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Giblin KA, Basili D, Afzal AM, Rosenbrier-Ribeiro L, Greene N, Barrett I, Hughes SJ, Bender A. New Associations between Drug-Induced Adverse Events in Animal Models and Humans Reveal Novel Candidate Safety Targets. Chem Res Toxicol 2020; 34:438-451. [PMID: 33338378 DOI: 10.1021/acs.chemrestox.0c00311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To improve our ability to extrapolate preclinical toxicity to humans, there is a need to understand and quantify the concordance of adverse events (AEs) between animal models and clinical studies. In the present work, we discovered 3011 statistically significant associations between preclinical and clinical AEs caused by drugs reported in the PharmaPendium database of which 2952 were new associations between toxicities encoded by different Medical Dictionary for Regulatory Activities terms across species. To find plausible and testable candidate off-target drug activities for the derived associations, we investigated the genetic overlap between the genes linked to both a preclinical and a clinical AE and the protein targets found to interact with one or more drugs causing both AEs. We discuss three associations from the analysis in more detail for which novel candidate off-target drug activities could be identified, namely, the association of preclinical mutagenicity readouts with clinical teratospermia and ovarian failure, the association of preclinical reflexes abnormal with clinical poor-quality sleep, and the association of preclinical psychomotor hyperactivity with clinical drug withdrawal syndrome. Our analysis successfully identified a total of 77% of known safety targets currently tested in in vitro screening panels plus an additional 431 genes which were proposed for investigation as future safety targets for different clinical toxicities. This work provides new translational toxicity relationships beyond AE term-matching, the results of which can be used for risk profiling of future new chemical entities for clinical studies and for the development of future in vitro safety panels.
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Affiliation(s)
- Kathryn A Giblin
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Danilo Basili
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Avid M Afzal
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Lyn Rosenbrier-Ribeiro
- Safety Platforms, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Nigel Greene
- Data Science and Artificial Intelligence, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Ian Barrett
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Samantha J Hughes
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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2
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Hoenerhoff MJ, Meyerholz DK, Brayton C, Beck AP. Challenges and Opportunities for the Veterinary Pathologist in Biomedical Research. Vet Pathol 2020; 58:258-265. [PMID: 33327888 DOI: 10.1177/0300985820974005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Animal models have critical roles in biomedical research in promoting understanding of human disease and facilitating development of new therapies and diagnostic techniques to improve human and animal health. In the study of myriad human conditions, each model requires in-depth characterization of its assets and limitations in order for it to be used to greatest advantage. Veterinary pathology expertise is critical in understanding the relevance and translational validity of animal models to conditions under study, assessing morbidity and mortality, and validating outcomes as relevant or not to the study interventions. Clear communication with investigators and education of research personnel on the use and interpretation of pathology endpoints in animal models are critical to the success of any research program. The veterinary pathologist is underutilized in biomedical research due to many factors including misconceptions about high fiscal costs, lack of perceived value, limited recognition of their expertise, and the generally low number of veterinary pathologists currently employed in biomedical research. As members of the multidisciplinary research team, veterinary pathologists have an important role to educate scientists, ensure accurate interpretation of pathology data, maximize rigor, and ensure reproducibility to provide the most reliable data for animal models in biomedical research.
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Onaciu A, Munteanu R, Munteanu VC, Gulei D, Raduly L, Feder RI, Pirlog R, Atanasov AG, Korban SS, Irimie A, Berindan-Neagoe I. Spontaneous and Induced Animal Models for Cancer Research. Diagnostics (Basel) 2020; 10:E660. [PMID: 32878340 PMCID: PMC7555044 DOI: 10.3390/diagnostics10090660] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Considering the complexity of the current framework in oncology, the relevance of animal models in biomedical research is critical in light of the capacity to produce valuable data with clinical translation. The laboratory mouse is the most common animal model used in cancer research due to its high adaptation to different environments, genetic variability, and physiological similarities with humans. Beginning with spontaneous mutations arising in mice colonies that allow for pursuing studies of specific pathological conditions, this area of in vivo research has significantly evolved, now capable of generating humanized mice models encompassing the human immune system in biological correlation with human tumor xenografts. Moreover, the era of genetic engineering, especially of the hijacking CRISPR/Cas9 technique, offers powerful tools in designing and developing various mouse strains. Within this article, we will cover the principal mouse models used in oncology research, beginning with behavioral science of animals vs. humans, and continuing on with genetically engineered mice, microsurgical-induced cancer models, and avatar mouse models for personalized cancer therapy. Moreover, the area of spontaneous large animal models for cancer research will be briefly presented.
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Affiliation(s)
- Anca Onaciu
- Research Center for Advanced Medicine - Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.O.); (R.M.); (R.-I.F.)
| | - Raluca Munteanu
- Research Center for Advanced Medicine - Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.O.); (R.M.); (R.-I.F.)
| | - Vlad Cristian Munteanu
- Department of Urology, The Oncology Institute “Prof Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
- Department of Anatomy and Embryology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Diana Gulei
- Research Center for Advanced Medicine - Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.O.); (R.M.); (R.-I.F.)
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (L.R.); (R.P.)
| | - Richard-Ionut Feder
- Research Center for Advanced Medicine - Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (A.O.); (R.M.); (R.-I.F.)
| | - Radu Pirlog
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (L.R.); (R.P.)
- Department of Morphological Sciences, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Atanas G. Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria;
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, 05-552 Magdalenka, Poland
- Institute of Neurobiology, Bulgarian Academy of Sciences, 23 Acad. G. Bonchev str., 1113 Sofia, Bulgaria
- Department of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Alexandru Irimie
- 11th Department of Surgical Oncology and Gynaecological Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania;
- Department of Surgery, The Oncology Institute Prof. Dr. Ion Chiricuta, 34–36 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; (L.R.); (R.P.)
