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Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023; 15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.
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Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
| | - John M Taylor
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mona Hashim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eduardo Calpena
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Pamela J Kaisaki
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Akiko Hashimoto
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edward Sanders
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ron Schwessinger
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lukas Lange
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Yesim Kesim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Vassilis Ragoussis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dimitrios V Vavoulis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Holger Allroggen
- Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Benito Baños-Piñero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Tal Ben-Ami
- Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Celeste Bento
- Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | - Edward Blair
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Katherine R Bull
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valerio Conti
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - E Graham Davies
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Fatima Dhalla
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
| | - Beatriz Diez Dacal
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Yin Dong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - James E Dunford
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jane Hartley
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Georg Hollander
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kassim Javaid
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
| | - Deirdre Kelly
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Dominic Kelly
- Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
| | - Samantha J L Knight
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Erika M Kvikstad
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Craig B Langman
- Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Kate E Lines
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Xin Lu
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sahar Mansour
- St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
| | - Adnan Manzur
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Brian Marsden
- Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Joanne Mason
- Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Steven Okoli
- Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Elizabeth Ormondroyd
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Lilian Bomme Ousager
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Smita Y Patel
- Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
| | - Melissa M Pentony
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
| | - Archana Ramesh
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Simone G Riva
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Irene Roberts
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Noémi Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Outi Salminen
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Kyleen D Schilling
- Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mark Stevenson
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Rajesh V Thakker
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Holm H Uhlig
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Richard van Wijk
- UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Steven Wall
- Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
| | - Jing Wang
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hugh Watkins
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Jaroslav Zak
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew O M Wilkie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
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Farmer DT, Mlcochova H, Zhou Y, Koelling N, Wang G, Ashley N, Bugacov H, Chen HJ, Parvez R, Tseng KC, Merrill AE, Maxson RE, Wilkie AOM, Crump JG, Twigg SRF. The developing mouse coronal suture at single-cell resolution. Nat Commun 2021; 12:4797. [PMID: 34376651 PMCID: PMC8355337 DOI: 10.1038/s41467-021-24917-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
Sutures separate the flat bones of the skull and enable coordinated growth of the brain and overlying cranium. The coronal suture is most commonly fused in monogenic craniosynostosis, yet the unique aspects of its development remain incompletely understood. To uncover the cellular diversity within the murine embryonic coronal suture, we generated single-cell transcriptomes and performed extensive expression validation. We find distinct pre-osteoblast signatures between the bone fronts and periosteum, a ligament-like population above the suture that persists into adulthood, and a chondrogenic-like population in the dura mater underlying the suture. Lineage tracing reveals an embryonic Six2+ osteoprogenitor population that contributes to the postnatal suture mesenchyme, with these progenitors being preferentially affected in a Twist1+/-; Tcf12+/- mouse model of Saethre-Chotzen Syndrome. This single-cell atlas provides a resource for understanding the development of the coronal suture and the mechanisms for its loss in craniosynostosis.
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Affiliation(s)
- D'Juan T Farmer
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Hana Mlcochova
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Yan Zhou
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Guanlin Wang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Neil Ashley
- Single cell facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Helena Bugacov
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Hung-Jhen Chen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Riana Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Kuo-Chang Tseng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, USA
| | - Robert E Maxson
- Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA.
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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Guo J, Nie X, Giebler M, Mlcochova H, Wang Y, Grow EJ, Kim R, Tharmalingam M, Matilionyte G, Lindskog C, Carrell DT, Mitchell RT, Goriely A, Hotaling JM, Cairns BR. The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty. Cell Stem Cell 2020; 26:262-276.e4. [PMID: 31928944 PMCID: PMC7298616 DOI: 10.1016/j.stem.2019.12.005] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/03/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022]
Abstract
The human testis undergoes dramatic developmental and structural changes during puberty, including proliferation and maturation of somatic niche cells, and the onset of spermatogenesis. To characterize this understudied process, we profiled and analyzed single-cell transcriptomes of ∼10,000 testicular cells from four boys spanning puberty and compared them to those of infants and adults. During puberty, undifferentiated spermatogonia sequentially expand and differentiate prior to the initiation of gametogenesis. Notably, we identify a common pre-pubertal progenitor for Leydig and myoid cells and delineate candidate factors controlling pubertal differentiation. Furthermore, pre-pubertal Sertoli cells exhibit two distinct transcriptional states differing in metabolic profiles before converging to an alternative single mature population during puberty. Roles for testosterone in Sertoli cell maturation, antimicrobial peptide secretion, and spermatogonial differentiation are further highlighted through single-cell analysis of testosterone-suppressed transfemale testes. Taken together, our transcriptional atlas of the developing human testis provides multiple insights into developmental changes and key factors accompanying male puberty.
