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Dey-Rao R, Shen S, Qu J, Melendy T. Proteomics analysis reveals novel phosphorylated residues and associated proteins of the polyomavirus DNA replication initiation complex. bioRxiv 2024:2024.02.08.579500. [PMID: 38370620 PMCID: PMC10871363 DOI: 10.1101/2024.02.08.579500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Polyomavirus ( PyV ) Large T-antigen ( LT ) is the major viral regulatory protein that targets numerous cellular factors/pathways: tumor suppressors, cell cycle regulators, transcription and chromatin regulators, as well as other factors for viral replication. LT directly recruits the cellular replication factors involved in LT's recognition of the viral origin, origin unwinding, and primer synthesis which is carried out by mutual interactions between LT, DNA polymerase alpha-primase ( Polprim ), and single strand (ss) DNA binding replication protein A ( RPA ). The activities as well as interactions of these three with each other as well as other factors, are known to be modulated by post-translational modifications (PTMs); however, modern high-sensitivity proteomic analyses of the PTMs as well as proteins associated with the three have been lacking. Elution from immunoprecipitation (IP) of the three factors were subjected to high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 479 novel phosphorylated amino acid residues (PAARs) on the three factors: 82 PAARs on SV40 LT, 305 on the Polprim heterotetrametric complex and 92 on the RPA heterotrimeric complex. LC-MS/MS analysis also identified proteins that co-immunoprecipitated (coIP-ed) with the three factors that were not previously reported: 374 with LT, 453 with Polprim and 183 with RPA. We used a bioinformatic-based approach to analyze the proteomics data and demonstrate a highly significant "enrichment" of transcription-related process associated uniquely with LT, consistent with its role as a transcriptional regulator, as opposed to Polprim and RPA associated proteins which showed no such enrichment. The most significant cell cycle related network was regulated by ETS proto-oncogene 1 (ETS1), indicating its involvement in regulatory control of DNA replication, repair, and metabolism. The interaction between LT and ETS1 is validated and shown to be independent of nucleic acids. One of the novel phosphorylated aa residues detected on LT from this study, has been demonstrated by us to affect DNA replication activities of SV40 Large T-antigen. Our data provide substantial additional novel information on PAARs, and proteins associated with PyV LT, and the cellular Polprim-, RPA- complexes which will benefit research in DNA replication, transformation, transcription, and other viral and host cellular processes.
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Karmakar M, Pérez Gómez AA, Carroll RJ, Lawley KS, Amstalden KAZ, Welsh CJ, Threadgill DW, Brinkmeyer-Langford C. Baseline Gait and Motor Function Predict Long-Term Severity of Neurological Outcomes of Viral Infection. Int J Mol Sci 2023; 24:ijms24032843. [PMID: 36769167 PMCID: PMC9917409 DOI: 10.3390/ijms24032843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Neurological dysfunction following viral infection varies among individuals, largely due to differences in their genetic backgrounds. Gait patterns, which can be evaluated using measures of coordination, balance, posture, muscle function, step-to-step variability, and other factors, are also influenced by genetic background. Accordingly, to some extent gait can be characteristic of an individual, even prior to changes in neurological function. Because neuromuscular aspects of gait are under a certain degree of genetic control, the hypothesis tested was that gait parameters could be predictive of neuromuscular dysfunction following viral infection. The Collaborative Cross (CC) mouse resource was utilized to model genetically diverse populations and the DigiGait treadmill system used to provide quantitative and objective measurements of 131 gait parameters in 142 mice from 23 CC and SJL/J strains. DigiGait measurements were taken prior to infection with the neurotropic virus Theiler's Murine Encephalomyelitis Virus (TMEV). Neurological phenotypes were recorded over 90 days post-infection (d.p.i.), and the cumulative frequency of the observation of these phenotypes was statistically associated with discrete baseline DigiGait measurements. These associations represented spatial and postural aspects of gait influenced by the 90 d.p.i. phenotype score. Furthermore, associations were found between these gait parameters with sex and outcomes considered to show resistance, resilience, or susceptibility to severe neurological symptoms after long-term infection. For example, higher pre-infection measurement values for the Paw Drag parameter corresponded with greater disease severity at 90 d.p.i. Quantitative trait loci significantly associated with these DigiGait parameters revealed potential relationships between 28 differentially expressed genes (DEGs) and different aspects of gait influenced by viral infection. Thus, these potential candidate genes and genetic variations may be predictive of long-term neurological dysfunction. Overall, these findings demonstrate the predictive/prognostic value of quantitative and objective pre-infection DigiGait measurements for viral-induced neuromuscular dysfunction.