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36 Republicii Street, 400015 Cluj-Napoca, Romania
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Comparison of Arthroscopic Partial Meniscectomy to Physical Therapy following Degenerative Meniscus Tears: A Systematic Review and Meta-analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1709415. [PMID: 32190650 PMCID: PMC7073498 DOI: 10.1155/2020/1709415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/14/2020] [Indexed: 11/17/2022]
Abstract
Objective To compare the effectiveness of arthroscopic partial meniscectomy (APM) and physical therapy (PT) for degenerative meniscus tears. Method We conducted a literature search through PubMed, Embase, the Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov. Randomized controlled trials in adults with degenerative meniscal tears without symptoms of locking were considered for inclusion. Two researchers independently performed the literature search, assessed the risk of bias, and selected eligible studies. The primary outcome was function at different follow-up time points and the secondary outcome was pain at different follow-up time points. Results We included 6 randomized controlled trials, with a total of 1006 participants, among which 495 were in the APM group and 511 were in the PT group. We found a small benefit in functional outcomes in the APM group until the 12 months follow-up time point (SMD = 0.20; 95%CI = 0.0-0.33; p = 0.002; I 2 = 34%), but no significant differences in function between groups at the 24-month follow-up time point (SMD = 0.12; 95%CI = -0.04 - 0.28; p = 0.002; I 2 = 34%), but no significant differences in function between groups at the 24-month follow-up time point (SMD = 0.12; 95%CI = -0.04 - 0.28; p = 0.002; I 2 = 34%), but no significant differences in function between groups at the 24-month follow-up time point (SMD = 0.12; 95%CI = -0.04 - 0.28; p = 0.002; I 2 = 34%), but no significant differences in function between groups at the 24-month follow-up time point (SMD = 0.12; 95%CI = -0.04 - 0.28. Conclusion In the treatment of degenerative meniscus tears, APM yielded better functional and pain outcomes compared with physical therapy in the short term until 12 months, but there were comparable results for pain and functional outcomes between the groups at the 24 months follow-up time point.
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PATHBIO: an international training program for precision mouse phenotyping. Mamm Genome 2020; 31:49-53. [PMID: 32088735 DOI: 10.1007/s00335-020-09829-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/15/2020] [Indexed: 10/24/2022]
Abstract
Design and production of genetically engineered mouse strains by individual research laboratories, research teams, large-scale consortia, and the biopharmaceutical industry have magnified the need for qualified personnel to identify, annotate, and validate (phenotype) these potentially new mouse models of human disease. The PATHBIO project has been recently established and funded by the European Union's ERASMUS+ Knowledge Alliance program to address the current shortfall in formally trained personnel. A series of teaching workshops will be given by experts on anatomy, histology, embryology, imaging, and comparative pathology to increase the availability of individuals with formal training to contribute to this important niche of Europe's biomedical research enterprise. These didactic and hands-on workshops are organized into three modules: (1) embryology, anatomy, histology, and the anatomical basis of imaging, (2) image-based phenotyping, and (3) pathology. The workshops are open to all levels of participants from recent graduates to Ph.D., M.D., and veterinary scientists. Participation is available on a competitive basis at no cost for attending. The first series of Workshop Modules was held in 2019 and these will continue for the next 2 years.
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Elmore SA, Cardiff R, Cesta MF, Gkoutos GV, Hoehndorf R, Keenan CM, McKerlie C, Schofield PN, Sundberg JP, Ward JM. A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals. ILAR J 2019; 59:29-39. [PMID: 30476141 DOI: 10.1093/ilar/ily005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/04/2018] [Indexed: 12/14/2022] Open
Abstract
The need for international collaboration in rodent pathology has evolved since the 1970s and was initially driven by the new field of toxicologic pathology. First initiated by the World Health Organization's International Agency for Research on Cancer for rodents, it has evolved to include pathology of the major species (rats, mice, guinea pigs, nonhuman primates, pigs, dogs, fish, rabbits) used in medical research, safety assessment, and mouse pathology. The collaborative effort today is driven by the needs of the regulatory agencies in multiple countries, and by needs of research involving genetically engineered animals, for "basic" research and for more translational preclinical models of human disease. These efforts led to the establishment of an international rodent pathology nomenclature program. Since that time, multiple collaborations for standardization of laboratory animal pathology nomenclature and diagnostic criteria have been developed, and just a few are described herein. Recently, approaches to a nomenclature that is amenable to sophisticated computation have been made available and implemented for large-scale programs in functional genomics and aging. Most terminologies continue to evolve as the science of human and veterinary pathology continues to develop, but standardization and successful implementation remain critical for scientific communication now as ever in the history of veterinary nosology.
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Affiliation(s)
- Susan A Elmore
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Robert Cardiff
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Mark F Cesta
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Georgios V Gkoutos
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Robert Hoehndorf
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Charlotte M Keenan
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Colin McKerlie
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Paul N Schofield
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - John P Sundberg
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
| | - Jerrold M Ward
- Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine
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7
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Cooper TK, Silva KA, Kennedy VE, Alghamdi S, Hoehndorf R, Sundberg BA, Schofield PN, Sundberg JP. Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice. Vet Pathol 2019; 56:799-806. [PMID: 31060453 DOI: 10.1177/0300985819844822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
During a screen for vascular phenotypes in aged laboratory mice, a unique discrete phenotype of hyaline arteriolosclerosis of the intertubular arteries and arterioles of the testes was identified in several inbred strains. Lesions were limited to the testes and did not occur as part of any renal, systemic, or pulmonary arteriopathy or vasculitis phenotype. There was no evidence of systemic or pulmonary hypertension, and lesions did not occur in ovaries of females. Frequency was highest in males of the SM/J (27/30, 90%) and WSB/EiJ (19/26, 73%) strains, aged 383 to 847 days. Lesions were sporadically present in males from several other inbred strains at a much lower (<20%) frequency. The risk of testicular hyaline arteriolosclerosis is at least partially underpinned by a genetic predisposition that is not associated with other vascular lesions (including vasculitis), separating out the etiology of this form and site of arteriolosclerosis from other related conditions that often co-occur in other strains of mice and in humans. Because of their genetic uniformity and controlled dietary and environmental conditions, mice are an excellent model to dissect the pathogenesis of human disease conditions. In this study, a discrete genetically driven phenotype of testicular hyaline arteriolosclerosis in aging mice was identified. These observations open the possibility of identifying the underlying genetic variant(s) associated with the predisposition and therefore allowing future interrogation of the pathogenesis of this condition.
