1
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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Ardery S, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros MC, Drushal M, Ferris MT, Fry RC, Gaines C, Gu B, Heise MT, Hock P, Hodges RA, Hulgin M, Kafri T, Lynch RM, Magnuson T, Miller DR, Murphy CEY, Nguyen DT, Noll KE, Proulx MK, Sassetti CM, Schoenrock SA, Shaw GD, Simon JM, Smith CM, Styblo M, Tarantino LM, Woo J, Pardo Manuel de Villena F. The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice. G3 (BETHESDA, MD.) 2024; 14:jkae193. [PMID: 39271181 PMCID: PMC11457065 DOI: 10.1093/g3journal/jkae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/18/2024] [Indexed: 09/15/2024]
Abstract
The MiniMUGA genotyping array is a popular tool for genetic quality control of laboratory mice and genotyping samples from most experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve the array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA. Here, we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for classical inbred strains and substrains, and increase the number of constructs reliably detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have updated the layout of the report to simplify the interpretation and completeness of the analysis and added a section summarizing the ideogram in table format. These changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.
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Affiliation(s)
- Matthew W Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John Sebastian Sigmon
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jennifer Brennan
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chidima Ahulamibe
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michelle E Allen
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sam Ardery
- Genetics and Molecular Biology Curriculum, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph Farrington
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dominic Ciavatta
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Marta C Cruz Cisneros
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Genetics and Molecular Biology Curriculum, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Madison Drushal
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christiann Gaines
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bin Gu
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard Austin Hodges
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mia Hulgin
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tal Kafri
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel M Lynch
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Caroline E Y Murphy
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Truong Nguyen
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kelsey E Noll
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Megan K Proulx
- Department of Microbiology, UMass Chan Medical School, Worchester, MA 01655, USA
| | | | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Miroslav Styblo
- Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa M Tarantino
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joyce Woo
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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2
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Lloyd KCK. Commentary: The International Mouse Phenotyping Consortium: high-throughput in vivo functional annotation of the mammalian genome. Mamm Genome 2024:10.1007/s00335-024-10068-x. [PMID: 39254744 DOI: 10.1007/s00335-024-10068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is a worldwide effort producing and phenotyping knockout mouse lines to expose the pathophysiological roles of all genes in human diseases and make mice and data available and accessible to the global research community. It has created new knowledge on the function of thousands of genes for which little to anything was known. This new knowledge has informed the genetic basis of rare diseases, posited gene product influences on common diseases, influenced research on targeted therapies, revealed functional pleiotropy, essentiality, and sexual dimorphism, and many more insights into the role of genes in health and disease. Its scientific contributions have been many and widespread, however there remain thousands of "dark" genes yet to be illuminated. Nearing the end of its current funding cycle, IMPC is at a crossroads. The vision forward is clear, the path to proceed less so.
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Affiliation(s)
- K C Kent Lloyd
- Department of Surgery, School of Medicine, University of California, Davis, California, USA.
- Mouse Biology Program, University of California, Davis, California, USA.
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3
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King A, Reichl PI, Metson JS, Parker R, Munro D, Oliveira C, Sommerova L, Becker JR, Biggs D, Preece C, Davies B, Chapman JR. Shieldin and CST co-orchestrate DNA polymerase-dependent tailed-end joining reactions independently of 53BP1-governed repair pathway choice. Nat Struct Mol Biol 2024:10.1038/s41594-024-01381-9. [PMID: 39227718 DOI: 10.1038/s41594-024-01381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 08/01/2024] [Indexed: 09/05/2024]
Abstract
Tumor suppressor p53-binding protein 1 (53BP1) regulates DNA end joining in lymphocytes, diversifying immune antigen receptors. This involves nucleosome-bound 53BP1 at DNA double-stranded breaks (DSBs) recruiting Rap1-interacting factor 1 homolog (RIF1) and shieldin, a poorly understood DNA-binding complex. The 53BP1-RIF1-shieldin axis is pathological in BRCA1-mutated cancers, blocking homologous recombination (HR) and driving illegitimate nonhomologous end joining (NHEJ). However, how this axis regulates DNA end joining and HR suppression remains unresolved. We investigated shieldin and its interplay with the Ctc1-Stn1-Ten1 (CST) complex, which was recently implicated downstream of 53BP1. Immunophenotypically, mice lacking shieldin or CST are equivalent, with class-switch recombination coreliant on both complexes. Ataxia-telangiectasia mutated kinase-dependent DNA damage signaling underpins this cooperation, inducing physical interactions between these complexes that reveal shieldin as a DSB-responsive CST adaptor. Furthermore, DNA polymerase ζ functions downstream of shieldin, establishing DNA fill-in synthesis as the physiological function of shieldin-CST. Lastly, we demonstrate that 53BP1 suppresses HR and promotes NHEJ in BRCA1-deficient mice and cells independently of shieldin. These findings showcase the versatility of the 53BP1 pathway, achieved through the collaboration of chromatin-bound 53BP1 complexes and DNA end-processing effector proteins.
