendelian Randomization to evaluate the association between TB and lung adenocarcinoma using three genome-wide significant variants from previous TB-GWAS in East Asians. The TB-related gene-set was associated with lung adenocarcinoma (p = 0.016). Additionally, the Mendelian Randomization showed an association between TB and lung adenocarcinoma (OR = 1.31, 95% CI: 1.03, 1.66, p = 0.027). Our findings support TB as a causal risk factor for lung cancer development among never-smoking Asian women.
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Affiliation(s)
- Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Maria Pik Wong
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Jie Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Minsun Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Department of Statistics, Sookmyung Women's University, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Kinki University School of Medicine, Sayama, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul, Republic of Korea
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ping Wang
- Department of Radiotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Central Hospital, Nagoya, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea; Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Japan; Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kyota Ashikawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takayuki Honda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology and Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Shun-Ichi Watanabe
- Division of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Kanagawa, Japan
| | - Shingo Matsumoto
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Japan
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita City, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita City, Japan
| | - Kimihiro Shimizu
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea; Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Gee-Chen Chang
- School of Medicine, Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, E-Da Cancer Hospital, School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Li-Hsin Chien
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea; Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Kyoung-Mu Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Department of Environmental Health, Korea National Open University, Seoul, Republic of Korea
| | - Batel Blechter
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Haixin Li
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Human Genetics, Genome Institute of Singapore, Singapore; School of Life Sciences, Anhui Medical University, Hefei, China
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Herbert Pang
- School of BioMedical Sciences, The University of Hong Kong, Hong Kong
| | - Yuqing Li
- Cancer Prevention Institute of California, Fremont, CA, USA
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul St Mary's Hospital, The Catholic University of Korea, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - C H Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chung-Hsing Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Michael Hsin
- Department of Cardiothoracic Surgery, Queen Mary Hospital, The University of Hong Kong, China
| | - Ko-Yung Sit
- Department of Cardiothoracic Surgery, Queen Mary Hospital, The University of Hong Kong, China
| | - James Ho
- Department of Medicine, The University of Hong Kong, China
| | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jen-Yu Hung
- Department of Internal Medicine, E-Da Cancer Hospital, School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Jun Suk Kim
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Chien-Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel Corporation Staff Worker Hospital, Wuhan, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | | | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Kun-Chieh Chen
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Jen Li
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Sanjiangdadao, Qujing, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Ping Cui
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Ying Chen
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Kaiyun Yang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Hsien-Chin Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Hui-Ling Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yao-Huei Fang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wan-Shan Hsieh
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Crystal N Marconett
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda Rieswijk
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Ann Chao
- Center for Global Health, National Cancer Institute, Bethesda, MD, USA
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Tangchun Wu
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Y L Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Yun-Chao Huang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Mullen DJ, Stueve TR, Yan C, Siegmund KD, Laird-Offringa IA. Abstract A08: Widespread tobacco smoking-associated changes in DNA methylation and gene expression in lung tissue of smokers. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-a08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Significance: Epigenome-wide association studies (EWAS) have identified thousands of CpGs showing smoking-associated DNA methylation changes in blood cell DNA of smokers. Several of these CpGs are strongly associated with lung cancer risk. Until recently, the relationship of such DNA methylation changes in the blood and epigenetic alterations in the lung, as well as their molecular link to lung cancer development, remained poorly understood. Using a limited EWAS of 237 lung tissue samples, we recently identified seven smoking-associated hypomethylated CpGs in lung tissue, five of which had been previously reported in blood, and one of which had been strongly associated with lung cancer risk. We showed that the latter CpG flanked a smoking-inducible enhancer element driving expression of a xenobiotic response gene. Here we expand these observations to identify tobacco-affected regulatory elements implicated in lung cancer.
Methods: We performed an EWAS using Inifinium HumanMethylation450K BeadChip data from The Cancer Genome Atlas (TCGA) corresponding to 393 eligible lung adenocarcinoma tumor samples. We replicated our findings in 27 adjacent normal lung tissue samples, then examined epigenetic enhancer marks near the smoking-associated altered CpGs using epigenomic data from primary lung cells and lung adenocarcinoma cell lines. We next identified potential responsive target genes of these enhancers by examining smoking-associated changes in gene expression on the 1 megabase flanks of the enhancers.
Results: 37,372 CpGs were significantly differentially methylated with respect to smoking in TCGA adenocarcinoma tumor samples after Benjamini Hochberg correction (p<0.05). 2,941 probes replicated at a nominal level in the adjacent normal samples (p<0.05), including 145 probes previously associated with smoking in at least one blood-based EWAS. 1,150 of the 2,941 replicated probes were located within 2 kb of a likely functional region carrying a histone mark of active enhancers in primary lung cells and/or lung cancer cell lines. 949 of these were within 1 Mb of a gene showing a significant, smoking-associated expression difference. One of the top-ranked CpGs we identified was among the 10 most-replicated CpGs in blood-based smoking EWAS, and was linked to smoking-induced upregulation of the aryl hydrocarbon receptor repressor (AHRR) gene, which is involved in the cellular xenobiotic response and has been implicated in lung cancer risk.
Conclusion: Many smoking-associated methylation changes in lung tissue are located in the vicinity of epigenetic regulators in lung tissue, and could be driving expression of smoking-associated genes that may affect lung cancer risk.
Funding: R01 HL114094 to IALO, P30 CA014089, USC Provost’s fellowship and Roy E. Thomas Foundation Graduate Scholarship to DJM.
Citation Format: Daniel J. Mullen, T. Ryan Stueve, Chunli Yan, Kimberly D. Siegmund, Ite A. Laird-Offringa. Widespread tobacco smoking-associated changes in DNA methylation and gene expression in lung tissue of smokers [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A08.
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Affiliation(s)
| | | | - Chunli Yan
- University of Southern California, Los Angeles, CA
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Stueve TR, Yang C, Marconett CN, Yan C, Zhou B, Borok Z, Laird-Offringa IA. Abstract A37: Tobacco smoke increases lung adenocarcinoma risk by downregulating TGF-beta and AhR-regulated focal adhesion proteins involved in injury resolution. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-a37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The most prevalent type of lung cancer—lung adenocarcinoma—arises from the most distal reaches of the lung in the alveolar epithelium. The alveolar epithelium consists of two cell types: (i) thin type I alveolar epithelial cells (AT1) that facilitate gas exchange and constitute more than 90% of the alveolar surface, and (ii) cuboidal surfactant-producing type II (AT2) cells. Following injury, dynamic interactions between extracellular matrix components, integrins, focal adhesion proteins, and cytoskeletal components allow AT2 progenitor cells to migrate, spread, and transdifferentiate into AT1 cells to restore the denuded epithelial barrier.
Methods: Utilizing primary human AT2 cells isolated from lung transplant remnants, our lab has established and extensively profiled an in vitro model of epithelial restitution, wherein AT2 cells differentiate over a period of six days into terminally differentiated AT1-like cells. Because cigarette smoking is the most recognized risk factor for lung adenocarcinoma (LUAD), and because the alveolar space is the primary target of tobacco smoke, we also compared the RNA-seq profiles of AT2>AT1 differentiation to those of A549 LUAD cells exposed to cigarette smoke condensate (CSC).
Results: We find that CSC downregulates many factors that are upregulated in the AT2>AT1 restitution model, particularly integrins, extracellular matrix components, and novel focal adhesion proteins that are also downregulated in LUAD relative to adjacent normal tissue. We describe regulation of four such novel focal adhesion proteins, specifically by TGF-β and aryl hydrocarbon receptor (AhR)-mediated mechanisms.
Conclusions: Our findings shed light on early mechanisms in the carcinogenic process, and support the notion that alveolar cells engaged in repeated cycles of injury and repair are critical actors in LUAD risk trajectories.
Note: This abstract was not presented at the conference.
Citation Format: Theresa Ryan Stueve, Chenchen Yang, Crystal N. Marconett, Chunli Yan, Beiyun Zhou, Zea Borok, Ite A. Laird-Offringa. Tobacco smoke increases lung adenocarcinoma risk by downregulating TGF-beta and AhR-regulated focal adhesion proteins involved in injury resolution [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A37.
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Affiliation(s)
| | | | | | - Chunli Yan
- University of Southern California, Los Angeles, CA
| | - Beiyun Zhou
- University of Southern California, Los Angeles, CA
| | - Zea Borok
- University of Southern California, Los Angeles, CA
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4
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Zhou B, Flodby P, Luo J, Castillo DR, Liu Y, Yu FX, McConnell A, Varghese B, Li G, Chimge NO, Sunohara M, Koss MN, Elatre W, Conti P, Liebler JM, Yang C, Marconett CN, Laird-Offringa IA, Minoo P, Guan K, Stripp BR, Crandall ED, Borok Z. Claudin-18-mediated YAP activity regulates lung stem and progenitor cell homeostasis and tumorigenesis. J Clin Invest 2018; 128:970-984. [PMID: 29400695 DOI: 10.1172/jci90429] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/05/2017] [Indexed: 12/19/2022] Open
Abstract
Claudins, the integral tight junction (TJ) proteins that regulate paracellular permeability and cell polarity, are frequently dysregulated in cancer; however, their role in neoplastic progression is unclear. Here, we demonstrated that knockout of Cldn18, a claudin family member highly expressed in lung alveolar epithelium, leads to lung enlargement, parenchymal expansion, increased abundance and proliferation of known distal lung progenitors, the alveolar epithelial type II (AT2) cells, activation of Yes-associated protein (YAP), increased organ size, and tumorigenesis in mice. Inhibition of YAP decreased proliferation and colony-forming efficiency (CFE) of Cldn18-/- AT2 cells and prevented increased lung size, while CLDN18 overexpression decreased YAP nuclear localization, cell proliferation, CFE, and YAP transcriptional activity. CLDN18 and YAP interacted and colocalized at cell-cell contacts, while loss of CLDN18 decreased YAP interaction with Hippo kinases p-LATS1/2. Additionally, Cldn18-/- mice had increased propensity to develop lung adenocarcinomas (LuAd) with age, and human LuAd showed stage-dependent reduction of CLDN18.1. These results establish CLDN18 as a regulator of YAP activity that serves to restrict organ size, progenitor cell proliferation, and tumorigenesis, and suggest a mechanism whereby TJ disruption may promote progenitor proliferation to enhance repair following injury.
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Affiliation(s)
- Beiyun Zhou
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Per Flodby
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Jiao Luo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Dan R Castillo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Yixin Liu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Fa-Xing Yu
- Department of Pharmacology and Moores Cancer Center, UCSD, La Jolla, California, USA.,Childrens Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Alicia McConnell
- Lung and Regenerative Medicine Institutes, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - Guanglei Li
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Nyam-Osor Chimge
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Mitsuhiro Sunohara
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | | | | | | | - Janice M Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and
| | - Chenchen Yang
- Department of Surgery.,Department of Biochemistry and Molecular Medicine, and
| | - Crystal N Marconett
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Surgery
| | - Ite A Laird-Offringa
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Surgery.,Department of Biochemistry and Molecular Medicine, and
| | - Parviz Minoo
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Kunliang Guan
- Department of Pharmacology and Moores Cancer Center, UCSD, La Jolla, California, USA
| | - Barry R Stripp
- Lung and Regenerative Medicine Institutes, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Edward D Crandall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and.,Department of Pathology.,Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine.,Hastings Center for Pulmonary Research.,Will Rogers Institute Pulmonary Research Center, and.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Biochemistry and Molecular Medicine, and
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5
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Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M. Publisher Correction: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nat Commun 2018; 9:160. [PMID: 29311577 PMCID: PMC5758615 DOI: 10.1038/s41467-017-02485-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ivan Vannini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Petra M Wise
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Kishore B Challagundla
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Meropi Plousiou
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Mirco Raffini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Erika Bandini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Francesca Fanini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Giorgia Paliaga
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, Meldola, FC, 47014, Italy
| | - Melissa Crawford
- Department of Internal Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine- DIMES, University of Bologna, Bologna, 40126, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linda Fabris
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ramana V Davuluri
- Departments of Preventive Medicine and Neurological Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Zhiyi Guo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria Angelica Cortez
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinna Zhang
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, MD, 20850, USA
| | - Shuxing Zhang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cecilia Fernandez-Cymering
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Silvia Carloni
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, Meldola, FC, 47014, Italy
| | - Samanta Salvi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, Meldola, FC, 47014, Italy
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mariam Murtadha
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Paolo Neviani
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Barbara J Gitlitz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ite A Laird-Offringa
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, 44121, Italy
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dino Amadori
- Department of Oncology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Meldola, FC, 47014, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, Naples, 80131, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Muller Fabbri
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.
