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Wimer LA, Davis-Castillo A, Galkina S, Ciotlos S, Patterson C, Prado L, Munoz MC, Martin N, Epstein S, Schaum N, Melov S. Characterizing phenotypic data of Peromyscus leucopus compared to C57BL/6J Mus musculus and diversity outbred (DO) Mus musculus. GeroScience 2024; 46:4647-4656. [PMID: 38871964 PMCID: PMC11335981 DOI: 10.1007/s11357-024-01175-3] [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: 12/04/2023] [Accepted: 04/24/2024] [Indexed: 06/15/2024] Open
Abstract
Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
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Affiliation(s)
- Lauren A Wimer
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Asia Davis-Castillo
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Sofiya Galkina
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Serban Ciotlos
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Cavan Patterson
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Leandro Prado
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Maria Castro Munoz
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Nicolas Martin
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | - Sharon Epstein
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA
| | | | - Simon Melov
- Buck Institute for Research On Aging, 8001 Redwood Blvd, Novato, CA, 94949, USA.
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2
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Arlt E, Kindermann A, Fritsche AK, Navarrete Santos A, Kielstein H, Bazwinsky-Wutschke I. A Flow Cytometry-Based Examination of the Mouse White Blood Cell Differential in the Context of Age and Sex. Cells 2024; 13:1583. [PMID: 39329764 PMCID: PMC11430320 DOI: 10.3390/cells13181583] [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: 07/31/2024] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Analysis of the white blood cell differential as part of a flow cytometry-based approach is a common routine diagnostic tool used in clinics and research. For human blood, the methodological approach, suitable markers, and gating strategies are well-established. However, there is a lack of information regarding the mouse blood count. In this article, we deliver a fast and easy protocol for reprocessing mouse blood for the purpose of flow cytometric analysis, as well as suitable markers and gating strategies. We also present two possible applications: for the analysis of the whole blood count, with blood from a cardiac puncture, and for the analysis of a certain leukocyte subset at multiple time points in the framework of a mouse experiment, using blood from the facial vein. Additionally, we provide orientation values by applying the method to 3-month-old and 24-month-old male and female C57BL/6J mice. Our analyses demonstrate differences in the leukocyte fractions depending on age and sex. We discuss the influencing factors and limitations that can affect the results and that, therefore, need to be considered when applying this method. The present study fills the gap in the knowledge related to the rare information on flow cytometric analysis of mouse blood and, thus, lays the foundation for further investigations in this area.
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Affiliation(s)
- Elise Arlt
- Institute of Anatomy and Cell Biology, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany; (A.K.); (A.-K.F.); (H.K.); (I.B.-W.)
| | - Andrea Kindermann
- Institute of Anatomy and Cell Biology, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany; (A.K.); (A.-K.F.); (H.K.); (I.B.-W.)
| | - Anne-Kristin Fritsche
- Institute of Anatomy and Cell Biology, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany; (A.K.); (A.-K.F.); (H.K.); (I.B.-W.)
- Institute of Anatomy, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Alexander Navarrete Santos
- Core Facility Flow Cytometry, Center for Basic Medical Research, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany;
| | - Heike Kielstein
- Institute of Anatomy and Cell Biology, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany; (A.K.); (A.-K.F.); (H.K.); (I.B.-W.)
| | - Ivonne Bazwinsky-Wutschke
- Institute of Anatomy and Cell Biology, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06108 Halle (Saale), Germany; (A.K.); (A.-K.F.); (H.K.); (I.B.-W.)
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3
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Bertorello S, Cei F, Fink D, Niccolai E, Amedei A. The Future Exploring of Gut Microbiome-Immunity Interactions: From In Vivo/Vitro Models to In Silico Innovations. Microorganisms 2024; 12:1828. [PMID: 39338502 PMCID: PMC11434319 DOI: 10.3390/microorganisms12091828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/30/2024] Open
Abstract
Investigating the complex interactions between microbiota and immunity is crucial for a fruitful understanding progress of human health and disease. This review assesses animal models, next-generation in vitro models, and in silico approaches that are used to decipher the microbiome-immunity axis, evaluating their strengths and limitations. While animal models provide a comprehensive biological context, they also raise ethical and practical concerns. Conversely, modern in vitro models reduce animal involvement but require specific costs and materials. When considering the environmental impact of these models, in silico approaches emerge as promising for resource reduction, but they require robust experimental validation and ongoing refinement. Their potential is significant, paving the way for a more sustainable and ethical future in microbiome-immunity research.
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Affiliation(s)
- Sara Bertorello
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy; (S.B.); (F.C.); (D.F.); (A.A.)
| | - Francesco Cei
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy; (S.B.); (F.C.); (D.F.); (A.A.)
| | - Dorian Fink
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy; (S.B.); (F.C.); (D.F.); (A.A.)
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy; (S.B.); (F.C.); (D.F.); (A.A.)
- Laboratorio Congiunto MIA-LAB (Microbiome-Immunity Axis Research for a Circular Health), University of Florence, 50134 Florence, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50139 Florence, Italy; (S.B.); (F.C.); (D.F.); (A.A.)
- Laboratorio Congiunto MIA-LAB (Microbiome-Immunity Axis Research for a Circular Health), University of Florence, 50134 Florence, Italy
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4
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Gabriel de Almeida G, Bolin AP, Batistuzzo A, Fonseca TL, Ribeiro MO, Bianco AC. Genetic Background Strongly Influences the Impact of Carrying the Thr92Ala-DIO2 Polymorphism in the Male Mouse. Endocrinology 2024; 165:bqae064. [PMID: 38836615 PMCID: PMC11181002 DOI: 10.1210/endocr/bqae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
About half of the world population carries at least one allele of the Ala92-DIO2, which slows down the activity of the type 2 deiodinase (D2), the enzyme that activates T4 to T3. Carrying the Ala92-DIO2 allele has been associated with increased body mass index and insulin resistance, but this has not been reproduced in all populations. To test if the genetic background affects the impact of this polymorphism, here we studied the genetically distant C57Bl/6J (B6) and FVB/N (FVB) mice carrying the Ala92-Dio2 allele as compared to control mice carrying the Thr92-Dio2 allele. Whereas B6-Ala92-Dio2 and B6-Thr92-Dio2 mice-fed chow or high-fat diet-behaved metabolically similar in studies using indirect calorimetry, glucose- and insulin tolerance tests, and measuring white adipose tissue (WAT) weight and liver steatosis, major differences were observed between FVB-Ala92-Dio2 and FVB-Thr92-Dio2 mice: carrying the Ala92-Dio2 allele (on a chow diet) resulted in hypercholesterolemia, smaller WAT pads, hepatomegaly, steatosis, and transcriptome changes in the interscapular brown adipose tissue (iBAT) typical of ER stress and apoptosis. Acclimatization at thermoneutrality (30 °C) eliminated most of the metabolic phenotype, indicating that impaired adaptive (BAT) thermogenesis can be involved. In conclusion, the metabolic impact of carrying the Ala92-Dio2 allele depends greatly on the genetic background of the mouse, varying from no phenotype in B6 mice to a major phenotype in FVB mice. These results will help the planning of future clinical trials studying the Thr92Ala-DIO2 polymorphism and may explain why some clinical studies performed in different populations across the globe have obtained inconsistent results.
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Affiliation(s)
- Guilherme Gabriel de Almeida
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Anaysa P Bolin
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo 05508, Brazil
| | - Alice Batistuzzo
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tatiana L Fonseca
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Miriam O Ribeiro
- Human Developmental Sciences Graduate Program, Center for Biological and Health Sciences, Presbyterian Mackenzie University, São Paulo, SP 01302, Brazil
| | - Antonio C Bianco
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, University of Chicago Medical Center, Chicago, IL 60637, USA
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5
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Šimon M, Mikec Š, Atanur SS, Konc J, Morton NM, Horvat S, Kunej T. Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes. Genes Genomics 2024; 46:557-575. [PMID: 38483771 PMCID: PMC11024027 DOI: 10.1007/s13258-024-01507-9] [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: 05/04/2023] [Accepted: 02/25/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Analysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts. OBJECTIVE To analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations. METHODS Genetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database. RESULTS WGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536. CONCLUSION WGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity.
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Affiliation(s)
- Martin Šimon
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
| | - Špela Mikec
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Santosh S Atanur
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, 1000, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Simon Horvat
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
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6
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Castaño-González K, Köppl C, Pyott SJ. The crucial role of diverse animal models to investigate cochlear aging and hearing loss. Hear Res 2024; 445:108989. [PMID: 38518394 DOI: 10.1016/j.heares.2024.108989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024]
Abstract
Age-related hearing loss affects a large and growing segment of the population, with profound impacts on quality of life. Age-related pathology of the cochlea-the mammalian hearing organ-underlies age-related hearing loss. Because investigating age-related changes in the cochlea in humans is challenging and often impossible, animal models are indispensable to investigate these mechanisms as well as the complex consequences of age-related hearing loss on the brain and behavior. In this review, we advocate for a comparative and interdisciplinary approach while also addressing the challenges of comparing age-related hearing loss across species with varying lifespans. We describe the experimental advantages and limitations as well as areas for future research in well-established models of age-related hearing loss, including mice, rats, gerbils, chinchillas, and birds. We also indicate the need to expand characterization of age-related hearing loss in other established animal models, especially guinea pigs, cats, and non-human primates, in which auditory function is well characterized but age-related cochlear pathology is understudied. Finally, we highlight the potential of emerging animal models for advancing our understanding of age-related hearing loss, including deer mice, with their notably extended lifespans and preserved hearing, naked mole rats, with their exceptional longevity and extensive vocal communications, as well as zebrafish, which offer genetic tractability and suitability for drug screening. Ultimately, a comparative and interdisciplinary approach in auditory research, combining insights from various animal models with human studies, is key to robust and reliable research outcomes that better advance our understanding and treatment of age-related hearing loss.