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Affiliation(s)
- Ashleigh King
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Pia I Reichl
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jean S Metson
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniella Munro
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Catarina Oliveira
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucia Sommerova
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jordan R Becker
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Preece
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - J Ross Chapman
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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4
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Vidović D, Waller A, Holmes J, Sklar LA, Schürer SC. Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. Drug Discov Today 2024; 29:103953. [PMID: 38508231 PMCID: PMC11335350 DOI: 10.1016/j.drudis.2024.103953] [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] [Received: 10/15/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
The Illuminating the Druggable Genome (IDG) consortium generated reagents, biological model systems, data, informatic databases, and computational tools. The Resource Dissemination and Outreach Center (RDOC) played a central administrative role, organized internal meetings, fostered collaboration, and coordinated consortium-wide efforts. The RDOC developed and deployed a Resource Management System (RMS) to enable efficient workflows for collecting, accessing, validating, registering, and publishing resource metadata. IDG policies for repositories and standardized representations of resources were established, adopting the FAIR (findable, accessible, interoperable, reusable) principles. The RDOC also developed metrics of IDG impact. Outreach initiatives included digital content, the Protein Illumination Timeline (representing milestones in generating data and reagents), the Target Watch publication series, the e-IDG Symposium series, and leveraging social media platforms.
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Affiliation(s)
- Dušica Vidović
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anna Waller
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Larry A Sklar
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Autophagy, Inflammation, & Metabolism (AIM) Center, University of New Mexico, Albuquerque, NM, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA; Frost Institute for Data Science & Computing, University of Miami, Miami, FL, USA.
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5
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Knuth MM, Campos CV, Smith K, Hutchins EK, Lewis S, York M, Coghill LM, Franklin C, MacFarlane A, Ericsson AC, Magnuson T, Ideraabdullah F. Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587032. [PMID: 38585881 PMCID: PMC10996631 DOI: 10.1101/2024.03.28.587032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Standard chow diet contributes to reproducibility in animal model experiments since chows differ in nutrient composition, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here, we measured the impact of diet (5V5M, 5V0G, 2920X, and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE), and developmental exposure (DE)) on growth & development, metabolic health indicators, and gut bacterial microbiota profiles across genetically identical C57BL6/J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on measured outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight, and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. Diet-induced beta diversity profiles were sex-dependent for LE mice. Compared to AE, LE drove 9X more diet-driven differentially abundant genera, majority of which were the result of inverse effects of 2920X and 5058. Our findings demonstrate that lifetime exposure to different chow diets has the greatest impact on reproducibility of experimental measures that are common components of preclinical mouse model studies. Importantly, weaning DE mice onto a uniform diet is likely an effective way to reduce unwanted phenotypic variability among experimental models.