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6
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Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M. Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nat Commun 2017; 8:1801. [PMID: 29180617 PMCID: PMC5703849 DOI: 10.1038/s41467-017-01562-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/27/2017] [Indexed: 01/05/2023] Open
Abstract
The transcribed ultraconserved regions (T-UCRs) encode long non-coding RNAs implicated in human carcinogenesis. Their mechanisms of action and the factors regulating their expression in cancers are poorly understood. Here we show that high expression of uc.339 correlates with lower survival in 210 non-small cell lung cancer (NSCLC) patients. We provide evidence from cell lines and primary samples that TP53 directly regulates uc.339. We find that transcribed uc.339 is upregulated in archival NSCLC samples, functioning as a decoy RNA for miR-339-3p, -663b-3p, and -95-5p. As a result, Cyclin E2, a direct target of all these microRNAs is upregulated, promoting cancer growth and migration. Finally, we find that modulation of uc.339 affects microRNA expression. However, overexpression or downregulation of these microRNAs causes no significant variations in uc.339 levels, suggesting a type of interaction for uc.339 that we call "entrapping". Our results support a key role for uc.339 in lung cancer.
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Affiliation(s)
- Ivan Vannini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Petra M Wise
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Meropi Plousiou
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Mirco Raffini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Erika Bandini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Francesca Fanini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Giorgia Paliaga
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Melissa Crawford
- Department of Internal Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine-DIMES, University of Bologna, 40126, Bologna, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Linda Fabris
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Ramana V Davuluri
- Departments of Preventive Medicine and Neurological Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Zhiyi Guo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria Angelica Cortez
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinna Zhang
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.,Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shuxing Zhang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cecilia Fernandez-Cymering
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Silvia Carloni
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, 47014, Meldola (FC), Italy
| | - Samanta Salvi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, 47014, Meldola (FC), Italy
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mariam Murtadha
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Paolo Neviani
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Barbara J Gitlitz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ite A Laird-Offringa
- Departments of Surgery and Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121, Ferrara, Italy
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dino Amadori
- Department of Oncology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, 47014, Meldola (FC), Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, 80131, Naples, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.
| | - Muller Fabbri
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.
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7
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Stueve TR, Li WQ, Shi J, Marconett CN, Zhang T, Yang C, Mullen D, Yan C, Wheeler W, Hua X, Zhou B, Borok Z, Caporaso NE, Pesatori AC, Duan J, Laird-Offringa IA, Landi MT. Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers. Hum Mol Genet 2017; 26:3014-3027. [PMID: 28854564 PMCID: PMC5886283 DOI: 10.1093/hmg/ddx188] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/30/2017] [Accepted: 05/07/2017] [Indexed: 11/14/2022] Open
Abstract
Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. We identified seven smoking-associated hypomethylated CpGs (P < 1.0 × 10-7), which were replicated in NTL data from The Cancer Genome Atlas. Five of these loci were previously reported as hypomethylated in smokers' blood, suggesting that blood-based biomarkers can reflect changes in the target tissue for these loci. Four CpGs border sequences carrying aryl hydrocarbon receptor binding sites and enhancer-specific histone modifications in primary alveolar epithelium and A549 lung adenocarcinoma cells. A549 cell exposure to cigarette smoke condensate increased these enhancer marks significantly and stimulated expression of predicted target xenobiotic response-related genes AHRR (P = 1.13 × 10-62) and CYP1B1 (P < 2.49 × 10-61). Expression of both genes was linked to smoking-related transversion mutations in lung tumors. Thus, smoking-associated hypomethylation may be a consequence of enhancer activation, revealing environmentally-induced regulatory elements implicated in lung carcinogenesis.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Preventive Medicine
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
- Department of Dermatology, Warren Alpert Medical School
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI 02903, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Crystal N. Marconett
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Chenchen Yang
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel Mullen
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Chunli Yan
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - William Wheeler
- Information Management Services, Inc., Rockville, MD 20852, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Beiyun Zhou
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90089, USA
| | - Zea Borok
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90089, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Angela C. Pesatori
- Unit of Epidemiology, IRCCS Fondazione Ca’ Granda Ospedale Maggiore Policlinico and Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Ite A. Laird-Offringa
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
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8
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Flodby P, Li C, Liu Y, Wang H, Marconett CN, Laird-Offringa IA, Minoo P, Lee AS, Zhou B. The 78-kD Glucose-Regulated Protein Regulates Endoplasmic Reticulum Homeostasis and Distal Epithelial Cell Survival during Lung Development. Am J Respir Cell Mol Biol 2017; 55:135-49. [PMID: 26816051 DOI: 10.1165/rcmb.2015-0327oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD), a chronic lung disease of prematurity, has been linked to endoplasmic reticulum (ER) stress. To investigate a causal role for ER stress in BPD pathogenesis, we generated conditional knockout (KO) mice (cGrp78(f/f)) with lung epithelial cell-specific KO of Grp78, a gene encoding the ER chaperone 78-kD glucose-regulated protein (GRP78), a master regulator of ER homeostasis and the unfolded protein response (UPR). Lung epithelial-specific Grp78 KO disrupted lung morphogenesis, causing developmental arrest, increased alveolar epithelial type II cell apoptosis, and decreased surfactant protein and type I cell marker expression in perinatal lungs. cGrp78(f/f) pups died immediately after birth, likely owing to respiratory distress. Importantly, Grp78 KO triggered UPR activation with marked induction of the proapoptotic transcription factor CCAAT/enhancer-binding proteins (C/EBP) homologous protein (CHOP). Increased expression of genes involved in oxidative stress and cell death and decreased expression of genes encoding antioxidant enzymes suggest a role for oxidative stress in alveolar epithelial cell (AEC) apoptosis. Increased Smad3 phosphorylation and expression of transforming growth factor-β/Smad3 targets Cdkn1a (encoding p21) and Gadd45a suggest that interactions among the apoptotic arm of the UPR, oxidative stress, and transforming growth factor-β/Smad signaling pathways contribute to Grp78 KO-induced AEC apoptosis and developmental arrest. Chemical chaperone Tauroursodeoxycholic acid reduced UPR activation and apoptosis in cGrp78(f/f) lungs cultured ex vivo, confirming a role for ER stress in observed AEC abnormalities. These results demonstrate a key role for GRP78 in AEC survival and gene expression during lung development through modulation of ER stress, and suggest the UPR as a potential therapeutic target in BPD.
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Affiliation(s)
- Per Flodby
- Departments of 1 Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine
| | | | - Yixin Liu
- Departments of 1 Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine
| | - Hongjun Wang
- Departments of 1 Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine
| | - Crystal N Marconett
- 3 Surgery, and.,4 Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, California
| | - Ite A Laird-Offringa
- 3 Surgery, and.,5 Biochemistry and Molecular Biology, and.,4 Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, California
| | | | - Amy S Lee
- 5 Biochemistry and Molecular Biology, and.,4 Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, California
| | - Beiyun Zhou
- Departments of 1 Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine.,4 Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, California
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9
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Marconett CN, Zhou B, Sunohara M, Pouldar TM, Wang H, Liu Y, Rieger ME, Tran E, Flodby P, Siegmund KD, Crandall ED, Laird-Offringa IA, Borok Z. Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol 2017; 56:310-321. [PMID: 27749084 DOI: 10.1165/rcmb.2016-0071oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma. Accurate labeling of specific cell types is critical for determining the contribution of each to the pathogenesis of these diseases. The distal lung alveolar epithelium is composed of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells. Although cell type-specific markers, most prominently surfactant protein C, have allowed detailed lineage tracing studies of AT2 cell differentiation and the cells' roles in disease, studies of AT1 cells have been hampered by a lack of genes with expression unique to AT1 cells. In this study, we performed genome-wide expression profiling of multiple rat organs together with purified rat AT2, AT1, and in vitro differentiated AT1-like cells, resulting in the identification of 54 candidate AT1 cell markers. Cross-referencing with genes up-regulated in human in vitro differentiated AT1-like cells narrowed the potential list to 18 candidate genes. Testing the top four candidate genes at RNA and protein levels revealed GRAM domain 2 (GRAMD2), a protein of unknown function, as highly specific to AT1 cells. RNA sequencing (RNAseq) confirmed that GRAMD2 is transcriptionally silent in human AT2 cells. Immunofluorescence verified that GRAMD2 expression is restricted to the plasma membrane of AT1 cells and is not expressed in bronchial epithelial cells, whereas reverse transcription-polymerase chain reaction confirmed that it is not expressed in endothelial cells. Using GRAMD2 as a new AT1 cell-specific gene will enhance AT1 cell isolation, the investigation of alveolar epithelial cell differentiation potential, and the contribution of AT1 cells to distal lung diseases.
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Affiliation(s)
- Crystal N Marconett
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Beiyun Zhou
- 3 Norris Comprehensive Cancer Center.,4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Mitsuhiro Sunohara
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | | | - Hongjun Wang
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Yixin Liu
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Megan E Rieger
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Evelyn Tran
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Per Flodby
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Kimberly D Siegmund
- 5 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Edward D Crandall
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Ite A Laird-Offringa
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Zea Borok
- 2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center.,4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
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10
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Seow WJ, Matsuo K, Hsiung CA, Shiraishi K, Song M, Kim HN, Wong MP, Hong YC, Hosgood HD, Wang Z, Chang IS, Wang JC, Chatterjee N, Tucker M, Wei H, Mitsudomi T, Zheng W, Kim JH, Zhou B, Caporaso NE, Albanes D, Shin MH, Chung LP, An SJ, Wang P, Zheng H, Yatabe Y, Zhang XC, Kim YT, Shu XO, Kim YC, Bassig BA, Chang J, Ho JCM, Ji BT, Kubo M, Daigo Y, Ito H, Momozawa Y, Ashikawa K, Kamatani Y, Honda T, Sakamoto H, Kunitoh H, Tsuta K, Watanabe SI, Nokihara H, Miyagi Y, Nakayama H, Matsumoto S, Tsuboi M, Goto K, Yin Z, Shi J, Takahashi A, Goto A, Minamiya Y, Shimizu K, Tanaka K, Wu T, Wei F, Wong JY, Matsuda F, Su J, Kim YH, Oh IJ, Song F, Lee VHF, Su WC, Chen YM, Chang GC, Chen KY, Huang MS, Yang PC, Lin HC, Xiang YB, Seow A, Park JY, Kweon SS, Chen CJ, Li H, Gao YT, Wu C, Qian B, Lu D, Liu J, Jeon HS, Hsiao CF, Sung JS, Tsai YH, Jung YJ, Guo H, Hu Z, Wang WC, Chung CC, Lawrence C, Burdett L, Yeager M, Jacobs KB, Hutchinson A, Berndt SI, He X, Wu W, Wang J, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Hu L, Chen CH, Yang TY, Xu J, Guan P, Tan W, Wang CL, Sihoe ADL, Chen Y, Choi YY, Hung JY, Kim JS, Yoon HI, Cai Q, Lin CC, Park IK, Xu P, Dong J, Kim C, He Q, Perng RP, Chen CY, Vermeulen R, Wu J, Lim WY, Chen KC, Chan JK, Chu M, Li YJ, Li J, Chen H, Yu CJ, Jin L, Lo YL, Chen YH, Fraumeni JF, Liu J, Yamaji T, Yang Y, Hicks B, Wyatt K, Li SA, Dai J, Ma H, Jin G, Song B, Wang Z, Cheng S, Li X, Ren Y, Cui P, Iwasaki M, Shimazu T, Tsugane S, Zhu J, Jiang G, Fei K, Wu G, Chien LH, Chen HL, Su YC, Tsai FY, Chen YS, Yu J, Stevens VL, Laird-Offringa IA, Marconett CN, Lin D, Chen K, Wu YL, Landi MT, Shen H, Rothman N, Kohno T, Chanock SJ, Lan Q. Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations. Hum Mol Genet 2017; 26:454-465. [PMID: 28025329 PMCID: PMC5856088 DOI: 10.1093/hmg/ddw414] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 01/12/2023] Open
Abstract
To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking controls from Asia confirmed associations with eight known single nucleotide polymorphisms (SNPs). Two new signals were observed at genome-wide significance (P < 5 × 10-8), namely, rs7216064 (17q24.3, BPTF), for overall lung adenocarcinoma risk, and rs3817963 (6p21.3, BTNL2) which is specific to cases with EGFR mutations. In further sub-analyses by EGFR status, rs9387478 (ROS1/DCBLD1) and rs2179920 (HLA-DPB1) showed stronger estimated associations in EGFR-positive compared to EGFR-negative cases. Comparison of the overall associations with published results in Western populations revealed that the majority of these findings were distinct, underscoring the importance of distinct contributing factors for smoking and non-smoking lung cancer. Our results extend the catalogue of regions associated with lung adenocarcinoma in non-smoking Asian women and highlight the importance of how the germline could inform risk for specific tumour mutation patterns, which could have important translational implications.