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Affiliation(s)
- Moumita Karmakar
- Department of Statistics, College of Science, Texas A & M University, College Station, TX 77843, USA
| | - Aracely A. Pérez Gómez
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
| | - Raymond J. Carroll
- Department of Statistics, College of Science, Texas A & M University, College Station, TX 77843, USA
| | - Koedi S. Lawley
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
| | - Katia A. Z. Amstalden
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
| | - C. Jane Welsh
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
| | - David W. Threadgill
- Department of Molecular and Cellular Medicine, Texas A & M Health Science Center, Texas A & M University, College Station, TX 77843, USA
| | - Candice Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A & M University, College Station, TX 77843, USA
- Correspondence:
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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Park Y, Kim MJ, Choi Y, Kim NH, Kim L, Hong SPD, Cho HG, Yu E, Chae YK. Role of mass spectrometry-based serum proteomics signatures in predicting clinical outcomes and toxicity in patients with cancer treated with immunotherapy. J Immunother Cancer 2022; 10:jitc-2021-003566. [PMID: 35347071 PMCID: PMC8961104 DOI: 10.1136/jitc-2021-003566] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 02/03/2023] Open
Abstract
Immunotherapy has fundamentally changed the landscape of cancer treatment. However, only a subset of patients respond to immunotherapy, and a significant portion experience immune-related adverse events (irAEs). In addition, the predictive ability of current biomarkers such as programmed death-ligand 1 (PD-L1) remains unreliable and establishing better potential candidate markers is of great importance in selecting patients who would benefit from immunotherapy. Here, we focus on the role of serum-based proteomic tests in predicting the response and toxicity of immunotherapy. Serum proteomic signatures refer to unique patterns of proteins which are associated with immune response in patients with cancer. These protein signatures are derived from patient serum samples based on mass spectrometry and act as biomarkers to predict response to immunotherapy. Using machine learning algorithms, serum proteomic tests were developed through training data sets from advanced non-small cell lung cancer (Host Immune Classifier, Primary Immune Response) and malignant melanoma patients (PerspectIV test). The tests effectively stratified patients into groups with good and poor treatment outcomes independent of PD-L1 expression. Here, we review current evidence in the published literature on three liquid biopsy tests that use biomarkers derived from proteomics and machine learning for use in immuno-oncology. We discuss how these tests may inform patient prognosis as well as guide treatment decisions and predict irAE of immunotherapy. Thus, mass spectrometry-based serum proteomics signatures play an important role in predicting clinical outcomes and toxicity.
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Affiliation(s)
- Yeonggyeong Park
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Min Jeong Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yoonhee Choi
- Department of Internal Medicine, NewYork-Presbyterian Queens, Flushing, New York, USA
| | - Na Hyun Kim
- Department of Internal Medicine, AMITA Health Saint Joseph Hospital Chicago, Chicago, Illinois, USA
| | - Leeseul Kim
- Department of Internal Medicine, AMITA Health Saint Francis Hospital Evanston, Evanston, Illinois, USA
| | - Seung Pyo Daniel Hong
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hyung-Gyo Cho
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emma Yu
- Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Young Kwang Chae
- Department of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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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 Genom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Boso G, Lam O, Bamunusinghe D, Oler AJ, Wollenberg K, Liu Q, Shaffer E, Kozak CA. Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. Viruses 2021; 13:v13091864. [PMID: 34578445 PMCID: PMC8472935 DOI: 10.3390/v13091864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/04/2021] [Accepted: 09/15/2021] [Indexed: 10/26/2022] Open
Abstract
The classical laboratory mouse strains are genetic mosaics of three Mus musculus subspecies that occupy distinct regions of Eurasia. These strains and subspecies carry infectious and endogenous mouse leukemia viruses (MLVs) that can be pathogenic and mutagenic. MLVs evolved in concert with restrictive host factors with some under positive selection, including the XPR1 receptor for xenotropic/polytropic MLVs (X/P-MLVs) and the post-entry restriction factor Fv1. Since positive selection marks host-pathogen genetic conflicts, we examined MLVs for counter-adaptations at sites that interact with XPR1, Fv1, and the CAT1 receptor for ecotropic MLVs (E-MLVs). Results describe different co-adaptive evolutionary paths within the ranges occupied by these virus-infected subspecies. The interface of CAT1, and the otherwise variable E-MLV envelopes, is highly conserved; antiviral protection is afforded by the Fv4 restriction factor. XPR1 and X/P-MLVs variants show coordinate geographic distributions, with receptor critical sites in envelope, under positive selection but with little variation in envelope and XPR1 in mice carrying P-ERVs. The major Fv1 target in the viral capsid is under positive selection, and the distribution of Fv1 alleles is subspecies-correlated. These data document adaptive, spatial and temporal, co-evolutionary trajectories at the critical interfaces of MLVs and the host factors that restrict their replication.
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Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Oscar Lam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Devinka Bamunusinghe
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (A.J.O.); (K.W.)
| | - Kurt Wollenberg
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (A.J.O.); (K.W.)
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Esther Shaffer
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA; (G.B.); (O.L.); (D.B.); (Q.L.); (E.S.)