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Affiliation(s)
- Karen Castaño-González
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Groningen; The Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands
| | - Christine Köppl
- Cluster of Excellence "Hearing4All", Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky Universität; Research Center Neurosensory Science, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Sonja J Pyott
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Groningen; The Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands.
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7
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Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res 2024; 34:145-159. [PMID: 38290977 PMCID: PMC10903950 DOI: 10.1101/gr.278157.123] [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] [Received: 08/08/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Hundreds of inbred mouse strains and intercross populations have been used to characterize the function of genetic variants that contribute to disease. Thousands of disease-relevant traits have been characterized in mice and made publicly available. New strains and populations including consomics, the collaborative cross, expanded BXD, and inbred wild-derived strains add to existing complex disease mouse models, mapping populations, and sensitized backgrounds for engineered mutations. The genome sequences of inbred strains, along with dense genotypes from others, enable integrated analysis of trait-variant associations across populations, but these analyses are hampered by the sparsity of genotypes available. Moreover, the data are not readily interoperable with other resources. To address these limitations, we created a uniformly dense variant resource by harmonizing multiple data sets. Missing genotypes were imputed using the Viterbi algorithm with a data-driven technique that incorporates local phylogenetic information, an approach that is extendable to other model organisms. The result is a web- and programmatically accessible data service called GenomeMUSter, comprising single-nucleotide variants covering 657 strains at 106.8 million segregating sites. Interoperation with phenotype databases, analytic tools, and other resources enable a wealth of applications, including multitrait, multipopulation meta-analysis. We show this in cross-species comparisons of type 2 diabetes and substance use disorder meta-analyses, leveraging mouse data to characterize the likely role of human variant effects in disease. Other applications include refinement of mapped loci and prioritization of strain backgrounds for disease modeling to further unlock extant mouse diversity for genetic and genomic studies in health and disease.
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Affiliation(s)
- Robyn L Ball
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA;
| | - Molly A Bogue
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - David G Ashbrook
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | | | | | - Alexander S Hatoum
- Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Artificial Intelligence and the Internet of Things Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Matthew J Kim
- University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hao He
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Jake Emerson
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | | | | | | | | | - Lu Lu
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - John Bluis
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Sejal Desai
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Robert W Williams
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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8
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Hullahalli K, Dailey KG, Hasegawa Y, Torres E, Suzuki M, Zhang H, Threadgill DW, Navarro VM, Waldor MK. Genetic and immune determinants of E. coli liver abscess formation. Proc Natl Acad Sci U S A 2023; 120:e2310053120. [PMID: 38096412 PMCID: PMC10743367 DOI: 10.1073/pnas.2310053120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Systemic infections can yield distinct outcomes in different tissues. In mice, intravenous inoculation of Escherichia coli leads to bacterial replication within liver abscesses, while other organs such as the spleen clear the pathogen. Abscesses are macroscopic necrotic regions that comprise the vast majority of the bacterial burden in the animal, yet little is known about the processes underlying their formation. Here, we characterize E. coli liver abscesses and identify host determinants of abscess susceptibility. Spatial transcriptomics revealed that liver abscesses are associated with heterogenous immune cell clusters comprised of macrophages, neutrophils, dendritic cells, innate lymphoid cells, and T-cells that surround necrotic regions of the liver. Abscess susceptibility is heightened in the C57BL lineage, particularly in C57BL/6N females. Backcross analyses demonstrated that abscess susceptibility is a polygenic trait inherited in a sex-dependent manner without direct linkage to sex chromosomes. As early as 1 d post infection, the magnitude of E. coli replication in the liver distinguishes abscess-susceptible and abscess-resistant strains of mice, suggesting that the immune pathways that regulate abscess formation are induced within hours. We characterized the early hepatic response with single-cell RNA sequencing and found that mice with reduced activation of early inflammatory responses, such as those lacking the LPS receptor TLR4 (Toll-like receptor 4), are resistant to abscess formation. Experiments with barcoded E. coli revealed that TLR4 mediates a tradeoff between abscess formation and bacterial clearance. Together, our findings define hallmarks of E. coli liver abscess formation and suggest that hyperactivation of the hepatic innate immune response drives liver abscess susceptibility.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Yuko Hasegawa
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Encarnacion Torres
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Masataka Suzuki
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Hailong Zhang
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - David W. Threadgill
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX76549
- Department of Nutrition, Texas A&M University, College Station, TX76549
| | - Victor M. Navarro
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
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9
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Zushin PJH, Mukherjee S, Wu JC. FDA Modernization Act 2.0: transitioning beyond animal models with human cells, organoids, and AI/ML-based approaches. J Clin Invest 2023; 133:e175824. [PMID: 37909337 PMCID: PMC10617761 DOI: 10.1172/jci175824] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Affiliation(s)
- Peter-James H. Zushin
- Stanford Cardiovascular Institute and
- Department of Medicine (Division of Cardiology), Stanford University, Stanford, California, USA
| | | | - Joseph C. Wu
- Stanford Cardiovascular Institute and
- Department of Medicine (Division of Cardiology), Stanford University, Stanford, California, USA
- Greenstone Biosciences, Palo Alto, California, USA
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10
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Emfinger CH, Clark LE, Yandell B, Schueler KL, Simonett SP, Stapleton DS, Mitok KA, Merrins MJ, Keller MP, Attie AD. Novel regulators of islet function identified from genetic variation in mouse islet Ca 2+ oscillations. eLife 2023; 12:RP88189. [PMID: 37787501 PMCID: PMC10547476 DOI: 10.7554/elife.88189] [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: 10/04/2023] Open
Abstract
Insufficient insulin secretion to meet metabolic demand results in diabetes. The intracellular flux of Ca2+ into β-cells triggers insulin release. Since genetics strongly influences variation in islet secretory responses, we surveyed islet Ca2+ dynamics in eight genetically diverse mouse strains. We found high strain variation in response to four conditions: (1) 8 mM glucose; (2) 8 mM glucose plus amino acids; (3) 8 mM glucose, amino acids, plus 10 nM glucose-dependent insulinotropic polypeptide (GIP); and (4) 2 mM glucose. These stimuli interrogate β-cell function, α- to β-cell signaling, and incretin responses. We then correlated components of the Ca2+ waveforms to islet protein abundances in the same strains used for the Ca2+ measurements. To focus on proteins relevant to human islet function, we identified human orthologues of correlated mouse proteins that are proximal to glycemic-associated single-nucleotide polymorphisms in human genome-wide association studies. Several orthologues have previously been shown to regulate insulin secretion (e.g. ABCC8, PCSK1, and GCK), supporting our mouse-to-human integration as a discovery platform. By integrating these data, we nominate novel regulators of islet Ca2+ oscillations and insulin secretion with potential relevance for human islet function. We also provide a resource for identifying appropriate mouse strains in which to study these regulators.
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Affiliation(s)
| | - Lauren E Clark
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Brian Yandell
- Department of Statistics, University of Wisconsin-MadisonMadisonUnited States
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Shane P Simonett
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Donnie S Stapleton
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Kelly A Mitok
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Matthew J Merrins
- Department of Medicine, Division of Endocrinology, University of Wisconsin-MadisonMadisonUnited States
- William S. Middleton Memorial Veterans HospitalMadisonUnited States
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine, Division of Endocrinology, University of Wisconsin-MadisonMadisonUnited States
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
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11
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Josefson CC, Hood WR. Understanding Patterns of Life History Trait Covariation in an Untapped Resource, the Lab Mouse. Physiol Biochem Zool 2023; 96:321-331. [PMID: 37713715 DOI: 10.1086/725435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
AbstractThrough artificial selection and inbreeding, strains of laboratory mice have been developed that vary in the expression of a single or suite of desired traits valuable to biomedical research. In addition to the selected trait(s), these strains also display variation in pelage color, body size, physiology, and life history. This article exploits the broad phenotypic variation across lab mouse strains to evaluate the relationships between life history and metabolism. Life history variation tends to exist along a fast-slow continuum. There has been considerable interest in understanding the ecological and evolutionary factors underlying life history variation and the physiological and metabolic processes that support them. Yet it remains unclear how these key traits scale across hierarchical levels, as ambiguous empirical support has been garnered at the intraspecific level. Within-species investigations have been thwarted by methodological constraints and environmental factors that obscure the genetic architecture underlying the hypothesized functional integration of life history and metabolic traits. In this analysis, we used the publicly available Mouse Phenome Database by the Jackson Laboratory to investigate the relationships among life history traits (e.g., body size, reproduction, and life span) and metabolic traits (e.g., daily energy expenditure and insulin-like growth factor 1 concentration). Our findings revealed significant variation in reproductive characteristics across strains of mice as well as relationships among life history and metabolic traits. We found evidence of variation along the fast-slow life history continuum, though the direction of some relationships among these traits deviated from interspecific predictions laid out in previous literature. Furthermore, our results suggest that the strength of these relationships are strongest earlier in life.
