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Hu H, Zhang Q, Hu FF, Liu CJ, Guo AY. A comprehensive survey for human transcription factors on expression, regulation, interaction, phenotype and cancer survival. Brief Bioinform 2021; 22:6124917. [PMID: 33517372 DOI: 10.1093/bib/bbab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/30/2020] [Accepted: 01/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) act as key regulators in biological processes through controlling gene expression. Here, we conducted a systematic study for all human TFs on the expression, regulation, interaction, mutation, phenotype and cancer survival. We revealed that the average expression levels of TFs in normal tissues were lower than 50% expression of non-TFs, whereas TF expression was increased in cancers. TFs that are specifically expressed in an individual tissue or cancer may be potential marker genes. For instance, TGIF2LX/Y were preferentially expressed in testis and NEUROG1, PRDM14, SRY, ZNF705A and ZNF716 were specifically highly expressed in germ cell tumors. We found different distributions of target genes and TF co-regulations in different TF families. Some small TF families have huge protein interaction pairs, suggesting their central roles in transcriptional regulation. The bZIP family is a small family involving many signaling pathways. Survival analysis indicated that most TFs significantly affect survival of one or more cancers. Some survival-related TFs were also specifically highly expressed in the corresponding cancer types, which may be potential targets for cancer therapy. Finally, we identified 43 TFs whose mutations were closely correlated to survival, suggesting their cancer-driven roles. The systematic analysis of TFs provides useful clues for further investigation of TF regulatory mechanisms and the role of TFs in diseases.
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Affiliation(s)
- Hui Hu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fei-Fei Hu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-Jie Liu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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Justice CM, Cuellar A, Bala K, Sabourin JA, Cunningham ML, Crawford K, Phipps JM, Zhou Y, Cilliers D, Byren JC, Johnson D, Wall SA, Morton JEV, Noons P, Sweeney E, Weber A, Rees KEM, Wilson LC, Simeonov E, Kaneva R, Yaneva N, Georgiev K, Bussarsky A, Senders C, Zwienenberg M, Boggan J, Roscioli T, Tamburrini G, Barba M, Conway K, Sheffield VC, Brody L, Mills JL, Kay D, Sicko RJ, Langlois PH, Tittle RK, Botto LD, Jenkins MM, LaSalle JM, Lattanzi W, Wilkie AOM, Wilson AF, Romitti PA, Boyadjiev SA. A genome-wide association study implicates the BMP7 locus as a risk factor for nonsyndromic metopic craniosynostosis. Hum Genet 2020; 139:1077-1090. [PMID: 32266521 PMCID: PMC7415527 DOI: 10.1007/s00439-020-02157-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/25/2020] [Indexed: 12/31/2022]
Abstract
Our previous genome-wide association study (GWAS) for sagittal nonsyndromic craniosynostosis (sNCS) provided important insights into the genetics of midline CS. In this study, we performed a GWAS for a second midline NCS, metopic NCS (mNCS), using 215 non-Hispanic white case-parent triads. We identified six variants with genome-wide significance (P ≤ 5 × 10-8): rs781716 (P = 4.71 × 10-9; odds ratio [OR] = 2.44) intronic to SPRY3; rs6127972 (P = 4.41 × 10-8; OR = 2.17) intronic to BMP7; rs62590971 (P = 6.22 × 10-9; OR = 0.34), located ~ 155 kb upstream from TGIF2LX; and rs2522623, rs2573826, and rs2754857, all intronic to PCDH11X (P = 1.76 × 10-8, OR = 0.45; P = 3.31 × 10-8, OR = 0.45; P = 1.09 × 10-8, OR = 0.44, respectively). We performed a replication study of these variants using an independent non-Hispanic white sample of 194 unrelated mNCS cases and 333 unaffected controls; only the association for rs6127972 (P = 0.004, OR = 1.45; meta-analysis P = 1.27 × 10-8, OR = 1.74) was replicated. Our meta-analysis examining single nucleotide polymorphisms common to both our mNCS and sNCS studies showed the strongest association for rs6127972 (P = 1.16 × 10-6). Our imputation analysis identified a linkage disequilibrium block encompassing rs6127972, which contained an enhancer overlapping a CTCF transcription factor binding site (chr20:55,798,821-55,798,917) that was significantly hypomethylated in mesenchymal stem cells derived from fused metopic compared to open sutures from the same probands. This study provides additional insights into genetic factors in midline CS.
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Affiliation(s)
- Cristina M Justice
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Araceli Cuellar
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA
| | - Krithi Bala
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA
| | - Jeremy A Sabourin
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Michael L Cunningham
- Department of Pediatrics, Division of Craniofacial Medicine, Seattle Children's Craniofacial Center, Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Karen Crawford
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Julie M Phipps
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Yan Zhou
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jo C Byren
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Katie E M Rees
- Clinical Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Emil Simeonov
- National Institute of Pediatrics, Sofia Medical University, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nadezhda Yaneva
- National Genetic Laboratory, University Hospital of Obstetrics and Gynecology "Maichin Dom", Medical University of Sofia, Sofia, Bulgaria
| | - Kiril Georgiev
- Department of Neurosurgery, University Hospital 'St. Ivan Rilski', Medical University of Sofia, Sofia, Bulgaria
| | - Assen Bussarsky
- Department of Neurosurgery, University Hospital 'St. Ivan Rilski', Medical University of Sofia, Sofia, Bulgaria
| | - Craig Senders
- Department of Otolaryngology, Head and Neck Surgery, University of California Davis, Sacramento, CA, USA
| | - Marike Zwienenberg
- Department of Neurosurgery, University of California Davis, Sacramento, CA, USA
| | - James Boggan
- Department of Neurosurgery, University of California Davis, Sacramento, CA, USA
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, Australia
| | - Gianpiero Tamburrini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Neurosurgery, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marta Barba
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Experimental Biology, Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Kristin Conway
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA
| | - Val C Sheffield
- Department of Pediatrics, Division of Medical Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Lawrence Brody
- Gene and Environment Interaction Section, NHGRI, Bethesda, NIHMD, USA
| | - James L Mills
- Epidemiology Branch, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD, USA
| | - Denise Kay
- Division of Genetics, NYS Department of Health, Wadsworth CenterAlbany, NY, USA
| | - Robert J Sicko
- Division of Genetics, NYS Department of Health, Wadsworth CenterAlbany, NY, USA
| | - Peter H Langlois
- Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, TX, USA
| | - Rachel K Tittle
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Lorenzo D Botto
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Wanda Lattanzi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Experimental Biology, Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander F Wilson
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA.
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA.
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