- Correspondence:
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Majhi PD, Griner NB, Mayfield JA, Compton S, Kane JJ, Baptiste TA, Dunphy KA, Roberts AL, Schneider SS, Savage EM, Patel D, Blackburn AC, Maurus KJ, Wiesmüller L, Jerry DJ. Genetic modifiers regulating DNA replication and double-strand break repair are associated with differences in mammary tumors in mouse models of Li-Fraumeni syndrome. Oncogene 2021; 40:5026-37. [PMID: 34183771 DOI: 10.1038/s41388-021-01892-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/16/2021] [Accepted: 06/04/2021] [Indexed: 01/04/2023]
Abstract
Breast cancer is the most common tumor among women with inherited variants in the TP53 tumor suppressor, but onset varies widely suggesting interactions with genetic or environmental factors. Rodent models haploinsufficent for Trp53 also develop a wide variety of malignancies associated with Li-Fraumeni Syndrome, but BALB/c mice are uniquely susceptible to mammary tumors and is genetically linked to the Suprmam1 locus on chromosome 7. To define mechanisms that interact with deficiencies in p53 to alter susceptibility to mammary tumors, we fine-mapped the Suprmam1 locus in females from an N2 backcross of BALB/cMed and C57BL/6J mice. A major modifier was localized within a 10 cM interval on chromosome 7. The effect of the locus on DNA damage responses was examined in the parental strains and mice that are congenic for C57BL/6J alleles on the BALB/cMed background (SM1-Trp53+/−). The mammary epithelium of C57BL/6J-Trp53+/− females exhibited little radiation-induced apoptosis compared to BALB/cMed-Trp53+/− and SM1-Trp53+/− females indicating that the Suprmam1B6/B6 alleles could not rescue repair of radiation-induced DNA double-strand breaks mostly relying on non-homologous end joining. In contrast, the Suprmam1B6/B6 alleles in SM1-Trp53+/− mice were sufficient to confer the C57BL/6J-Trp53+/− phenotypes in homology-directed repair and replication fork progression. The Suprmam1B6/B6 alleles in SM1-Trp53+/− mice appear to act in trans to regulate a panel of DNA repair and replication genes which lie outside the locus.
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Mansfield MJ, Tremblay BJ, Zeng J, Wei X, Hodgins H, Worley J, Bry L, Dong M, Doxey AC. Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathog 2020; 16:e1009181. [PMID: 33370413 DOI: 10.1371/journal.ppat.1009181] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/02/2021] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile is the major worldwide cause of antibiotic-associated gastrointestinal infection. A pathogenicity locus (PaLoc) encoding one or two homologous toxins, toxin A (TcdA) and toxin B (TcdB), is essential for C. difficile pathogenicity. However, toxin sequence variation poses major challenges for the development of diagnostic assays, therapeutics, and vaccines. Here, we present a comprehensive phylogenomic analysis of 8,839 C. difficile strains and their toxins including 6,492 genomes that we assembled from the NCBI short read archive. A total of 5,175 tcdA and 8,022 tcdB genes clustered into 7 (A1-A7) and 12 (B1-B12) distinct subtypes, which form the basis of a new method for toxin-based subtyping of C. difficile. We developed a haplotype coloring algorithm to visualize amino acid variation across all toxin sequences, which revealed that TcdB has diversified through extensive homologous recombination throughout its entire sequence, and formed new subtypes through distinct recombination events. In contrast, TcdA varies mainly in the number of repeats in its C-terminal repetitive region, suggesting that recombination-mediated diversification of TcdB provides a selective advantage in C. difficile evolution. The application of toxin subtyping is then validated by classifying 351 C. difficile clinical isolates from Brigham and Women's Hospital in Boston, demonstrating its clinical utility. Subtyping partitions TcdB into binary functional and antigenic groups generated by intragenic recombinations, including two distinct cell-rounding phenotypes, whether recognizing frizzled proteins as receptors, and whether it can be efficiently neutralized by monoclonal antibody bezlotoxumab, the only FDA-approved therapeutic antibody. Our analysis also identifies eight universally conserved surface patches across the TcdB structure, representing ideal targets for developing broad-spectrum therapeutics. Finally, we established an open online database (DiffBase) as a central hub for collection and classification of C. difficile toxins, which will help clinicians decide on therapeutic strategies targeting specific toxin variants, and allow researchers to monitor the ongoing evolution and diversification of C. difficile.
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Abstract
Hybrid male sterility (HMS) contributes to reproductive isolation commonly observed among house mouse (Mus musculus) subspecies, both in the wild and in laboratory crosses. Incompatibilities involving specific Prdm9 alleles and certain Chromosome (Chr) X genotypes are known determinants of fertility and HMS, and previous work in the field has demonstrated that genetic background modifies these two major loci. We constructed hybrids that have identical genotypes at Prdm9 and identical X chromosomes, but differ widely across the rest of the genome. In each case, we crossed female PWK/PhJ mice representative of the M. m. musculus subspecies to males from a classical inbred strain representative of M. m. domesticus: 129S1/SvImJ, A/J, C57BL/6J, or DBA/2J. We detected three distinct trajectories of fertility among the hybrids using breeding experiments. The PWK129S1 males were always infertile. PWKDBA2 males were fertile, despite their genotypes at the major HMS loci. We also observed age-dependent changes in fertility parameters across multiple genetic backgrounds. The PWKB6 and PWKAJ males were always infertile before 12 weeks and after 35 weeks. However, some PWKB6 and PWKAJ males were transiently fertile between 12 and 35 weeks. This observation could resolve previous contradictory reports about the fertility of PWKB6. Taken together, these results point to multiple segregating HMS modifier alleles, some of which have age-related modes of action. The ultimate identification of these alleles and their age-related mechanisms will advance understanding both of the genetic architecture of HMS and of how reproductive barriers are maintained between house mouse subspecies.