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12
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Wang J, Han GZ. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat Commun 2023; 14:4968. [PMID: 37591904 PMCID: PMC10435555 DOI: 10.1038/s41467-023-40732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
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Affiliation(s)
- Jianhua Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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13
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Jin J, Yang X, Gong H, Li X. Time- and Gender-Dependent Alterations in Mice during the Aging Process. Int J Mol Sci 2023; 24:12790. [PMID: 37628974 PMCID: PMC10454612 DOI: 10.3390/ijms241612790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Compared to young people and adults, there are differences in the ability of elderly people to resist diseases or injuries, with some noticeable features being gender-dependent. However, gender differences in age-related viscera alterations are not clear. To evaluate a potential possibility of gender differences during the natural aging process, we used three age groups to investigate the impact on spleens, kidneys, and adrenal glands. The immunofluorescence results showed that male-specific p21 proteins were concentrated in the renal tubule epithelial cells of the kidney. Histological staining revealed an increase in the frequencies of fat vacuoles located in the renal tubule epithelial cells of the cortex, under the renal capsule in the kidneys of male mice with age. In female mice, we found that the width of the globular zone in the adrenal gland cortex was unchanged with age. On the contrary, the male displayed a reduction in width. Compared to females, the content of epinephrine in adrenal gland tissue according to ELISA analysis was higher in adults, and a greater decline was observed in aged males particularly. These data confirmed the age-dependent differences between female and male mice; therefore, gender should be considered one of the major factors for personalized treatment in clinical diagnosis and treatment.
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Affiliation(s)
- Jing Jin
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China (H.G.)
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China (H.G.)
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215004, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China (H.G.)
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215004, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China (H.G.)
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215004, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
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14
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Watanabe N, Hirose M, Hasegawa A, Mochida K, Ogura A, Inoue K. Derivation of embryonic stem cells from wild-derived mouse strains by nuclear transfer using peripheral blood cells. Sci Rep 2023; 13:11175. [PMID: 37430017 DOI: 10.1038/s41598-023-38341-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Wild-derived mouse strains have been extensively used in biomedical research because of the high level of inter-strain polymorphisms and phenotypic variations. However, they often show poor reproductive performance and are difficult to maintain by conventional in vitro fertilization and embryo transfer. In this study, we examined the technical feasibility of derivation of nuclear transfer embryonic stem cells (ntESCs) from wild-derived mouse strains for their safe genetic preservation. We used leukocytes collected from peripheral blood as nuclear donors without sacrificing them. We successfully established 24 ntESC lines from two wild-derived strains of CAST/Ei and CASP/1Nga (11 and 13 lines, respectively), both belonging to Mus musculus castaneus, a subspecies of laboratory mouse. Most (23/24) of these lines had normal karyotype, and all lines examined showed teratoma formation ability (4 lines) and pluripotent marker gene expression (8 lines). Two male lines examined (one from each strain) were proven to be competent to produce chimeric mice following injection into host embryos. By natural mating of these chimeric mice, the CAST/Ei male line was confirmed to have germline transmission ability. Our results demonstrate that inter-subspecific ntESCs derived from peripheral leukocytes could provide an alternative strategy for preserving invaluable genetic resources of wild-derived mouse strains.
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Affiliation(s)
- Naomi Watanabe
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michiko Hirose
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Ayumi Hasegawa
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Keiji Mochida
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Atsuo Ogura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Kimiko Inoue
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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15
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Huang B, Lin Z, Chen Z, Chen J, Shi B, Jia J, Li Y, Pan Y, Liang Y, Cai Z. Strain differences in the drug transport capacity of intestinal glucose transporters in Sprague-Dawley versus Wistar rats, C57BL/6J versus Kunming mice. Int J Pharm 2023; 640:123000. [PMID: 37254285 DOI: 10.1016/j.ijpharm.2023.123000] [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: 02/20/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023]
Abstract
Designing oral drug delivery systems using intestinal glucose transporters (IGTs) may be one of the strategies for improving oral bioavailability of drugs. However, little is known about the biological factors affecting the drug transport capacity of IGTs. Gastrodin is a sedative drug with a structure very similar to glucose. It is a highly water-soluble phenolic glucoside. It can hardly enter the intestine through simple diffusion but exhibits good oral bioavailability of over 80%. We confirmed that gastrodin is absorbed via the intestinal glucose transport pathway. It has the highest oral bioavailability among the reported glycosides' active ingredients through this pathway. Thus, gastrodin is the most selective drug substrate of IGTs and can be used to evaluate the drug transport capacity of IGTs. Obviously, strain is one of the main biological factors affecting drug absorption. This study firstly compared the drug transport capacity of IGTs between SD rats and Wistar rats and between C57 mice and KM mice by pharmacokinetic experiments and single-pass intestinal perfusion experiments of gastrodin. Then, the sodium-dependent glucose transporter type 1 (SGLT1) and sodium-independent glucose transporters type 2 (GLUT2) in the duodenum, jejunum, ileum and colon of these animals were quantified using RT-qPCR and Western blot. The results showed that the oral bioavailability of gastrodin in Wistar rats was significantly higher than in SD rats and significantly higher in KM mice than in C57 mice. Gastrodin absorption significantly differed among different intestinal segments in SD rats, C57 mice and KM mice, except Wistar rats. RT-qPCR and Western blot demonstrated that the intestinal expression distribution of SGLT1 and GLUT2 in SD rats and C57 mice was duodenum ≈ jejunum > ileum > colon. SGLT1 expression did not differ among different intestinal segments in KM mice, whereas the intestinal expression distribution of GLUT2 was duodenum ≈ jejunum ≈ ileum > colon. However, the expression of SGLT1 and GLUT2 did not differ among different intestinal segments in Wistar rats. It was reported that the intestinal expression distribution of SGLT1 and GLUT2 in humans is duodenum > jejunum > ileum > colon. Hence, the intestinal expression distribution of SGLT1 and GLUT2 of SD rats and C57 mice was more similar to that in humans. In conclusion, the drug transport capacity of IGTs differs in different strains of rats and mice. SD rats and C57 mice are more suitable for evaluating the pharmacokinetics of glycosides' active ingredients absorbed via the intestinal glucose transport pathway.
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Affiliation(s)
- Baolin Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China; The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500 Qingyuan, China
| | - Zimin Lin
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Zhenzhen Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Jiasheng Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Birui Shi
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China; The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500 Qingyuan, China
| | - Jingjing Jia
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500 Qingyuan, China
| | - Yuan Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Yueqing Pan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Yuntao Liang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Zheng Cai
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China; Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China.
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16
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Echevarria-Cooper DM, Hawkins NA, Kearney JA. Strain-dependent effects on neurobehavioral and seizure phenotypes in Scn2aK1422E mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543929. [PMID: 37333275 PMCID: PMC10274703 DOI: 10.1101/2023.06.06.543929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Pathogenic variants in SCN2A are associated with a range of neurodevelopmental disorders (NDD). Despite being largely monogenic, SCN2A-related NDD show considerable phenotypic variation and complex genotype-phenotype correlations. Genetic modifiers can contribute to variability in disease phenotypes associated with rare driver mutations. Accordingly, different genetic backgrounds across inbred rodent strains have been shown to influence disease-related phenotypes, including those associated with SCN2A-related NDD. Recently, we developed a mouse model of the variant SCN2A-p.K1422E that was maintained as an isogenic line on the C57BL/6J (B6) strain. Our initial characterization of NDD phenotypes in heterozygous Scn2aK1422E mice revealed alterations in anxiety-related behavior and seizure susceptibility. To determine if background strain affects phenotype severity in the Scn2aK1422E mouse model, phenotypes of mice on B6 and [DBA/2J×B6]F1 hybrid (F1D2) strains were compared. Convergent evidence from neurobehavioral assays demonstrated lower anxiety-like behavior in Scn2aK1422E mice compared to wild-type and further suggested that this effect is more pronounced on the B6 background compared to the F1D2 background. Although there were no strain-dependent differences in occurrence of rare spontaneous seizures, response to the chemoconvulsant kainic acid revealed differences in seizure generalization and lethality risk, with variation based on strain and sex. Continued examination of strain-dependent effects in the Scn2aK1422E mouse model could reveal genetic backgrounds with unique susceptibility profiles that would be relevant for future studies on specific traits and enable the identification of highly penetrant phenotypes and modifier genes that could provide clues about the primary pathogenic mechanism of the K1422E variant.
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Affiliation(s)
- Dennis M. Echevarria-Cooper
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Nicole A. Hawkins
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jennifer A. Kearney
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
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17
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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18
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Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Commun Biol 2023; 6:244. [PMID: 36879097 PMCID: PMC9988836 DOI: 10.1038/s42003-023-04603-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Histamine plays pivotal role in normal physiology and dysregulated production of histamine or signaling through histamine receptors (HRH) can promote pathology. Previously, we showed that Bordetella pertussis or pertussis toxin can induce histamine sensitization in laboratory inbred mice and is genetically controlled by Hrh1/HRH1. HRH1 allotypes differ at three amino acid residues with P263-V313-L331 and L263-M313-S331, imparting sensitization and resistance respectively. Unexpectedly, we found several wild-derived inbred strains that carry the resistant HRH1 allotype (L263-M313-S331) but exhibit histamine sensitization. This suggests the existence of a locus modifying pertussis-dependent histamine sensitization. Congenic mapping identified the location of this modifier locus on mouse chromosome 6 within a functional linkage disequilibrium domain encoding multiple loci controlling sensitization to histamine. We utilized interval-specific single-nucleotide polymorphism (SNP) based association testing across laboratory and wild-derived inbred mouse strains and functional prioritization analyses to identify candidate genes for this modifier locus. Atg7, Plxnd1, Tmcc1, Mkrn2, Il17re, Pparg, Lhfpl4, Vgll4, Rho and Syn2 are candidate genes within this modifier locus, which we named Bphse, enhancer of Bordetella pertussis induced histamine sensitization. Taken together, these results identify, using the evolutionarily significant diversity of wild-derived inbred mice, additional genetic mechanisms controlling histamine sensitization.