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Affiliation(s)
- Jingtao Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; The Andrology Laboratory, Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Xichen Nie
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Maria Giebler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK
| | - Hana Mlcochova
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK
| | - Yueqi Wang
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Edward J Grow
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Robin Kim
- Section of Transplantation, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Melissa Tharmalingam
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK; Royal Hospital for Children and Young People, Edinburgh EH91LF, UK
| | - Gabriele Matilionyte
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK; Royal Hospital for Children and Young People, Edinburgh EH91LF, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Douglas T Carrell
- The Andrology Laboratory, Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Rod T Mitchell
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK; Royal Hospital for Children and Young People, Edinburgh EH91LF, UK
| | - Anne Goriely
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK
| | - James M Hotaling
- The Andrology Laboratory, Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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4
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Goos JAC, Vogel WK, Mlcochova H, Millard CJ, Esfandiari E, Selman WH, Calpena E, Koelling N, Carpenter EL, Swagemakers SMA, van der Spek PJ, Filtz TM, Schwabe JWR, Iwaniec UT, Mathijssen IMJ, Leid M, Twigg SRF. A de novo substitution in BCL11B leads to loss of interaction with transcriptional complexes and craniosynostosis. Hum Mol Genet 2019; 28:2501-2513. [PMID: 31067316 PMCID: PMC6644156 DOI: 10.1093/hmg/ddz072] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
Craniosynostosis, the premature ossification of cranial sutures, is a developmental disorder of the skull vault, occurring in approximately 1 in 2250 births. The causes are heterogeneous, with a monogenic basis identified in ~25% of patients. Using whole-genome sequencing, we identified a novel, de novo variant in BCL11B, c.7C>A, encoding an R3S substitution (p.R3S), in a male patient with coronal suture synostosis. BCL11B is a transcription factor that interacts directly with the nucleosome remodelling and deacetylation complex (NuRD) and polycomb-related complex 2 (PRC2) through the invariant proteins RBBP4 and RBBP7. The p.R3S substitution occurs within a conserved amino-terminal motif (RRKQxxP) of BCL11B and reduces interaction with both transcriptional complexes. Equilibrium binding studies and molecular dynamics simulations show that the p.R3S substitution disrupts ionic coordination between BCL11B and the RBBP4-MTA1 complex, a subassembly of the NuRD complex, and increases the conformational flexibility of Arg-4, Lys-5 and Gln-6 of BCL11B. These alterations collectively reduce the affinity of BCL11B p.R3S for the RBBP4-MTA1 complex by nearly an order of magnitude. We generated a mouse model of the BCL11B p.R3S substitution using a CRISPR-Cas9-based approach, and we report herein that these mice exhibit craniosynostosis of the coronal suture, as well as other cranial sutures. This finding provides strong evidence that the BCL11B p.R3S substitution is causally associated with craniosynostosis and confirms an important role for BCL11B in the maintenance of cranial suture patency.
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Affiliation(s)
- Jacqueline A C Goos
- Departments of Plastic and Reconstructive Surgery and Hand Surgery
- Bioinformatics, Erasmus MC, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Walter K Vogel
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Hana Mlcochova
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Christopher J Millard
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Elahe Esfandiari
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Wisam H Selman
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- College of Veterinary Medicine, University of Al-Qadisiyah, Al Diwaniyah, Iraq
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Evan L Carpenter
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sigrid M A Swagemakers
- Bioinformatics, Erasmus MC, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Peter J van der Spek
- Bioinformatics, Erasmus MC, University Medical Center Rotterdam, CA Rotterdam, The Netherlands
| | - Theresa M Filtz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - John W R Schwabe
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Urszula T Iwaniec
- Skeletal Biology Laboratory, School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Mark Leid
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, OR, USA
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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5
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Maher GJ, Ralph HK, Ding Z, Koelling N, Mlcochova H, Giannoulatou E, Dhami P, Paul DS, Stricker SH, Beck S, McVean G, Wilkie AOM, Goriely A. Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes. Genome Res 2018; 28:1779-1790. [PMID: 30355600 PMCID: PMC6280762 DOI: 10.1101/gr.239186.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [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: 05/04/2018] [Accepted: 10/20/2018] [Indexed: 02/07/2023]
Abstract
Mosaic mutations present in the germline have important implications for reproductive risk and disease transmission. We previously demonstrated a phenomenon occurring in the male germline, whereby specific mutations arising spontaneously in stem cells (spermatogonia) lead to clonal expansion, resulting in elevated mutation levels in sperm over time. This process, termed "selfish spermatogonial selection," explains the high spontaneous birth prevalence and strong paternal age-effect of disorders such as achondroplasia and Apert, Noonan and Costello syndromes, with direct experimental evidence currently available for specific positions of six genes (FGFR2, FGFR3, RET, PTPN11, HRAS, and KRAS). We present a discovery screen to identify novel mutations and genes showing evidence of positive selection in the male germline, by performing massively parallel simplex PCR using RainDance technology to interrogate mutational hotspots in 67 genes (51.5 kb in total) in 276 biopsies of testes from five men (median age, 83 yr). Following ultradeep sequencing (about 16,000×), development of a low-frequency variant prioritization strategy, and targeted validation, we identified 61 distinct variants present at frequencies as low as 0.06%, including 54 variants not previously directly associated with selfish selection. The majority (80%) of variants identified have previously been implicated in developmental disorders and/or oncogenesis and include mutations in six newly associated genes (BRAF, CBL, MAP2K1, MAP2K2, RAF1, and SOS1), all of which encode components of the RAS-MAPK pathway and activate signaling. Our findings extend the link between mutations dysregulating the RAS-MAPK pathway and selfish selection, and show that the aging male germline is a repository for such deleterious mutations.