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Affiliation(s)
- Samuel J Widmayer
- Department of Biological Science, W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
- Graduate Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | | | - David L Aylor
- Department of Biological Science, W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
- Bioinformatics Research Center, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695
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Fernandez Lahore G, Raposo B, Lagerquist M, Ohlsson C, Sabatier P, Xu B, Aoun M, James J, Cai X, Zubarev RA, Nandakumar KS, Holmdahl R. Vitamin D3 receptor polymorphisms regulate T cells and T cell-dependent inflammatory diseases. Proc Natl Acad Sci U S A 2020; 117:24986-97. [PMID: 32958661 DOI: 10.1073/pnas.2001966117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It has proven difficult to identify the underlying genes in complex autoimmune diseases. Here, we use forward genetics to identify polymorphisms in the vitamin D receptor gene (Vdr) promoter, controlling Vdr expression and T cell activation. We isolated these polymorphisms in a congenic mouse line, allowing us to study the immunomodulatory properties of VDR in a physiological context. Congenic mice overexpressed VDR selectively in T cells, and thus did not suffer from calcemic effects. VDR overexpression resulted in an enhanced antigen-specific T cell response and more severe autoimmune phenotypes. In contrast, vitamin D3-deficiency inhibited T cell responses and protected mice from developing autoimmune arthritis. Our observations are likely translatable to humans, as Vdr is overexpressed in rheumatic joints. Genetic control of VDR availability codetermines the proinflammatory behavior of T cells, suggesting that increased presence of VDR at the site of inflammation might limit the antiinflammatory properties of its ligand.
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Edmondson EF, Gatti DM, Ray FA, Garcia EL, Fallgren CM, Kamstock DA, Weil MM. Genomic mapping in outbred mice reveals overlap in genetic susceptibility for HZE ion- and γ-ray-induced tumors. Sci Adv 2020; 6:eaax5940. [PMID: 32494593 PMCID: PMC7159905 DOI: 10.1126/sciadv.aax5940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 01/14/2020] [Indexed: 05/02/2023]
Abstract
Cancer risk from galactic cosmic radiation exposure is considered a potential "showstopper" for a manned mission to Mars. Calculating the actual risks confronted by spaceflight crews is complicated by our limited understanding of the carcinogenic effects of high-charge, high-energy (HZE) ions, a radiation type for which no human exposure data exist. Using a mouse model of genetic diversity, we find that the histotype spectrum of HZE ion-induced tumors is similar to the spectra of spontaneous and γ-ray-induced tumors and that the genomic loci controlling susceptibilities overlap between groups for some tumor types. Where it occurs, this overlap indicates shared tumorigenesis mechanisms regardless of the type of radiation exposure and supports the use of human epidemiological data from γ-ray exposures to predict cancer risks from galactic cosmic rays.
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Affiliation(s)
- E. F. Edmondson
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Colorado State University, Fort Collins, CO 80523, USA
| | - D. M. Gatti
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - F. A. Ray
- Colorado State University, Fort Collins, CO 80523, USA
| | - E. L. Garcia
- Colorado State University, Fort Collins, CO 80523, USA
| | | | | | - M. M. Weil
- Colorado State University, Fort Collins, CO 80523, USA
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12
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Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genet 2020; 16:e1008537. [PMID: 31961859 PMCID: PMC7010298 DOI: 10.1371/journal.pgen.1008537] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 02/10/2020] [Accepted: 11/23/2019] [Indexed: 01/08/2023] Open
Abstract
Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues-liver, lung, and kidney-in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.