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Affiliation(s)
- Timothy K Cooper
- 1 Department of Comparative Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA.,2 Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | | | | | - Sarah Alghamdi
- 4 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Robert Hoehndorf
- 4 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | | | - Paul N Schofield
- 3 The Jackson Laboratory, Bar Harbor, ME, USA.,5 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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8
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Gibaud B, Forestier G, Feldmann C, Ferrigno G, Gonçalves P, Haidegger T, Julliard C, Katić D, Kenngott H, Maier-Hein L, März K, de Momi E, Nagy DÁ, Nakawala H, Neumann J, Neumuth T, Rojas Balderrama J, Speidel S, Wagner M, Jannin P. Toward a standard ontology of surgical process models. Int J Comput Assist Radiol Surg 2018; 13:1397-1408. [PMID: 30006820 DOI: 10.1007/s11548-018-1824-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE The development of common ontologies has recently been identified as one of the key challenges in the emerging field of surgical data science (SDS). However, past and existing initiatives in the domain of surgery have mainly been focussing on individual groups and failed to achieve widespread international acceptance by the research community. To address this challenge, the authors of this paper launched a European initiative-OntoSPM Collaborative Action-with the goal of establishing a framework for joint development of ontologies in the field of SDS. This manuscript summarizes the goals and the current status of the international initiative. METHODS A workshop was organized in 2016, gathering the main European research groups having experience in developing and using ontologies in this domain. It led to the conclusion that a common ontology for surgical process models (SPM) was absolutely needed, and that the existing OntoSPM ontology could provide a good starting point toward the collaborative design and promotion of common, standard ontologies on SPM. RESULTS The workshop led to the OntoSPM Collaborative Action-launched in mid-2016-with the objective to develop, maintain and promote the use of common ontologies of SPM relevant to the whole domain of SDS. The fundamental concept, the architecture, the management and curation of the common ontology have been established, making it ready for wider public use. CONCLUSION The OntoSPM Collaborative Action has been in operation for 24 months, with a growing dedicated membership. Its main result is a modular ontology, undergoing constant updates and extensions, based on the experts' suggestions. It remains an open collaborative action, which always welcomes new contributors and applications.
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Affiliation(s)
| | | | - Carolin Feldmann
- Division of Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Paulo Gonçalves
- Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal.,IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Tamás Haidegger
- Antal Bejczy Center for Intelligent Robotics, Óbuda University, Budapest, Hungary.,Austrian Center for Medical Innovation and Technology (ACMIT), Wiener Neustadt, Austria
| | - Chantal Julliard
- Inserm, LTSI - UMR_S 1099, Univ Rennes, Rennes, France.,LIRMM, Université de Montpellier, Montpellier, France.,Stryker GmbH, Freiburg, Germany
| | - Darko Katić
- Karlsruhe Institute of Technology, Institute for Anthropomatics and Robotics, Karlsruhe, Germany.,ArtiMinds Robotics GmbH, Karlsruhe, Germany
| | - Hannes Kenngott
- Department of General, Abdominal and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Lena Maier-Hein
- Division of Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keno März
- Division of Computer Assisted Medical Interventions, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Dénes Ákos Nagy
- Antal Bejczy Center for Intelligent Robotics, Óbuda University, Budapest, Hungary.,Austrian Center for Medical Innovation and Technology (ACMIT), Wiener Neustadt, Austria
| | | | - Juliane Neumann
- Innovation Center Computer Assisted Surgery, Leipzig University, Leipzig, Germany
| | - Thomas Neumuth
- Innovation Center Computer Assisted Surgery, Leipzig University, Leipzig, Germany
| | | | | | - Martin Wagner
- Department of General, Abdominal and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Pierre Jannin
- Inserm, LTSI - UMR_S 1099, Univ Rennes, Rennes, France
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9
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Schofield PN, Ward JM, Sundberg JP. Show and tell: disclosure and data sharing in experimental pathology. Dis Model Mech 2017; 9:601-5. [PMID: 27483498 PMCID: PMC4920154 DOI: 10.1242/dmm.026054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reproducibility of data from experimental investigations using animal models is increasingly under scrutiny because of the potentially negative impact of poor reproducibility on the translation of basic research. Histopathology is a key tool in biomedical research, in particular for the phenotyping of animal models to provide insights into the pathobiology of diseases. Failure to disclose and share crucial histopathological experimental details compromises the validity of the review process and reliability of the conclusions. We discuss factors that affect the interpretation and validation of histopathology data in publications and the importance of making these data accessible to promote replicability in research. Summary: Reproducibility of findings in experiments using model organisms has recently become a source of concern, particularly for translational science. We discuss factors affecting the interpretation and reliability of experimental pathology findings in the mouse, and how disclosure and transparent reporting are crucial for replicability.
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Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK The Jackson Laboratory, Bar Harbor, ME 04609, USA
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10
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Ward JM, Schofield PN, Sundberg JP. Reproducibility of histopathological findings in experimental pathology of the mouse: a sorry tail. Lab Anim (NY) 2017; 46:146-151. [PMID: 28328876 DOI: 10.1038/laban.1214] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
Reproducibility of in vivo research using the mouse as a model organism depends on many factors, including experimental design, strain or stock, experimental protocols, and methods of data evaluation. Gross and histopathology are often the endpoints of such research and there is increasing concern about the accuracy and reproducibility of diagnoses in the literature. To reproduce histopathological results, the pathology protocol, including necropsy methods and slide preparation, should be followed by interpretation of the slides by a pathologist familiar with reading mouse slides and familiar with the consensus medical nomenclature used in mouse pathology. Likewise, it is important that pathologists are consulted as reviewers of manuscripts where histopathology is a key part of the investigation. The absence of pathology expertise in planning, executing and reviewing in vivo research using mice leads to questionable pathology-based findings and conclusions from studies, even in high-impact journals. We discuss the various aspects of this problem, give some examples from the literature and suggest solutions.