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Affiliation(s)
- Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Minsun Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Department of Statistics, Sookmyung Women’s University, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Maria Pik Wong
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - H. Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jiu-Cun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hu Wei
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Kinki University School of Medicine, Sayama, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul, Republic of Korea
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, People’s Republic of China
| | - Ping Wang
- Department of Radiotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, People’s Republic of China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Central Hospital, Nagoya, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, People’s Republic of China
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Bryan A. Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Japan
| | - Hidemi Ito
- Division of Epidemiology & Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kyota Ashikawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takayuki Honda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Shun-Ichi Watanabe
- Division of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroshi Nokihara
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Kanagawa, Japan
| | - Shingo Matsumoto
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Japan
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita City, Japan
| | - Kimihiro Shimizu
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Tangchun Wu
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, People’s Republic of China
| | - Jason Y.Y. Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, People’s Republic of China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Gee-Chen Chang
- School of Medicine, Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kuan-Yu Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsien-Chih Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, People’s Republic of China
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun, Hwasun Hospital, Republic of Korea
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Haixin Li
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, People’s Republic of China
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Department of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- School of Life Sciences, Anhui Medical University, Hefei, People’s Republic of China
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Charles C. Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | | | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Kevin B. Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xingzhou He
- Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
| | - Junwen Wang
- Department of Health Sciences Research
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Yuqing Li
- Cancer Prevention Institute of California, Fremont, CA, USA
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul St Mary's Hospital, The Catholic University of Korea, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Chang Hyun Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Lingmin Hu
- Ministry of Education Key Laboratory of Modern Toxicology
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, People’s Republic of China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Alan Dart Loon Sihoe
- Department of Surgery, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jen-Yu Hung
- Department of Internal Medicine, Kaohsiung Medical University Hospital, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jun Suk Kim
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho-Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Chien-Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel (Group) Corporation Staff-Worker Hospital, Wuhan, People’s Republic of China
| | - Jing Dong
- Ministry of Education Key Laboratory of Modern Toxicology
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Christopher Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
| | | | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | | | - Kun-Chieh Chen
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - John K.C. Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, People’s Republic of China
| | - Minjie Chu
- Ministry of Education Key Laboratory of Modern Toxicology
- Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Yao-Jen Li
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Qujing, People’s Republic of China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yen-Li Lo
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Ying-Hsiang Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Joseph F. Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, People’s Republic of China
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Shengchao A. Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, People’s Republic of China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, People’s Republic of China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, People’s Republic of China
| | - Ping Cui
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, People’s Republic of China
| | - Gening Jiang
- Shanghai Pulmonary Hospital, Shanghai, People’s Republic of China
| | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, People’s Republic of China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, People’s Republic of China
| | - Li-Hsin Chien
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Hui-Ling Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Chun Su
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Song Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | | | - Ite A. Laird-Offringa
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Crystal N. Marconett
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People’s Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, People’s Republic of China
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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11
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Pulido MA, DerHartunian MK, Qin Z, Chung EM, Kang DS, Woodham AW, Tsou JA, Klooster R, Akbari O, Wang L, Kast WM, Liu SV, Verschuuren JJ, Aswad DW, Laird-Offringa IA. Isoaspartylation appears to trigger small cell lung cancer-associated autoimmunity against neuronal protein ELAVL4. J Neuroimmunol 2016; 299:70-78. [PMID: 27725125 PMCID: PMC5152694 DOI: 10.1016/j.jneuroim.2016.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022]
Abstract
Autoantibodies against SCLC-associated neuronal antigen ELAVL4 (HuD) have been linked to smaller tumors and improved survival, but the antigenic epitope and mechanism of autoimmunity have never been solved. We report that recombinant human ELAVL4 protein incubated under physiological conditions acquires isoaspartylation, a type of immunogenic protein damage. Specifically, the N-terminal region of ELAVL4, previously implicated in SCLC-associated autoimmunity, undergoes isoaspartylation in vitro, is recognized by sera from anti-ELAVL4 positive SCLC patients and is highly immunogenic in subcutaneously injected mice and in vitro stimulated human lymphocytes. Our data suggest that isoaspartylated ELAVL4 is the trigger for the SCLC-associated anti-ELAVL4 autoimmune response.
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Affiliation(s)
- Mario A. Pulido
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Meleeneh Kazarian DerHartunian
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Zhenxia Qin
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA
| | - Eric M. Chung
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Diane S. Kang
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Andrew W. Woodham
- Department of Molecular Microbiology and Immunology Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jeffrey A. Tsou
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Omid Akbari
- Department of Molecular Microbiology and Immunology Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Wang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - W. Martin Kast
- Department of Molecular Microbiology and Immunology Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Stephen V. Liu
- Department of Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Dana W. Aswad
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA
| | - Ite A. Laird-Offringa
- Departments of Surgery and of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
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12
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Zuber V, Marconett CN, Shi J, Hua X, Wheeler W, Yang C, Song L, Dale AM, Laplana M, Risch A, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Zhou B, Borok Z, van der Heijden HFM, de Graaf J, Swinkels D, Aben KK, McKay J, Hung RJ, Bikeböller H, Stevens VL, Albanes D, Caporaso NE, Han Y, Wei Y, Panadero MA, Mayordomo JI, Christiani DC, Kiemeney L, Andreassen OA, Houlston R, Amos CI, Chatterjee N, Laird-Offringa IA, Mills IG, Landi MT. Pleiotropic Analysis of Lung Cancer and Blood Triglycerides. J Natl Cancer Inst 2016; 108:djw167. [PMID: 27565901 DOI: 10.1093/jnci/djw167] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/31/2016] [Indexed: 01/05/2023] Open
Abstract
Epidemiologically related traits may share genetic risk factors, and pleiotropic analysis could identify individual loci associated with these traits. Because of their shared epidemiological associations, we conducted pleiotropic analysis of genome-wide association studies of lung cancer (12 160 lung cancer case patients and 16 838 control subjects) and cardiovascular disease risk factors (blood lipids from 188 577 subjects, type 2 diabetes from 148 821 subjects, body mass index from 123 865 subjects, and smoking phenotypes from 74 053 subjects). We found that 6p22.1 (rs6904596, ZNF184) was associated with both lung cancer (P = 5.50x10(-6)) and blood triglycerides (P = 1.39x10(-5)). We replicated the association in 6097 lung cancer case patients and 204 657 control subjects (P = 2.40 × 10(-4)) and in 71 113 subjects with triglycerides data (P = .01). rs6904596 reached genome-wide significance in lung cancer meta-analysis (odds ratio = 1.15, 95% confidence interval = 1.10 to 1.21 ,: Pcombined = 5.20x10(-9)). The large sample size provided by the lipid GWAS data and the shared genetic risk factors between the two traits contributed to the uncovering of a hitherto unidentified genetic locus for lung cancer.
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Affiliation(s)
- Verena Zuber
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Crystal N Marconett
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Jianxin Shi
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Xing Hua
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - William Wheeler
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Chenchen Yang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Lei Song
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Anders M Dale
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Marina Laplana
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Angela Risch
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Aree Witoelar
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Wesley K Thompson
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Andrew J Schork
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Beiyun Zhou
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Zea Borok
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Henricus F M van der Heijden
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Jacqueline de Graaf
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Dorine Swinkels
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Katja K Aben
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - James McKay
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Rayjean J Hung
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Heike Bikeböller
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Victoria L Stevens
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Demetrius Albanes
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Neil E Caporaso
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Younghun Han
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Yongyue Wei
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Maria Angeles Panadero
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Jose I Mayordomo
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - David C Christiani
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Lambertus Kiemeney
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Richard Houlston
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Christopher I Amos
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Nilanjan Chatterjee
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Ite A Laird-Offringa
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Ian G Mills
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
| | - Maria Teresa Landi
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine (VZ, AW, FB, YW, OAA), and Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership (VZ, IGM), University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway (VZ, AW, FB, YW, OAA); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK (VZ); Departments of Surgery and of Biochemistry and Molecular Biology (CNM, CY, IALO) and Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (BZ, ZB), Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA (CNM, CY, IALO); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Public Health Service, Bethesda, MD (JS, XH, LS, DA, NEC, NC, MTL); Information Management Services, Inc.; Rockville, MD (WW); Multimodal Imaging Laboratory (AMD, AJS), Center for Human Development (AMD, AJS), Department of Radiology (AMD), Department of Neurosciences (AMD), Department of Psychiatry (WKT), and Cognitive Sciences Graduate Program (AJS), University of California, San Diego, La Jolla, CA; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany (ML, AR); Department of Molecular Biology, University of Salzburg, Salzburg, Austria (AR); Translational Lung Research Center Heidelberg TLRC-H, Member of the German Center for Lung Research DZL, Heidelberg, Germany (AR); Department of Medical Genetics (SD) and Department of Molecular Oncology, Institute of Cancer Research and Department of Urology (IGM), Oslo University Hospital, Oslo, Norway (SD); NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway (SD); Radboud Unive
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13
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Crawford DW, Blakeley BD, Chen PH, Sherpa C, Le Grice SF, Laird-Offringa IA, McNaughton BR. An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chem Biol 2016; 11:2206-15. [PMID: 27253715 DOI: 10.1021/acschembio.6b00145] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potent and selective recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA recognition motif as a scaffold for tailoring new RNA hairpin recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5'-untranslated region, inhibits the interaction between TAR RNA and an HIV trans-activator of transcription (Tat)-derived peptide, and suppresses Tat/TAR-dependent transcription. Proteins described in this work are among the tightest TAR RNA-binding reagents-small molecule, nucleic acid, or protein-reported to date and thus have potential utility as therapeutics and basic research tools. Moreover, our findings demonstrate how a naturally occurring RNA recognition motif can be dramatically resurfaced through mutation, leading to potent and selective recognition-and modulation-of disease-relevant RNA.
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Affiliation(s)
| | | | - Po-Han Chen
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
| | - Chringma Sherpa
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stuart F.J. Le Grice
- Basic
Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ite A. Laird-Offringa
- Department of Surgery and Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, United States
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14
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Abstract
The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zea Borok
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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15
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Yang C, Stueve TR, Marconett CN, Rhie SK, Luo J, Zhou B, Borok Z, Laird-Offringa IA. Functional lung adenocarcinoma risk SNPs identified through positional integration with human alveolar epithelial cell epigenomes. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2015.12.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Liebler JM, Marconett CN, Juul N, Wang H, Liu Y, Flodby P, Laird-Offringa IA, Minoo P, Zhou B. Combinations of differentiation markers distinguish subpopulations of alveolar epithelial cells in adult lung. Am J Physiol Lung Cell Mol Physiol 2015; 310:L114-20. [PMID: 26545903 DOI: 10.1152/ajplung.00337.2015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/02/2015] [Indexed: 11/22/2022] Open
Abstract
Distal lung epithelium is maintained by proliferation of alveolar type II (AT2) cells and, for some daughter AT2 cells, transdifferentiation into alveolar type I (AT1) cells. We investigated if subpopulations of alveolar epithelial cells (AEC) exist that represent various stages in transdifferentiation from AT2 to AT1 cell phenotypes in normal adult lung and if they can be identified using combinations of cell-specific markers. Immunofluorescence microscopy showed that, in distal rat and mouse lungs, ∼ 20-30% of NKX2.1(+) (or thyroid transcription factor 1(+)) cells did not colocalize with pro-surfactant protein C (pro-SP-C), a highly specific AT2 cell marker. In distal rat lung, NKX2.1(+) cells coexpressed either pro-SP-C or the AT1 cell marker homeodomain only protein x (HOPX). Not all HOPX(+) cells colocalize with the AT1 cell marker aquaporin 5 (AQP5), and some AQP5(+) cells were NKX2.1(+). HOPX was expressed earlier than AQP5 during transdifferentiation in rat AEC primary culture, with robust expression of both by day 7. We speculate that NKX2.1 and pro-SP-C colocalize in AT2 cells, NKX2.1 and HOPX or AQP5 colocalize in intermediate or transitional cells, and HOPX and AQP5 are expressed without NKX2.1 in AT1 cells. These findings suggest marked heterogeneity among cells previously identified as exclusively AT1 or AT2 cells, implying the presence of subpopulations of intermediate or transitional AEC in normal adult lung.