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Affiliation(s)
- Abbas Raza
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Sean A Diehl
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
| | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Laure K Case
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dawei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Jason Kost
- Catalytic Data Science, Charleston, SC, 29403, USA
| | - Robyn L Ball
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Rui Huang
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Chen
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Runlin Ma
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Anna L Tyler
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - J Matthew Mahoney
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA.
- Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
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19
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Tao Y, Young‐Stubbs C, Yazdizadeh Shotorbani P, Su D, Mathis KW, Ma R. Sex and strain differences in renal hemodynamics in mice. Physiol Rep 2023; 11:e15644. [PMID: 36946063 PMCID: PMC10031302 DOI: 10.14814/phy2.15644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 03/23/2023] Open
Abstract
The present study was to examine sex and strain differences in glomerular filtration rate (GFR) and renal blood flow (RBF) in C57BL6, 129/Sv, and C57BLKS/J mice, three commonly used mouse strains in renal research. GFR was measured by transdermal measurement of FITC-sinitrin clearance in conscious mice. RBF was measured by a flow probe placed in the renal artery under an anesthetic state. In C57BL6 mice, there were no sex differences in both GFR and RBF. In 129/Sv mice, females had significantly greater GFR than males at age of 24 weeks, but not at 8 weeks. However, males had higher RBF and lower renal vascular resistance (RVR). Similar to 129/Sv, female C57BLKS/J had significantly greater GFR at both 8 and 24 weeks, lower RBF, and higher RVR than males. Across strains, male 129/Sv had lower GFR and higher RBF than male C57BL6, but no significant difference in GFR and greater RBF than male C57BLKS/J. No significant difference in GFR or RBF was observed between C57BL6 and C57BLKS/J mice. Deletion of eNOS in C57BLKS/J mice reduced GFR in both sexes, but decreased RBF in males. Furthermore, there were no sex differences in the severity of renal injury in eNOS-/- dbdb mice. Taken together, our study suggests that sex differences in renal hemodynamics in mice are strain and age dependent. eNOS was not involved in the sex differences in GFR, but in RBF. Furthermore, the sexual dimorphism did not impact the severity of renal injury in diabetic nephropathy.
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Affiliation(s)
- Yu Tao
- Department of Physiology and AnatomyUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Cassandra Young‐Stubbs
- Department of Physiology and AnatomyUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | | | - Dong‐Ming Su
- Department of Microbiology, Immunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Keisa W. Mathis
- Department of Physiology and AnatomyUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Rong Ma
- Department of Physiology and AnatomyUniversity of North Texas Health Science CenterFort WorthTexasUSA
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20
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Gu J, Cui S, Tang X, Liu Z, Zhao J, Zhang H, Mao B, Chen W. Fructooligosaccharides (FOS) significantly increased the relative abundance of intestinal B. pseudolongum in mice with different genotypes. Curr Res Food Sci 2022; 5:2178-2189. [PMID: 36387600 PMCID: PMC9661384 DOI: 10.1016/j.crfs.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Fructooligosaccharides (FOS) promote the proliferation of Bifidobacterium, especially Bifidobacterium pseudolongum in C57BL/6J mice. However, the response of intestinal microbes to FOS is influenced by host genotypes. Therefore, we compared the intestinal microbiota of four commonly used mice before and after FOS intervention, including C57BL/6J, BALB/c, Institute Cancer Research (ICR), and Kunming (KM) mice. The intestinal microbiota of the four genotypes exhibited similarities in composition but differences in relative abundance. Bifidobacterium was significantly increased to different degrees in the four genotypes of mice after FOS intervention, and Akkermansia and Bacteroides were also significantly increased in BALB/c and KM mice. Lactobacillus and Alistipes levels were unchanged or decreased. Within the genus Bifidobacterium, B. pseudolongum was the dominant species in the four genotypes of mice and proliferated significantly after FOS intervention, with dramatic proliferation in C57BL/6J mice (9.49%). Furthermore, eight strains of B. pseudolongum were screened from the feces of mice with four genotypes, and there was a great difference in the ability and manner of utilizing FOS among the strains. The strains from C57BL/6J mice exhibited the strongest utilization of 1-kestose (GF2), whereas other strains could utilize both GF2 and nistose (GF3) weakly. The gut microbial analysis of mice with different genotypes complemented our previous studies. The results provided the background strains of the different mouse genotypes and suggested a correlation between the utilization ability and the response of the strains to FOS. Further studies on the utilization ability of strains and competition in the intestine will contribute to the understanding of the mechanisms of the intestinal microbial response to diet. The intestinal microbiota is similar in composition for mice of different genotypes. B. pseudolongum predominates in bifidobacteria in mice of different genotypes. The relative abundance of B. pseudolongum increases after FOS intake. B. pseudolongum strains show different abilities in utilizing FOS.
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21
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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22
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Liu M, Yu C, Zhang Z, Song M, Sun X, Piálek J, Jacob J, Lu J, Cong L, Zhang H, Wang Y, Li G, Feng Z, Du Z, Wang M, Wan X, Wang D, Wang YL, Li H, Wang Z, Zhang B, Zhang Z. Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice. Genome Biol 2022; 23:203. [PMID: 36163035 PMCID: PMC9511766 DOI: 10.1186/s13059-022-02772-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. Results We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. Conclusion Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02772-1.
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Affiliation(s)
- Ming Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,International Society of Zoological Sciences, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhichao Zhang
- Novogene Bioinformatics Institute, Beijing, China.,Glbizzia Biosciences, Beijing, China
| | - Mingjing Song
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiuping Sun
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Jaroslav Piálek
- House Mouse Group, Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests / Institute for Epidemiology and Pathogen Diagnostics, Münster, Germany
| | - Jiqi Lu
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Lin Cong
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Hongmao Zhang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yong Wang
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Feng
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenglin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xinru Wan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan-Ling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongjun Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zuoxin Wang
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, FL, 32306, USA
| | - Bing Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,International Society of Zoological Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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23
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Yasuda SP, Miyasaka Y, Hou X, Obara Y, Shitara H, Seki Y, Matsuoka K, Takahashi A, Wakai E, Hibino H, Takada T, Shiroishi T, Kominami R, Kikkawa Y. Two Loci Contribute to Age-Related Hearing Loss Resistance in the Japanese Wild-Derived Inbred MSM/Ms Mice. Biomedicines 2022; 10:biomedicines10092221. [PMID: 36140322 PMCID: PMC9496148 DOI: 10.3390/biomedicines10092221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
An MSM/Ms strain was established using Japanese wild mice, which exhibit resistance to several phenotypes associated with aging, such as obesity, inflammation, and tumorigenesis, compared to common inbred mouse strains. MSM/Ms strain is resistant to age-related hearing loss, and their auditory abilities are sustained for long durations. The age-related hearing loss 3 (ahl3) locus contributes to age-related hearing in MSM/Ms strain. We generated ahl3 congenic strains by transferring a genomic region on chromosome 17 from MSM/Ms mice into C57BL/6J mice. Although C57BL/6J mice develop age-related hearing loss because of the ahl allele of the cadherin 23 gene, the development of middle- to high-frequency hearing loss was significantly delayed in an ahl3 congenic strain. Moreover, the novel age-related hearing loss 10 (ahl10) locus associated with age-related hearing resistance in MSM/Ms strain was mapped to chromosome 12. Although the resistance effects in ahl10 congenic strain were slightly weaker than those in ahl3 congenic strain, slow progression of age-related hearing loss was confirmed in ahl10 congenic strain despite harboring the ahl allele of cadherin 23. These results suggest that causative genes and polymorphisms of the ahl3 and ahl10 loci are important targets for the prevention and treatment of age-related hearing loss.
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Affiliation(s)
- Shumpei P. Yasuda
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yuki Miyasaka
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan
| | - Xuehan Hou
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yo Obara
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroshi Shitara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yuta Seki
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Kunie Matsuoka
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Ai Takahashi
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Eri Wakai
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Division of Glocal Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hiroshi Hibino
- Division of Glocal Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | | | - Ryo Kominami
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yoshiaki Kikkawa
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
- Correspondence:
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24
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Devlin R, Roberts E. Building a healthy mouse model ecosystem to interrogate cancer biology. Dis Model Mech 2022; 15:276587. [PMID: 36098988 PMCID: PMC9509886 DOI: 10.1242/dmm.049795] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In a recent study, Sargent et al. characterise several novel Rag1-/- mouse strains and demonstrate that genetic background strongly influences xenograft development and phenotype. Here, we discuss this work within the broader context of cancer mouse modelling. We argue that new technologies will enable insights into how specific models align with human disease states and that this knowledge can be used to develop a diverse ecosystem of complementary mouse models of cancer. By utilising these diverse, well-characterised models to provide multiple perspectives on specific cancers, it should be possible to reduce the inappropriate attrition of sound hypotheses while protecting against false positives. Furthermore, careful re-introduction of biological variation, be that through outbred populations, environmental diversity or including animals of both sexes, can ensure that results are more broadly applicable and are less impacted by particular traits of homogeneous experimental populations. Thus, careful characterisation and judicious use of an array of mouse models provides an opportunity to address some of the issues surrounding both the reproducibility and translatability crises often referenced in pre-clinical cancer research.