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Affiliation(s)
- Geoffrey J Maher
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Hannah K Ralph
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Zhihao Ding
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Nils Koelling
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Hana Mlcochova
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Eleni Giannoulatou
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Pawan Dhami
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Stefan H Stricker
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Gilean McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Anne Goriely
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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6
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Guo J, Grow EJ, Mlcochova H, Maher GJ, Lindskog C, Nie X, Guo Y, Takei Y, Yun J, Cai L, Kim R, Carrell DT, Goriely A, Hotaling JM, Cairns BR. The adult human testis transcriptional cell atlas. Cell Res 2018; 28:1141-1157. [PMID: 30315278 PMCID: PMC6274646 DOI: 10.1038/s41422-018-0099-2] [Citation(s) in RCA: 352] [Impact Index Per Article: 58.7] [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: 08/30/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Human adult spermatogenesis balances spermatogonial stem cell (SSC) self-renewal and differentiation, alongside complex germ cell-niche interactions, to ensure long-term fertility and faithful genome propagation. Here, we performed single-cell RNA sequencing of ~6500 testicular cells from young adults. We found five niche/somatic cell types (Leydig, myoid, Sertoli, endothelial, macrophage), and observed germline-niche interactions and key human-mouse differences. Spermatogenesis, including meiosis, was reconstructed computationally, revealing sequential coding, non-coding, and repeat-element transcriptional signatures. Interestingly, we identified five discrete transcriptional/developmental spermatogonial states, including a novel early SSC state, termed State 0. Epigenetic features and nascent transcription analyses suggested developmental plasticity within spermatogonial States. To understand the origin of State 0, we profiled testicular cells from infants, and identified distinct similarities between adult State 0 and infant SSCs. Overall, our datasets describe key transcriptional and epigenetic signatures of the normal adult human testis, and provide new insights into germ cell developmental transitions and plasticity.
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Affiliation(s)
- Jingtao Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.,Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Edward J Grow
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Hana Mlcochova
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Geoffrey J Maher
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Xichen Nie
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Yixuan Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robin Kim
- Section of Transplantation, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Douglas T Carrell
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Anne Goriely
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - James M Hotaling
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Bradley R Cairns
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
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7
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Guo J, Grow EJ, Yi C, Mlcochova H, Maher GJ, Lindskog C, Murphy PJ, Wike CL, Carrell DT, Goriely A, Hotaling JM, Cairns BR. Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. Cell Stem Cell 2018; 21:533-546.e6. [PMID: 28985528 PMCID: PMC5832720 DOI: 10.1016/j.stem.2017.09.003] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/12/2017] [Accepted: 09/01/2017] [Indexed: 12/20/2022]
Abstract
Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4+ hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4+ hSSCs and differentiating c-KIT+ spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic "poising" in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed. Interestingly, open chromatin in hSSCs was strikingly enriched in binding sites for pioneer factors (NFYA/B, DMRT1, and hormone receptors). Remarkably, single-cell RNA-seq clustering analysis identified four cellular/developmental states during hSSC differentiation, involving major transitions in cell-cycle and transcriptional regulators, splicing and signaling factors, and glucose/mitochondria regulators. Overall, our results outline the dynamic chromatin/transcription landscape operating in hSSCs and identify crucial molecular pathways that accompany the transition from quiescence to proliferation and differentiation.
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Affiliation(s)
- Jingtao Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Edward J Grow
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Chongil Yi
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK
| | - Geoffrey J Maher
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Patrick J Murphy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Douglas T Carrell
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT 84122, USA
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX39DS, UK
| | - James M Hotaling
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT 84122, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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8
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Iliev R, Fedorko M, Machackova T, Mlcochova H, Svoboda M, Pacik D, Dolezel J, Stanik M, Slaby O. Expression Levels of PIWI-interacting RNA, piR-823, Are Deregulated in Tumor Tissue, Blood Serum and Urine of Patients with Renal Cell Carcinoma. Anticancer Res 2017. [PMID: 27919963 DOI: 10.21873/antic anres.11239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Renal cell carcinoma (RCC) is the most common neoplasm of adult kidney accounting for about 3% of adult malignancies. P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of naturally occurring, short non-coding RNAs involved in silencing of transposable elements and in sequence-specific chromatin modifications. There were preliminary data published indicating that piR-823 expression is deregulated in circulating tumor cells and tumor tissue in gastric and kidney cancer, respectively. PATIENTS AND METHODS In our study, we analyzed piR-823 levels in 588 biological specimens: tumor tissue (N=153), adjacent renal parenchyma (N=121), blood serum (N=178) and urine (N=20) of patients undergoing nephrectomy for RCC; and in blood serum (N=101) and urine (N=15) of matched healthy controls. Expression levels of piR-823 were determined in all biological specimens by quantitative real-time polymerase chain reaction, compared in patients and controls, and correlated with clinicopathological features of RCC. RESULTS We identified a significant down-regulation of piR-823 in tumor tissue [p<0.0001, area under the curve (AUC)=0.7945]. On the contrary in blood serum and urine, the expression of piR-823 was significantly higher in patients with RCC compared to healthy individuals (p=0.0005, AUC=0.6264 and p=0.0157, AUC=0.7433, respectively). We further observed higher levels of piR-823 in tumor tissue to be associated with shorter disease-free survival of patients (p=0.0186) and a trend for higher piR-823 levels in serum to be associated with advanced clinical stages of RCC (p=0.0691). There were no other significant associations of piR-823 levels in any type of biological specimen with clinicopathological features of RCC. CONCLUSION piR-823 is down-regulated in tumor tissue, but positively correlated with worse outcome, indicating its complex role in RCC pathogenesis. In blood serum, piR-823 is up-regulated, but with unsatisfactory analytical performance. Preliminary data indicate the promising diagnostic utility of urinary piR-823 in patients with RCC.
