| Reference | 1. Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Robertson AG(1), Shih J(2), Yau C(3), Gibb EA(1), Oba J(4), Mungall KL(1), Hess JM(5), Uzunangelov V(6), Walter V(7), Danilova L(8), Lichtenberg TM(9), Kucherlapati M(10), Kimes PK(11), Tang M(12), Penson A(13), Babur O(14), Akbani R(15), Bristow CA(16), Hoadley KA(17), Iype L(18), Chang MT(19); TCGA Research Network, Cherniack AD(2), Benz C(3), Mills GB(20), Verhaak RGW(21), Griewank KG(22), Felau I(23), Zenklusen JC(23), Gershenwald JE(24), Schoenfield L(25), Lazar AJ(26), Abdel-Rahman MH(27), Roman-Roman S(28), Stern MH(28), Cebulla CM(29), Williams MD(26), Jager MJ(30), Coupland SE(31), Esmaeli B(32), Kandoth C(33), Woodman SE(34). Collaborators: Abdel-Rahman MH, Akbani R, Ally A, Auman JT, Babur O, Balasundaram M, Balu S, Benz C, Beroukhim R, Birol I, Bodenheimer T, Bowen J, Bowlby R, Bristow CA, Brooks D, Carlsen R, Cebulla CM, Chang MT, Cherniack AD, Chin L, Cho J, Chuah E, Chudamani S, Cibulskis C, Cibulskis K, Cope L, Coupland SE, Danilova L, Defreitas T, Demchok JA, Desjardins L, Dhalla N, Esmaeli B, Felau I, Ferguson ML, Frazer S, Gabriel SB, Gastier-Foster JM, Gehlenborg N, Gerken M, Gershenwald JE, Getz G, Gibb EA, Griewank KG, Grimm EA, Hayes DN, Hegde AM, Heiman DI, Helsel C, Hess JM, Hoadley KA, Hobensack S, Holt RA, Hoyle AP, Hu X, Hutter CM, Jager MJ, Jefferys SR, Jones CD, Jones SJM, Kandoth C, Kasaian K, Kim J, Kimes PK, Kucherlapati M, Kucherlapati R, Lander E, Lawrence MS, Lazar AJ, Lee S, Leraas KM, Lichtenberg TM, Lin P, Liu J, Liu W, Lolla L, Lu Y, Iype L, Ma Y, Mahadeshwar HS, Mariani O, Marra MA, Mayo M, Meier S, Meng S, Meyerson M, Mieczkowski PA, Mills GB, Moore RA, Mose LE, Mungall AJ, Mungall KL, Murray BA, Naresh R, Noble MS, Oba J, Pantazi A, Parfenov M, Park PJ, Parker JS, Penson A, Perou CM, Pihl T, Pilarski R, Protopopov A, Radenbaugh A, Rai K, Ramirez NC, Ren X, Reynolds SM, Roach J, Robertson AG, Roman-Roman S, Roszik J, Sadeghi S, Saksena G, Sastre X, Schadendorf D, Schein JE, Schoenfield L, Schumacher SE, Seidman J, Seth S, Sethi G, Sheth M, Shi Y, Shields C, Shih J, Shmulevich I, Simons JV, Singh AD, Sipahimalani P, Skelly T, Sofia H, Soloway MG, Song X, Stern MH, Stuart J, Sun Q, Sun H, Tam A, Tan D, Tang M, Tang J, Tarnuzzer R, Taylor BS, Thiessen N, Thorsson V, Tse K, Uzunangelov V, Veluvolu U, Verhaak RGW, Voet D, Walter V, Wan Y, Wang Z, Weinstein JN, Wilkerson MD, Williams MD, Wise L, Woodman SE, Wong T, Wu Y, Yang L, Yang L, Yau C, Zenklusen JC, Zhang J, Zhang H, Zmuda E. Author information: (1)Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada. (2)The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. (3)Buck Institute for Research on Aging, Novato, CA 94945, USA. (4)Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (5)The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. (6)Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, CA 95064, USA. (7)Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Public Health Sciences, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA. (8)The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21287, USA. (9)The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA. (10)Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA. (11)Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. (12)Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (13)Human Oncology and Pathogenesis Program, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA. (14)Molecular and Medical Genetics, Computational Biology, Oregon Health and Science University, Portland, OR 97239, USA. (15)Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (16)Institute for Applied Cancer Science, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (17)Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. (18)Institute for Systems Biology, Seattle, WA 98109, USA. (19)Human Oncology and Pathogenesis Program, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94122, USA. (20)Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (21)Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (22)Department of Dermatology, University Hospital Essen, 45157 Essen, Germany. (23)Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA. (24)Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (25)Department of Pathology, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA. (26)Department