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Affiliation(s)
- Gregory R. Keele
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Bryan C. Quach
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Omics Discovery and Epidemiology, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, United States of America
| | - Jennifer W. Israel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace A. Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Lauren Lewis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Alexias Safi
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paul Cotney
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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13
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Watson CT, Kos JT, Gibson WS, Newman L, Deikus G, Busse CE, Smith ML, Jackson KJ, Collins AM. A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunol Cell Biol 2019; 97:888-901. [PMID: 31441114 DOI: 10.1111/imcb.12288] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/05/2019] [Accepted: 08/20/2019] [Indexed: 01/20/2023]
Abstract
The genomes of classical inbred mouse strains include genes derived from all three major subspecies of the house mouse, Mus musculus. We recently posited that genetic diversity in the immunoglobulin heavy chain (IGH) gene loci of C57BL/6 and BALB/c mice reflects differences in subspecies origin. To investigate this hypothesis, we conducted high-throughput sequencing of IGH gene rearrangements to document IGH variable (IGHV), joining (IGHJ) and diversity (IGHD) genes in four inbred wild-derived mouse strains (CAST/EiJ, LEWES/EiJ, MSM/MsJ and PWD/PhJ) and a single disease model strain (NOD/ShiLtJ), collectively representing genetic backgrounds of several major mouse subspecies. A total of 341 germline IGHV sequences were inferred in the wild-derived strains, including 247 not curated in the international ImMunoGeneTics information system. By contrast, 83/84 inferred NOD IGHV genes had previously been observed in C57BL/6 mice. Variability among the strains examined was observed for only a single IGHJ gene, involving a description of a novel allele. By contrast, unexpected variation was found in the IGHD gene loci, with four previously unreported IGHD gene sequences being documented. Very few IGHV sequences of C57BL/6 and BALB/c mice were shared with strains representing major subspecies, suggesting that their IGH loci may be complex mosaics of genes of disparate origins. This suggests a similar level of diversity is likely present in the IGH loci of other classical inbred strains. This must now be documented if we are to properly understand interstrain variation in models of antibody-mediated disease.
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Affiliation(s)
- Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Leah Newman
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Melissa L Smith
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Katherine Jl Jackson
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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14
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Skorski M, Bamunusinghe D, Liu Q, Shaffer E, Kozak CA. Distribution of endogenous gammaretroviruses and variants of the Fv1 restriction gene in individual mouse strains and strain subgroups. PLoS One 2019; 14:e0219576. [PMID: 31291374 PMCID: PMC6619830 DOI: 10.1371/journal.pone.0219576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/26/2019] [Indexed: 01/16/2023] Open
Abstract
Inbred laboratory mouse strains carry endogenous retroviruses (ERVs) classed as ecotropic, xenotropic or polytropic mouse leukemia viruses (E-, X- or P-MLVs). Some of these MLV ERVs produce infectious virus and/or contribute to the generation of intersubgroup recombinants. Analyses of selected mouse strains have linked the appearance of MLVs and virus-induced disease to the strain complement of MLV E-ERVs and to host genes that restrict MLVs, particularly Fv1. Here we screened inbred strain DNAs and genome assemblies to describe the distribution patterns of 45 MLV ERVs and Fv1 alleles in 58 classical inbred strains grouped in two ways: by common ancestry to describe ERV inheritance patterns, and by incidence of MLV-associated lymphomagenesis. Each strain carries a unique set of ERVs, and individual ERVs are present in 5–96% of the strains, often showing lineage-specific distributions. Two ERVs are alternatively present as full-length proviruses or solo long terminal repeats. High disease incidence strains carry the permissive Fv1n allele, tested strains have highly expressed E-ERVs and most have the Bxv1 X-ERV; these three features are not present together in any low-moderate disease strain. The P-ERVs previously implicated in P-MLV generation are not preferentially found in high leukemia strains, but the three Fv1 alleles that restrict inbred strain E-MLVs are found only in low-moderate leukemia strains. This dataset helps define the genetic basis of strain differences in spontaneous lymphomagenesis, describes the distribution of MLV ERVs in strains with shared ancestry, and should help annotate sequenced strain genomes for these insertionally polymorphic and functionally important proviruses.
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Affiliation(s)
- Matthew Skorski
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Devinka Bamunusinghe
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Esther Shaffer
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- * E-mail:
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15
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Vogel H, Kamitz A, Hallahan N, Lebek S, Schallschmidt T, Jonas W, Jähnert M, Gottmann P, Zellner L, Kanzleiter T, Damen M, Altenhofen D, Burkhardt R, Renner S, Dahlhoff M, Wolf E, Müller TD, Blüher M, Joost HG, Chadt A, Al-Hasani H, Schürmann A. A collective diabetes cross in combination with a computational framework to dissect the genetics of human obesity and Type 2 diabetes. Hum Mol Genet 2019; 27:3099-3112. [PMID: 29893858 PMCID: PMC6097155 DOI: 10.1093/hmg/ddy217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
To explore the genetic determinants of obesity and Type 2 diabetes (T2D), the German Center for Diabetes Research (DZD) conducted crossbreedings of the obese and diabetes-prone New Zealand Obese mouse strain with four different lean strains (B6, DBA, C3H, 129P2) that vary in their susceptibility to develop T2D. Genome-wide linkage analyses localized more than 290 quantitative trait loci (QTL) for obesity, 190 QTL for diabetes-related traits and 100 QTL for plasma metabolites in the outcross populations. A computational framework was developed that allowed to refine critical regions and to nominate a small number of candidate genes by integrating reciprocal haplotype mapping and transcriptome data. The efficiency of the complex procedure was demonstrated for one obesity QTL. The genomic interval of 35 Mb with 502 annotated candidate genes was narrowed down to six candidates. Accordingly, congenic mice retained the obesity phenotype owing to an interval that contains three of the six candidate genes. Among these the phospholipase PLA2G4A exhibited an elevated expression in adipose tissue of obese human subjects and is therefore a critical regulator of the obesity locus. Together, our broad and complex approach demonstrates that combined- and comparative-cross analysis exhibits improved mapping resolution and represents a valid tool for the identification of disease genes.