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Affiliation(s)
- Robert Iliev
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Michal Fedorko
- Department of Urology, University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Tana Machackova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Mlcochova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marek Svoboda
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dalibor Pacik
- Department of Urology, University Hospital Brno, Masaryk University, Brno, Czech Republic
| | - Jan Dolezel
- Department of Urologic Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Michal Stanik
- Department of Urologic Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic .,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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9
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Mlcochova H, Machackova T, Rabien A, Radova L, Fabian P, Iliev R, Slaba K, Poprach A, Kilic E, Stanik M, Redova-Lojova M, Svoboda M, Dolezel J, Vyzula R, Jung K, Slaby O. Epithelial-mesenchymal transition-associated microRNA/mRNA signature is linked to metastasis and prognosis in clear-cell renal cell carcinoma. Sci Rep 2016; 6:31852. [PMID: 27549611 PMCID: PMC4994011 DOI: 10.1038/srep31852] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 02/22/2016] [Accepted: 07/28/2016] [Indexed: 02/06/2023] Open
Abstract
Clear-cell renal cell carcinomas (ccRCCs) are genetically heterogeneous tumors presenting diverse clinical courses. Epithelial-mesenchymal transition (EMT) is a crucial process involved in initiation of metastatic cascade. The aim of our study was to identify an integrated miRNA/mRNA signature associated with metastasis and prognosis in ccRCC through targeted approach based on analysis of miRNAs/mRNAs associated with EMT. A cohort of 230 ccRCC was included in our study and further divided into discovery, training and validation cohorts. EMT markers were evaluated in ccRCC tumor samples, which were grouped accordingly to EMT status. By use of large-scale miRNA/mRNA expression profiling, we identified miRNA/mRNA with significantly different expression in EMT-positive tumors and selected 41 miRNAs/mRNAs for training phase of the study to evaluate their diagnostic and prognostic potential. Fifteen miRNAs/mRNAs were analyzed in the validation phase, where all evaluated miRNA/mRNA candidates were confirmed to be significantly deregulated in tumor tissue. Some of them significantly differed in metastatic tumors, correlated with clinical stage, with Fuhrman grade and with overall survival. Further, we established an EMT-based stage-independent prognostic scoring system enabling identification of ccRCC patients at high-risk of cancer-related death. Finally, we confirmed involvement of miR-429 in EMT regulation in RCC cells in vitro.
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Affiliation(s)
- Hana Mlcochova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Tana Machackova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Anja Rabien
- University Hospital Charite, Humboldt University, Department of Urology, Schumannstrasse 20/21, D-10117 Berlin, Germany.,Berlin Institute for Urologic Research, Robert-Koch Platz 7, 10115 Berlin, Germany
| | - Lenka Radova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Pavel Fabian
- Masaryk Memorial Cancer Institute, Department of Diagnostic and Experimental Pathology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Robert Iliev
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Katerina Slaba
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Alexandr Poprach
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Ergin Kilic
- University Hospital Charite, Humboldt University, Institute of Pathology, Schumannstrasse 20/21, D-10117 Berlin, Germany
| | - Michal Stanik
- Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Martina Redova-Lojova
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic
| | - Marek Svoboda
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Jan Dolezel
- Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Rostislav Vyzula
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Klaus Jung
- University Hospital Charite, Humboldt University, Department of Urology, Schumannstrasse 20/21, D-10117 Berlin, Germany.,Berlin Institute for Urologic Research, Robert-Koch Platz 7, 10115 Berlin, Germany
| | - Ondrej Slaby
- Masaryk University, Central European Institute of Technology (CEITEC), Kamenice 5, 625 00, Brno, Czech Republic.,Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic
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Iliev R, Vychytilova-Faltejskova P, Juracek J, Mlcochova H, Stanik M, Dolezel J, Fedorko M, Pacik D, Svoboda M, Slaby O. Abstract 237: Piwi genes and tissue/serum piR-651 are related to clinicopathologic features of renal cell carcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-237] [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
Introduction: Piwi-interacting RNAs (piRNAs) consists a newly discovered class of non-coding RNA. PiRNAs were first identified in the germ cells of various animal species. They bind to Piwi proteins which are a subfamily of Argonaut proteins. In humans were identified four Ago genes and four Piwi genes. Human Piwi genes include PIWIL1, PIWIL2, PIWIL3 and PIWIL4. Recent studies suggest that deregulated expression of Piwi proteins is common to many types of tumors and also correlate with clinicopathologic features and worse prognosis in patients with breast, cervical, ovarian, colorectal and other cancers. PiRNAs are short single-stranded RNAs with 26-31 nucleotides in length. They are involved in silencing of transposable elements and it is assumed that also participate in sequence-specific chromatin modifications. The differential expression of piRNAs was found in gastric and breast cancer. In our pilot study we analyzed expression of Piwi genes and piR-651, which was previously found to be deregulated in various types of tumors.
Patients and Methods: In our study, we have used the tumor tissue and the paired renal parenchyma tissue of 56 patients with renal cell carcinoma (RCC). From the tissue was isolated total RNA and by RT-qPCR were examined the expression of Piwi genes and piR-651. For the analysis of circulating piR-651, blood serum samples of 75 patients with RCC and 75 age, gender-matched healthy donors were used. We have compared expression levels of the studied genes in tumor and non-tumor tissues, serum samples, and also correlated them with clinicopathologic features of RCC patients (stage, grade, RFS, OS).