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Affiliation(s)
- Megan M. Knuth
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Vieira Campos
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Translational Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-881, Brazil
| | - Kirsten Smith
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Postbaccalaureate Research Education Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth K. Hutchins
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shantae Lewis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Postbaccalaureate Research Education Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mary York
- University of Missouri (MU) Bioinformatics and Analytics Core, Bond Life Sciences Center, Columbia, MO 65201, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Lyndon M. Coghill
- University of Missouri (MU) Bioinformatics and Analytics Core, Bond Life Sciences Center, Columbia, MO 65201, USA
- Department of Veterinary Pathobiology, MU, Columbia, MO 65201, USA
| | - Craig Franklin
- Department of Veterinary Pathobiology, MU, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center at the University of Missouri (MU MMRRC), Columbia, MO 65201, USA
- MU Metagenomics Center (MUMC), University of Missouri, Columbia, MO 65201, USA
| | - Amanda MacFarlane
- Texas A&M Agriculture, Food, and Nutrition Evidence Center, Fort Worth, TX 76102, USA
- Department of Nutrition, Texas A&M University, College Station TX 77843, USA
| | - Aaron C. Ericsson
- Department of Veterinary Pathobiology, MU, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center at the University of Missouri (MU MMRRC), Columbia, MO 65201, USA
- MU Metagenomics Center (MUMC), University of Missouri, Columbia, MO 65201, USA
| | - Terry Magnuson
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Mutant Mouse Resource and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Folami Ideraabdullah
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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6
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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros M, Drushal M, Ferris MT, Fry R, Gaines C, Gu B, Heise MT, Hodges RA, Kafri T, Lynch R, Magnuson T, Miller D, Murphy CEY, Nguyen DT, Noll KE, Proulx M, Sassetti C, Shaw GD, Simon JM, Smith C, Styblo M, Tarantino L, Woo J, Pardo Manuel de Villena F. The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582794. [PMID: 38464063 PMCID: PMC10925293 DOI: 10.1101/2024.02.29.582794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.
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7
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Parada-Parra OJ, Hernández-Cruz A. Effects of reversible SERCA inhibition on catecholamine exocytosis and intracellular [Ca 2+] signaling in chromaffin cells from normotensive Wistar Kyoto rats and spontaneously hypertensive rats. Pflugers Arch 2024; 476:123-144. [PMID: 37775569 PMCID: PMC10758371 DOI: 10.1007/s00424-023-02859-z] [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] [Received: 03/17/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]
Abstract
Intracellular Ca2+ ([Ca2+]i) signaling and catecholamine (CA) exocytosis from adrenal chromaffin cells (CCs) differ between mammalian species. These differences partly result from the different contributions of Ca2+-induced Ca2+-release (CICR) from internal stores, which boosts intracellular Ca2+ signals. Transient inhibition of the sarcoendoplasmic reticulum (SERCA) Ca2+ pump with cyclopiazonic acid (CPA) reduces CICR. Recently, Martínez-Ramírez et al. found that CPA had contrasting effects on catecholamine secretion and intracellular Ca2+ signals in mouse and bovine CCs, where it enhanced and inhibited exocytosis, respectively. After CPA withdrawal, exocytosis diminished in mouse CCs and increased in bovine CCs. These differences can be explained if mouse CCs have weak CICR and strong Ca2+ uptake, and the reverse is true for bovine CCs. Surprisingly, CPA slightly reduced the amplitude of Ca2+ signals in both mouse and bovine CCs. Here we examined the effects of CPA on stimulated CA exocytosis and Ca2+ signaling in rat CCs and investigated if it alters differently the responses of CCs from normotensive (WKY) or hypertensive (SHR) rats, which differ in the gain of CICR. Our results demonstrate that CPA application strongly inhibits voltage-gated exocytosis and Ca2+ transients in rat CCs, regardless of strain (SHR or WKY). Thus, despite the greater phylogenetic distance from the most recent common ancestors, suppression of endoplasmic reticulum (ER) Ca2+ uptake through CPA inhibits the CA secretion in rat CCs more similarly to bovine than mouse CCs, unveiling divergent evolutionary relationships in the mechanism of CA exocytosis of CCs between rodents. Agents that inhibit the SERCA pump, such as CPA, suppress catecholamine secretion equally well in WKY and SHR CCs and are not potential therapeutic agents for hypertension. Rat CCs display Ca2+ signals of varying widths. Some even show early and late Ca2+ components. Narrowing the Ca2+ transients by CPA and ryanodine suggests that the late component is mainly due to CICR. Simultaneous recordings of Ca2+ signaling and amperometry in CCs revealed the existence of a robust and predictable correlation between the kinetics of the whole-cell intracellular Ca2+ signal and the rate of exocytosis at the single-cell level.