of Pathology, Dermatology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (27)Departments of Ophthalmology and Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH 43210, USA. (28)Department of Translational Research, Institut Curie, PSL Research University, Paris 75248, France. (29)Havener Eye Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43212, USA. (30)Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands. (31)Department of Molecular & Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool L7 8TX, UK; Department of Cellular Pathology, Royal Liverpool University Hospital, Liverpool, L69 3GA, UK. (32)Orbital Oncology & Ophthalmic Plastic Surgery, Department of Plastic Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: [email protected]. (33)Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA. Electronic address: [email protected]. (34)Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: [email protected]. Erratum in Cancer Cell. 2018 Jan 8;33(1):151. Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved. DOI: 10.1016/j.ccell.2017.07.003 PMCID: PMC5619925 PMID: 28810145 [Indexed for MEDLINE]<br />
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2. Nature. 2013 Dec 19;504(7480):401-5. doi: 10.1038/nature12870. Epub 2013 Dec 11. DWARF 53 acts as a repressor of strigolactone signalling in rice. Jiang L(1), Liu X(1), Xiong G(1), Liu H(1), Chen F(2), Wang L(2), Meng X(2), Liu G(2), Yu H(2), Yuan Y(2), Yi W(3), Zhao L(3), Ma H(3), He Y(4), Wu Z(4), Melcher K(4), Qian Q(5), Xu HE(6), Wang Y(2), Li J(2). Author information: (1)1] State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2]. (2)State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. (3)VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. (4)Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, Michigan 49503, USA. (5)State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China. (6)1] VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China [2] Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue Northeast, Grand Rapids, Michigan 49503, USA. Erratum in Nature. 2014 Feb 20;506(7488):396. Comment in Nature. 2013 Dec 19;504(7480):384-5. Mol Plant. 2014 May;7(5):761-3. Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex. DOI: 10.1038/nature12870 PMCID: PMC5802366 PMID: 24336200 [Indexed for MEDLINE] Conflict of interest statement: The authors declare no competing financial interests.<br />
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3. Metabolism of Thyroid Hormone. Peeters RP(1), Visser TJ(2). In: Feingold KR(3), Anawalt B(4), Boyce A(5), Chrousos G(6), de Herder WW(7), Dhatariya K(8), Dungan K(9), Hershman JM(10), Hofland J(11), Kalra S(12), Kaltsas G(13), Koch C(14), Kopp P(15), Korbonits M(16), Kovacs CS(17), Kuohung W(18), Laferrère B(19), Levy M(20), McGee EA(21), McLachlan R(22), Morley JE(23), New M(24), Purnell J(25), Sahay R(26), Singer F(27), Sperling MA(28), Stratakis CA(29), Trence DL(30), Wilson DP(31), editors. Endotext [Internet]. South Dartmouth (MA): MDText.com, Inc.; 2000–. 2017 Jan 1. Author information: (1)Dept. of Endocrinology, Room D-442, Erasmus University Medical Center, Wytemaweg, 3015 CE, Rotterdam The Netherlands (2)Department of Internal Medicine III Erasmus University Medical School Molewater Plein 50 Dr. 3015 GE, Rotterdam THE NETHERLANDS Tel: 011-31-10-463-5463 Fax: 011-31-10-463-5430 (3)Emeritus Professor of Medicine, University of California, San Francisco, CA (4)Chief of Medicine at the University of Washington Medical Center and Professor and Vice Chair of the Department of Medicine, University of Washington (5)Pediatric Endocrinologist and Associate Research Physician in the Skeletal Diseases and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health (6)Professor of Pediatrics and Endocrinology, Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece (7)Professor of Endocrine Oncology, Erasmus MC and Erasmus MC Cancer Center, Rotterdam, the Netherlands (8)Consultant in Diabetes, Endocrinology and General Medicine, Norfolk and Norwich University Hospitals NHS Foundation Trust and University of East Anglia, Norwich, UK (9)Professor of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Ohio State University (10)Distinguished Professor Emeritus of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA; Endocrinology