Results: We found a significant down-regulation of PIWIL1 (p<0,0001) and piR-651 (p<0,0001) expression levels in tumor tissue when compared to paired renal parenchyma samples. The expression levels of PIWIL2, PIWIL3 and PIWIL4 were not significantly deregulated in tumor tissue. Interestingly, levels of PIWIL2 and PIWIL4 correlated significantly with the stage (p = 0,002 and p = 0,003, resp.) and grade (p = 0.007 and p<0.0001, resp.) of RCC. We found also a correlation between higher levels of PIWIL1 and overall survival (p<0.05). We have observed significantly decreased expression levels of piR-651 in blood serum samples of RCC patients when compared to healthy donors and accordingly to ROC analysis we were able to distinguish blood serum of RCC patients and control subjects with the sensitivity of 77.33% and a specificity of 72.37%. Expression levels of serum piR-651 were not in correlation with the stage and grade of RCC.
Conclusion: Accordingly to our pilot data expression of Piwi genes is altered in tumor tissue and is correlated to selected clinicopathologic features of RCC. We also suggest the potential of piR-651 in blood serum as novel non-invasive diagnostic biomarker in RCC.
Acknowledgments: IGA MZCR No: NT/13860-4/2012, NT/13549-4/2012, NT/13547-4/2012, NT/13514-4/2012
Citation Format: Robert Iliev, Petra Vychytilova-Faltejskova, Jaroslav Juracek, Hana Mlcochova, Michal Stanik, Jan Dolezel, Michal Fedorko, Dalibor Pacik, Marek Svoboda, Ondrej Slaby. Piwi genes and tissue/serum piR-651 are related to clinicopathologic features of renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 237. doi:10.1158/1538-7445.AM2015-237
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Affiliation(s)
- Robert Iliev
- 1Molecular Oncology II, CEITEC, Masaryk University, Brno, Czech Republic
| | | | - Jaroslav Juracek
- 2Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Brno, Czech Republic
| | - Hana Mlcochova
- 1Molecular Oncology II, CEITEC, Masaryk University, Brno, Czech Republic
| | - Michal Stanik
- 3Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Brno, Czech Republic
| | - Jan Dolezel
- 3Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Brno, Czech Republic
| | - Michal Fedorko
- 4Faculty Hospital Brno, Department of Urology, Brno, Czech Republic
| | - Dalibor Pacik
- 4Faculty Hospital Brno, Department of Urology, Brno, Czech Republic
| | - Marek Svoboda
- 2Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Brno, Czech Republic
| | - Ondrej Slaby
- 1Molecular Oncology II, CEITEC, Masaryk University, Brno, Czech Republic
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Sana J, Besse A, Ondracek J, Vecera M, Fadrus P, Kren L, Mlcochova H, Illiev R, Mlcochova J, Vychytilova P, Hezova R, Juracek J, Slaby O. Abstract 5256: MiRNA-31-5p expression in glioblastoma tissue and effects of its replacement in glioblastoma cells. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-5256] [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
Introduction:
Glioblastoma multiforme (GBM) is the most malignant primary tumor of the central nervous system of adults. Our previous study has showed significant alterations in expression of microRNAs (miRNAs) in GBM tissue. Some of these miRNAs were also correlated with overall survival, whereas miR-31-5p was the most significant, indicating its tumor suppressive functioning. In this study, miR-31-5p was studied on larger cohort of GBM patients and also in vitro of selected GBM cell lines.
Patients, Cell lines and Methods:
Expression of miR-31-5p was validated on cohort of 58 GBM patients and 10 samples of non-tumor brain tissue. We have increased expression level of miR-31-5p using transient transfection of specific miRNA mimic in GBM cell lines A172, U87MG, T98MG, and U251. Cell viability and proliferation were analyzed using MTT assay and cell counting, respectively. Cell cycle analyses were performed by flow-cytometry using propidium iodide. Migration and invasion potential were measured by the wound healing assay and transwell invasion assay, respectively. Finally, potential targets of miR-31-5p were discovered using combination of bioinformatics algorithms for target prediction and GeneChip Human Gene 2.0 ST Array (Affymetrix) whole-genome expression profiling.
Results:
Down-regulation of miR-31-5p was successfully validated on cohort of 58 GBM patients and 10 samples of non-tumor brain tissue (p<0.001). MiR-31-5p was significantly associated also with progression-free and overall survival of GBM patients. Transient expression of miR-31-5p led to the significant decrease of GBM cell proliferation and viability in A172, U87MG, T98G, and U251 cell lines (t-test; p < 0.05) due to the cell cycle arrest in G1 phase. Moreover, transfected A172 and U251 cells had a lower migration and invasiveness potential in comparison with control cells (t-test; p < 0.05). Finally, analysis of global gene expression profiles together with predicted mRNA targets revealed several interesting targets of miR-31-5p, which are involved in crucial signaling pathways of GBM.
Conclusion:
Taken together, our data suggest that miR-31-5p is not only powerful diagnostic marker as showed previously but seems to be promising therapeutic target in GBM patients. This work was supported by grants of Internal Grant Agency of the Czech Ministry of Health no. NT13514-4/2012, NT/13860-4/2012, NT/13549-4/2012, NT/13547-4/2012; and project “CEITEC - Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068).