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Affiliation(s)
- Janice M Liebler
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Nicholas Juul
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Hongjun Wang
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Yixin Liu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Per Flodby
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Parviz Minoo
- Division of Newborn Medicine, Department of Pediatrics, and Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Beiyun Zhou
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California;
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17
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Schliekelman MJ, Taguchi A, Zhu J, Dai X, Rodriguez J, Celiktas M, Zhang Q, Chin A, Wong CH, Wang H, McFerrin L, Selamat SA, Yang C, Kroh EM, Garg KS, Behrens C, Gazdar AF, Laird-Offringa IA, Tewari M, Wistuba II, Thiery JP, Hanash SM. Molecular portraits of epithelial, mesenchymal, and hybrid States in lung adenocarcinoma and their relevance to survival. Cancer Res 2015; 75:1789-800. [PMID: 25744723 DOI: 10.1158/0008-5472.can-14-2535] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a key process associated with tumor progression and metastasis. To define molecular features associated with EMT states, we undertook an integrative approach combining mRNA, miRNA, DNA methylation, and proteomic profiles of 38 cell populations representative of the genomic heterogeneity in lung adenocarcinoma. The resulting data were integrated with functional profiles consisting of cell invasiveness, adhesion, and motility. A subset of cell lines that were readily defined as epithelial or mesenchymal based on their morphology and E-cadherin and vimentin expression elicited distinctive molecular signatures. Other cell populations displayed intermediate/hybrid states of EMT, with mixed epithelial and mesenchymal characteristics. A dominant proteomic feature of aggressive hybrid cell lines was upregulation of cytoskeletal and actin-binding proteins, a signature shared with mesenchymal cell lines. Cytoskeletal reorganization preceded loss of E-cadherin in epithelial cells in which EMT was induced by TGFβ. A set of transcripts corresponding to the mesenchymal protein signature enriched in cytoskeletal proteins was found to be predictive of survival in independent datasets of lung adenocarcinomas. Our findings point to an association between cytoskeletal and actin-binding proteins, a mesenchymal or hybrid EMT phenotype and invasive properties of lung adenocarcinomas.
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Affiliation(s)
- Mark J Schliekelman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York
| | - Xudong Dai
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, New York
| | - Jaime Rodriguez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muge Celiktas
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Zhang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Alice Chin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Chee-Hong Wong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Hong Wang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lisa McFerrin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Suhaida A Selamat
- Department of Surgery, Biochemistry and Molecular Biology, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Chenchen Yang
- Department of Surgery, Biochemistry and Molecular Biology, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Evan M Kroh
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kavita S Garg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ite A Laird-Offringa
- Department of Surgery, Biochemistry and Molecular Biology, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Muneesh Tewari
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jean P Thiery
- Institute of Molecular Cell Biology, Singapore. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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18
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Marconett CN, Zhou B, Siegmund KD, Borok Z, Laird-Offringa IA. Transcriptomic Profiling of Primary Alveolar Epithelial Cell Differentiation in Human and Rat. Genom Data 2014; 2:105-109. [PMID: 25343132 PMCID: PMC4203668 DOI: 10.1016/j.gdata.2014.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell-type specific gene regulation is a key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how changes in transcriptional activation during alveolar epithelial cell (AEC) differentiation determine phenotype. We performed transcriptomic profiling using in vitro differentiation of human and rat primary AEC. This model recapitulates in vitro an in vivo process in which AEC transition from alveolar type 2 (AT2) cells to alveolar type 1 (AT1) cells during normal maintenance and regeneration following lung injury. Here we describe in detail the quality control, preprocessing, and normalization of microarray data presented within the associated study (Marconett et al., 2013). We also include R code for reproducibility of the referenced data and easily accessible processed data tables.
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Affiliation(s)
- Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Will Rogers Institute Pulmonary Research Center and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D Siegmund
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zea Borok
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Will Rogers Institute Pulmonary Research Center and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America ; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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Pulido MA, Lombardi V, Lee D, Wang Y, Chung E, Wang L, Kast WM, Akbari O, Laird-Offringa IA. Abstract 3623: Fluctuating antibody response and CD4-positive T-cells in a small-cell lung cancer mouse model. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patients with small-cell lung cancer (SCLC), a highly metastatic type of lung cancer, show a dismal 5-year survival of only 5%. Effective therapies are urgently needed. Notably, about fifteen-percent of SCLC-patients harbor anti-Hu autoantibodies, which are associated with improved survival. This suggests that the anti-Hu response might be harnessed for immunotherapy. A conditional SCLC mouse model with floxed Rb1 and p53 alleles, in which the cancer is induced by instilling Cre-recombinase into the lungs via intratracheal intubation, offers a unique opportunity to study the immune response in detail. We have previously shown that, just like human SCLC patients, a fraction of these SCLC-carrying mice show an anti-Hu autoantibody response. Here we examine the presence of anti-Hu reactive T-cells using a prospective cohort (n=45) of SCLC-induced mice. All mice develop SCLC, showing systemic disease in 4-7 months following inactivation of floxed Rb1 and p53 alleles. Monthly autoantibody analysis by western blotting revealed an antibody response in a subset of mice, sometimes as early as 1 month after induction. Reactivity usually peaked approximately 3-4 months after induction and declined as disease progressed. This suggests an immune escape mechanism and/or antibody adsorption by the rapidly proliferating tumors. T-cells were isolated at euthanasia from the spleens of moribund mice. Proliferating anti-HuD CD4-positive T-cells were detected in fifty-one-percent of mice (eighteen out of thirty-five) by flow cytometry. Anti-HuD T-cell proliferation from spleen cells was validated in a subsequent prospective cohort (n=45) of SCLC-induced mice using thymidine incorporation. Stratifying for antibody positive and negative mice using an stringent cutoff, there was no significant difference in T cell response between the two groups (p=0.11), however four mice in the antibody positive group showed the most elevated anti-HuD T-cell response. Our observations warrant a much larger study, in which in-depth characterization of the humoral and cellular the anti-HuD immune response is carried out at multiple time points and correlated with a detailed analysis of the stage of tumor development and mestastasis. Preliminary data hints at a negative correlation between the anti-HuD antibody and T-cell response on one hand and tumor size and metastasis on the other. The observation that the Hu antigen in mice with SCLC is a target for both humoral and cellular immune responses underscores the utility of this mouse model in the preclinical evaluation the anti-Hu immune response for therapy and clinical translation.
Citation Format: Mario A. Pulido, Vincent Lombardi, Diane Lee, Yiwei Wang, Eric Chung, Lina Wang, W. Martin Kast, Omid Akbari, Ite A. Laird-Offringa. Fluctuating antibody response and CD4-positive T-cells in a small-cell lung cancer mouse model. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3623. doi:10.1158/1538-7445.AM2014-3623
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Affiliation(s)
| | | | - Diane Lee
- USC Keck School of Medicine, Los Angeles, CA
| | - Yiwei Wang
- USC Keck School of Medicine, Los Angeles, CA
| | - Eric Chung
- USC Keck School of Medicine, Los Angeles, CA
| | - Lina Wang
- USC Keck School of Medicine, Los Angeles, CA
| | | | - Omid Akbari
- USC Keck School of Medicine, Los Angeles, CA
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20
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Shi J, Marconett C, Duan J, Hyland P, Li P, Wang Z, Wheeler W, Campan M, Huang J, Zhou W, Triche T, Amundadottir L, Hutchinson A, Chen PH, Zhou B, Chung B, Bertazzi PA, Bergen AW, Freedman M, Lee D, Siegmund K, Warner AC, Berman B, Pesatori AC, Borok Z, Consonni D, Chatterjee N, Tucker M, Caporaso N, Chanock SJ, Laird-Offringa IA, Landi MT. Abstract 287: Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters, and CpG islands (CGIs) while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, 4 of the 5 established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
Citation Format: Jianxin Shi, Crystal Marconett, Jubao Duan, Paula Hyland, Peng Li, Zhaoming Wang, William Wheeler, Mihaela Campan, Jing Huang, Weiyin Zhou, Tim Triche, Laufey Amundadottir, Amy Hutchinson, Po-Han Chen, Beiyun Zhou, Brian Chung, Pier Alberto Bertazzi, Andrew W. Bergen, Mathew Freedman, Diane Lee, Kim Siegmund, Andrew Clay Warner, Ben Berman, Angela C. Pesatori, Zea Borok, Dario Consonni, Nilanjan Chatterjee, Margaret Tucker, Neil Caporaso, Stephen J. Chanock, Ite A. Laird-Offringa, Maria Teresa Landi. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 287. doi:10.1158/1538-7445.AM2014-287
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Affiliation(s)
| | | | | | | | - Peng Li
- 1National Cancer Insititute, Bethesda, MD
| | | | | | | | - Jing Huang
- 1National Cancer Insititute, Bethesda, MD
| | | | - Tim Triche
- 2University of Southern California, Los Angeles, CA
| | | | | | - Po-Han Chen
- 2University of Southern California, Los Angeles, CA
| | - Beiyun Zhou
- 2University of Southern California, Los Angeles, CA
| | - Brian Chung
- 2University of Southern California, Los Angeles, CA
| | | | | | | | - Diane Lee
- 2University of Southern California, Los Angeles, CA
| | - Kim Siegmund
- 2University of Southern California, Los Angeles, CA
| | | | - Ben Berman
- 2University of Southern California, Los Angeles, CA
| | | | - Zea Borok
- 2University of Southern California, Los Angeles, CA
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21
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Li G, Flodby P, Luo J, Kage H, Sipos A, Gao D, Ji Y, Beard LL, Marconett CN, DeMaio L, Kim YH, Kim KJ, Laird-Offringa IA, Minoo P, Liebler JM, Zhou B, Crandall ED, Borok Z. Knockout mice reveal key roles for claudin 18 in alveolar barrier properties and fluid homeostasis. Am J Respir Cell Mol Biol 2014; 51:210-22. [PMID: 24588076 DOI: 10.1165/rcmb.2013-0353oc] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Claudin proteins are major constituents of epithelial and endothelial tight junctions (TJs) that regulate paracellular permeability to ions and solutes. Claudin 18, a member of the large claudin family, is highly expressed in lung alveolar epithelium. To elucidate the role of claudin 18 in alveolar epithelial barrier function, we generated claudin 18 knockout (C18 KO) mice. C18 KO mice exhibited increased solute permeability and alveolar fluid clearance (AFC) compared with wild-type control mice. Increased AFC in C18 KO mice was associated with increased β-adrenergic receptor signaling together with activation of cystic fibrosis transmembrane conductance regulator, higher epithelial sodium channel, and Na-K-ATPase (Na pump) activity and increased Na-K-ATPase β1 subunit expression. Consistent with in vivo findings, C18 KO alveolar epithelial cell (AEC) monolayers exhibited lower transepithelial electrical resistance and increased solute and ion permeability with unchanged ion selectivity. Claudin 3 and claudin 4 expression was markedly increased in C18 KO mice, whereas claudin 5 expression was unchanged and occludin significantly decreased. Microarray analysis revealed changes in cytoskeleton-associated gene expression in C18 KO mice, consistent with observed F-actin cytoskeletal rearrangement in AEC monolayers. These findings demonstrate a crucial nonredundant role for claudin 18 in the regulation of alveolar epithelial TJ composition and permeability properties. Increased AFC in C18 KO mice identifies a role for claudin 18 in alveolar fluid homeostasis beyond its direct contributions to barrier properties that may, at least in part, compensate for increased permeability.
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Affiliation(s)
- Guanglei Li
- 1 Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine
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22
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Wilson IM, Vucic EA, Enfield KSS, Thu KL, Zhang YA, Chari R, Lockwood WW, Radulovich N, Starczynowski DT, Banáth JP, Zhang M, Pusic A, Fuller M, Lonergan KM, Rowbotham D, Yee J, English JC, Buys TPH, Selamat SA, Laird-Offringa IA, Liu P, Anderson M, You M, Tsao MS, Brown CJ, Bennewith KL, MacAulay CE, Karsan A, Gazdar AF, Lam S, Lam WL. EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk. Oncogene 2013; 33:4464-73. [PMID: 24096489 PMCID: PMC4527534 DOI: 10.1038/onc.2013.396] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/30/2013] [Accepted: 08/06/2013] [Indexed: 02/07/2023]
Abstract
In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.