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Affiliation(s)
| | - Paul N Schofield
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK.,The Jackson Laboratory, Bar Harbor, Maine, USA
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11
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Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11, and 15 for age-related cardiac fibrosis. Mamm Genome 2016; 27:179-90. [PMID: 27126641 DOI: 10.1007/s00335-016-9634-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/24/2016] [Indexed: 10/21/2022]
Abstract
Dystrophic cardiac calcinosis (DCC), also called epicardial and myocardial fibrosis and mineralization, has been detected in mice of a number of laboratory inbred strains, most commonly C3H/HeJ and DBA/2J. In previous mouse breeding studies between these DCC susceptible and the DCC-resistant strain C57BL/6J, 4 genetic loci harboring genes involved in DCC inheritance were identified and subsequently termed Dyscalc loci 1 through 4. Here, we report susceptibility to cardiac fibrosis, a sub-phenotype of DCC, at 12 and 20 months of age and close to natural death in a survey of 28 inbred mouse strains. Eight strains showed cardiac fibrosis with highest frequency and severity in the moribund mice. Using genotype and phenotype information of the 28 investigated strains, we performed genome-wide association studies (GWAS) and identified the most significant associations on chromosome (Chr) 15 at 72 million base pairs (Mb) (P < 10(-13)) and Chr 4 at 122 Mb (P < 10(-11)) and 134 Mb (P < 10(-7)). At the Chr 15 locus, Col22a1 and Kcnk9 were identified. Both have been reported to be morphologically and functionally important in the heart muscle. The strongest Chr 4 associations were located approximately 6 Mb away from the Dyscalc 2 quantitative trait locus peak within the boundaries of the Extl1 gene and in close proximity to the Trim63 and Cap1 genes. In addition, a single-nucleotide polymorphism association was found on chromosome 11. This study provides evidence for more than the previously reported 4 genetic loci determining cardiac fibrosis and DCC. The study also highlights the power of GWAS in the mouse for dissecting complex genetic traits.
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12
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Ladiges W, Ikeno Y, Niedernhofer L, McIndoe RA, Ciol MA, Ritchey J, Liggitt D. The Geropathology Research Network: An Interdisciplinary Approach for Integrating Pathology Into Research on Aging. J Gerontol A Biol Sci Med Sci 2016; 71:431-4. [PMID: 26243216 PMCID: PMC5014185 DOI: 10.1093/gerona/glv079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/14/2015] [Indexed: 01/22/2023] Open
Abstract
Geropathology is the study of aging and age-related lesions and diseases in the form of whole necropsies/autopsies, surgical biopsies, histology, and molecular biomarkers. It encompasses multiple subspecialties of geriatrics, anatomic pathology, molecular pathology, clinical pathology, and gerontology. In order to increase the consistency and scope of communication in the histologic and molecular pathology assessment of tissues from preclinical and clinical aging studies, a Geropathology Research Network has been established consisting of pathologists and scientists with expertise in the comparative pathology of aging, the design of aging research studies, biostatistical methods for analysis of aging data, and bioinformatics for compiling and annotating large sets of data generated from aging studies. The network provides an environment to promote learning and exchange of scientific information and ideas for the aging research community through a series of symposia, the development of uniform ways of integrating pathology into aging studies, and the statistical analysis of pathology data. The efforts of the network are ultimately expected to lead to a refined set of sentinel biomarkers of molecular and anatomic pathology that could be incorporated into preclinical and clinical aging intervention studies to increase the relevance and productivity of these types of investigations.
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Affiliation(s)
- Warren Ladiges
- Department of Comparative Medicine, University of Washington, Seattle.
| | - Yuji Ikeno
- Department of Pathology, University of Texas at San Antonio, San Antonio
| | | | | | - Marcia A Ciol
- Department of Rehabilitation Medicine, University of Washington, Seattle
| | - Jerry Ritchey
- Department of Veterinary Pathology, College of Veterinary Medicine, Oklahoma State University, Stillwater
| | - Denny Liggitt
- Department of Comparative Medicine, University of Washington, Seattle
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13
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Sundberg JP, Berndt A, Sundberg BA, Silva KA, Kennedy V, Smith RS, Cooper TK, Schofield PN. Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study. Vet Pathol 2016; 53:456-67. [PMID: 26936752 PMCID: PMC5297262 DOI: 10.1177/0300985815612556] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inbred mice are a unique model system for studying aging because of the genetic homogeneity within inbred strains, the short life span of mice relative to humans, and the rich array of analytic tools that are available. A large-scale aging study was conducted on 28 inbred strains representing great genetic diversity to determine, via histopathology, the type and diversity of spontaneous diseases that aging mice develop. A total of 20 885 different diagnoses were made, with an average of 12 diagnoses per mouse in the study. Eighteen inbred strains have had their genomes sequenced, and many others have been partially sequenced to provide large repositories of data on genetic variation among the strains. This vast amount of genomic information can be utilized in genome-wide association studies to find candidate genes that are involved in the pathogenesis of spontaneous diseases. As an illustration, this article presents a genome-wide association study of the genetic associations of age-related intestinal amyloidosis, which implicated 3 candidate genes: translocating chain-associated membrane protein 1 (Tram1); splicing factor 3b, subunit 5 (Sf3b5); and syntaxin 11 (Stx11). Representative photomicrographs are available on the Mouse Tumor Biology Database and Pathbase to serve as a reference when evaluating inbred mice used in other genetic or experimental studies to rule out strain background lesions. Many of the age-related mouse diseases are similar, if not identical, to human diseases; therefore, the genetic discoveries have direct translational benefit.