Citation Format: Jiri Sana, Andrej Besse, Jakub Ondracek, Marek Vecera, Pavel Fadrus, Leos Kren, Hana Mlcochova, Robert Illiev, Jitka Mlcochova, Petra Vychytilova, Renata Hezova, Jaroslav Juracek, Ondrej Slaby. MiRNA-31-5p expression in glioblastoma tissue and effects of its replacement in glioblastoma cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5256. doi:10.1158/1538-7445.AM2015-5256
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Affiliation(s)
- Jiri Sana
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Andrej Besse
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Jakub Ondracek
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Marek Vecera
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Pavel Fadrus
- 2University Hospital Brno, Department of Neurosurgery, Brno, Czech Republic
| | - Leos Kren
- 3University Hospital Brno, Department of Pathology, Brno, Czech Republic
| | - Hana Mlcochova
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Robert Illiev
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Jitka Mlcochova
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Petra Vychytilova
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
| | - Renata Hezova
- 4Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Brno, Czech Republic
| | - Jaroslav Juracek
- 4Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Brno, Czech Republic
| | - Ondrej Slaby
- 1Masaryk University, Central European Institute of Technology - CEITEC, Brno, Czech Republic
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression. In the last decade, number of evidences showing miRNAs contribution to the regulation of apoptosis, cellular proliferation, differentiation, and other important cellular processes is constantly growing. Specific miRNA expression signatures have been identified in variety of human cancers as well as pathologies of cardiovascular and urinary systems. Our chapter focuses on the potential of urinary miRNAs to serve as biomarkers in uro-oncology, nephrology, and cardiology. We discuss in detail recent knowledge about the origin of urinary miRNAs, their stability, quality control, and their utility as a potential new class of biomarkers in medicine. Finally, we summarize the studies focusing on detection and characterization of urinary miRNAs as potential biomarkers in urologic cancers, nephrology, and cardiology.
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Affiliation(s)
- Hana Mlcochova
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
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Mlcochova H, Hezova R, Stanik M, Slaby O. Urine microRNAs as potential noninvasive biomarkers in urologic cancers. Urol Oncol 2013; 32:41.e1-9. [PMID: 24035473 DOI: 10.1016/j.urolonc.2013.04.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 01/18/2023]
Abstract
Micro-ribonucleic acids (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression. The ability of miRNAs to inhibit translation of oncogenes and tumor suppressors implies that they may be involved in carcinogenesis. Our review focuses on the potential of urinary miRNAs to serve as biomarkers of urologic cancers. We discuss in detail the recent knowledge about the origin of urinary miRNAs, their stability, quality control, and their utility as a potential new class of biomarkers in urologic cancer. Finally, we summarize the studies focusing on detection and characterization of urinary miRNAs as potential biomarkers in bladder, prostate, and kidney cancers.
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Affiliation(s)
- Hana Mlcochova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Renata Hezova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Michal Stanik
- Masaryk Memorial Cancer Institute, Department of Urologic Oncology, Brno, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53 Brno, Czech Republic.
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Cooklin M, Rhode K, Razavi R, O'neill M, Gill J, Kusa S, Komatsu Y, Kakita K, Takayama K, Taniguchi H, Otomo K, Iesaka Y, Ammar S, Reents T, Fichtner S, Wu J, Zhu P, Olimulder MAGM, Galjee MA, Van Dessel PFHM, Van Der Palen J, Wilde AAM, Scholten MF, Chouchou F, Poupard L, Philippe C, Court-Fortune I, Kolb C, Barthelemy JC, Roche F, Deshko MS, Snezhitsky VA, Dolgoshey TS, Madekina GA, Stempen TP, Sugiura S, Fujii E, Senga M, Hessling G, Dohi K, Sugiura E, Nakamura M, Ito M, Eitel C, Hindricks G, Sommer P, Gaspar T, Bollmann A, Arya A, Deisenhofer I, Piorkowski C, Mendell J, Lasseter K, Shi M, Urban L, Hatala R, Hlivak P, De Melis M, Garutti C, Corbucci G, Di Biase L, Mlcochova H, Maxian R, Cihak R, Wichterle D, Peichl P, Kautzner J, Arbelo E, Dogac A, Luepkes C, Ploessnig M, Gilbert G, Chronaki C, Hinterbuchner L, Guillen A, Brugada J, Bun SS, Latcu DG, Franceschi F, Prevot S, Koutbi L, Ricard