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Affiliation(s)
- Oscar J Parada-Parra
- Departamento Neurociencia Cognitiva, and Laboratorio Nacional de Canalopatías, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito de La Investigación Científica S/N, Ciudad Universitaria, Mexico City CDMX, C.P. 04510, México
| | - Arturo Hernández-Cruz
- Departamento Neurociencia Cognitiva, and Laboratorio Nacional de Canalopatías, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito de La Investigación Científica S/N, Ciudad Universitaria, Mexico City CDMX, C.P. 04510, México.
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8
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King A, Reichl P, Metson JS, Parker R, Munro D, Oliveira C, Becker JR, Biggs D, Preece C, Davies B, Chapman JR. Shieldin and CST co-orchestrate DNA polymerase-dependent tailed-end joining reactions independently of 53BP1-governed repair pathway choice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572534. [PMID: 38187711 PMCID: PMC10769304 DOI: 10.1101/2023.12.20.572534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
53BP1 regulates DNA end-joining in lymphocytes, diversifying immune antigen receptors. This involves nucleosome-bound 53BP1 at DNA double-stranded breaks (DSBs) recruiting RIF1 and shieldin, a poorly understood DNA-binding complex. The 53BP1-RIF1-shieldin axis is pathological in BRCA1-mutated cancers, blocking homologous recombination (HR) and driving illegitimate non-homologous end-joining (NHEJ). However, how this axis regulates DNA end-joining and HR suppression remains unresolved. We investigated shieldin and its interplay with CST, a complex recently implicated in 53BP1-dependent activities. Immunophenotypically, mice lacking shieldin or CST are equivalent, with class-switch recombination co-reliant on both complexes. ATM-dependent DNA damage signalling underpins this cooperation, inducing physical interactions between these complexes that reveal shieldin as a DSB-responsive CST adaptor. Furthermore, DNA polymerase ζ functions downstream of shieldin, establishing DNA fill-in synthesis as the physiological function of shieldin-CST. Lastly, 53BP1 suppresses HR and promotes NHEJ in BRCA1-deficient mice and cells independently of shieldin. These findings showcase the resilience of the 53BP1 pathway, achieved through the collaboration of chromatin-bound 53BP1 complexes and DNA end-processing effector proteins.
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Affiliation(s)
- Ashleigh King
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Pia Reichl
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Jean S. Metson
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Robert Parker
- Centre for ImmunoOncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniella Munro
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Catarina Oliveira
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Jordan R. Becker
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Preece
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, 1 Midland Rd, London, UK
| | - J. Ross Chapman
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
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9
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Bustin KA, Shishikura K, Chen I, Lin Z, McKnight N, Chang Y, Wang X, Li JJ, Arellano E, Pei L, Morton PD, Gregus AM, Buczynski MW, Matthews ML. Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception. Mol Cell Neurosci 2023; 125:103842. [PMID: 36924917 PMCID: PMC10247460 DOI: 10.1016/j.mcn.2023.103842] [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] [Received: 01/16/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Chemical platforms that facilitate both the identification and elucidation of new areas for therapeutic development are necessary but lacking. Activity-based protein profiling (ABPP) leverages active site-directed chemical probes as target discovery tools that resolve activity from expression and immediately marry the targets identified with lead compounds for drug design. However, this approach has traditionally focused on predictable and intrinsic enzyme functionality. Here, we applied our activity-based proteomics discovery platform to map non-encoded and post-translationally acquired enzyme functionalities (e.g. cofactors) in vivo using chemical probes that exploit the nucleophilic hydrazine pharmacophores found in a classic antidepressant drug (e.g. phenelzine, Nardil®). We show the probes are in vivo active and can map proteome-wide tissue-specific target engagement of the drug. In addition to engaging targets (flavoenzymes monoamine oxidase A/B) that are associated with the known therapeutic mechanism as well as several other members of the flavoenzyme family, the probes captured the previously discovered N-terminal glyoxylyl (Glox) group of Secernin-3 (SCRN3) in vivo through a divergent mechanism, indicating this functional feature has biochemical activity in the brain. SCRN3 protein is ubiquitously expressed in the brain, yet gene expression is regulated by inflammatory stimuli. In an inflammatory pain mouse model, behavioral assessment of nociception showed Scrn3 male knockout mice selectively exhibited impaired thermal nociceptive sensitivity. Our study provides a guided workflow to entangle molecular (off)targets and pharmacological mechanisms for therapeutic development.