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Affiliation(s)
| | - A Berndt
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - K A Silva
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - V Kennedy
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - R S Smith
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - T K Cooper
- Department of Comparative Medicine, Department of Pathology, Penn State Milton S. Hershey Medical Center, College of Medicine, Hershey, PA, USA
| | - P N Schofield
- The Jackson Laboratory, Bar Harbor, ME, USA Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK
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14
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Sundberg JP, Silva KA, King LE, Pratt CH. Skin Diseases in Laboratory Mice: Approaches to Drug Target Identification and Efficacy Screening. Methods Mol Biol 2016; 1438:199-224. [PMID: 27150092 PMCID: PMC5301944 DOI: 10.1007/978-1-4939-3661-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2023]
Abstract
A large variety of mouse models for human skin, hair, and nail diseases are readily available from investigators and vendors worldwide. Mouse skin is a simple organ to observe lesions and their response to therapy, but identifying and monitoring the progress of treatments of mouse skin diseases can still be challenging. This chapter provides an overview on how to use the laboratory mouse as a preclinical tool to evaluate efficacy of new compounds or test potential new uses for compounds approved for use for treating an unrelated disease. Basic approaches to handling mice, applying compounds, and quantifying effects of the treatment are presented.
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Affiliation(s)
- John P Sundberg
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA.
| | - Kathleen A Silva
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA
| | - Lloyd E King
- Division of Dermatology, Department of Medicine, Vanderbilt Medical Center, Nashville, TN, USA
| | - C Herbert Pratt
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA
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15
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Berndt A, Ackert-Bicknell C, Silva KA, Kennedy VE, Sundberg BA, Cates JM, Schofield PN, Sundberg JP. Genetic determinants of fibro-osseous lesions in aged inbred mice. Exp Mol Pathol 2015; 100:92-100. [PMID: 26589134 DOI: 10.1016/j.yexmp.2015.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 12/12/2022]
Abstract
Fibro-osseous lesions in mice are progressive aging changes in which the bone marrow is replaced to various degrees by fibrovascular stroma and bony trabeculae in a wide variety of bones. The frequency and severity varied greatly among 28 different inbred mouse stains, predominantly affecting females, ranging from 0% for 10 strains to 100% for KK/HlJ and NZW/LacJ female mice. Few lesions were observed in male mice and for 23 of the strains, no lesions were observed in males for any of the cohorts. There were no significant correlations between strain-specific severities of fibro-osseous lesions and ovarian (r=0.11; P=0.57) or endometrial (r=0.03; P=0.89) cyst formation frequency or abnormalities in parathyroid glands. Frequency of fibro-osseous lesions was most strongly associated (P<10(-6)) with genome variations on chromosome (Chr) 8 at 90.6 and 90.8Mb (rs33108071, rs33500669; P=5.0·10(-10), 1.3·10(-6)), Chr 15 at 23.6 and 23.8Mb (rs32087871, rs45770368; P=7.3·10(-7), 2.7·10(-6)), and Chr 19 at 33.2, 33.4, and 33.6Mb (rs311004232, rs30524929, rs30448815; P=2.8·10(-6), 2.8·10(-6), 2.8·10(-6)) in genome-wide association studies (GWAS). The relatively large number of candidate genes identified in the GWAS analyses suggests that this may be an extremely complex polygenic disease. These results indicate that fibro-osseous lesions are surprisingly common in many inbred strains of laboratory mice as they age. While this presents little problem in most studies that utilize young animals, it may complicate aging studies, particularly those focused on bone.
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Affiliation(s)
- Annerose Berndt
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.
| | | | | | | | | | - Justin M Cates
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States.
| | - Paul N Schofield
- The Jackson Laboratory, Bar Harbor, ME, United States; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.
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16
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Begley DA, Sundberg JP, Krupke DM, Neuhauser SB, Bult CJ, Eppig JT, Morse HC, Ward JM. Finding mouse models of human lymphomas and leukemia's using the Jackson laboratory mouse tumor biology database. Exp Mol Pathol 2015; 99:533-6. [PMID: 26302176 DOI: 10.1016/j.yexmp.2015.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 01/22/2023]
Abstract
Many mouse models have been created to study hematopoietic cancer types. There are over thirty hematopoietic tumor types and subtypes, both human and mouse, with various origins, characteristics and clinical prognoses. Determining the specific type of hematopoietic lesion produced in a mouse model and identifying mouse models that correspond to the human subtypes of these lesions has been a continuing challenge for the scientific community. The Mouse Tumor Biology Database (MTB; http://tumor.informatics.jax.org) is designed to facilitate use of mouse models of human cancer by providing detailed histopathologic and molecular information on lymphoma subtypes, including expertly annotated, on line, whole slide scans, and providing a repository for storing information on and querying these data for specific lymphoma models.
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Affiliation(s)
| | | | | | | | | | | | - Herbert C Morse
- Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, NIH, Bethesda, MD USA
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17
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McInnes EF, Scudamore CL. Aging Lesions: Background Versus Phenotype. CURRENT PATHOBIOLOGY REPORTS 2015. [DOI: 10.1007/s40139-015-0078-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Bult CJ, Krupke DM, Begley DA, Richardson JE, Neuhauser SB, Sundberg JP, Eppig JT. Mouse Tumor Biology (MTB): a database of mouse models for human cancer. Nucleic Acids Res 2014; 43:D818-24. [PMID: 25332399 PMCID: PMC4384039 DOI: 10.1093/nar/gku987] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Mouse Tumor Biology (MTB; http://tumor.informatics.jax.org) database is a unique online compendium of mouse models for human cancer. MTB provides online access to expertly curated information on diverse mouse models for human cancer and interfaces for searching and visualizing data associated with these models. The information in MTB is designed to facilitate the selection of strains for cancer research and is a platform for mining data on tumor development and patterns of metastases. MTB curators acquire data through manual curation of peer-reviewed scientific literature and from direct submissions by researchers. Data in MTB are also obtained from other bioinformatics resources including PathBase, the Gene Expression Omnibus and ArrayExpress. Recent enhancements to MTB improve the association between mouse models and human genes commonly mutated in a variety of cancers as identified in large-scale cancer genomics studies, provide new interfaces for exploring regions of the mouse genome associated with cancer phenotypes and incorporate data and information related to Patient-Derived Xenograft models of human cancers.