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Affiliation(s)
- Ryan Devlin
- Beatson Institute for Cancer Research, University of Glasgow, Glasgow G61 1BD, UK
| | - Ed Roberts
- Beatson Institute for Cancer Research, University of Glasgow, Glasgow G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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25
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Malin K, Witkowska-Piłaszewicz O, Papis K. The many problems of somatic cell nuclear transfer in reproductive cloning of mammals. Theriogenology 2022; 189:246-254. [DOI: 10.1016/j.theriogenology.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 11/24/2022]
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26
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Swain P, Mortreux M, Laws JM, Kyriacou H, De Martino E, Winnard A, Caplan N. Skeletal muscle deconditioning during partial weight-bearing in rodents - A systematic review and meta-analysis. LIFE SCIENCES IN SPACE RESEARCH 2022; 34:68-86. [PMID: 35940691 DOI: 10.1016/j.lssr.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Space agencies are planning to send humans back to the Lunar surface, in preparation for crewed exploration of Mars. However, the effect of hypogravity on human skeletal muscle is largely unknown. A recently established rodent partial weight-bearing model has been employed to mimic various levels of hypogravity loading and may provide valuable insights to better understanding how human muscle might respond to this environment. The aim of this study was to perform a systematic review regarding the effects of partial weight-bearing on the morphology and function of rodent skeletal muscle. Five online databases were searched with the following inclusion criteria: population (rodents), intervention (partial weight-bearing for ≥1 week), control (full weight-bearing), outcome(s) (skeletal muscle morphology/function), and study design (animal intervention). Of the 2,993 studies identified, eight were included. Partial weight-bearing at 20%, 40%, and 70% of full loading caused rapid deconditioning of skeletal muscle morphology and function within the first one to two weeks of exposure. Calf circumference, hindlimb wet muscle mass, myofiber cross-sectional area, front/rear paw grip force, and nerve-stimulated plantarflexion force were reduced typically by medium to very large effects. Higher levels of partial weight-bearing often attenuated deconditioning but failed to entirely prevent it. Species and sex mediated the deconditioning response. Risk of bias was low/unclear for most studies. These findings suggest that there is insufficient stimulus to mitigate muscular deconditioning in hypogravity settings highlighting the need to develop countermeasures for maintaining astronaut/cosmonaut muscular health on the Moon and Mars.
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Affiliation(s)
- Patrick Swain
- Aerospace Medicine and Rehabilitation Laboratory, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom.
| | - Marie Mortreux
- Harvard Medical School, Department of Neurology, Beth Israel Deaconess Medical Center Boston, Massachusetts, United States
| | - Jonathan M Laws
- Aerospace Medicine and Rehabilitation Laboratory, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Harry Kyriacou
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Enrico De Martino
- Aerospace Medicine and Rehabilitation Laboratory, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Andrew Winnard
- Aerospace Medicine and Rehabilitation Laboratory, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Nick Caplan
- Aerospace Medicine and Rehabilitation Laboratory, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
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27
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. CELL GENOMICS 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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28
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Genetically modified mice for research on human diseases: A triumph for Biotechnology or a work in progress? THE EUROBIOTECH JOURNAL 2022. [DOI: 10.2478/ebtj-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022] Open
Abstract
Abstract
Genetically modified mice are engineered as models for human diseases. These mouse models include inbred strains, mutants, gene knockouts, gene knockins, and ‘humanized’ mice. Each mouse model is engineered to mimic a specific disease based on a theory of the genetic basis of that disease. For example, to test the amyloid theory of Alzheimer’s disease, mice with amyloid precursor protein genes are engineered, and to test the tau theory, mice with tau genes are engineered. This paper discusses the importance of mouse models in basic research, drug discovery, and translational research, and examines the question of how to define the “best” mouse model of a disease. The critiques of animal models and the caveats in translating the results from animal models to the treatment of human disease are discussed. Since many diseases are heritable, multigenic, age-related and experience-dependent, resulting from multiple gene-gene and gene-environment interactions, it will be essential to develop mouse models that reflect these genetic, epigenetic and environmental factors from a developmental perspective. Such models would provide further insight into disease emergence, progression and the ability to model two-hit and multi-hit theories of disease. The summary examines the biotechnology for creating genetically modified mice which reflect these factors and how they might be used to discover new treatments for complex human diseases such as cancers, neurodevelopmental and neurodegenerative diseases.
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29
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Mulley JF. Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains. J Anat 2022; 240:735-745. [PMID: 34747015 PMCID: PMC8930804 DOI: 10.1111/joa.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/08/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
A series of elegant embryo transfer experiments in the 1950s demonstrated that the uterine environment could alter vertebral patterning in inbred mouse strains. In the intervening decades, attention has tended to focus on the technical achievements involved and neglected the underlying biological question: how can genetically homogenous individuals have a heterogenous number of vertebrae? Here I revisit these experiments and, with the benefit of knowledge of the molecular-level processes of vertebral patterning gained over the intervening decades, suggest a novel hypothesis for homeotic transformation of the last lumbar vertebra to the adjacent sacral type through regulation of Hox genes by sex steroids. Hox genes are involved in both axial patterning and development of male and female reproductive systems and have been shown to be sensitive to sex steroids in vitro and in vivo. Regulation of these genes by sex steroids and resulting alterations to vertebral patterning may hint at a deep evolutionary link between the ribless lumbar region of mammals and the switch from egg-laying to embryo implantation. An appreciation of the impact of sex steroids on Hox genes may explain some puzzling aspects of human disease, and highlights the spine as a neglected target for in utero exposure to endocrine disruptors.
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30
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Mortazavi M, Ren Y, Saini S, Antaki D, St. Pierre CL, Williams A, Sohni A, Wilkinson MF, Gymrek M, Sebat J, Palmer AA. SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains. CELL GENOMICS 2022; 2:100102. [PMID: 35720252 PMCID: PMC9205302 DOI: 10.1016/j.xgen.2022.100102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 11/22/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022]
Abstract
Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 indels, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs), and 2,826 differentially expressed genes (DE genes) among these 14 strains; 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs, and frameshifting indels that were associated with DE genes. Our results can be used for both forward and reverse genetic approaches and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.
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Affiliation(s)
- Milad Mortazavi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Yangsu Ren
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Shubham Saini
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Danny Antaki
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Celine L. St. Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - April Williams
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
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31
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Peltz G, Tan Y. What Have We Learned (or Expect to) From Analysis of Murine Genetic Models Related to Substance Use Disorders? Front Psychiatry 2022; 12:793961. [PMID: 35095607 PMCID: PMC8790171 DOI: 10.3389/fpsyt.2021.793961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
The tremendous public health problem created by substance use disorders (SUDs) presents a major opportunity for mouse genetics. Inbred mouse strains exhibit substantial and heritable differences in their responses to drugs of abuse (DOA) and in many of the behaviors associated with susceptibility to SUD. Therefore, genetic discoveries emerging from analysis of murine genetic models can provide critically needed insight into the neurobiological effects of DOA, and they can reveal how genetic factors affect susceptibility drug addiction. There are already indications, emerging from our prior analyses of murine genetic models of responses related to SUDs that mouse genetic models of SUD can provide actionable information, which can lead to new approaches for alleviating SUDs. Lastly, we consider the features of murine genetic models that enable causative genetic factors to be successfully identified; and the methodologies that facilitate genetic discovery.
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Affiliation(s)
- Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, United States
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32
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Cooper TK, Meyerholz DK, Beck AP, Delaney MA, Piersigilli A, Southard TL, Brayton CF. Research-Relevant Conditions and Pathology of Laboratory Mice, Rats, Gerbils, Guinea Pigs, Hamsters, Naked Mole Rats, and Rabbits. ILAR J 2022; 62:77-132. [PMID: 34979559 DOI: 10.1093/ilar/ilab022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/12/2021] [Indexed: 12/31/2022] Open
Abstract
Animals are valuable resources in biomedical research in investigations of biological processes, disease pathogenesis, therapeutic interventions, safety, toxicity, and carcinogenicity. Interpretation of data from animals requires knowledge not only of the processes or diseases (pathophysiology) under study but also recognition of spontaneous conditions and background lesions (pathology) that can influence or confound the study results. Species, strain/stock, sex, age, anatomy, physiology, spontaneous diseases (noninfectious and infectious), and neoplasia impact experimental results and interpretation as well as animal welfare. This review and the references selected aim to provide a pathology resource for researchers, pathologists, and veterinary personnel who strive to achieve research rigor and validity and must understand the spectrum of "normal" and expected conditions to accurately identify research-relevant experimental phenotypes as well as unusual illness, pathology, or other conditions that can compromise studies involving laboratory mice, rats, gerbils, guinea pigs, hamsters, naked mole rats, and rabbits.
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Affiliation(s)
- Timothy K Cooper
- Department of Comparative Medicine, Penn State Hershey Medical Center, Hershey, PA, USA
| | - David K Meyerholz
- Department of Pathology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa, USA
| | - Amanda P Beck
- Department of Pathology, Yeshiva University Albert Einstein College of Medicine, Bronx, New York, USA
| | - Martha A Delaney
- Zoological Pathology Program, University of Illinois at Urbana-Champaign College of Veterinary Medicine, Urbana-Champaign, Illinois, USA
| | - Alessandra Piersigilli
- Laboratory of Comparative Pathology and the Genetically Modified Animal Phenotyping Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Teresa L Southard
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Cory F Brayton
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021; 15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
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Affiliation(s)
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada
| | | | - Olga Shevtsova
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Emma van der Slagt
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Hai Lam Nguyen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Penelope A Young
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.,Department of Molecular Medicine, Université de Laval, Québec City, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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A Combined Adjuvant TF-Al Consisting of TFPR1 and Aluminum Hydroxide Augments Strong Humoral and Cellular Immune Responses in Both C57BL/6 and BALB/c Mice. Vaccines (Basel) 2021; 9:vaccines9121408. [PMID: 34960154 PMCID: PMC8705145 DOI: 10.3390/vaccines9121408] [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: 10/26/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
TFPR1 is a novel adjuvant for protein and peptide antigens, which has been demonstrated in BALB/c mice in our previous studies; however, its adjuvanticity in mice with different genetic backgrounds remains unknown, and its adjuvanticity needs to be improved to fit the requirements for various vaccines. In this study, we first compared the adjuvanticity of TFPR1 in two commonly used inbred mouse strains, BALB/c and C57BL/6 mice, in vitro and in vivo, and demonstrated that TFPR1 activated TLR2 to exert its immune activity in vivo. Next, to prove the feasibility of TFPR1 acting as a major component of combined adjuvants, we prepared a combined adjuvant, TF-Al, by formulating TFPR1 and alum at a certain ratio and compared its adjuvanticity with that of TFPR1 and alum alone using OVA and recombinant HBsAg as model antigens in both BALB/c and C57BL/6 mice. Results showed that TFPR1 acts as an effective vaccine adjuvant in both BALB/c mice and C57BL/6 mice, and further demonstrated the role of TLR2 in the adjuvanticity of TFPR1 in vivo. In addition, we obtained a novel combined adjuvant, TF-Al, based on TFPR1, which can augment antibody and cellular immune responses in mice with different genetic backgrounds, suggesting its promise for vaccine development in the future.