P, Mohanty P, Saoudi N, Deharo JC, Nazari N, Alizadeh A, Sayah S, Hekmat M, Assadian M, 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J, Johansson B, Houltz B, Edvardsson N, Schersten H, Karlsson T, Wandt B, Berglin E, Hoyt RH, Jenson BP, Trines SAIP, Braun J, Tjon Joek Tjien A, Zeppenfeld K, Tavilla G, Klautz RJM, Schalij MJ, Krausova R, Cihak R, Peichl P, Wichterle D, Kautzner J, Pirk J, Skalsky I, Maly J, Imai K, Sueda T, Orihashi K, Picarra BC, Santos AR, Dionisio P, Semedo P, Matos R, Leitao M, Banha M, Trinca M, Elder DHJ, George J, Jain R, Lang CC, Choy AM, Konert M, Loescher S, Hartmann A, Aversa E, Chirife R, Sztyglic E, Mazzetti H, Mascheroni O, Tentori MC, Pop RM, Margulescu AD, Dulgheru R, Enescu O, Siliste C, Vinereanu D, Menezes Junior A, Castro Carneiro AR, De Oliveira BL, Shah AN, Kantharia B, De Lucia R, Soldati E, Segreti L, Di Cori A, Zucchelli G, Viani S, Paperini L, Bongiorni MG, Kutarski A, Czajkowski M, Pietura R, Malecka B, Heintze J, Eckardt L, Bauer A, Meine M, Van Erven L, Bloch Thomsen PE, Lopez Chicharro MP, Merhi O, Nagashima M, Goya M, Soga Y, Hayashi K, Ohe M, Andou K, Hiroshima K, 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Pytkowski M, Firek B, Jankowska A, Szwed H, Nakajima I, Noda T, Okamura H, Satomi K, Aiba T, Shimizu W, Aihara N, Kamakura S, Brzozowski W, Tomaszewski A, Kutarski A, Wysokinski A, Bertoldi EG, Rohde LE, Zimerman LI, Pimentel M, Polanczyk CA, Boriani G, Lunati M, Gasparini M, Landolina M, Lonardi G, Pecora D, Santini M, Valsecchi S, Rubinstein BJ, Wang DY, Cabreriza SE, Richmond ME, Rusanov A, Quinn TA, Cheng B, Spotnitz HM, Kristiansen HM, Vollan G, Hovstad T, Keilegavlen H, Faerestrand S, Kawata H, Phan H, Anand K, Feld G, Brigesdotter-Green U, Nawar AMR, Ragab DALIA, Eluhsseiny RANIA, Abdelaziz AHMED, Nof E, Abu Shama R, Buber J, Kuperstein R, Feinberg MS, Barlev D, Eldar M, Glikson M, Badran H, Samir R, Tawfik M, Amin M, Eldamnhoury H, Khaled S, Tolosana JM, Martin AM, Hernandez-Madrid A, Macias A, Fernandez-Lozano I, Osca J, Quesada A, Mont L, Boriani G, Gasparini M, Landolina M, Lunati M, Santini M, Padeletti L, Botto GL, De Santo T, Lunati M, Szwed A, Martinez JG, Degand B, Villani GQ, Leclercq C, Rousseauplasse A, Ritter P, Estrada A, Doiny D, Castrejon Castrejon S, Perez-Silva A, Ortega M, Lopez-Sendon JL, Merino JL, Watanabe I, Nagashima K, Okumura Y, Kofune M, Ohkubo K, Nakai T, Hirayama A, Mikhaylov E, Vander M, Lebedev D, Zarse M, Suleimann H, Bogossian H, Stegelmeyer J, Ninios I, Karosienne Z, Kloppe A, Lemke B, John S, Gaspar T, Rolf S, Sommer P, Hindricks G, Piorkowski C, Berruezo A, Fernandez-Armenta J, Mont LL, Zeljko H, Andreu D, Herzcku C, Boussy T, Brugada J, Yamauchi Y, Okada H, Maeda S, Tao S, Obayahi T, Aonuma K, Hegrenes J, Lim E, Mediratta V, Bautista R, Teplitsky L, Van Huls Van Taxis CFB, Wijnmaalen AP, Gawrysiak M, Schuijf JD, Bax JJ, Schalij MJ, Zeppenfeld K, Huo Y, Richter S, Hindricks G, Arya A, Gaspar T, Bollmann A, Akca F, Bauernfeind T, Schwagten B, De Groot NMS, Jordaens L, Szili-Torok T, Hegrenes J, Miller S, Kastner G, Teplitsky L, Maury P, Della Bella P, Delacretaz E, Sacher F, Maccabelli G, Brenner R, Rollin A, Jais P, Vergara P, Trevisi N, Ricco A, Petracca F, Bisceglia C, Baratto F, Maccabelli G, Della Bella P, Salguero Bodes R, Fontenla Cerezuela A, De Riva Silva M, Lopez Gil M, Mejia Martinez E, Jurado Roman A, Montero Alvarez M, Arribas Ynsaurriaga F, Baszko A, Krzyzanowski K, Bobkowski W, Surmacz R, Zinka E, Siwinska A, Szyszka A, Perez Silva A, Doiny D, Castrejon Castrejon S, Estrada Mucci A, Ortega Molina M, Lopez Sendon JL, Merino Llorens JL, Kaitani K, Hanazawa K, Izumi C, Nakagawa Y, Yamanaka I, Hirahara T, Sugawara Y, Suga C, Ako J, Momomura S, Galizio N, Gonzalez J, Robles F, Palazzo A, Favaloro L, Diez M, Guevara E, Fernandez A, Greenberg S, Epstein A, Deering T, Goldman DS, Sangli C, Keeney JA, Lee K, Piers SRD, Van Rees JB, Thijssen J, Borleffs CJW, Van Der Velde ET, Van Erven L, Schalij MJ, Leclercq CH, Hero M, Mizobuchi M, Enjoji Y, Yazaki Y, Shibata K, Funatsu A, Kobayashi T, Nakamura S, Amit G, Pertzov B, Katz A, Zahger D, Robles F, Galizio N, Gonzalez J, Medesani L, Rana R, Palazzo A, Albano F, Fraguas H, Pedersen SS, Hoogwegt MT, Jordaens L, Theuns DAMJ, Van Den Broek KC, Tekle FB, Habibovic M, Alings M, Van Der Voort P, Denollet J, Vrazic H, Jilek C, Badran H, Lesevic H, Tzeis S, Semmler V, Deisenhofer I, Kolb C, Theuns DAMJ, Gold MR, Burke MC, Bardy GH, Varma N, Pavri B, Stambler B, Michalski J, Investigators TRUST, Safak E, Schmitz D, Konorza T, Wende C, Schirdewan A, Neuzner J, Simmers T, Erglis A, Gradaus R, Alings M, Goetzke J, Coutrot L, Goehl K, Bazan Gelizo V, Grau N, Valles E, Felez M, Sanjuas C, Bruguera J, Marti-Almor J, Chu SY, Li PW, Ding WH, Schukro C, Leitner L, Siebermair J, Stix G, Pezawas T, Kastner J, Wolzt