Consultant, Endocrine Clinic, West Los Angeles VA Medical Center, Los Angeles, CA (11)Consultant Endocrinologist, Erasmus MC and Erasmus MC Cancer Center, Rotterdam, the Netherlands (12)Consultant Endocrinologist, Department of Endocrinology, Bharti Hospital, Karnal, India (13)Professor of General Medicine-Endocrinology, 1st Department of Propaedeutic Medicine, National and Kapodistrian University of Athens, Athens, Greece (14)Professor, The University of Tennessee Health Science Center, Memphis, Tennessee (15)Professor of Medicine and Chief of the Division of Endocrinology, Diabetology and Metabolism, University of Lausanne, Switzerland (16)Professor of Endocrinology and Metabolism, Centre Lead for Endocrinology and Deputy Institute Director, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, England (17)University Research Professor and Professor of Medicine (Endocrinology and Metabolism), Obstetrics & Gynecology, and BioMedical Sciences, at Memorial University of Newfoundland in St. John’s, Newfoundland, Canada (18)Director of the Division of Reproductive Endocrinology at Boston Medical Center and an Associate Professor of Obstetrics and Gynecology at the Boston University School of Medicine (19)Professor of Medicine, New York Obesity Research Center, Division of Endocrinology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA (20)Consultant endocrinologist at University Hospitals of Leicester and Honorary Associate Professor at Leicester University (21)Professor of Obstetrics and Gynecology at the University of Vermont and Director of the Division of Reproductive Endocrinology and Infertility. Burlington, Vermont (22)Director of Clinical Research, Hudson Institute of Medical Research; Consultant Endocrinologist, Monash Medical Centre, Melbourne, Australia (23)Dammert Professor of Gerontology and Director, Division of Geriatric Medicine and Director of the Division of Endocrinology, Saint Louis University Medical Center (24)Professor of Pediatrics, Professor of Genetics and Genomic Sciences, and Chief of the Adrenal Steroid Disorders Program, Icahn School of Medicine, Mount Sinai School of Medicine, New York, NY (25)Professor of Medicine, Knight Cardiovascular Institute and the Division of Endocrinology, and Associate Director, Bob and Charlee Moore Institute for Nutrition and Wellness, Oregon Health and Science University, Portland, OR (26)Professor and Head of Department of Endocrinology, Osmania Medical College and Osmania General Hospital, Hyderabad, India (27)Director of the Endocrine/Bone Disease Program, Saint Johns Cancer Institute at Saint John’s Health Center, Santa Monica, CA; Clinical Professor of Medicine, UCLA School of Medicine, Los Angeles, CA (28)Professorial Lecturer, Division of Pediatric Endocrinology and Diabetes, Icahn School of Medicine at Mount Sinai, New York, NY. Emeritus Professor and Chair, Department of Pediatrics, University of Pittsburgh (29)CSO, ELPEN, Inc. & Director, Research Institute, Athens, Greece & Senior Investigator, Human Genetics & Precision Medicine, FORTH (ITE), Heraklion, Greece. Emeritus Scientific Director & Senior Investigator, NICHD, NIH, Bethesda, MD, USA (30)Professor of Medicine, Emeritus, University of Washington, Seattle, WA (31)Endowed Chair, Cardiovascular Health and Risk Prevention, Pediatric Endocrinology and Diabetes, Cook Children's Medical Center, Fort Worth, TX Thyroid hormone is indispensable for normal development and metabolism of most cells and tissues. Thyroid hormones are metabolized by different pathways: glucuronidation, sulfation, and deiodination, the latter being the most important. Three enzymes catalyzing deiodination have been identified, called type 1 (D1), type 2 (D2) and type 3 (D3) iodothyronine deiodinases. D1 and D2 have outer ring deiodinase activity, converting the prohormone T4 to its bioactive form T3 and degrading rT3 to 3,3’-T2. D3 has inner ring deiodinase activity and degrades T4 to rT3 and T3 to 3,3’-T2. D1 is largely expressed in liver and kidney. Its main role is clearance of rT3 from the circulation and it also contributes to production of plasma T3. D2 is importantly expressed in the central nervous system, pituitary, brown adipose tissue and muscle and, generally, its expression reciprocally responds to changes in thyroid state. D2 serves to adapt cellular thyroid