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Affiliation(s)
- Katelyn A Bustin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyosuke Shishikura
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Irene Chen
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA
| | - Zongtao Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nate McKnight
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxuan Chang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xie Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jing Jing Li
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eric Arellano
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Paul D Morton
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic and State University, Blacksburg, VA, 24060, USA
| | - Ann M Gregus
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA.
| | - Matthew W Buczynski
- School of Neuroscience, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA.
| | - Megan L Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182874. [PMID: 37274208 PMCID: PMC10234152 DOI: 10.3389/fnins.2023.1182874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Protein synthesis is a fundamental process that underpins almost every aspect of cellular functioning. Intriguingly, despite their common function, recessive mutations in aminoacyl-tRNA synthetases (ARSs), the family of enzymes that pair tRNA molecules with amino acids prior to translation on the ribosome, cause a diverse range of multi-system disorders that affect specific groups of tissues. Neurological development is impaired in most ARS-associated disorders. In addition to central nervous system defects, diseases caused by recessive mutations in cytosolic ARSs commonly affect the liver and lungs. Patients with biallelic mutations in mitochondrial ARSs often present with encephalopathies, with variable involvement of peripheral systems. Many of these disorders cause severe disability, and as understanding of their pathogenesis is currently limited, there are no effective treatments available. To address this, accurate in vivo models for most of the recessive ARS diseases are urgently needed. Here, we discuss approaches that have been taken to model recessive ARS diseases in vivo, highlighting some of the challenges that have arisen in this process, as well as key results obtained from these models. Further development and refinement of animal models is essential to facilitate a better understanding of the pathophysiology underlying recessive ARS diseases, and ultimately to enable development and testing of effective therapies.
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Affiliation(s)
- Elizabeth Kalotay
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gary D. Housley
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
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11
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Bustin KA, Shishikura K, Chen I, Lin Z, McKnight N, Chang Y, Wang X, Li JJ, Arellano E, Pei L, Morton PD, Gregus AM, Buczynski MW, Matthews ML. Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526866. [PMID: 36778412 PMCID: PMC9915563 DOI: 10.1101/2023.02.02.526866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemical platforms that facilitate both the identification and elucidation of new areas for therapeutic development are necessary but lacking. Activity-based protein profiling (ABPP) leverages active site-directed chemical probes as target discovery tools that resolve activity from expression and immediately marry the targets identified with lead compounds for drug design. However, this approach has traditionally focused on predictable and intrinsic enzyme functionality. Here, we applied our activity-based proteomics discovery platform to map non-encoded and post-translationally acquired enzyme functionalities (e.g. cofactors) in vivo using chemical probes that exploit the nucleophilic hydrazine pharmacophores found in a classic antidepressant drug (e.g. phenelzine, Nardil ® ). We show the probes are in vivo active and can map proteome-wide tissue-specific target engagement of the drug. In addition to engaging targets (flavoenzymes monoamine oxidase A/B) that are associated with the known therapeutic mechanism as well as several other members of the flavoenzyme family, the probes captured the previously discovered N -terminal glyoxylyl (Glox) group of Secernin-3 (SCRN3) in vivo through a divergent mechanism, indicating this functional feature has biochemical activity in the brain. SCRN3 protein is ubiquitously expressed in the brain, yet gene expression is regulated by inflammatory stimuli. In an inflammatory pain mouse model, behavioral assessment of nociception showed Scrn3 male knockout mice selectively exhibited impaired thermal nociceptive sensitivity. Our study provides a guided workflow to entangle molecular (off)targets and pharmacological mechanisms for therapeutic development.