M, Schmidinger H, Behar NATHALIE, Kervio G, Petit B, Maison-Balnche P, Bodi S, Mabo P, Foley PWX, Mutch E, Brashaw-Smith J, Ball L, Leyva F, Kim DH, Lee MJ, Lee WS, Park SD, Shin SH, Woo SI, Kwan J, Park KS, Munetsugu Y, Tanno K, Kikuchi M, Ito H, Miyoshi F, Kawamura M, Kobayashi Y, Man S, Algra AM, Schreurs CA, Van Erven L, Van Der Wall EE, Cannegieter SC, Schalij MJ, Swenne CA, Adachi M, Yano A, Miake J, Ogura K, Kato M, Iitsuka K, Kondo T, Zarse M, Goebbert K, Bogossian H, Karossiene Z, Stegelmeyer J, Ninios I, Kloppe A, Lemke B, Goldman D, Kallen B, Kerpi E, Sardo J, Arsenos P, Gatzoulis K, Manis G, Dilaveris P, Tsiachris D, Mytas D, Asimakopoulos S, Stefanadis C, Arsenos P, Gatzoulis K, Manis G, Dilaveris P, Sideris S, Kartsagoulis E, Mytas D, Stefanadis C, Barbosa O, Marocolo Junior M, Silva Cortes R, Moraes Brandolis RA, Oliveira LF, Pertili Rodrigues De Resende LA, Vieira Da Silva MA, Dias Da Silva VJ, Hegazy RA, Sharaf IA, Fadel F, Bazaraa H, Esam R, Deshko MS, Snezhitsky VA, Stempen TP, Kuroki K, Tada H, Igawa M, Yoshida K, Igarashi M, Sekiguchi Y, Kuga K, Aonuma K, Ferreira Santos L, Dionisio T, Nunes L, Machado J, Castedo S, Henriques C, Matos A, Oliveira Santos J, Kraaier K. Poster Session 3. Europace 2011. [DOI: 10.1093/europace/eur229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schwagten B, Schwagten BKR, Szili-Torok T, Rivero-Ayerza M, Thornton A, Van Belle Y, Jordaens L, Leiria TLL, Kus T, Hadjis TA, Essebag V, Sturmer ML, Soubelet E, Krum D, Delavelle A, Varray F, Hare J, Vaillant R, Choudhuri I, Sra J, Vollmann D, Luethje L, Seegers J, Hasenfuss G, Zabel M, Johar S, Jones DG, Lyne JC, Kaba RA, Wong T, Markides V, Clague JR, Ernst S, Hlivak P, Mlcochova H, Peichl P, Cihak R, Wichterle D, Kautzner J. Abstracts: Tools to facilitate ablation procedures. Europace 2009. [DOI: 10.1093/europace/euq197] [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: 11/12/2022] Open
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Halaska MG, Vlk R, Feldmar P, Hrehorcak M, Krcmar M, Mlcochova H, Mala I, Rob L. Predicting term birth weight using ultrasound and maternal characteristics. Eur J Obstet Gynecol Reprod Biol 2006; 128:231-5. [PMID: 16530919 DOI: 10.1016/j.ejogrb.2006.01.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 10/02/2005] [Revised: 01/09/2006] [Accepted: 01/16/2006] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The aim of the study was to compare an ultrasound-based prediction formula of Shepard, Hadlock, our new equation and equation of Nahum based on maternal characteristics. STUDY DESIGN Two groups of 125 (group A) and 130 (group B) healthy term pregnant women were sampled. Standard ultrasonographic measurements were performed and maternal characteristics recorded. A new birth weight equation was developed by multiple stepwise regression analysis from the group A data and then compared to the different birth weight prediction equations of Hadlock, Shepard and Nahum on group B. RESULTS New prediction equation: log(10) EFW=0.64041xBPD-0.03257xBPD(2)+0.00154xACxFL. Our new (Halaska) and Hadlock's ultrasound estimations are comparable. Both equations are superior to Shepard and Nahum's equations. The Nahum equation is comparable to the Shepard estimation. Halaska equation tends to have the highest overall accuracy, Hadlock's estimation predicts better fetuses over 4000g, but this needs to be further validated. CONCLUSIONS The Halaska and Hadlock's estimations are comparable to one another; the Nahum equation is comparable to Shepard's and can be used as simple, inexpensive and approximative estimate.
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Affiliation(s)
- Michael George Halaska
- Department of Obstetrics and Gynecology, 2nd Medical Faculty of the Charles University, Prague, Czech Republic.
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Cihak R, Mlcochova H, Kautzner J, Peichl P. 567 Radiofrequency ablation for atrial fibrillation guided by circular catheter, electro-anatomical mapping and intracardiac echocardiography. Europace 2005. [DOI: 10.1016/eupace/7.supplement_1.125-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- R. Cihak
- Institut for Clinical and Exp. Medicine, Clinic of Cardiology, Prague
| | - H. Mlcochova
- IKEM, Department of Cardiology, Prague, Czech Republic
| | - J. Kautzner
- IKEM, Department of Cardiology, Prague, Czech Republic
| | - P. Peichl
- IKEM, Department of Cardiology, Prague, Czech Republic
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Peichl P, Kautzner J, Cihak R, Bytesnik J, Mlcochova H. P-414 The role of baseline intraventricular conduction defect on the degree of fusion in patients undergoing CRT. Europace 2003. [DOI: 10.1016/eupace/4.supplement_2.b163-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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