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Cheng KC, Burdine RD, Dickinson ME, Ekker SC, Lin AY, Lloyd KCK, Lutz CM, MacRae CA, Morrison JH, O'Connor DH, Postlethwait JH, Rogers CD, Sanchez S, Simpson JH, Talbot WS, Wallace DC, Weimer JM, Bellen HJ. Promoting validation and cross-phylogenetic integration in model organism research. Dis Model Mech 2022; 15:dmm049600. [PMID: 36125045 PMCID: PMC9531892 DOI: 10.1242/dmm.049600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organism-based chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
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Affiliation(s)
- Keith C. Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, Park, PA 16802, USA
| | - Rebecca D. Burdine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77007, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77007, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55906, USA
| | - Alex Y. Lin
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - K. C. Kent Lloyd
- Mouse Biology Program, School of Medicinel, University of California Davis, Davis, CA 95618, USA
- Department of Surgery, School of Medicine, University of California Davis, Davis, CA 95618, USA
| | - Cathleen M. Lutz
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609, USA
| | - Calum A. MacRae
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 360 Longwood Avenue, Boston, MA 02215, USA
| | - John H. Morrison
- California National Primate Research Center, University of California Davis, Davis, CA 95616, USA
- Department of Neurology, University of California Davis, Davis, CA 95616, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University ofWisconsin-Madison, Madison, WI 53711, USA
| | | | - Crystal D. Rogers
- School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA
| | - Julie H. Simpson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93117, USA
| | - William S. Talbot
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Douglas C. Wallace
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jill M. Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute (TCH), Baylor College of Medicine, Houston, TX 77007, USA
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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