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Iglesias-Carres L, Neilson AP. Utilizing preclinical models of genetic diversity to improve translation of phytochemical activities from rodents to humans and inform personalized nutrition. Food Funct 2021; 12:11077-11105. [PMID: 34672309 DOI: 10.1039/d1fo02782d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mouse models are an essential tool in different areas of research, including nutrition and phytochemical research. Traditional inbred mouse models have allowed the discovery of therapeutical targets and mechanisms of action and expanded our knowledge of health and disease. However, these models lack the genetic variability typically found in human populations, which hinders the translatability of the results found in mice to humans. The development of genetically diverse mouse models, such as the collaborative cross (CC) or the diversity outbred (DO) models, has been a useful tool to overcome this obstacle in many fields, such as cancer, immunology and toxicology. However, these tools have not yet been widely adopted in the field of phytochemical research. As demonstrated in other disciplines, use of CC and DO models has the potential to provide invaluable insights for translation of phytochemicals from rodents to humans, which are desperately needed given the challenges and numerous failed clinical trials in this field. These models may prove informative for personalized use of phytochemicals in humans, including: predicting interindividual variability in phytochemical bioavailability and efficacy, identifying genetic loci or genes governing response to phytochemicals, identifying phytochemical mechanisms of action and therapeutic targets, and understanding the impact of genetic variability on individual response to phytochemicals. Such insights would prove invaluable for personalized implementation of phytochemicals in humans. This review will focus on the current work performed with genetically diverse mouse populations, and the research opportunities and advantages that these models can offer to phytochemical research.
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Affiliation(s)
- Lisard Iglesias-Carres
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, USA.
| | - Andrew P Neilson
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, USA.
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Choi J, Kim SJ, Fujiyama T, Miyoshi C, Park M, Suzuki-Abe H, Yanagisawa M, Funato H. The Role of Reproductive Hormones in Sex Differences in Sleep Homeostasis and Arousal Response in Mice. Front Neurosci 2021; 15:739236. [PMID: 34621154 PMCID: PMC8491770 DOI: 10.3389/fnins.2021.739236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
There are various sex differences in sleep/wake behaviors in mice. However, it is unclear whether there are sex differences in sleep homeostasis and arousal responses and whether gonadal hormones are involved in these sex differences. Here, we examined sleep/wake behaviors under baseline condition, after sleep deprivation by gentle handling, and arousal responses to repeated cage changes in male and female C57BL/6 mice that are hormonally intact, gonadectomized, or gonadectomized with hormone supplementation. Compared to males, females had longer wake time, shorter non-rapid eye movement sleep (NREMS) time, and longer rapid eye movement sleep (REMS) episodes. After sleep deprivation, males showed an increase in NREMS delta power, NREMS time, and REMS time, but females showed a smaller increase. Females and males showed similar arousal responses. Gonadectomy had only a modest effect on homeostatic sleep regulation in males but enhanced it in females. Gonadectomy weakened arousal response in males and females. With hormone replacement, baseline sleep in gonadectomized females was similar to that of intact females, and baseline sleep in gonadectomized males was close to that of intact males. Gonadal hormone supplementation restored arousal response in males but not in females. These results indicate that male and female mice differ in their baseline sleep-wake behavior, homeostatic sleep regulation, and arousal responses to external stimuli, which are differentially affected by reproductive hormones.
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Affiliation(s)
- Jinhwan Choi
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Staci J Kim
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tomoyuki Fujiyama
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Chika Miyoshi
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Minjeong Park
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Haruka Suzuki-Abe
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan.,Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Japan.,Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
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Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. [PMID: 34615869 PMCID: PMC8494802 DOI: 10.1038/s41467-021-26097-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell L Leibowitz
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Zeid D, Mooney-Leber S, Seemiller LR, Goldberg LR, Gould TJ. Terc Gene Cluster Variants Predict Liver Telomere Length in Mice. Cells 2021; 10:2623. [PMID: 34685603 PMCID: PMC8533930 DOI: 10.3390/cells10102623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/19/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Variants in a gene cluster upstream-adjacent to TERC on human chromosome 3, which includes genes APRM, LRRC31, LRRC34 and MYNN, have been associated with telomere length in several human populations. Currently, the mechanism by which variants in the TERC gene cluster influence telomere length in humans is unknown. Given the proximity between the TERC gene cluster and TERC (~0.05 Mb) in humans, it is speculated that cluster variants are in linkage disequilibrium with a TERC causal variant. In mice, the Terc gene/Terc gene cluster are also located on chromosome 3; however, the Terc gene cluster is located distantly downstream of Terc (~60 Mb). Here, we initially aim to investigate the interactions between genotype and nicotine exposure on absolute liver telomere length (aTL) in a panel of eight inbred mouse strains. Although we found no significant impact of nicotine on liver aTL, this first experiment identified candidate single nucleotide polymorphisms (SNPs) in the murine Terc gene cluster (within genes Lrrc31, Lrriq4 and Mynn) co-varying with aTL in our panel. In a second experiment, we tested the association of these Terc gene cluster variants with liver aTL in an independent panel of eight inbred mice selected based on candidate SNP genotype. This supported our initial finding that Terc gene cluster polymorphisms impact aTL in mice, consistent with data in human populations. This provides support for mice as a model for telomere dynamics, especially for studying mechanisms underlying the association between Terc cluster variants and telomere length. Finally, these data suggest that mechanisms independent of linkage disequilibrium between the Terc/TERC gene cluster and the Terc/TERC gene mediate the cluster's regulation of telomere length.
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Affiliation(s)
- Dana Zeid
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Sean Mooney-Leber
- Department of Psychology, University of Wisconsin-Stevens Point, Stevens Point, WI 54481, USA;
| | - Laurel R. Seemiller
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Lisa R. Goldberg
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Thomas J. Gould
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
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Wang M, Fang Z, Yoo B, Bejerano G, Peltz G. The Effect of Population Structure on Murine Genome-Wide Association Studies. Front Genet 2021; 12:745361. [PMID: 34589118 PMCID: PMC8475632 DOI: 10.3389/fgene.2021.745361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 - 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated.
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Affiliation(s)
- Meiyue Wang
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
| | - Zhuoqing Fang
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
| | - Boyoung Yoo
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, United States
| | - Gill Bejerano
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, United States
| | - Gary Peltz
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, United States
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Cheng AA, Li W, Hernandez LL. Investigating the effect of positional variation on mid-lactation mammary gland transcriptomics in mice fed either a low-fat or high-fat diet. PLoS One 2021; 16:e0255770. [PMID: 34437559 PMCID: PMC8389404 DOI: 10.1371/journal.pone.0255770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 07/24/2021] [Indexed: 11/18/2022] Open
Abstract
Little attention has been given to the effect of positional variation of gene expression in the mammary gland. However, more research is shedding light regarding the physiological differences that mammary gland location can have on the murine mammary gland. Here we examined the differentially expressed genes between mammary gland positions under either a low-fat diet (LFD) or a high-fat diet (HFD) in the mid-lactation mammary gland (lactation day 11; L11). Three-week old WT C57BL/6 mice were randomly assigned to either a low-fat diet (LFD) or high fat diet (HFD) (n = 3/group) and either the right thoracic mammary gland (TMG) or inguinal mammary gland (IMG) was collected from each dam for a total of 12 unique glands. Within each diet, differentially expressed genes (DEGs) were first filtered by adjusted p-value (cutoff ≤ 0.05) and fold-change (FC, cutoff ≥2). Genes were further filtered by mean normalized read count with a cutoff≥10. We observed that mammary gland position had a significant impact on mammary gland gene expression with either LFD or HFD diet, with 1264 DEGs in LFD dams and 777 DEGs in HFD dams. We found that genes related to snRNP binding and translation initiation were most significantly altered between the TMG and IMG. Although we were not able to discern a molecular mechanism, many small nuclear RNAs and small nucleolar RNAs were differentially expressed between the TMG and IMG responsible for cellular functions such as splicing and ribosome biogenesis, which provides and interesting avenue for future research. Our study supports the hypothesis that collection of the mammary gland from a particular location influences mammary gland gene expression, thereby highlighting the importance for researchers to be vigilant in documenting and reporting which mammary gland they are using for their studies.