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Affiliation(s)
- I M Wilson
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - E A Vucic
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K S S Enfield
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K L Thu
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Y A Zhang
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R Chari
- 1] Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada [2] Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - W W Lockwood
- 1] Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada [2] National Human Genome Research Institute, Cancer Genetics Branch, Bethesda, MD, USA
| | - N Radulovich
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON, Canada
| | - D T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - J P Banáth
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - M Zhang
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A Pusic
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - M Fuller
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K M Lonergan
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - D Rowbotham
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - J Yee
- Department of Surgery, Vancouver General Hospital, Vancouver, BC, Canada
| | - J C English
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - T P H Buys
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - S A Selamat
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - I A Laird-Offringa
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - P Liu
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M Anderson
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M You
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M S Tsao
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON, Canada
| | - C J Brown
- Department of Medical Genetics, University of British Columbia, Life Sciences Centre, Vancouver, BC, Canada
| | - K L Bennewith
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - C E MacAulay
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A Karsan
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A F Gazdar
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - S Lam
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - W L Lam
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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23
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Blakeley BD, Shattuck J, Coates MB, Tran E, Laird-Offringa IA, McNaughton BR. Analysis of protein-RNA complexes involving a RNA recognition motif engineered to bind hairpins with seven- and eight-nucleotide loops. Biochemistry 2013; 52:4745-7. [PMID: 23806102 DOI: 10.1021/bi400801q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
U1A binds U1hpII, a hairpin RNA with a 10-nucleotide loop. A U1A mutant (ΔK50ΔM51) binds U1hpII-derived hairpins with shorter loops, making it an interesting scaffold for engineering or evolving proteins that bind similarly sized disease-related hairpin RNAs. However, a more detailed understanding of complexes involving ΔK50ΔM51 is likely a prerequisite to generating such proteins. Toward this end, we measured mutational effects for complexes involving U1A ΔK50ΔM51 and U1hpII-derived hairpin RNAs with seven- or eight-nucleotide loops and identified contacts that are critical to the stabilization of these complexes. Our data provide valuable insight into sequence-selective recognition of seven- or eight-nucleotide loop hairpins by an engineered RNA binding protein.
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Affiliation(s)
- Brett D Blakeley
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, Colorado State University , Fort Collins, Colorado 80523, United States
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24
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Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, Lynch SK, Stueve TR, Siegmund KD, Berman BP, Borok Z, Laird-Offringa IA. Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. PLoS Genet 2013; 9:e1003513. [PMID: 23818859 PMCID: PMC3688557 DOI: 10.1371/journal.pgen.1003513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 04/04/2013] [Indexed: 12/16/2022] Open
Abstract
Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation. Understanding the role of epigenetic control of gene expression is critical to the full description of biological processes, such as development and regeneration. Herein we utilize the differentiation of cells from the distal lung to gain insight into the correlation between the epigenetic landscape, molecular signaling events, and eventual changes in transcription and phenotype. We found that by integrating epigenetic profiling with whole genome transcriptomic data we were able to determine which molecular signaling events were activated and repressed during adult alveolar epithelial cell differentiation, and we identified epigenetic changes that contributed to these changes. Furthermore, we validated the role of one of these predicted but not previously identified pathways, retinoid X receptor signaling, in this process.
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Affiliation(s)
- Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Megan E. Rieger
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Suhaida A. Selamat
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Mickael Dubourd
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Xiaohui Fang
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine/Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Sean K. Lynch
- Department of Product Engineering, Division of Manufacturing Operations, MAXIM Integrated Products, Sunnyvale, California, United States of America
| | - Theresa Ryan Stueve
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D. Siegmund
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Benjamin P. Berman
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- University of Southern California Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zea Borok
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ite A. Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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25
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Abstract
Epigenetic deregulation of gene function has been strongly implicated in carcinogenesis and is one of the mechanisms contributing to the development of lung cancer. The inherent reversibility of epigenetic alterations makes them viable therapeutic targets. Here, we review the therapeutic implications of epigenetic changes in lung cancer, and recent advances in therapeutic strategies targeting DNA methylation and histone acetylation.
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Affiliation(s)
- Stephen V Liu
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles, CA , USA
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26
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Law MJ, Lee DS, Lee CS, Anglim PP, Haworth IS, Laird-Offringa IA. The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA. Nucleic Acids Res 2013; 41:7092-100. [PMID: 23703211 PMCID: PMC3737524 DOI: 10.1093/nar/gkt326] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Previous kinetic investigations of the N-terminal RNA Recognition Motif (RRM) domain of spliceosomal A protein of the U1 small nuclear ribonucleoprotein particle (U1A) interacting with its RNA target U1 hairpin II (U1hpII) provided experimental evidence for a ‘lure and lock’ model of binding. The final step of locking has been proposed to involve conformational changes in an α-helix immediately C-terminal to the RRM domain (helix C), which occludes the RNA binding surface in the unbound protein. Helix C must shift its position to accommodate RNA binding in the RNA–protein complex. This results in a new hydrophobic core, an intraprotein hydrogen bond and a quadruple stacking interaction between U1A and U1hpII. Here, we used a surface plasmon resonance-based biosensor to gain mechanistic insight into the role of helix C in mediating the interaction with U1hpII. Truncation, removal or disruption of the helix exposes the RNA-binding surface, resulting in an increase in the association rate, while simultaneously reducing the ability of the complex to lock, reflected in a loss of complex stability. Disruption of the quadruple stacking interaction has minor kinetic effects when compared with removal of the intraprotein hydrogen bonds. These data provide new insights into the mechanism whereby sequences C-terminal to an RRM can influence RNA binding.
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Affiliation(s)
- Michael J Law
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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27
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Chen Y, Bates DL, Dey R, Chen PH, Machado ACD, Laird-Offringa IA, Rohs R, Chen L. DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation. Cell Rep 2012; 2:1197-206. [PMID: 23142663 DOI: 10.1016/j.celrep.2012.10.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 08/13/2012] [Accepted: 10/01/2012] [Indexed: 12/17/2022] Open
Abstract
GATA transcription factors regulate transcription during development and differentiation by recognizing distinct GATA sites with a tandem of two conserved zinc fingers, and by mediating long-range DNA looping. However, the molecular basis of these processes is not well understood. Here, we determined three crystal structures of the full DNA-binding domain (DBD) of human GATA3 protein, which contains both zinc fingers, in complex with different DNA sites. In one structure, both zinc fingers wrap around a palindromic GATA site, cooperatively enhancing the binding affinity and kinetic stability. Strikingly, in the other two structures, the two fingers of GATA DBD bind GATA sites on different DNA molecules, thereby bridging two separate DNA fragments. This was confirmed in solution by an in-gel fluorescence resonance energy transfer analysis. These findings not only provide insights into the structure and function of GATA proteins but also shed light on the molecular basis of long-range gene regulation.
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Affiliation(s)
- Yongheng Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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28
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Johnson CJ, Galler JS, Anglim PP, Tsou JA, Selamt SA, Rom WN, Laird-Offringa IA. Abstract B10: Detection of DNA methylation in the serum of lung cancer cases and controls using Digital MethyLight. Clin Cancer Res 2012. [DOI: 10.1158/1078-0432.12aacriaslc-b10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Lung cancer is the leading cause of cancer death worldwide. Over 1.3 million people succumbed to lung cancer in 2008 according to the World Health Organization (WHO). The predicted five year survival rate for non-small cell lung cancer (NSCLC) for the year 2010 is 16%. An early diagnosis would significantly increase survival of lung cancer patients. Low dose computed tomography (LDCT) detects tumors as small as T0. However, in a recent study by The National Lung Screening Trial Research Team, the false positive rate was 96%. DNA methylation, which has been shown to be associated with gene inactivation in various cancers, exhibits cancer-specific profiles. We hypothesize that DNA methylation in plasma/serum could be a powerful biomarker to complement LDCT when a lesion is detected.
Results: Using candidate gene analysis in combination with epigenetic profiling we have identified 12 DNA methylation markers based on comparisons between archival lung cancer samples and matched adjacent non-tumor lung: 2C35, GDNF, HOXA1, HOXB4, MT1G, NEUROD1, NID2, OPCML/HNT, SFRP1, TNFRSF25, TRIM58, TWIST1 are all highly significantly and frequently hypermethylated in lung cancer tissues. Because detection of shed DNA in bodily fluids requires a very sensitive method, we have adapted Digital MethyLight to interrogate the 12 markers simultaneously on 384-well plates. Digital MethyLight is a sensitive real time-based limiting dilution method in which free floating DNA extracted from bodily fluids is diluted over a large number of wells (in our case 90) so that the number of detectable methylated DNA molecules can be counted. We used three different colors of probes to generate four sets of multiplexed probes, covering our 12-marker panel. Using this method, we examined the serum of 90 patients with lung cancer and 90 high-risk controls from New York City. We also examined serum from an additional 30 low risk, non-smoker controls. Many of our markers showed a statistically significant difference in methylation when comparing cases to non-smoker controls, but the difference with the high risk smokers was much less pronounced. Several subjects from the high-risk controls showed DNA methylation levels comparable to the cases, and several of these controls were ultimately diagnosed with cancer. Interestingly, we found no correlation between tumor stage and amount of DNA shed, and were able to detect methylated DNA in the serum of several stage 1A patients.
Conclusion: Elevated DNA methylation is observed in lung cancer cases, as well as in a number of high risk control subjects. Serum DNA methylation levels are markedly lower in non-smoking controls. While sensitivity is low, methylated DNA can be detected in stage 1A patients, suggesting that even small tumors can shed sufficient DNA to allow detection. It is not clear why some patients do not show detectable DNA, even with progressed disease. This merits further investigation.
Funding: R01 CA 119029, R01 CA120869, Canary Foundation and Thomas G. Labrecque Foundation.
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Affiliation(s)
- Candace J.S Johnson
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - Janice S. Galler
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - Paul P. Anglim
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - Jeffery A. Tsou
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - Suhaida A. Selamt
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - William N. Rom
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
| | - Ite A. Laird-Offringa
- 1University of Southern California, Los Angeles, CA, 2New York University, New York, NY
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Campan M, Moffitt M, Houshdaran S, Shen H, Widschwendter M, Daxenbichler G, Long T, Marth C, Laird-Offringa IA, Press MF, Dubeau L, Siegmund KD, Wu AH, Groshen S, Chandavarkar U, Roman LD, Berchuck A, Pearce CL, Laird PW. Genome-scale screen for DNA methylation-based detection markers for ovarian cancer. PLoS One 2011; 6:e28141. [PMID: 22163280 PMCID: PMC3233546 DOI: 10.1371/journal.pone.0028141] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 11/02/2011] [Indexed: 01/04/2023] Open
Abstract
Background The identification of sensitive biomarkers for the detection of ovarian cancer is of high clinical relevance for early detection and/or monitoring of disease recurrence. We developed a systematic multi-step biomarker discovery and verification strategy to identify candidate DNA methylation markers for the blood-based detection of ovarian cancer. Methodology/Principal Findings We used the Illumina Infinium platform to analyze the DNA methylation status of 27,578 CpG sites in 41 ovarian tumors. We employed a marker selection strategy that emphasized sensitivity by requiring consistency of methylation across tumors, while achieving specificity by excluding markers with methylation in control leukocyte or serum DNA. Our verification strategy involved testing the ability of identified markers to monitor disease burden in serially collected serum samples from ovarian cancer patients who had undergone surgical tumor resection compared to CA-125 levels. We identified one marker, IFFO1 promoter methylation (IFFO1-M), that is frequently methylated in ovarian tumors and that is rarely detected in the blood of normal controls. When tested in 127 serially collected sera from ovarian cancer patients, IFFO1-M showed post-resection kinetics significantly correlated with serum CA-125 measurements in six out of 16 patients. Conclusions/Significance We implemented an effective marker screening and verification strategy, leading to the identification of IFFO1-M as a blood-based candidate marker for sensitive detection of ovarian cancer. Serum levels of IFFO1-M displayed post-resection kinetics consistent with a reflection of disease burden. We anticipate that IFFO1-M and other candidate markers emerging from this marker development pipeline may provide disease detection capabilities that complement existing biomarkers.