state to changing physiological needs. D3 is importantly expressed in fetal tissues and in adult brain tissue. In addition, D3 can be re-expressed under certain pathological conditions such as critical illness or in specific cancers. In recent years, the paradigm has evolved that D2 and D3 can locally modify thyroid hormone bioactivity independent of serum thyroid hormone concentrations. Its physiological relevance has been shown in various developmental and regenerative conditions. Future studies may reveal if modifying (local) deiodinase activity can be of use under certain circumstances. For complete coverage of all related areas of Endocrinology, please see our online FREE web-book, www.endotext.org. and WWW.THYROIDMANAGER.ORG. Copyright © 2000-2022, MDText.com, Inc. PMID: 25905401<br />
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4. Front Genet. 2019 Feb 12;10:102. doi: 10.3389/fgene.2019.00102. eCollection 2019. Structural Biology of the FGF7 Subfamily. Zinkle A(1), Mohammadi M(1). Author information: (1)Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY, United States. Mammalian fibroblast growth factor (FGF) signaling is intricately regulated via selective binding interactions between 18 FGF ligands and four FGF receptors (FGFR1-4), three of which (FGFR1-3) are expressed as either epithelial ("b") or mesenchymal ("c") splice isoforms. The FGF7 subfamily, consisting of FGF3, FGF7, FGF10, and FGF22, is unique among FGFs in that its members are secreted exclusively by the mesenchyme, and specifically activate the "b" isoforms of FGFR1 (FGFR1b) and FGFR2 (FGFR2b) present in the overlying epithelium. This unidirectional mesenchyme-to-epithelium signaling contributes to the development of essentially all organs, glands, and limbs. Structural analysis has shown that members of the FGF7 subfamily achieve their restricted specificity for FGFR1b/FGFR2b by engaging in specific contacts with two alternatively spliced loop regions in the immunoglobulin-like domain 3 (D3) of these receptors. Weak basal receptor-binding affinity further constrains the FGF7 subfamily's specificity for FGFR1b/2b. In this review, we elaborate on the structural determinants of FGF7 subfamily receptor-binding specificity, and discuss how affinity differences among the four members for the heparin sulfate (HS) co-receptor contribute to their disparate biological activities. DOI: 10.3389/fgene.2019.00102 PMCID: PMC6379346 PMID: 30809251<br />
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5. J Endocrinol. 2018 Jan;236(1):R57-R68. doi: 10.1530/JOE-16-0611. Epub 2017 Oct 19. Role of thyroid hormone in skeletal muscle physiology. Bloise FF(1), Cordeiro A(2), Ortiga-Carvalho TM(2). Author information: (1)Institute of Biophysics Carlos Chagas FilhoLaboratory of Translational Endocrinology, Rio de Janeiro, Brazil [email protected]. (2)Institute of Biophysics Carlos Chagas FilhoLaboratory of Translational Endocrinology, Rio de Janeiro, Brazil. Thyroid hormones (TH) are crucial for development, growth, differentiation, metabolism and thermogenesis. Skeletal muscle (SM) contractile function, myogenesis and bioenergetic metabolism are influenced by TH. These effects depend on the presence of the TH transporters MCT8 and MCT10 in the plasma membrane, the expression of TH receptors (THRA or THRB) and hormone availability, which is determined either by the activation of thyroxine (T4) into triiodothyronine (T3) by type 2 iodothyronine deiodinases (D2) or by the inactivation of T4 into reverse T3 by deiodinases type 3 (D3). SM relaxation and contraction rates depend on T3 regulation of myosin expression and energy supplied by substrate oxidation in the mitochondria. The balance between D2 and D3 expression determines TH intracellular levels and thus influences the proliferation and differentiation of satellite cells, indicating an important role of TH in muscle repair and myogenesis. During critical illness, changes in TH levels and in THR and deiodinase expression negatively affect SM function and repair. This review will discuss the influence of TH action on SM contraction, bioenergetics metabolism, myogenesis and repair in health and illness conditions. © 2018 Society for Endocrinology. DOI: 10.1530/JOE-16-0611 PMID: 29051191 [Indexed for MEDLINE]
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