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Affiliation(s)
- Adrienne A. Cheng
- Department of Nutritional Sciences, UW-Madison, Madison, Wisconsin, United States of America
- Department of Animal and Dairy Sciences, UW-Madison, Madison, Wisconsin, United States of America
| | - Wenli Li
- Cell Wall Biology and Utilization Research Unit, US Dairy Forage Research Center, Agricultural Research Service, US Department of Agriculture, Madison, Wisconsin, United States of America
| | - Laura L. Hernandez
- Department of Animal and Dairy Sciences, UW-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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TARANG MITEK, KUMAR PUSHPENDRA, KUMAR AMIT, SAINI BL, KAUSHAL SHOBHANA, SACHAN SHWETA, CHAUHAN ANUJ, PRAKASH JAI, BHUSHAN BHARAT. Genetic characterization of F0 outbred and F1 inbred Swiss albino mice using microsatellite markers and their performance evaluation. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v91i3.114144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Swiss albino mice have been widely utilized in various biological researches worldwide. Phenotypic and fitness related traits of F0 and F1 inbred mice were estimated on 918 and 707 individual offsprings, respectively. The influence of fixed effects (litter size and sex) on birth weight (BW), weaning weight (WW) and adult body weight (ABW) in both the generations were found to be statistically significant. Genetic characterization of F0 outbred and the F1 inbred strain of Swiss albino mice were evaluated by using 10 microsatellites markers. The results indicated that total number of alleles per locus ranged from 3 (D2Mit61, D3Mit55, D8Mit14, D9Mit27, D10Mit180, D11Mit167) to 4 (D1Mit15, D2Mit51, D5Mit18, D7Mit323) in F0 and F1 inbred population, with a mean value of 3.4 indicating polymorphism in all 10 loci. The mean of effective number of alleles was 2.935 and 2.733 in F0 and F1 population, respectively. Estimates of the FIS ranged from 0.139 (D10Mit180) to 0.999 (D9Mit27); and from 0.109 (D3Mit55) to 0.679 (D2Mit51) in F0 and F1 inbred population, respectively. The estimated mean markerbased FIS was 0.294 and 0.372 in F0 and F1 populations, respectively. The mean values of observed heterozygosity (Ho) and expected heterozygosity (He) were 0.460 and 0.654, respectively for F0 and 0.390 and 0.627, respectively for F1 inbred mice population. Slight reduction in heterozygosity and 7.8% increase in inbreeding coefficient were observed in F1 inbred in comparison to F0 population. The results suggested that genome wide microsatellite genotyping might be more useful for accurate measuring and reliable estimation of population genetic parameters and inbreeding coefficient.
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Young GR, Ferron AKW, Panova V, Eksmond U, Oliver PL, Kassiotis G, Stoye JP. Gv1, a Zinc Finger Gene Controlling Endogenous MLV Expression. Mol Biol Evol 2021; 38:2468-2474. [PMID: 33560369 PMCID: PMC8136514 DOI: 10.1093/molbev/msab039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genomes of inbred mice harbor around 50 endogenous murine leukemia virus (MLV) loci, although the specific complement varies greatly between strains. The Gv1 locus is known to control the transcription of endogenous MLVs and to be the dominant determinant of cell-surface presentation of MLV envelope, the GIX antigen. Here, we identify a single Krüppel-associated box zinc finger protein (ZFP) gene, Zfp998, as Gv1 and show it to be necessary and sufficient to determine the GIX+ phenotype. By long-read sequencing of bacterial artificial chromosome clones from 129 mice, the prototypic GIX+ strain, we reveal the source of sufficiency and deficiency as splice-acceptor variations and highlight the varying origins of the chromosomal region encompassing Gv1. Zfp998 becomes the second identified ZFP gene responsible for epigenetic suppression of endogenous MLVs in mice and further highlights the prominent role of this gene family in control of endogenous retroviruses.
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Affiliation(s)
- George R Young
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Aaron K W Ferron
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Veera Panova
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Urszula Eksmond
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | | | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
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Wilzopolski J, Kietzmann M, Mishra SK, Stark H, Bäumer W, Rossbach K. TRPV1 and TRPA1 Channels Are Both Involved Downstream of Histamine-Induced Itch. Biomolecules 2021; 11:1166. [PMID: 34439832 PMCID: PMC8391774 DOI: 10.3390/biom11081166] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 01/17/2023] Open
Abstract
Two histamine receptor subtypes (HR), namely H1R and H4R, are involved in the transmission of histamine-induced itch as key components. Although exact downstream signaling mechanisms are still elusive, transient receptor potential (TRP) ion channels play important roles in the sensation of histaminergic and non-histaminergic itch. The aim of this study was to investigate the involvement of TRPV1 and TRPA1 channels in the transmission of histaminergic itch. The potential of TRPV1 and TRPA1 inhibitors to modulate H1R- and H4R-induced signal transmission was tested in a scratching assay in mice in vivo as well as via Ca2+ imaging of murine sensory dorsal root ganglia (DRG) neurons in vitro. TRPV1 inhibition led to a reduction of H1R- and H4R- induced itch, whereas TRPA1 inhibition reduced H4R- but not H1R-induced itch. TRPV1 and TRPA1 inhibition resulted in a reduced Ca2+ influx into sensory neurons in vitro. In conclusion, these results indicate that both channels, TRPV1 and TRPA1, are involved in the transmission of histamine-induced pruritus.
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Affiliation(s)
- Jenny Wilzopolski
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (M.K.); (K.R.)
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; (S.K.M.); (W.B.)
- Department of Veterinary Medicine, Institute of Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Manfred Kietzmann
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (M.K.); (K.R.)
| | - Santosh K. Mishra
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; (S.K.M.); (W.B.)
| | - Holger Stark
- Institute of Pharmaceutical and Medical Chemistry, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany;
| | - Wolfgang Bäumer
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; (S.K.M.); (W.B.)
- Department of Veterinary Medicine, Institute of Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kristine Rossbach
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany; (M.K.); (K.R.)
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Schaffenrath J, Huang SF, Wyss T, Delorenzi M, Keller A. Characterization of the blood-brain barrier in genetically diverse laboratory mouse strains. Fluids Barriers CNS 2021; 18:34. [PMID: 34321020 PMCID: PMC8317333 DOI: 10.1186/s12987-021-00269-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background Genetic variation in a population has an influence on the manifestation of monogenic as well as multifactorial disorders, with the underlying genetic contribution dependent on several interacting variants. Common laboratory mouse strains used for modelling human disease lack the genetic variability of the human population. Therefore, outcomes of rodent studies show limited relevance to human disease. The functionality of brain vasculature is an important modifier of brain diseases. Importantly, the restrictive interface between blood and brain—the blood–brain barrier (BBB) serves as a major obstacle for the drug delivery into the central nervous system (CNS). Using genetically diverse mouse strains, we aimed to investigate the phenotypic and transcriptomic variation of the healthy BBB in different inbred mouse strains. Methods We investigated the heterogeneity of brain vasculature in recently wild-derived mouse strains (CAST/EiJ, WSB/EiJ, PWK/PhJ) and long-inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, DBA/2J, NOD/ShiLtJ) using different phenotypic arms. We used immunohistochemistry and confocal laser microscopy followed by quantitative image analysis to determine vascular density and pericyte coverage in two brain regions—cortex and hippocampus. Using a low molecular weight fluorescence tracer, sodium fluorescein and spectrophotometry analysis, we assessed BBB permeability in young and aged mice of selected strains. For further phenotypic characterization of endothelial cells in inbred mouse strains, we performed bulk RNA sequencing of sorted endothelial cells isolated from cortex and hippocampus. Results Cortical vessel density and pericyte coverage did not differ among the investigated strains, except in the cortex, where PWK/PhJ showed lower vessel density compared to NOD/ShiLtJ, and a higher pericyte coverage than DBA/2J. The vascular density in the hippocampus differed among analyzed strains but not the pericyte coverage. The staining patterns of endothelial arteriovenous zonation markers were similar in different strains. BBB permeability to a small fluorescent tracer, sodium fluorescein, was also similar in different strains, except in the hippocampus where the CAST/EiJ showed higher permeability than NOD/ShiLtJ. Transcriptomic analysis of endothelial cells revealed that sex of the animal was a major determinant of gene expression differences. In addition, the expression level of several genes implicated in endothelial function and BBB biology differed between wild-derived and long-inbred mouse strains. In aged mice of three investigated strains (DBA/2J, A/J, C57BL/6J) vascular density and pericyte coverage did not change—expect for DBA/2J, whereas vascular permeability to sodium fluorescein increased in all three strains. Conclusions Our analysis shows that although there were no major differences in parenchymal vascular morphology and paracellular BBB permeability for small molecular weight tracer between investigated mouse strains or sexes, transcriptomic differences of brain endothelial cells point to variation in gene expression of the intact BBB. These baseline variances might be confounding factors in pathological conditions that may lead to a differential functional outcome dependent on the sex or genetic polymorphism. Supplementary Information The online version contains supplementary material available at 10.1186/s12987-021-00269-w.
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Affiliation(s)
- Johanna Schaffenrath
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zürich, Zürich University, Zürich, Switzerland.,Neuroscience Center Zürich, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Sheng-Fu Huang
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zürich, Zürich University, Zürich, Switzerland.,Neuroscience Center Zürich, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Tania Wyss
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Oncology, University Lausanne, Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Oncology, University Lausanne, Lausanne, Switzerland
| | - Annika Keller
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zürich, Zürich University, Zürich, Switzerland. .,Neuroscience Center Zürich, University of Zürich and ETH Zürich, Zürich, Switzerland.
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Coding variants in mouse and rat model organisms: mousepost and ratpost. Mamm Genome 2021; 33:81-87. [PMID: 34313794 DOI: 10.1007/s00335-021-09898-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
Mice and rats are the most commonly used vertebrate model organisms in biomedical research. The availability of a reference genome in both animals combined with the deep sequencing of several doze of popular inbred lines also provides rich sequence variation data in these species. In some cases, such sequence variants can be linked directly to a distinctive phenotype. In previous work, we created the mouse and rat online searchable databases ("Mousepost" and "Ratpost") where small variant information for protein coding transcripts in mouse and rat inbred strains can be easily retrieved at the amino acid level. These tools are directly useful in forward genetics strategies or as a repository of existing sequence variations. Here, we perform a comparison between the "Mousepost" and "Ratpost" databases and we couple these two tools to a database of human sequence variants ClinVar. We investigated the level of redundancy and complementarity of known variants in protein coding transcripts and found that the large majority of variants is species-specific. However, a small set of positions is conserved in an inbred line between both species. We conclude that both databases are highly complementary, but this may change with further sequencing efforts in both species.