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12
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Expression of LIM domain-binding 3 (LDB3), a striated muscle Z-band alternatively spliced PDZ-motif protein in the nervous system. Sci Rep 2023; 13:270. [PMID: 36609526 PMCID: PMC9822979 DOI: 10.1038/s41598-023-27531-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
LIM domain-binding 3 (LDB3) is a member of the Enigma family of PDZ-LIM proteins. LDB3 has been reported as a striated muscle-specific Z-band alternatively spliced protein that plays an important role in mechanosensory actin cytoskeleton remodeling. This study shows that LDB3 is broadly expressed in the central and peripheral nervous system of human and mouse. LDB3 is predominantly expressed in the adult stages compared to early development and at a significantly higher level in the spinal cord than in the brain. As in skeletal muscle and heart, LDB3 is extensively alternatively spliced in the neurons. Three novel splice isoforms were identified suggesting splicing-dependent regulation of LDB3 expression in the nervous system. Expression of LDB3 in the motor cortex, cerebellum, spinal motor neuron, peripheral nerve, and neuromuscular junction in addition to skeletal muscle indicates important roles for this PDZ-LIM family protein in motor planning and execution. Moreover, expression in the hippocampal neurons suggests roles for LDB3 in learning and memory. LDB3 interactors filamin C and myotilin are also expressed in the spinal motor neuron, nerve, and neuromuscular junction, thereby providing the basis for neurogenic manifestations in myopathies associated with mutations in these so-called muscle proteins.
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13
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Guo J, Wang S, Gao Q. Can next-generation humanized mice that reconstituted with both functional human immune system and hepatocytes model the progression of viral hepatitis to hepatocarcinogenesis? Front Med (Lausanne) 2022; 9:1002260. [PMID: 36213658 PMCID: PMC9537463 DOI: 10.3389/fmed.2022.1002260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Hepatitis B virus (HBV) and Hepatitis C virus (HCV) chronic infections cause liver immunopathological diseases such as hepatitis, fibrosis, cirrhosis, and hepatocellular carcinomas, which are difficult to treat and continue to be major health problems globally. Due to the species-specific hepato-tropism of HBV and HCV, conventional rodent models are limited in their utility for studying the infection and associated liver immunopathogenesis. Humanized mice reconstituted with both functional human immune system and hepatocytes (HIS-HuHEP mice) have been extremely instrumental for in vivo studies of HBV or HCV infection and human-specific aspects of the progression of liver immunopathogenesis. However, none of the current HIS-HuHEP mice can model the progression of viral hepatitis to hepatocarcinogenesis which may be a notorious result of HBV or HCV chronic infection in patients, suggesting that they were functionally compromised and that there is still significant space to improve and establish next-generation of HIS-HuHEP mice with more sophisticated functions. In this review, we first summarize the principal requirements to establish HIS-HuHEP mice. We then discuss the respective protocols for current HIS-HuHEP mice and their applications, as well as their advantages and disadvantages. We also raise perspectives for further improving and establishing next-generation HIS-HuHEP mice.
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Affiliation(s)
- Jinglong Guo
- Department of Cardiovascular Disease, The First Hospital of Jilin University, Changchun, China
| | - Siyue Wang
- Graduate Program in Immunology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, United States
| | - Qi Gao
- Department of Cardiovascular Disease, The First Hospital of Jilin University, Changchun, China
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14
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Ringwald M, Richardson JE, Baldarelli RM, Blake JA, Kadin JA, Smith C, Bult CJ. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Mamm Genome 2021; 33:4-18. [PMID: 34698891 PMCID: PMC8913530 DOI: 10.1007/s00335-021-09921-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022]
Abstract
The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org .
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