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Affiliation(s)
- Heike Vogel
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Anne Kamitz
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Nicole Hallahan
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Sandra Lebek
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Tanja Schallschmidt
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Wenke Jonas
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Lisa Zellner
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Timo Kanzleiter
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Mareike Damen
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Delsi Altenhofen
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Ralph Burkhardt
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig D-04303, Germany
| | - Simone Renner
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Chair for Molecular Animal Breeding and Biotechnology, Gene Center.,Department of Veterinary Sciences, Center for Innovative Medical Models (CiMM), LMU Munich, D-81377 Munich, Germany
| | - Maik Dahlhoff
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Chair for Molecular Animal Breeding and Biotechnology, Gene Center.,Department of Veterinary Sciences, Center for Innovative Medical Models (CiMM), LMU Munich, D-81377 Munich, Germany
| | - Eckhard Wolf
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Chair for Molecular Animal Breeding and Biotechnology, Gene Center.,Department of Veterinary Sciences, Center for Innovative Medical Models (CiMM), LMU Munich, D-81377 Munich, Germany
| | - Timo D Müller
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany.,Division of Metabolic Diseases, Department of Medicine, Technische Universität München, Munich D-80333, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig D-04103, Germany
| | - Hans-Georg Joost
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany
| | - Alexandra Chadt
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Hadi Al-Hasani
- German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Düsseldorf D-40225, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal D-14558, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg D-85764, Germany.,Institute of Nutritional Science, University of Potsdam, Nuthetal D-14558, Germany
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16
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Nishino R, Petri S, Handel MA, Kunieda T, Fujiwara Y. Hybrid Sterility with Meiotic Metaphase Arrest in Intersubspecific Mouse Crosses. J Hered 2019; 110:183-193. [PMID: 30452700 PMCID: PMC6399516 DOI: 10.1093/jhered/esy060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
Although organisms belonging to different species and subspecies sometimes produce fertile offspring, a hallmark of the speciation process is reproductive isolation, characterized by hybrid sterility (HS) due to failure in gametogenesis. In mammals, HS is usually exhibited by males, the heterogametic sex. The phenotypic manifestations of HS are complex. The most frequently observed are abnormalities in both autosomal and sex chromosome interactions that are linked to meiotic prophase arrest or postmeiotic spermiogenesis aberrations and lead to defective or absent gametes. The aim of this study was to determine the HS phenotypes in intersubspecific F1 mice produced by matings between Mus musculus molossinus-derived strains and diverse Mus musculus domesticus-inbred laboratory mouse strains. Most of these crosses produced fertile F1 offspring. However, when female BALB/cJ (domesticus) mice were mated to male JF1/MsJ (molossinus) mice, the (BALBdomxJF1mol)F1 males were sterile, whereas the (JF1molxBALBdom)F1 males produced by the reciprocal crossings were fertile; thus the sterility phenotype was asymmetric. The sterile (BALBdomxJF1mol) F1 males exhibited a high rate of meiotic metaphase arrest with misaligned chromosomes, probably related to a high frequency of XY dissociation. Intriguingly, in the sterile (BALBdomxJF1mol)F1 males we observed aberrant allele-specific expression of several meiotic genes, that play critical roles in important meiotic events including chromosome pairing. Together, these observations of an asymmetrical HS phenotype in intersubspecific F1 males, probably owing to meiotic defects in the meiotic behavior of the XY chromosomes pair and possibly also transcriptional misregulation of meiotic genes, provide new models and directions for understanding speciation mechanisms in mammals.
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Affiliation(s)
- Risako Nishino
- Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Okayama, Japan
- Institute of Environmental Toxicology, Joso, Ibaraki, Japan
| | | | | | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, Okayama, Japan
| | - Yasuhiro Fujiwara
- Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Okayama, Japan
- The Jackson Laboratory, Bar Harbor, ME, Japan
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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17
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Collins AM, Watson CT. Immunoglobulin Light Chain Gene Rearrangements, Receptor Editing and the Development of a Self-Tolerant Antibody Repertoire. Front Immunol 2018; 9:2249. [PMID: 30349529 PMCID: PMC6186787 DOI: 10.3389/fimmu.2018.02249] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Discussion of the antibody repertoire usually emphasizes diversity, but a conspicuous feature of the light chain repertoire is its lack of diversity. The diversity of reported allelic variants of germline light chain genes is also limited, even in well-studied species. In this review, the implications of this lack of diversity are considered. We explore germline and rearranged light chain genes in a variety of species, with a particular focus on human and mouse genes. The importance of the number, organization and orientation of the genes for the control of repertoire development is discussed, and we consider how primary rearrangements and receptor editing together shape the expressed light chain repertoire. The resulting repertoire is dominated by just a handful of IGKV and IGLV genes. It has been hypothesized that an important function of the light chain is to guard against self-reactivity, and the role of secondary rearrangements in this process could explain the genomic organization of the light chain genes. It could also explain why the light chain repertoire is so limited. Heavy and light chain genes may have co-evolved to ensure that suitable light chain partners are usually available for each heavy chain that forms early in B cell development. We suggest that the co-evolved loci of the house mouse often became separated during the inbreeding of laboratory mice, resulting in new pairings of loci that are derived from different sub-species of the house mouse. A resulting vulnerability to self-reactivity could explain at least some mouse models of autoimmune disease.