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Affiliation(s)
- Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Debra M Krupke
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Dale A Begley
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | | | | | - John P Sundberg
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
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19
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Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Schofield PN, Bult CJ, Eppig JT, Sundberg JP. Identifying mouse models for skin cancer using the Mouse Tumor Biology Database. Exp Dermatol 2014; 23:761-3. [PMID: 25040013 PMCID: PMC4183210 DOI: 10.1111/exd.12512] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2014] [Indexed: 11/29/2022]
Abstract
In recent years, the scientific community has generated an ever-increasing amount of data from a growing number of animal models of human cancers. Much of these data come from genetically engineered mouse models. Identifying appropriate models for skin cancer and related relevant genetic data sets from an expanding pool of widely disseminated data can be a daunting task. The Mouse Tumor Biology Database (MTB) provides an electronic archive, search and analysis system that can be used to identify dermatological mouse models of cancer, retrieve model-specific data and analyse these data. In this report, we detail MTB's contents and capabilities, together with instructions on how to use MTB to search for skin-related tumor models and associated data.
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Affiliation(s)
| | | | | | | | - Paul N. Schofield
- The Jackson Laboratory, Bar Harbor, ME USA
- Dept. of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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20
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Cardiff RD, Miller CH, Munn RJ. Analysis of mouse model pathology: a primer for studying the anatomic pathology of genetically engineered mice. Cold Spring Harb Protoc 2014; 2014:561-80. [PMID: 24890215 DOI: 10.1101/pdb.top069922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This primer of pathology is intended to introduce investigators to the structure (morphology) of cancer with an emphasis on genetically engineered mouse (GEM) models (GEMMs). We emphasize the necessity of using the entire biological context for the interpretation of anatomic pathology. Because the primary investigator is responsible for almost all of the information and procedures leading up to microscopic examination, they should also be responsible for documentation of experiments so that the microscopic interpretation can be rendered in context of the biology. The steps involved in this process are outlined, discussed, and illustrated. Because GEMMs are unique experimental subjects, some of the more common pitfalls are discussed. Many of these errors can be avoided with attention to detail and continuous quality assurance.
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
| | - Claramae H Miller
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
| | - Robert J Munn
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
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21
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Scudamore CL, Busk N, Vowell K. A simplified necropsy technique for mice: making the most of unscheduled deaths. Lab Anim 2014; 48:342-4. [DOI: 10.1177/0023677214536555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sudden or unexpected deaths in experimental mice can be potential causes of lost data or lost opportunities to diagnose health problems. In small animal units and in particular out of normal working hours there may not be the time or expertise available to attempt a careful dissection on unscheduled mortalities or moribund animals. This paper outlines a robust and easy necropsy technique which can be easily learnt, uses minimal equipment and can be used to implement the 3Rs (replacement, refinement and reduction) by maximizing the amount of information gained from experimental animals.
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Affiliation(s)
| | - Naomi Busk
- Mary Lyon Centre, MRC Harwell, Oxfordshire, UK
| | - Kate Vowell
- Mary Lyon Centre, MRC Harwell, Oxfordshire, UK
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22
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Scudamore CL. Acquiring, recording, and analyzing pathology data from experimental mice: an overview. ACTA ACUST UNITED AC 2014; 4:1-10. [PMID: 25715673 DOI: 10.1002/9780470942390.mo130200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pathology is often underutilized as an end point in mouse studies in academic research because of a lack of experience and expertise. The use of traditional pathology techniques including necropsy and microscopic analysis can be useful in identifying the basic processes underlying a phenotype and facilitating comparison with equivalent human diseases. This overview aims to provide a guide and reference to the acquisition, recording, and analysis of high-quality pathology data from experimental mice in an academic research setting.
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Affiliation(s)
- Cheryl L Scudamore
- Mary Lyon Centre, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, United Kingdom
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23
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Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y, Carragher DM, Clarke K, Karp NA, Newbigging S, Jones N, Morikawa L, White JK, McKerlie C. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen. Dis Model Mech 2014; 7:515-24. [PMID: 24652767 PMCID: PMC4007403 DOI: 10.1242/dmm.015263] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.
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Affiliation(s)
- Hibret A Adissu
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, 25 Orde Street, Toronto, ON M5T 3H7, Canada
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24
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Dadras SS, Silva KA, King LE, Sundberg JP. Transplantable malignant melanoma in LT.B6 congenic mice resembling pigmented epithelioid melanocytoma in humans. J Invest Dermatol 2014; 134:1772-1775. [PMID: 24476622 DOI: 10.1038/jid.2014.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Soheil S Dadras
- Department of Dermatology and Genetics/Developmental Biology, University of Connecticut, Farmington, Connecticut, USA.
| | | | - Lloyd E King
- Vanderbilt University, Nashville, Tennessee, USA
| | - John P Sundberg
- The Jackson Laboratory, Bar Harbor, Maine, USA; Vanderbilt University, Nashville, Tennessee, USA
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25
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Cardiff RD, Miller CH, Munn RJ, Galvez JJ. Structured reporting in anatomic pathology for coclinical trials: the caELMIR model. Cold Spring Harb Protoc 2014; 2014:32-43. [PMID: 24173313 DOI: 10.1101/pdb.top078790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Electronic media, with their tremendous potential for storing, retrieving, and integrating data, are an essential part of modern collaborative multidisciplinary science. Structured reporting is a fundamental aspect of keeping accurate, searchable electronic records. This discussion on structured reporting in anatomic pathology for pre- and coclinical trials in animal models provides background information for scientists who are not familiar with structured reporting. Practical examples are provided using a working database system for preclinical research-caELMIR (Cancer Electronic Laboratory Management Information and Retrieval)-developed by the U.S. National Cancer Institute's (NCI's) Mouse Models of Human Cancers Consortium (MMHCC).
