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Mishra A, Lai GC, Yao LJ, Aung TT, Shental N, Rotter-Maskowitz A, Shepherdson E, Singh GSN, Pai R, Shanti A, Wong RMM, Lee A, Khyriem C, Dutertre CA, Chakarov S, Srinivasan KG, Shadan NB, Zhang XM, Khalilnezhad S, Cottier F, Tan ASM, Low G, Chen P, Fan Y, Hor PX, Lee AKM, Choolani M, Vermijlen D, Sharma A, Fuks G, Straussman R, Pavelka N, Malleret B, McGovern N, Albani S, Chan JKY, Ginhoux F. Microbial exposure during early human development primes fetal immune cells. Cell 2021; 184:3394-3409.e20. [PMID: 34077752 PMCID: PMC8240556 DOI: 10.1016/j.cell.2021.04.039] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.
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Affiliation(s)
- Archita Mishra
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Ghee Chuan Lai
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Leong Jing Yao
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Thet Tun Aung
- Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Noam Shental
- Department of Mathematics and Computer Science, Open University of Israel, Ra'anana 4353701, Israel
| | - Aviva Rotter-Maskowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edwin Shepherdson
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Gurmit Singh Naranjan Singh
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Rhea Pai
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Adhika Shanti
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Regina Men Men Wong
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore
| | - Andrea Lee
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Costerwell Khyriem
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Charles Antoine Dutertre
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Svetoslav Chakarov
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - K G Srinivasan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Xiao-Meng Zhang
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Fabien Cottier
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Gillian Low
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Yiping Fan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Pei Xiang Hor
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Avery Khoo May Lee
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228, Singpore
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Ankur Sharma
- Genome Institute of Singapore (GIS), A(∗)STAR, 60 Biopolis Street, Singapore 138672, Singapore; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia; Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117597, Singapore
| | - Naomi McGovern
- Department of Pathology and Centre for Trophoblast Research, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore.
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; OBGYN-Academic Clinical Program, Duke-NUS, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore 119077, Singapore.
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China.
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Annamalai AK, Sampathkumar K, Kane S, Shetty NS, Kulkarni S, Rangarajan V, Purandare N, Pai PS, Mahuvakar AD, Shanthi R, Suriyakumar G, Puri V, Aram S, Gopalakrishnan C, Chelian M, Srinivasan KG, Gill AJ, Gurnell M, Clifton-Bligh R. Needle(s) in the Haystack-Synchronous Multifocal Tumor-Induced Osteomalacia. J Clin Endocrinol Metab 2016; 101:390-3. [PMID: 26691889 DOI: 10.1210/jc.2015-3854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- Anand K Annamalai
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Krishnaswamy Sampathkumar
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Shubhada Kane
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Nitin S Shetty
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Suyash Kulkarni
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Venkatesh Rangarajan
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Nilendu Purandare
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Prathamesh S Pai
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Ankit D Mahuvakar
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Radhakrishnan Shanthi
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Govindarajulu Suriyakumar
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Vipla Puri
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Subramaniam Aram
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Chandrasekhar Gopalakrishnan
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Mathirajan Chelian
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - K G Srinivasan
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Anthony J Gill
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Mark Gurnell
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
| | - Roderick Clifton-Bligh
- Departments of Endocrinology (A.K.A.) and Surgery and Anaesthesiology (S.A., C.G., M.C.), Ashwin Speciality Hospital, Madurai 625020, India; Department of Nephrology (K.S.), Meenakshi Mission Hospital and Research Centre, Madurai 625107, India; Departments of Cytopathology (S.Ka.), Radio-Diagnosis (N.S.S., S.Ku.), Nuclear Medicine (V.R., N.P.), and Head and Neck Surgery (P.S.P., A.D.M.), Tata Memorial Centre and Research Centre, Mumbai 400012, India; Department of Pathology (R.S.), Aravind Eye Care Hospitals, Madurai 625020, India; HCG Anderson PET Center (G.S.), Chennai 600084, India; RIA, Department of Laboratory Medicine (V.P.), Hinduja Hospital, Mumbai 400016, India; KGS Scan Center (K.G.S.), Madurai 625020, India; Cancer Diagnosis and Pathology Group (A.J.G.), Kolling Institute of Medical Research, University of Sydney, St Leonards NSW 2065, Australia; Wellcome Trust-Medical Research Council Institute of Metabolic Science (M.G.), University of Cambridge and National Institute for Health Research Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; and Department of Endocrinology (R.C.-B.), Kolling Institute, Royal N Shore Hospital, Sydney, NSW 2065, Australia
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Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SCJ, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816. [PMID: 17571346 PMCID: PMC2212820 DOI: 10.1038/nature05874] [Citation(s) in RCA: 3782] [Impact Index Per Article: 222.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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