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Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
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18
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Bamunusinghe D, Skorski M, Buckler-White A, Kozak CA. Xenotropic Mouse Gammaretroviruses Isolated from Pre-Leukemic Tissues Include a Recombinant. Viruses 2018; 10:v10080418. [PMID: 30096897 PMCID: PMC6116186 DOI: 10.3390/v10080418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/28/2018] [Accepted: 08/03/2018] [Indexed: 11/16/2022] Open
Abstract
Naturally-occurring lymphomagenesis is induced by mouse leukemia viruses (MLVs) carried as endogenous retroviruses (ERVs). Replicating the ecotropic MLVs recombines with polytropic (P-ERVs) and xenotropic ERVs (X-ERVs) to generate pathogenic viruses with an altered host range. While most recovered nonecotropic recombinants have a polytropic host range, the X-MLVs are also present in the pre-leukemic tissues. We analyzed two such isolates from the AKR mice to identify their ERV progenitors and to look for evidence of recombination. AKR40 resembles the active X-ERV Bxv1, while AKR6 has a Bxv1-like backbone with substitutions that alter the long terminal repeat (LTR) enhancer and the envelope (env). AKR6 has a modified xenotropic host range, and its Env residue changes all lie outside of the domain that governs the receptor choice. The AKR6 segment spanning the two substitutions, but not the entire AKR6 env-LTR, exists as an ERV, termed Xmv67, in AKR, but not in the C57BL/6 mice. This suggests that AKR6 is the product of one, not two, recombination events. Xmv67 originated in the Asian mice. These data indicate that the recombinant X-MLVs that can be generated during lymphomagenesis, describe a novel X-ERV subtype found in the AKR genome, but not in the C57BL/6 reference genome, and identify residues in the envelope C-terminus that may influence the host range.
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Affiliation(s)
- Devinka Bamunusinghe
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0460, USA.
| | - Matthew Skorski
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0460, USA.
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0460, USA.
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0460, USA.
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19
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Collins AM, Jackson KJL. On being the right size: antibody repertoire formation in the mouse and human. Immunogenetics 2018; 70:143-58. [DOI: 10.1007/s00251-017-1049-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023]
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20
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Abstract
Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales.
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Affiliation(s)
- Tom R Booker
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Ontario, L5L 1C6, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
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21
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Donoghue LJ, Livraghi-Butrico A, McFadden KM, Thomas JM, Chen G, Grubb BR, O'Neal WK, Boucher RC, Kelada SNP. Identification of trans Protein QTL for Secreted Airway Mucins in Mice and a Causal Role for Bpifb1. Genetics 2017; 207:801-12. [PMID: 28851744 DOI: 10.1534/genetics.117.300211] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
Abstract
Mucus hyper-secretion is a hallmark feature of asthma and other muco-obstructive airway diseases. The mucin proteins MUC5AC and MUC5B are the major glycoprotein components of mucus and have critical roles in airway defense. Despite the biomedical importance of these two proteins, the loci that regulate them in the context of natural genetic variation have not been studied. To identify genes that underlie variation in airway mucin levels, we performed genetic analyses in founder strains and incipient lines of the Collaborative Cross (CC) in a house dust mite mouse model of asthma. CC founder strains exhibited significant differences in MUC5AC and MUC5B, providing evidence of heritability. Analysis of gene and protein expression of Muc5ac and Muc5b in incipient CC lines (n = 154) suggested that post-transcriptional events were important regulators of mucin protein content in the airways. Quantitative trait locus (QTL) mapping identified distinct, trans protein QTL for MUC5AC (chromosome 13) and MUC5B (chromosome 2). These two QTL explained 18 and 20% of phenotypic variance, respectively. Examination of the MUC5B QTL allele effects and subsequent phylogenetic analysis allowed us to narrow the MUC5B QTL and identify Bpifb1 as a candidate gene. Bpifb1 mRNA and protein expression were upregulated in parallel to MUC5B after allergen challenge, and Bpifb1 knockout mice exhibited higher MUC5B expression. Thus, BPIFB1 is a novel regulator of MUC5B.