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine and Center for Genomic Pathology, University of California, Davis, Davis, California 95616
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26
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Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV. The mouse pathology ontology, MPATH; structure and applications. J Biomed Semantics 2013; 4:18. [PMID: 24033988 PMCID: PMC3851164 DOI: 10.1186/2041-1480-4-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated into data collection platforms (such as computerized medical record-keeping systems) to enable the pathologist to rapidly screen and accurately record observations. The MPATH ontology was originally constructed in 2,000 by a committee of pathologists for the annotation of rodent histopathology images, but is now widely used for coding and analysis of disease and phenotype data for rodents, humans and zebrafish. CONSTRUCTION AND CONTENT MPATH is divided into two main branches describing pathological processes and structures based on traditional histopathological principles. It does not aim to include definitive diagnoses, which would generally be regarded as disease concepts. It contains 888 core pathology terms in an almost exclusively is_a hierarchy nine layers deep. Currently, 86% of the terms have textual definitions and contain relationships as well as logical axioms to other ontologies such the Gene Ontology. APPLICATION AND UTILITY MPATH was originally devised for the annotation of histopathological images from mice but is now being used much more widely in the recording of diagnostic and phenotypic data from both mice and humans, and in the construction of logical definitions for phenotype and disease ontologies. We discuss the use of MPATH to generate cross-products with qualifiers derived from a subset of the Phenotype and Trait Ontology (PATO) and its application to large-scale high-throughput phenotyping studies. MPATH provides a largely species-agnostic ontology for the descriptions of anatomic pathology, which can be applied to most amniotes and is now finding extensive use in species other than mice. It enables investigators to interrogate large datasets at a variety of depths, use semantic analysis to identify the relations between diseases in different species and integrate pathology data with other data types, such as pharmacogenomics.
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Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3EG, Cambridge, UK.
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27
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Abstract
Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases.
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Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA.
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28
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Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2013; 2:30. [PMID: 24358873 DOI: 10.12688/f1000research.2-30.v1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2013] [Indexed: 12/30/2022] Open
Abstract
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Sandra C Doelken
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Barbara J Ruef
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - Sebastian Bauer
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | | | - Monte Westerfield
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - George Gkoutos
- Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK
| | - Paul Schofield
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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29
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Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2013; 2:30. [PMID: 24358873 PMCID: PMC3799545 DOI: 10.12688/f1000research.2-30.v2] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 12/11/2022] Open
Abstract
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from
http://purl.obolibrary.org/obo/hp/uberpheno/.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Sandra C Doelken
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | - Barbara J Ruef
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - Sebastian Bauer
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany
| | | | - Monte Westerfield
- ZFIN, Institute of Neuroscience, University of Oregon, Eugene OR, 97403-5291, USA
| | - George Gkoutos
- Department of Computer Science, University of Aberystwyth, Aberystwyth, SY23 2AX, UK
| | - Paul Schofield
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Berkeley CA, 94720, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Berlin-Brandenberg Center for Regenerative Therapies (BCRT), Charité-Universitatsmedizin Berlin, Berlin, 13353, Germany ; Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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30
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Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SAT, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M. ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res 2012; 41:D854-60. [PMID: 23074187 PMCID: PMC3531097 DOI: 10.1093/nar/gks938] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
ZFIN, the Zebrafish Model Organism Database (http://zfin.org), is the central resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN curators manually curate and integrate comprehensive data involving zebrafish genes, mutants, transgenics, phenotypes, genotypes, gene expressions, morpholinos, antibodies, anatomical structures and publications. Integrated views of these data, as well as data gathered through collaborations and data exchanges, are provided through a wide selection of web-based search forms. Among the vertebrate model organisms, zebrafish are uniquely well suited for rapid and targeted generation of mutant lines. The recent rapid production of mutants and transgenic zebrafish is making management of data associated with these resources particularly important to the research community. Here, we describe recent enhancements to ZFIN aimed at improving our support for mutant and transgenic lines, including (i) enhanced mutant/transgenic search functionality; (ii) more expressive phenotype curation methods; (iii) new downloads files and archival data access; (iv) incorporation of new data loads from laboratories undertaking large-scale generation of mutant or transgenic lines and (v) new GBrowse tracks for transgenic insertions, genes with antibodies and morpholinos.
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Affiliation(s)
- Douglas G Howe
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
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31
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Sundberg JP, HogenEsch H, Nikitin AY, Treuting PM, Ward JM. Training Mouse Pathologists: Ten Years of Workshops on the Pathology of Mouse Models of Human Disease. Toxicol Pathol 2012; 40:823-5. [DOI: 10.1177/0192623312439123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Harm HogenEsch
- Purdue University College of Veterinary Medicine, West Lafayette, Indiana, USA
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32
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Sundberg JP, Ward JM, HogenEsch H, Nikitin AY, Treuting PM, Macauley JB, Schofield PN. Training pathologists in mouse pathology. Vet Pathol 2012; 49:393-7. [PMID: 20817889 PMCID: PMC3329931 DOI: 10.1177/0300985810381244] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Expertise in the pathology of mice has expanded from traditional regulatory and drug safety screening (toxicologic pathology) primarily performed by veterinary pathologists to the highly specialized area of mouse research pathobiology performed by veterinary and medical pathologists encompassing phenotyping of mutant mice and analysis of research experiments exploiting inbred mouse strains and genetically engineered lines. With increasing use of genetically modified mice in research, mouse pathobiology and, by extension, expert mouse research-oriented pathologists have become integral to the success of basic and translational biomedical research. Training for today's research-oriented mouse pathologist must go beyond knowledge of anatomic features of mice and strain-specific background diseases to the specialized genetic nomenclature, husbandry, and genetics, including the methodology of genetic engineering and complex trait analysis. While training can be accomplished through apprenticeships in formal programs, these are often heavily service related and do not provide the necessary comprehensive training. Specialty courses and short-term mentoring with expert specialists are opportunities that, when combined with active practice and publication, will lead to acquisition of the skills required for cutting-edge mouse-based experimental science.
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Affiliation(s)
- J P Sundberg
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609-1500, USA.