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Affiliation(s)
- Mihaela Campan
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Melissa Moffitt
- Department of Obstetrics and Gynecology Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Sahar Houshdaran
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Hui Shen
- University of Southern California Epigenome Center, University of Southern California, Los Angeles, CA, United States of America
| | - Martin Widschwendter
- Department of Gynecological Oncology, Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, United Kingdom
| | - Günter Daxenbichler
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Tiffany Long
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Christian Marth
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Ite A. Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Louis Dubeau
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Susan Groshen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Uma Chandavarkar
- Department of Obstetrics and Gynecology Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lynda D. Roman
- Department of Obstetrics and Gynecology Division of Gynecologic Oncology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peter W. Laird
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- University of Southern California Epigenome Center, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
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Selamat SA, Galler JS, Joshi AD, Fyfe MN, Campan M, Siegmund KD, Kerr KM, Laird-Offringa IA. DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One 2011; 6:e21443. [PMID: 21731750 PMCID: PMC3121768 DOI: 10.1371/journal.pone.0021443] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/28/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is common in lung adenocarcinoma, but its timing in the phases of tumor development is largely unknown. Delineating when abnormal DNA methylation arises may provide insight into the natural history of lung adenocarcinoma and the role that DNA methylation alterations play in tumor formation. METHODOLOGY/PRINCIPAL FINDINGS We used MethyLight, a sensitive real-time PCR-based quantitative method, to analyze DNA methylation levels at 15 CpG islands that are frequently methylated in lung adenocarcinoma and that we had flagged as potential markers for non-invasive detection. We also used two repeat probes as indicators of global DNA hypomethylation. We examined DNA methylation in 249 tissue samples from 93 subjects, spanning the putative spectrum of peripheral lung adenocarcinoma development: histologically normal adjacent non-tumor lung, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS, formerly known as bronchioloalveolar carcinoma), and invasive lung adenocarcinoma. Comparison of DNA methylation levels between the lesion types suggests that DNA hypermethylation of distinct loci occurs at different time points during the development of lung adenocarcinoma. DNA methylation at CDKN2A ex2 and PTPRN2 is already significantly elevated in AAH, while CpG islands at 2C35, EYA4, HOXA1, HOXA11, NEUROD1, NEUROD2 and TMEFF2 are significantly hypermethylated in AIS. In contrast, hypermethylation at CDH13, CDX2, OPCML, RASSF1, SFRP1 and TWIST1 and global DNA hypomethylation appear to be present predominantly in invasive cancer. CONCLUSIONS/SIGNIFICANCE The gradual increase in DNA methylation seen for numerous loci in progressively more transformed lesions supports the model in which AAH and AIS are sequential stages in the development of lung adenocarcinoma. The demarcation of DNA methylation changes characteristic for AAH, AIS and adenocarcinoma begins to lay out a possible roadmap for aberrant DNA methylation events in tumor development. In addition, it identifies which DNA methylation changes might be used as molecular markers for the detection of preinvasive lesions.
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Affiliation(s)
- Suhaida A. Selamat
- Departments of Surgery and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Janice S. Galler
- Departments of Surgery and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amit D. Joshi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - M. Nicky Fyfe
- Department of Pathology, Aberdeen Royal Infirmary, University of Aberdeen, Aberdeen, United Kingdom
| | - Mihaela Campan
- Departments of Surgery and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Keith M. Kerr
- Department of Pathology, Aberdeen Royal Infirmary, University of Aberdeen, Aberdeen, United Kingdom
| | - Ite A. Laird-Offringa
- Departments of Surgery and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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Kazarian M, Laird-Offringa IA. Small-cell lung cancer-associated autoantibodies: potential applications to cancer diagnosis, early detection, and therapy. Mol Cancer 2011; 10:33. [PMID: 21450098 PMCID: PMC3080347 DOI: 10.1186/1476-4598-10-33] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 03/30/2011] [Indexed: 12/26/2022] Open
Abstract
Small-cell lung cancer (SCLC) is the most aggressive lung cancer subtype and lacks effective early detection methods and therapies. A number of rare paraneoplastic neurologic autoimmune diseases are strongly associated with SCLC. Most patients with such paraneoplastic syndromes harbor high titers of antibodies against neuronal proteins that are abnormally expressed in SCLC tumors. These autoantibodies may cross-react with the nervous system, possibly contributing to autoimmune disease development. Importantly, similar antibodies are present in many SCLC patients without autoimmune disease, albeit at lower titers. The timing of autoantibody development relative to cancer and the nature of the immune trigger remain to be elucidated. Here we review what is currently known about SCLC-associated autoantibodies, and describe a recently developed mouse model system of SCLC that appears to lend itself well to the study of the SCLC-associated immune response. We also discuss potential clinical applications for these autoantibodies, such as SCLC diagnosis, early detection, and therapy.
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Affiliation(s)
- Meleeneh Kazarian
- Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NOR 6420, Los Angeles, CA 90089-9176, USA
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Vázquez-Chantada M, Fernández-Ramos D, Embade N, Martínez-Lopez N, Varela-Rey M, Woodhoo A, Luka Z, Wagner C, Anglim PP, Finnell RH, Caballería J, Laird-Offringa IA, Gorospe M, Lu SC, Mato JM, Martínez-Chantar ML. HuR/methyl-HuR and AUF1 regulate the MAT expressed during liver proliferation, differentiation, and carcinogenesis. Gastroenterology 2010; 138:1943-53. [PMID: 20102719 PMCID: PMC2860011 DOI: 10.1053/j.gastro.2010.01.032] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 12/18/2009] [Accepted: 01/14/2010] [Indexed: 01/15/2023]
Abstract
BACKGROUND & AIMS Hepatic de-differentiation, liver development, and malignant transformation are processes in which the levels of hepatic S-adenosylmethionine are tightly regulated by 2 genes: methionine adenosyltransferase 1A (MAT1A) and methionine adenosyltransferase 2A (MAT2A). MAT1A is expressed in the adult liver, whereas MAT2A expression primarily is extrahepatic and is associated strongly with liver proliferation. The mechanisms that regulate these expression patterns are not completely understood. METHODS In silico analysis of the 3' untranslated region of MAT1A and MAT2A revealed putative binding sites for the RNA-binding proteins AU-rich RNA binding factor 1 (AUF1) and HuR, respectively. We investigated the posttranscriptional regulation of MAT1A and MAT2A by AUF1, HuR, and methyl-HuR in the aforementioned biological processes. RESULTS During hepatic de-differentiation, the switch between MAT1A and MAT2A coincided with an increase in HuR and AUF1 expression. S-adenosylmethionine treatment altered this homeostasis by shifting the balance of AUF1 and methyl-HuR/HuR, which was identified as an inhibitor of MAT2A messenger RNA (mRNA) stability. We also observed a similar temporal distribution and a functional link between HuR, methyl-HuR, AUF1, and MAT1A and MAT2A during fetal liver development. Immunofluorescent analysis revealed increased levels of HuR and AUF1, and a decrease in methyl-HuR levels in human livers with hepatocellular carcinoma (HCC). CONCLUSIONS Our data strongly support a role for AUF1 and HuR/methyl-HuR in liver de-differentiation, development, and human HCC progression through the posttranslational regulation of MAT1A and MAT2A mRNAs.
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Affiliation(s)
- Mercedes Vázquez-Chantada
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - Nieves Embade
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - Nuria Martínez-Lopez
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - Ashwin Woodhoo
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA
| | - Conrad Wagner
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA, Tennessee Valley Department of Medical Affairs Medical Center, Nashville, TN, USA
| | - Paul P. Anglim
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Richard H. Finnell
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, USA
| | | | - Ite A. Laird-Offringa
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Myriam Gorospe
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shelly C Lu
- Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University Southern California, Los Angeles, CA 90033, USA
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
| | - M Luz Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology Park of Bizkaia, 48160-Derio, Bizkaia, Spain
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Kazarian M, Calbo J, Proost N, Carpenter CL, Berns A, Laird-Offringa IA. Immune response in lung cancer mouse model mimics human anti-Hu reactivity. J Neuroimmunol 2009; 217:38-45. [PMID: 19765830 DOI: 10.1016/j.jneuroim.2009.08.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 08/28/2009] [Accepted: 08/28/2009] [Indexed: 01/26/2023]
Abstract
Most patients with paraneoplastic encephalomyelitis/sensory neuronopathy PEM/SN have small-cell lung cancer (SCLC) and develop antibodies against neuronal-specific Hu proteins, which are abnormally expressed in the tumor. Anti-Hu reactivity is present in ~16% of SCLC patients without PEM/SN. Here we test the hypothesis that engineered SCLC-prone mice may exhibit anti-Hu reactivity. We show that tumors from SCLC-prone mice misexpress Hu proteins, and 14% of mice harbor anti-Hu antibodies. Mice appear to show reactivity prior to clinical diagnosis of SCLC. This mouse model system will be useful to study SCLC-associated autoimmunity, its diagnostic value, and the potential protective role of oncoantigen-directed autoantibodies.
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Affiliation(s)
- Meleeneh Kazarian
- Departments of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California/Norris Cancer Center, 1441 Eastlake Ave. NOR 6420, Norris Cancer Center, Los Angeles, CA 90089, United States
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Tsou JA, Kazarian M, Patel A, Galler JS, Laird-Offringa IA, Carpenter CL, London SJ. Low level anti-Hu reactivity: A risk marker for small cell lung cancer? ACTA ACUST UNITED AC 2008; 32:292-9. [PMID: 19070439 DOI: 10.1016/j.cdp.2008.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2008] [Indexed: 10/21/2022]
Abstract
BACKGROUND Previous experimental and laboratory studies have implicated antibodies against Hu proteins (anti-Hu) as a potential marker for small cell lung cancer (SCLC); there are no estimates of the association between anti-Hu and SCLC using a population-based design. METHODS We used stored plasma specimens to evaluate anti-Hu reactivity in relationship to small cell lung cancer in a population-based case-control study. Using Western Blot analysis, we measured anti-Hu reactivity against recombinant Hu family member, HuD, in plasma samples from 41 SCLC cases and 79 controls individually matched for age, race, sex, and smoking status (never, past, current). We analyzed the association between anti-Hu reactivity and SCLC using conditional logistic regression. RESULTS Anti-Hu reactivity was associated with SCLC, both before and after adjustment for amount of smoking. We observed a smoking-adjusted odds ratio of 3.2 (95% confidence interval from 0.98 to 13.4) comparing subjects above 1800 units (the lower limit of the second tertile of the distribution among antibody positive controls) to subjects with lower reactivity. We also found suggestive evidence in follow-up of our cases that anti-Hu above 1800 units was related to longer-term survival from SCLC. The present research is the first report of anti-Hu reactivity and SCLC in a population-based study. CONCLUSIONS Given the suggestive evidence in this study, prospective analyses to examine whether anti-Hu reactivity might predict risk of developing SCLC, or whether anti-Hu reactivity could serve as an early marker for SCLC, may be warranted.
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Affiliation(s)
- Jeffrey A Tsou
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
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Anglim PP, Alonzo TA, Laird-Offringa IA. DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer 2008; 7:81. [PMID: 18947422 PMCID: PMC2585582 DOI: 10.1186/1476-4598-7-81] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/23/2008] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the number one cancer killer in the United States. This disease is clinically divided into two sub-types, small cell lung cancer, (10–15% of lung cancer cases), and non-small cell lung cancer (NSCLC; 85–90% of cases). Early detection of NSCLC, which is the more common and less aggressive of the two sub-types, has the highest potential for saving lives. As yet, no routine screening method that enables early detection exists, and this is a key factor in the high mortality rate of this disease. Imaging and cytology-based screening strategies have been employed for early detection, and while some are sensitive, none have been demonstrated to reduce lung cancer mortality. However, mortality might be reduced by developing specific molecular markers that can complement imaging techniques. DNA methylation has emerged as a highly promising biomarker and is being actively studied in multiple cancers. The analysis of DNA methylation-based biomarkers is rapidly advancing, and a large number of potential biomarkers have been identified. Here we present a detailed review of the literature, focusing on DNA methylation-based markers developed using primary NSCLC tissue. Viable markers for clinical diagnosis must be detectable in 'remote media' such as blood, sputum, bronchoalveolar lavage, or even exhaled breath condensate. We discuss progress on their detection in such media and the sensitivity and specificity of the molecular marker panels identified to date. Lastly, we look to future advancements that will be made possible with the interrogation of the epigenome.
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Affiliation(s)
- Paul P Anglim
- Departments of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089-9176, USA.
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Julien KR, Sumita M, Chen PH, Laird-Offringa IA, Hoogstraten CG. Conformationally restricted nucleotides as a probe of structure-function relationships in RNA. RNA 2008; 14:1632-1643. [PMID: 18596252 PMCID: PMC2491483 DOI: 10.1261/rna.866408] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 04/17/2008] [Indexed: 05/26/2023]
Abstract
We introduce the use of commercially available locked nucleic acids (LNAs) as a functional probe in RNA. LNA nucleotides contain a covalent linkage that restricts the pseudorotation phase of the ribose to C3'-endo (A-form). Introduction of an LNA at a single site thus allows the role of ribose structure and dynamics in RNA function to be assessed. We apply LNA probing at multiple sites to analyze self-cleavage in the lead-dependent ribozyme (leadzyme), thermodynamic stability in the UUCG tetraloop, and the kinetics of recognition of U1A protein by U1 snRNA hairpin II. In the leadzyme, locking a single guanosine residue into the C3'-endo pucker increases the catalytic rate by a factor of 20, despite the fact that X-ray crystallographic and NMR structures of the leadzyme ground state reported a C2'-endo conformation at this site. These results strongly suggest that a conformational change at this position is critical for catalytic function. Functional insights obtained in all three systems demonstrate the highly general applicability of LNA probing in analysis of the role of ribose orientation in RNA structure, dynamics, and function.