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Dorman A, Binenbaum I, Abu-Toamih Atamni HJ, Chatziioannou A, Tomlinson I, Mott R, Iraqi FA. Genetic mapping of novel modifiers for Apc Min induced intestinal polyps' development using the genetic architecture power of the collaborative cross mice. BMC Genomics 2021; 22:566. [PMID: 34294033 PMCID: PMC8299641 DOI: 10.1186/s12864-021-07890-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/14/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the Adenomatous polyposis coli (Apc) gene. Mice carrying a nonsense mutation in the Apc gene at R850, which is designated ApcMin/+ (Multiple intestinal neoplasia), develop intestinal adenomas. Several genetic modifier loci of Min (Mom) were previously mapped, but so far, most of the underlying genes have not been identified. To identify novel modifier loci associated with ApcMin/+, we performed quantitative trait loci (QTL) analysis for polyp development using 49 F1 crosses between different Collaborative Cross (CC) lines and C57BL/6 J-ApcMin/+mice. The CC population is a genetic reference panel of recombinant inbred lines, each line independently descended from eight genetically diverse founder strains. C57BL/6 J-ApcMin/+ males were mated with females from 49 CC lines. F1 offspring were terminated at 23 weeks and polyp counts from three sub-regions (SB1-3) of small intestinal and colon were recorded. RESULTS The number of polyps in all these sub-regions and colon varied significantly between the different CC lines. At 95% genome-wide significance, we mapped nine novel QTL for variation in polyp number, with distinct QTL associated with each intestinal sub-region. QTL confidence intervals varied in width between 2.63-17.79 Mb. We extracted all genes in the mapped QTL at 90 and 95% CI levels using the BioInfoMiner online platform to extract, significantly enriched pathways and key linker genes, that act as regulatory and orchestrators of the phenotypic landscape associated with the ApcMin/+ mutation. CONCLUSIONS Genomic structure of the CC lines has allowed us to identify novel modifiers and confirmed some of the previously mapped modifiers. Key genes involved mainly in metabolic and immunological processes were identified. Future steps in this analysis will be to identify regulatory elements - and possible epistatic effects - located in the mapped QTL.
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Affiliation(s)
- Alexandra Dorman
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
| | - Ilona Binenbaum
- Department of Biology, University of Patras, Patras, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Hanifa J. Abu-Toamih Atamni
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
| | | | - Ian Tomlinson
- Cancer Research UK Edinburgh Centre, Charles and Ethel Barr Chair of Cancer Research, University of Edinburgh, Edinburgh, UK
| | - Richard Mott
- Department of Genetics, University Collage of London, London, UK
| | - Fuad A. Iraqi
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
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Lu X, Tu SW, Chang W, Wan C, Wang J, Zang Y, Ramdas B, Kapur R, Lu X, Cao S, Zhang C. SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data. Brief Bioinform 2021; 22:bbaa307. [PMID: 33230549 PMCID: PMC8294548 DOI: 10.1093/bib/bbaa307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 01/04/2023] Open
Abstract
Deconvolution of mouse transcriptomic data is challenged by the fact that mouse models carry various genetic and physiological perturbations, making it questionable to assume fixed cell types and cell type marker genes for different data set scenarios. We developed a Semi-Supervised Mouse data Deconvolution (SSMD) method to study the mouse tissue microenvironment. SSMD is featured by (i) a novel nonparametric method to discover data set-specific cell type signature genes; (ii) a community detection approach for fixing cell types and their marker genes; (iii) a constrained matrix decomposition method to solve cell type relative proportions that is robust to diverse experimental platforms. In summary, SSMD addressed several key challenges in the deconvolution of mouse tissue data, including: (i) varied cell types and marker genes caused by highly divergent genotypic and phenotypic conditions of mouse experiment; (ii) diverse experimental platforms of mouse transcriptomics data; (iii) small sample size and limited training data source and (iv) capable to estimate the proportion of 35 cell types in blood, inflammatory, central nervous or hematopoietic systems. In silico and experimental validation of SSMD demonstrated its high sensitivity and accuracy in identifying (sub) cell types and predicting cell proportions comparing with state-of-the-arts methods. A user-friendly R package and a web server of SSMD are released via https://github.com/xiaoyulu95/SSMD.
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Affiliation(s)
- Xiaoyu Lu
- Department of BioHealth Informatics, Indiana University−Purdue University Indianapolis
| | - Szu-Wei Tu
- Department of BioHealth Informatics, Indiana University−Purdue University Indianapolis
| | - Wennan Chang
- Department of Electrical and Computer Engineering, Purdue University
| | - Changlin Wan
- Department of Electrical and Computer Engineering, Purdue University
| | - Jiashi Wang
- Biomedical Data Research Data (BDRD) Lab at Indiana University School of Medicine
| | - Yong Zang
- Department of Biostatistics and a member of the Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
| | - Baskar Ramdas
- Department of Pediatrics, Indiana University School of Medicine
| | - Reuben Kapur
- Department of Pediatrics, Indiana University School of Medicine
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - Sha Cao
- Computational Biology and Bioinformatics, Indiana University School of Medicine
| | - Chi Zhang
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
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Rescuing Auditory Temporal Processing with a Novel Augmented Acoustic Environment in an Animal Model of Congenital Hearing Loss. eNeuro 2021; 8:ENEURO.0231-21.2021. [PMID: 34155086 PMCID: PMC8281262 DOI: 10.1523/eneuro.0231-21.2021] [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: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Congenital sensorineural hearing loss (SNHL) affects thousands of infants each year and results in significant delays in speech and language development. Previous studies have shown that early exposure to a simple augmented acoustic environment (AAE) can limit the effects of progressive SNHL on hearing sensitivity. However, SNHL is also accompanied by hearing loss that is not assessed on standard audiological examinations, such as reduced temporal processing acuity. To assess whether sound therapy may improve these deficits, a mouse model of congenital SNHL was exposed to simple or temporally complex AAE. The DBA/2J mouse strain develops rapid, base to apex, progressive SNHL beginning at birth and is functionally deaf by six months of age. Hearing sensitivity and auditory brainstem function was measured using otoacoustic emissions, auditory brainstem response (ABR) and extracellular recording from the inferior colliculus (IC) in mice following exposure to 30 d of continuous AAE. Peripheral function and sound sensitivity in auditory midbrain neurons improved following exposure to both types of AAE. However, exposure to a novel, temporally complex AAE more strongly improved a measure of temporal processing acuity, neural gap-in-noise detection in the auditory midbrain. These experiments suggest that targeted sound therapy may be harnessed to improve hearing outcomes for children suffering from congenital SNHL.
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Bansal R, Nagel M, Stopkova R, Sofer Y, Kimchi T, Stopka P, Spehr M, Ben-Shaul Y. Do all mice smell the same? Chemosensory cues from inbred and wild mouse strains elicit stereotypic sensory representations in the accessory olfactory bulb. BMC Biol 2021; 19:133. [PMID: 34182994 PMCID: PMC8240315 DOI: 10.1186/s12915-021-01064-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background For many animals, chemosensory cues are vital for social and defensive interactions and are primarily detected and processed by the vomeronasal system (VNS). These cues are often inherently associated with ethological meaning, leading to stereotyped behaviors. Thus, one would expect consistent representation of these stimuli across different individuals. However, individuals may express different arrays of vomeronasal sensory receptors and may vary in the pattern of connections between those receptors and projection neurons in the accessory olfactory bulb (AOB). In the first part of this study, we address the ability of individuals to form consistent representations despite these potential sources of variability. The second part of our study is motivated by the fact that the majority of research on VNS physiology involves the use of stimuli derived from inbred animals. Yet, it is unclear whether neuronal representations of inbred-derived stimuli are similar to those of more ethologically relevant wild-derived stimuli. Results First, we compared sensory representations to inbred, wild-derived, and wild urine stimuli in the AOBs of males from two distinct inbred strains, using them as proxies for individuals. We found a remarkable similarity in stimulus representations across the two strains. Next, we compared AOB neuronal responses to inbred, wild-derived, and wild stimuli, again using male inbred mice as subjects. Employing various measures of neuronal activity, we show that wild-derived and wild stimuli elicit responses that are broadly similar to those from inbred stimuli: they are not considerably stronger or weaker, they show similar levels of sexual dimorphism, and when examining population-level activity, cluster with inbred mouse stimuli. Conclusions Despite strain-specific differences and apparently random connectivity, the AOB can maintain stereotypic sensory representations for broad stimulus categories, providing a substrate for common stereotypical behaviors. In addition, despite many generations of inbreeding, AOB representations capture the key ethological features (i.e., species and sex) of wild-derived and wild counterparts. Beyond these broad similarities, representations of stimuli from wild mice are nevertheless distinct from those elicited by inbred mouse stimuli, suggesting that laboratory inbreeding has indeed resulted in marked modifications of urinary secretions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01064-7.
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Affiliation(s)
- Rohini Bansal
- Department of Medical Neurobiology, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maximilian Nagel
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Romana Stopkova
- BIOCEV group, Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Yizhak Sofer
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Kimchi
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Pavel Stopka
- BIOCEV group, Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marc Spehr
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Yoram Ben-Shaul
- Department of Medical Neurobiology, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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