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33
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Schofield PN, Vogel P, Gkoutos GV, Sundberg JP. Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. Dis Model Mech 2012; 5:19-25. [PMID: 22028326 PMCID: PMC3255539 DOI: 10.1242/dmm.008334] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Recent advances in gene knockout techniques and the in vivo analysis of mutant mice, together with the advent of large-scale projects for systematic mouse mutagenesis and genome-wide phenotyping, have allowed the creation of platforms for the most complete and systematic analysis of gene function ever undertaken in a vertebrate. The development of high-throughput phenotyping pipelines for these and other large-scale projects allows investigators to search and integrate large amounts of directly comparable phenotype data from many mutants, on a genomic scale, to help develop and test new hypotheses about the origins of disease and the normal functions of genes in the organism. Histopathology has a venerable history in the understanding of the pathobiology of human and animal disease, and presents complementary advantages and challenges to in vivo phenotyping. In this review, we present evidence for the unique contribution that histopathology can make to a large-scale phenotyping effort, using examples from past and current programmes at Lexicon Pharmaceuticals and The Jackson Laboratory, and critically assess the role of histopathology analysis in high-throughput phenotyping pipelines.
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Affiliation(s)
- Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
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34
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Schofield PN, Sundberg JP, Hoehndorf R, Gkoutos GV. New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. Brief Funct Genomics 2011; 10:258-65. [PMID: 21987712 PMCID: PMC3189694 DOI: 10.1093/bfgp/elr031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The systematic investigation of the phenotypes associated with genotypes in model organisms holds the promise of revealing genotype-phenotype relations directly and without additional, intermediate inferences. Large-scale projects are now underway to catalog the complete phenome of a species, notably the mouse. With the increasing amount of phenotype information becoming available, a major challenge that biology faces today is the systematic analysis of this information and the translation of research results across species and into an improved understanding of human disease. The challenge is to integrate and combine phenotype descriptions within a species and to systematically relate them to phenotype descriptions in other species, in order to form a comprehensive understanding of the relations between those phenotypes and the genotypes involved in human disease. We distinguish between two major approaches for comparative phenotype analyses: the first relies on evolutionary relations to bridge the species gap, while the other approach compares phenotypes directly. In particular, the direct comparison of phenotypes relies heavily on the quality and coherence of phenotype and disease databases. We discuss major achievements and future challenges for these databases in light of their potential to contribute to the understanding of the molecular mechanisms underlying human disease. In particular, we discuss how the use of ontologies and automated reasoning can significantly contribute to the analysis of phenotypes and demonstrate their potential for enabling translational research.
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de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon P. The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res Notes 2011; 4:313. [PMID: 21878109 PMCID: PMC3192696 DOI: 10.1186/1756-0500-4-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 08/30/2011] [Indexed: 11/25/2022] Open
Abstract
Background The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models. Findings We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described. Conclusions RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.
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Affiliation(s)
- Bernard de Bono
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
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Sundberg JP, Berndt A, Sundberg BA, Silva KA, Kennedy V, Bronson R, Yuan R, Paigen B, Harrison D, Schofield PN. The mouse as a model for understanding chronic diseases of aging: the histopathologic basis of aging in inbred mice. PATHOBIOLOGY OF AGING & AGE RELATED DISEASES 2011; 1:PBA-1-7179. [PMID: 22953031 PMCID: PMC3417678 DOI: 10.3402/pba.v1i0.7179] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 04/28/2011] [Accepted: 04/29/2011] [Indexed: 11/30/2022]
Abstract
Inbred mice provide a unique tool to study aging populations because of the genetic homogeneity within an inbred strain, their short life span, and the tools for analysis which are available. A large-scale longitudinal and cross-sectional aging study was conducted on 30 inbred strains to determine, using histopathology, the type and diversity of diseases mice develop as they age. These data provide tools that when linked with modern in silico genetic mapping tools, can begin to unravel the complex genetics of many of the common chronic diseases associated with aging in humans and other mammals. In addition, novel disease models were discovered in some strains, such as rhabdomyosarcoma in old A/J mice, to diseases affecting many but not all strains including pseudoxanthoma elasticum, pulmonary adenoma, alopecia areata, and many others. This extensive data set is now available online and provides a useful tool to help better understand strain-specific background diseases that can complicate interpretation of genetically engineered mice and other manipulatable mouse studies that utilize these strains.
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Birschwilks M, Gruenberger M, Adelmann C, Tapio S, Gerber G, Schofield PN, Grosche B. The European Radiobiological Archives: Online Access to Data from Radiobiological Experiments. Radiat Res 2011; 175:526-31. [DOI: 10.1667/rr2471.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Schofield PN, Dubus P, Klein L, Moore M, McKerlie C, Ward JM, Sundberg JP. Pathology of the laboratory mouse: an International Workshop on Challenges for High Throughput Phenotyping. Toxicol Pathol 2011; 39:559-62. [PMID: 21444746 DOI: 10.1177/0192623311399789] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The fifth in a series of European workshops for veterinary and human pathologists, "Pathology of the Laboratory Mouse: An International Workshop on Challenges for High Throughput Phenotyping," was held in Bordeaux, France, from September 30 to October 1, 2010. In this report we outline the rationale for setting up this workshop series, summarize our experience, and suggest approaches for optimizing histopathology phenotyping for gene function discovery.
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Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Bult CJ, Eppig JT, Sundberg JP. The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data. Vet Pathol 2011; 49:218-23. [PMID: 21282667 DOI: 10.1177/0300985810395726] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Mouse Tumor Biology Database (MTB) is designed to provide an electronic data storage, search, and analysis system for information on mouse models of human cancer. The MTB includes data on tumor frequency and latency, strain, germ line, and somatic genetics, pathologic notations, and photomicrographs. The MTB collects data from the primary literature, other public databases, and direct submissions from the scientific community. The MTB is a community resource that provides integrated access to mouse tumor data from different scientific research areas and facilitates integration of molecular, genetic, and pathologic data. Current status of MTB, search capabilities, data types, and future enhancements are described in this article.
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Affiliation(s)
- D A Begley
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609-1500, USA
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