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Affiliation(s)
- Kristine R Julien
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Anglim PP, Galler JS, Koss MN, Hagen JA, Turla S, Campan M, Weisenberger DJ, Laird PW, Siegmund KD, Laird-Offringa IA. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer 2008; 7:62. [PMID: 18616821 PMCID: PMC2483990 DOI: 10.1186/1476-4598-7-62] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 07/10/2008] [Indexed: 02/06/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer death in men and women in the United States and Western Europe. Over 160,000 Americans die of this disease every year. The five-year survival rate is 15% – significantly lower than that of other major cancers. Early detection is a key factor in increasing lung cancer patient survival. DNA hypermethylation is recognized as an important mechanism for tumor suppressor gene inactivation in cancer and could yield powerful biomarkers for early detection of lung cancer. Here we focused on developing DNA methylation markers for squamous cell carcinoma of the lung. Using the sensitive, high-throughput DNA methylation analysis technique MethyLight, we examined the methylation profile of 42 loci in a collection of 45 squamous cell lung cancer samples and adjacent non-tumor lung tissues from the same patients. Results We identified 22 loci showing significantly higher DNA methylation levels in tumor tissue than adjacent non-tumor lung. Of these, eight showed highly significant hypermethylation in tumor tissue (p < 0.0001): GDNF, MTHFR, OPCML, TNFRSF25, TCF21, PAX8, PTPRN2 and PITX2. Used in combination on our specimen collection, this eight-locus panel showed 95.6% sensitivity and specificity. Conclusion We have identified 22 DNA methylation markers for squamous cell lung cancer, several of which have not previously been reported to be methylated in any type of human cancer. The top eight markers show great promise as a sensitive and specific DNA methylation marker panel for squamous cell lung cancer.
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Affiliation(s)
- Paul P Anglim
- Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089-9176, USA.
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Tsou JA, Galler JS, Wali A, Ye W, Siegmund KD, Groshen S, Laird PW, Turla S, Koss MN, Pass HI, Laird-Offringa IA. DNA methylation profile of 28 potential marker loci in malignant mesothelioma. Lung Cancer 2007; 58:220-30. [PMID: 17659810 PMCID: PMC2752414 DOI: 10.1016/j.lungcan.2007.06.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 05/28/2007] [Accepted: 06/19/2007] [Indexed: 11/24/2022]
Abstract
Patients with malignant mesothelioma (MM), an aggressive cancer associated with asbestos exposure, usually present clinically with advanced disease and this greatly reduces the likelihood of curative treatment. MM is difficult to diagnose without invasive techniques; the development of non-invasively detectable molecular markers would therefore be highly beneficial. DNA methylation changes in cancer cells provide powerful markers that are potentially detectable non-invasively in DNA shed into bodily fluids. Here we examined the methylation status of 28 loci in 52 MM tumors to investigate their potential as molecular markers for MM. To exclude candidate MM markers that might be positive in biopsies/pleural fluid due to contaminating surrounding non-tumor lung tissue/DNA, we also examined the methylation of these markers in lung samples (age- or environmentally induced hypermethylation is frequently observed in non-cancerous lung). Statistically significantly increased methylation in MM versus non-tumor lung samples was found for estrogen receptor 1 (ESR1; p = 0.0002), solute carrier family 6 member 20 (SLC6A20; p = 0.0022) and spleen tyrosine kinase (SYK; p=0.0003). Examination of associations between methylation levels of the 28 loci and clinical parameters suggest associations of the methylation status of metallothionein genes with gender, histology, asbestos exposure, and lymph node involvement, and the methylation status of leucine zipper tumor suppressor 1 (LZTS1) and SLC6A20 with survival.
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Affiliation(s)
- Jeffrey A. Tsou
- Norris Cancer Center and Departments of Surgery and of Biochemistry and Molecular Biology, Room NOR6420, 1441 Eastlake Ave., Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Janice S. Galler
- Norris Cancer Center and Departments of Surgery and of Biochemistry and Molecular Biology, Room NOR6420, 1441 Eastlake Ave., Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Anil Wali
- Department of Thoracic Surgery, Karamanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Wei Ye
- Biostatistics Core, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9175, USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9011, USA
| | - Susan Groshen
- Biostatistics Core, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9175, USA
| | - Peter W. Laird
- Norris Cancer Center and Departments of Surgery and of Biochemistry and Molecular Biology, Room NOR6420, 1441 Eastlake Ave., Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Sally Turla
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9092, USA
| | - Michael N. Koss
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9092, USA
| | - Harvey I. Pass
- Department of Thoracic Surgery, Karamanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Ite A. Laird-Offringa
- Norris Cancer Center and Departments of Surgery and of Biochemistry and Molecular Biology, Room NOR6420, 1441 Eastlake Ave., Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
- Corresponding author: Tel.: +1 323 865 0655; fax: +1 323 865 0158. E-mail address: (I.A. Laird-Offringa)
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Tsou JA, Galler JS, Siegmund KD, Laird PW, Turla S, Cozen W, Hagen JA, Koss MN, Laird-Offringa IA. Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer 2007; 6:70. [PMID: 17967182 PMCID: PMC2206053 DOI: 10.1186/1476-4598-6-70] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 10/29/2007] [Indexed: 02/04/2023] Open
Abstract
Background Lung cancer is the number one cancer killer of both men and women in the United States. Three quarters of lung cancer patients are diagnosed with regionally or distantly disseminated disease; their 5-year survival is only 15%. DNA hypermethylation at promoter CpG islands shows great promise as a cancer-specific marker that would complement visual lung cancer screening tools such as spiral CT, improving early detection. In lung cancer patients, such hypermethylation is detectable in a variety of samples ranging from tumor material to blood and sputum. To date the penetrance of DNA methylation at any single locus has been too low to provide great clinical sensitivity. We used the real-time PCR-based method MethyLight to examine DNA methylation quantitatively at twenty-eight loci in 51 primary human lung adenocarcinomas, 38 adjacent non-tumor lung samples, and 11 lung samples from non-lung cancer patients. Results We identified thirteen loci showing significant differential DNA methylation levels between tumor and non-tumor lung; eight of these show highly significant hypermethylation in adenocarcinoma: CDH13, CDKN2A EX2, CDX2, HOXA1, OPCML, RASSF1, SFPR1, and TWIST1 (p-value << 0.0001). Using the current tissue collection and 5-fold cross validation, the four most significant loci (CDKN2A EX2, CDX2, HOXA1 and OPCML) individually distinguish lung adenocarcinoma from non-cancer lung with a sensitivity of 67–86% and specificity of 74–82%. DNA methylation of these loci did not differ significantly based on gender, race, age or tumor stage, indicating their wide applicability as potential lung adenocarcinoma markers. We applied random forests to determine a good classifier based on a subset of our loci and determined that combined use of the same four top markers allows identification of lung cancer tissue from non-lung cancer tissue with 94% sensitivity and 90% specificity. Conclusion The identification of eight CpG island loci showing highly significant hypermethylation in lung adenocarcinoma provides strong candidates for evaluation in patient remote media such as plasma and sputum. The four most highly ranked loci, CDKN2A EX2, CDX2, HOXA1 and OPCML, which show significant DNA methylation even in stage IA tumor samples, merit further investigation as some of the most promising lung adenocarcinoma markers identified to date.
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Affiliation(s)
- Jeffrey A Tsou
- Norris Cancer Center and Department of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA.
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Abstract
The N-terminal RNA Recognition Motif (RRM1) of the spliceosomal protein U1A interacting with its target U1 hairpin II (U1hpII) has been used as a paradigm for RRM-containing proteins interacting with their RNA targets. U1A binds to U1hpII via direct interactions with a 7-nucleotide (nt) consensus binding sequence at the 5' end of a 10-nt loop, and via hydrogen bonds with the closing C-G base pair at the top of the RNA stem. Using surface plasmon resonance (Biacore), we have examined the role of structural features of U1hpII in binding to U1A RRM1. Mutational analysis of the closing base pair suggests it plays a minor role in binding and mainly prevents "breathing" of the loop. Lengthening the stem and nontarget part of the loop suggests that the increased negative charge of the RNA might slightly aid association. However, this is offset by an increase in dissociation, which may be caused by attraction of the RRM to nontarget parts of the RNA. Studies of a single stranded target and RNAs with untethered loops indicate that structure is not very relevant for association but is important for complex stability. In particular, breaking the link between the stem and the 5' side of the loop greatly increases complex dissociation, presumably by hindering simultaneous contacts between the RRM and stem and loop nucleotides. While binding of U1A to a single stranded target is much weaker than to U1hpII, it occurs with nanomolar affinity, supporting recent evidence that binding of unstructured RNA by U1A has physiological significance.
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Affiliation(s)
- Michael J Law
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
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Law MJ, Linde ME, Chambers EJ, Oubridge C, Katsamba PS, Nilsson L, Haworth IS, Laird-Offringa IA. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res 2006; 34:275-85. [PMID: 16407334 PMCID: PMC1326249 DOI: 10.1093/nar/gkj436] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes.
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Affiliation(s)
- Michael J. Law
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Michael E. Linde
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Eric J. Chambers
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Chris Oubridge
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 2QH, UK
| | - Phinikoula S. Katsamba
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences at NovumSE-141 57 Huddinge, Sweden
| | - Ian S. Haworth
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Ite A. Laird-Offringa
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- To whom correspondence should be addressed. Tel: +1 323 865 0655; Fax: +1 323 865 0158;
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Law MJ, Chambers EJ, Katsamba PS, Haworth IS, Laird-Offringa IA. Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. Nucleic Acids Res 2005; 33:2917-28. [PMID: 15914668 PMCID: PMC1140079 DOI: 10.1093/nar/gki602] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The A protein of the U1 small nuclear ribonucleoprotein particle, interacting with its stem-loop RNA target (U1hpII), is frequently used as a paradigm for RNA binding by recognition motif domains (RRMs). U1A/U1hpII complex formation has been proposed to consist of at least two steps: electrostatically mediated alignment of both molecules followed by locking into place, based on the establishment of close-range interactions. The sequence of events between alignment and locking remains obscure. Here we examine the roles of three critical residues, Tyr13, Phe56 and Gln54, in complex formation and stability using Biacore. Our mutational and kinetic data suggest that Tyr13 plays a more important role than Phe56 in complex formation. Mutational analysis of Gln54, combined with molecular dynamics studies, points to Arg52 as another key residue in association. Based on our data and previous structural and modeling studies, we propose that electrostatic alignment of the molecules is followed by hydrogen bond formation between the RNA and Arg52, and the sequential establishment of interactions with loop bases (including Tyr13). A quadruple stack, sandwiching two bases between Phe56 and Asp92, would occur last and coincide with the rearrangement of a C-terminal helix that partially occludes the RRM surface in the free protein.
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Affiliation(s)
| | - Eric J. Chambers
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | | | - Ian S. Haworth
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Ite A. Laird-Offringa
- To whom correspondence should be addressed. Tel: +1 323 865 0655; Fax: +1 323 865 0158;
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43
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Tsou JA, Shen LYC, Siegmund KD, Long TI, Laird PW, Seneviratne CK, Koss MN, Pass HI, Hagen JA, Laird-Offringa IA. Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung. Lung Cancer 2005; 47:193-204. [PMID: 15639718 DOI: 10.1016/j.lungcan.2004.08.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 07/30/2004] [Accepted: 08/18/2004] [Indexed: 01/17/2023]
Abstract
DNA methylation markers provide a powerful tool to make diagnoses based on genetic material obtained directly from tumors or from "remote" locations such as sputum, pleural fluid, or serum. In particular when limited cell numbers are available, amplifyable DNA markers can provide a very sensitive tool for cancer detection and classification. Malignant mesothelioma (MM), an aggressive cancer strongly associated with asbestos exposure, can be difficult to distinguish from adenocarcinoma of the lung when limited material is available. In an attempt to identify molecular markers for MM and adenocarcinoma, we examined the DNA methylation status of 14 loci. Analysis of methylation levels in 10 MM and 8 adenocarcinoma cell lines showed that methylation of APC was significantly elevated in adenocarcinoma compared to MM cell lines (P=0.0003), while methylation of CDH1 was higher in MM (P<0.02). Subsequent examination of the methylation status of the 14 loci in 6 MM and 7 adenocarcinoma primary tumors, which yielded similar methylation profiles, supported these observations. Comparison of methylation in MM cell lines and tumors versus non-tumor lung tissue indicated that APC exhibits less methylation in MM (P=0.003) while RASSF1, PGR1, ESR1, and CDH1 show more methylation in MM, the latter two showing the most significant difference between the two tissue types (P< or = 0.0001). Comparison of methylation in adenocarcinoma cell lines and tumors versus non-tumor lung tissue showed methylation of ESR1, PGR1 and RASSF1 to be significantly elevated in adenocarcinoma, with RASSF1 being most significant (P=0.0002). Thus, with the examination of 14 loci, we have identified 5 candidates that show potential for distinguishing between MM, adenocarcinoma and/or non-cancer lung. Our observations support the strong potential of methylation markers as tools for accurate diagnosis of neoplasms in and around the lung.
