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Rogers CD, Amemiya C, Arur S, Babonis L, Barresi M, Bartlett M, Behringer R, Benham-Pyle B, Bergmann D, Blackman B, Brown CT, Browne B, Camacho J, Chabu CY, Chow I, Cleaver O, Cool J, Dennis MY, Dickinson AJ, Di Talia S, Frank M, Gillmor S, Haag ES, Hariharan I, Harland R, Husbands A, Jerome-Majewska L, Koenig K, Labonne C, Layden M, Lowe C, Mani M, Martik M, McKown K, Moens C, Mosimann C, Onyenedum J, Reed R, Rivera A, Rokhsar D, Royer L, Rutaganira F, Shahan R, Sinha N, Swalla B, Van Norman JM, Wagner DE, Wikramanayake A, Zebell S, Brady SM. Pluripotency of a founding field: rebranding developmental biology. Development 2024; 151:dev202342. [PMID: 38345109 PMCID: PMC10986740 DOI: 10.1242/dev.202342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank' of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.
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Affiliation(s)
- Crystal D. Rogers
- Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Chris Amemiya
- University of California, Merced, Department of Molecular and Cell Biology and Quantitative and Systems Biology Program, 5200 N. Lake Road, SE1 262, Merced, CA 95343, USA
| | - Swathi Arur
- The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leslie Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Richard Behringer
- The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Blair Benham-Pyle
- Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dominique Bergmann
- Department of Biology and HHMI, Stanford University, Stanford, CA 94305, USA
| | - Ben Blackman
- University of California, Berkeley, Berkeley CA 94720, USA
| | - C. Titus Brown
- Population Health & Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Bill Browne
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Ida Chow
- Society for Developmental Biology, Rockville, MD 20852, USA
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, UT Southwestern Medical School, Dallas, TX 75390, USA
| | - Jonah Cool
- Chan Zuckerberg Initiative, Redwood City, CA 94063, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, School of Biological Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Margaret Frank
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Stewart Gillmor
- Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato, Guanajuato 36824, Mexico
| | - Eric S. Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Iswar Hariharan
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Richard Harland
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Aman Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Loydie Jerome-Majewska
- Department of Pediatrics, Human Genetics, Anatomy and Cell Biology, McGill University and Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada
| | | | - Carole Labonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Michael Layden
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Chris Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, USA
| | - Madhav Mani
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Megan Martik
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Katelyn McKown
- Department of Biology and Stanford Introductory Studies, Stanford University, Stanford, CA 94305, USA
| | - Cecilia Moens
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Christian Mosimann
- Children's Hospital Colorado, Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 E. 17th Avenue, RC1 South, 12114, Aurora, CO 80045, USA
| | - Joyce Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Robert Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ajna Rivera
- University of the Pacific, Stockton, CA 95211, USA
| | - Dan Rokhsar
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Loic Royer
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Flora Rutaganira
- Departments of Biochemistry and Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Billie Swalla
- Biology Department and Friday Harbor Labs, University of Washington, Seattle, WA 98195, USA
| | - Jaimie M. Van Norman
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Daniel E. Wagner
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, CA 94143, USA
| | | | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Siobhán M. Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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Sun YH, Wu YL, Liao BY. Phenotypic heterogeneity in human genetic diseases: ultrasensitivity-mediated threshold effects as a unifying molecular mechanism. J Biomed Sci 2023; 30:58. [PMID: 37525275 PMCID: PMC10388531 DOI: 10.1186/s12929-023-00959-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Phenotypic heterogeneity is very common in genetic systems and in human diseases and has important consequences for disease diagnosis and treatment. In addition to the many genetic and non-genetic (e.g., epigenetic, environmental) factors reported to account for part of the heterogeneity, we stress the importance of stochastic fluctuation and regulatory network topology in contributing to phenotypic heterogeneity. We argue that a threshold effect is a unifying principle to explain the phenomenon; that ultrasensitivity is the molecular mechanism for this threshold effect; and discuss the three conditions for phenotypic heterogeneity to occur. We suggest that threshold effects occur not only at the cellular level, but also at the organ level. We stress the importance of context-dependence and its relationship to pleiotropy and edgetic mutations. Based on this model, we provide practical strategies to study human genetic diseases. By understanding the network mechanism for ultrasensitivity and identifying the critical factor, we may manipulate the weak spot to gently nudge the system from an ultrasensitive state to a stable non-disease state. Our analysis provides a new insight into the prevention and treatment of genetic diseases.
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Affiliation(s)
- Y Henry Sun
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| | - Yueh-Lin Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wei-Gong Memorial Hospital, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institute, Zhunan, Miaoli, Taiwan
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