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Affiliation(s)
- Jeffrey A Tsou
- Norris Cancer Center and Department of Surgery and Biochemistry, Room NOR 6420, 1441 Eastlake Ave., Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9176, USA
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Marchevsky AM, Tsou JA, Laird-Offringa IA. Classification of individual lung cancer cell lines based on DNA methylation markers: use of linear discriminant analysis and artificial neural networks. J Mol Diagn 2004; 6:28-36. [PMID: 14736824 PMCID: PMC1867460 DOI: 10.1016/s1525-1578(10)60488-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The classification of small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) can pose diagnostic problems due to inter-observer variability and other limitations of histopathology. There is an interest in developing classificatory models of lung neoplasms based on the analysis of multivariate molecular data with statistical methods and/or neural networks. DNA methylation levels at 20 loci were measured in 41 SCLC and 46 NSCLC cell lines with the quantitative real-time PCR method MethyLight. The data were analyzed with artificial neural networks (ANN) and linear discriminant analysis (LDA) to classify the cell lines into SCLC or into NSCLC. Models used either data from all 20 loci, or from five significant DNA methylation loci that were selected by a step-wise back-propagation procedure (PTGS2, CALCA, MTHFR, ESR1, and CDKN2A). The data were sorted randomly by cell line into 10 different data sets, each with training and testing subsets composed of 71 and 16 of the cases, respectively. Ten ANN models were trained using the 10 data sets: five using 20 variables, and five using the five variables selected by step-wise back-propagation. The ANN models with 20 input variables correctly classified 100% of the cell lines, while the models with only five variables correctly classified 87 to 100% of cases. For comparison, 10 different LDA models were trained and tested using the same data sets with either the original data or with logarithmically transformed data. Again, half of the models used all 20 variables while the others used only the five significant variables. LDA models provided correct classifications in 62.5% to 87.5% of cases. The classifications provided by all of the different models were compared with kappa statistics, yielding kappa values ranging from 0.25 to 1.0. We conclude that ANN models based on DNA methylation profiles can objectively classify SCLC and NSCLC cells lines with substantial to perfect concordance, while LDA models based on DNA methylation profiles provide poor to substantial concordance. Our work supports the promise of ANN analysis of DNA methylation data as a powerful approach for the development of automated methods for lung cancer classification.
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Affiliation(s)
- Alberto M Marchevsky
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
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45
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Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA, Feigon J. Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target. J Mol Biol 2004; 337:799-816. [PMID: 15033352 DOI: 10.1016/j.jmb.2004.01.056] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Revised: 01/19/2004] [Accepted: 01/21/2004] [Indexed: 11/30/2022]
Abstract
Nucleolin is a 70 kDa multidomain protein involved in several steps of eukaryotic ribosome biogenesis. In vitro selection in combination with mutagenesis and structural analysis identified binding sites in pre-rRNA with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein contains four tandem RNA-binding domains (RBDs), of which the first two are responsible for the RNA-binding specificity and affinity for NREs. Here, we present the solution structure of the 28 kDa complex formed by the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural pre-rRNA target, b2NRE. The structure demonstrates that the sequence-specific recognition of the pre-rRNA NRE is achieved by intermolecular hydrogen bonds and stacking interactions involving mainly the beta-sheet surfaces of the two RBDs and the linker residues. A comparison with our previously determined NMR structure of RBD12 in complex with an in vitro selected RNA target, sNRE, shows that although the sequence-specific recognition of the loop consensus nucleotides is the same in the two complexes, they differ in several aspects. While the protein makes numerous specific contacts to the non-consensus nucleotides in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin RBD12 contacts only consensus nucleotides in b2NRE. The absence of these upper stem contacts from the RBD12/b2NRE complex results in a much less stable complex, as demonstrated by kinetic analyses. The role of the loop E motif in high-affinity binding is supported by gel-shift analyses with a series of sNRE mutants. The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding.
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Affiliation(s)
- Carina Johansson
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA
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46
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Abstract
MOTIVATION Aberrant DNA methylation is common in cancer. DNA methylation profiles differ between tumor types and subtypes and provide a powerful diagnostic tool for identifying clusters of samples and/or genes. DNA methylation data obtained with the quantitative, highly sensitive MethyLight technology is not normally distributed; it frequently contains an excess of zeros. Established tools to analyze this type of data do not exist. Here, we evaluate a variety of methods for cluster analysis to determine which is most reliable. RESULTS We introduce a Bernoulli-lognormal mixture model for clustering DNA methylation data obtained using MethyLight. We model the outcomes using a two-part distribution having discrete and continuous components. It is compared with standard cluster analysis approaches for continuous data and for discrete data. In a simulation study, we find that the two-part model has the lowest classification error rate for mixture outcome data compared with other approaches. The methods are illustrated using DNA methylation data from a study of lung cancer cell lines. Compared with competing hierarchical clustering methods, the mixture model approaches have the lowest cross-validation error for detecting lung cancer subtype (non-small versus small cell). The Bernoulli-lognormal mixture assigns observations to subgroups with the lowest uncertainty. AVAILABILITY Software is available upon request from the authors. SUPPLEMENTARY INFORMATION http://www-rcf.usc.edu/~kims/SupplementaryInfo.html
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Affiliation(s)
- Kimberly D Siegmund
- Department of Preventive Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA.
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Abstract
Hu proteins have been shown to bind to AU-rich elements (AREs) in the 3'-untranslated region of unstable mRNAs. They can thereby inhibit the decay of labile transcripts by antagonizing destabilizing proteins that target these AU-rich sequences. Here we examine the sequence preferences of HuD to elucidate its possible role in counteracting mRNA decay. Using repeats of the prototype destabilizing sequence UU(AUUU)nAUU, we show that all three HuD RNA-binding domains participate in binding to AU-tracts that can be as short as 13 residues, depending on the position of the remaining As. Removal of the A residues, resulting in a poly(U)-tract, increased the affinity of HuD for RNA, suggesting that the presence of As in destabilizing elements might favor the recruitment of other proteins and/or prevent HuD from binding too tightly to AREs. In vitro selection experiments with randomized RNAs confirmed the preference of HuD for poly(U). RNA binding analysis of the related protein HuB showed a similar preference for poly(U). In contrast, tristetraprolin, an mRNA destabilizing protein, strongly prefers AU-rich RNA. Many labile mRNAs contain U-tracts in or near their AREs. Individual AREs may thus differentially affect mRNA half-life by recruiting a unique complement of stabilizing and destabilizing factors.
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Affiliation(s)
- Sungmin Park-Lee
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90089-9176, USA
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Li H, Park S, Kilburn B, Jelinek MA, Henschen-Edman A, Aswad DW, Stallcup MR, Laird-Offringa IA. Lipopolysaccharide-induced methylation of HuR, an mRNA-stabilizing protein, by CARM1. Coactivator-associated arginine methyltransferase. J Biol Chem 2002; 277:44623-30. [PMID: 12237300 DOI: 10.1074/jbc.m206187200] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The RNA-binding protein HuR stabilizes labile mRNAs carrying AU-rich instability elements. This mRNA stabilization can be induced by hypoxia, lipopolysaccharide, and UV light. The mechanism by which these stimuli activate HuR is unclear and might be related to post-translational modification of this protein. Here we show that HuR can be methylated on arginine. However, HuR is not a substrate for PRMT1, the most prominent protein-arginine methyltransferase in mammalian cells, which methylates a number of heterogeneous nuclear ribonucleoproteins. Instead, HuR is specifically methylated by coactivator-associated arginine methyltransferase 1 (CARM1), a protein-arginine methyltransferase previously shown to serve as a transcriptional coactivator. By analyzing methylation of specific HuR arginine-to-lysine mutants and by sequencing radioactively methylated HuR peptides, Arg(217) was identified as the major HuR methylation site. Arg(217) is located in the hinge region between the second and third of the three HuR RNA recognition motif domains. Antibodies against a methylated HuR peptide were used to demonstrate in vivo methylation of HuR. HuR methylation increased in cells that overexpressed CARM1. Importantly, lipopolysaccharide stimulation of macrophages, which leads to HuR-mediated stabilization of tumor necrosis factor alpha mRNA in these cells, caused increased methylation of endogenous HuR. Thus, CARM1, which plays a role in transcriptional activation through histone H3 methylation, may also play a role in post-transcriptional gene regulation by methylating HuR.
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Affiliation(s)
- Hongwei Li
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, California 90089-9176, USA
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Katsamba PS, Bayramyan M, Haworth IS, Myszka DG, Laird-Offringa IA. Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA. J Biol Chem 2002; 277:33267-74. [PMID: 12082087 DOI: 10.1074/jbc.m200304200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA recognition motifs (RRMs) are characterized by highly conserved regions located centrally on a beta-sheet, which forms the RNA binding surface. Variable flanking regions, such as the loop connecting beta-strands 2 and 3, are thought to be important in determining the RNA-binding specificities of individual RRMs. The N-terminal RRM of the spliceosomal U1A protein mediates binding to an RNA hairpin (U1hpII) in the U1 small nuclear RNA. In this complex, the beta(2)-beta(3) loop protrudes through the 10-nucleotide RNA loop. Shortening of the RNA loop strongly perturbs binding, suggesting that an optimal "fit" of the beta(2)-beta(3) loop into the RNA loop is an important factor in complexation. To understand this interaction further, we mutated or deleted loop residues Lys(50) and Met(51), which protrude centrally into the RNA loop but do not make any direct contacts to the bases. Using BIACORE, we analyzed the ability of these U1A mutants to bind to wild type RNAs, or RNAs with shortened loops. Alanine replacement mutations only modestly affected binding to wild type U1hpII. Interestingly, simultaneous replacement of Lys(50) and Met(51) with alanine appeared to alleviate the loss of binding caused by shortening of the RNA loop. Deletion of Lys(50) or Met(51) caused a dramatic loss in stability of the U1A.U1hpII complex. However, deletion of both residues simultaneously was much less deleterious. Simulated annealing molecular dynamics analyses suggest this is due to the ability of this mutant to rearrange flanking amino acids to substitute for the two deleted residues. The double deletion mutant also exhibited substantially reduced negative effects of RNA loop shortening, suggesting the rearranged loop is better able to accommodate a short RNA loop. Our results indicate that one of the roles of the beta(2)-beta(3) loop is to provide a steric fit into the RNA loop, thereby stabilizing the RNA.protein complex.
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Affiliation(s)
- Phinikoula S Katsamba
- Norris Cancer Center/University of Southern California, Keck School of Medicine, Los Angeles, California 90089-9176, USA
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50
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Abstract
Carcinoma of the lung is the most common cause of cancer death worldwide. The estimated 5-year survival ranges from 6-16%, depending on the cell type. The best opportunity for improving survival of lung cancer patients is through early detection, when curative surgical resection is possible. Although the subjects at increased risk for developing carcinoma of the lung (long-term smokers) can be identified, only 10-20% of this group will ultimately develop the disease. Screening tests of long-term smokers employed to date (radiography and sputum cytology) have not been successful in reducing lung cancer mortality. The application of molecular markers specific for lung cancer offers new possibilities for early detection. Hypermethylation of CpG islands in the promoter regions of genes is a common phenomenon in lung cancer, as demonstrated by the analysis of the methylation status of over 40 genes from lung cancer tumors, cell lines, patient sputum and/or serum. Determination of the methylation patterns of multiple genes to obtain complex DNA methylation signatures promises to provide a highly sensitive and specific tool for lung cancer diagnosis. When combined with the development of non-invasive methods to detect such signatures, this may provide a viable method to screen subjects at risk for lung cancer.
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Affiliation(s)
- Jeffrey A Tsou
- Department of Biochemistry, University of Southern California, School of Medicine, Norris Comprehensive Cancer Center, NOR 6420, 1441 Eastlake Ave, Los Angeles, California, CA 90089-9176, USA
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