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Makhanova N, Morgan AP, Kayashima Y, Makhanov A, Hiller S, Zhilicheva S, Xu L, Pardo-Manuel de Villena F, Maeda N. Genetic architecture of atherosclerosis dissected by QTL analyses in three F2 intercrosses of apolipoprotein E-null mice on C57BL6/J, DBA/2J and 129S6/SvEvTac backgrounds. PLoS One 2017; 12:e0182882. [PMID: 28837567 PMCID: PMC5570285 DOI: 10.1371/journal.pone.0182882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/26/2017] [Indexed: 12/20/2022] Open
Abstract
Quantitative trait locus (QTL) analyses of intercross populations between widely used mouse inbred strains provide a powerful approach for uncovering genetic factors that influence susceptibility to atherosclerosis. Epistatic interactions are common in complex phenotypes and depend on genetic backgrounds. To dissect genetic architecture of atherosclerosis, we analyzed F2 progeny from a cross between apolipoprotein E-null mice on DBA/2J (DBA-apoE) and C57BL/6J (B6-apoE) genetic backgrounds and compared the results with those from two previous F2 crosses of apolipoprotein E-null mice on 129S6/SvEvTac (129-apoE) and DBA-apoE backgrounds, and B6-apoE and 129-apoE backgrounds. In these round-robin crosses, in which each parental strain was crossed with two others, large-effect QTLs are expected to be detectable at least in two crosses. On the other hand, observation of QTLs in one cross only may indicate epistasis and/or absence of statistical power. For atherosclerosis at the aortic arch, Aath4 on chromosome (Chr)2:66 cM follows the first pattern, with significant QTL peaks in (DBAx129)F2 and (B6xDBA)F2 mice but not in (B6x129)F2 mice. We conclude that genetic variants unique to DBA/2J at Aath4 confer susceptibility to atherosclerosis at the aortic arch. A similar pattern was observed for Aath5 on chr10:35 cM, verifying that the variants unique to DBA/2J at this locus protect against arch plaque development. However, multiple loci, including Aath1 (Chr1:49 cM), and Aath2 (Chr1:70 cM) follow the second type of pattern, showing significant peaks in only one of the three crosses (B6-apoE x 129-apoE). As for atherosclerosis at aortic root, the majority of QTLs, including Ath29 (Chr9:33 cM), Ath44 (Chr1:68 cM) and Ath45 (Chr2:83 cM), was also inconsistent, being significant in only one of the three crosses. Only the QTL on Chr7:37 cM was consistently suggestive in two of the three crosses. Thus QTL analysis of round-robin crosses revealed the genetic architecture of atherosclerosis.
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Affiliation(s)
- Natalia Makhanova
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Andrew P. Morgan
- Department of Genetics and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Yukako Kayashima
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Andrei Makhanov
- College of Computing, Georgia Institute of Technology, Atlanta, United States of America
| | - Sylvia Hiller
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Svetlana Zhilicheva
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Longquan Xu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Nobuyo Maeda
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
- * E-mail:
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Shorter JR, Odet F, Aylor DL, Pan W, Kao CY, Fu CP, Morgan AP, Greenstein S, Bell TA, Stevans AM, Feathers RW, Patel S, Cates SE, Shaw GD, Miller DR, Chesler EJ, McMillian L, O'Brien DA, Villena FP. Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross. Genetics 2017; 206:557-72. [PMID: 28592496 DOI: 10.1534/genetics.116.199596] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/09/2017] [Indexed: 11/18/2022] Open
Abstract
The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.
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Gatti DM, Weber SN, Goodwin NC, Lammert F, Churchill GA. Genetic background influences susceptibility to chemotherapy-induced hematotoxicity. Pharmacogenomics J 2018; 18:319-30. [PMID: 28607509 DOI: 10.1038/tpj.2017.23] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
Hematotoxicity is a life-threatening side effect of many chemotherapy regimens. While clinical factors influence patient responses, genetic factors may also play an important role. We sought to identify genomic loci that influence chemotherapy-induced hematotoxicity by dosing Diversity Outbred mice with one of three chemotherapy drugs; doxorubicin, cyclophosphamide or docetaxel. We observed that each drug had a distinct effect on both the changes in blood cell sub-populations and the underlying genetic architecture of hematotoxicity. For doxorubicin, we mapped the change in cell counts before and after dosing and found that alleles of ATP-binding cassette B1B (Abcb1b) on chromosome 5 influence all cell populations. For cyclophosphamide and docetaxel, we found that each cell population was influenced by distinct loci, none of which overlapped between drugs. These results suggest that susceptibility to chemotherapy-induced hematotoxicity is influenced by different genes for different chemotherapy drugs.
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Abstract
In this chapter, we will use the example of the identification of Tnni3k as a modulator of cardiac conduction to introduce you to the use of a murine F2-generation intercross as a powerful method for the identification of novel genes relevant for cardiovascular traits. Murine F2-progeny is a genetically diverse panel of mice with differences in phenotype manifestations, e.g. cardiovascular traits such as cardiomyopathy and ECG parameters. This chapter discusses the best strategies for using F2-mice for genetic mapping. Moreover, we provide an example of the feasibility of identification of new genes modulating cardiac function utilizing the technique of mapping quantitative trait loci (QTLs) and a systems genetics integration of available genetic, gene expression, and phenotypic data.
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Affiliation(s)
- Svitlana Podliesna
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Elisabeth M Lodder
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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Reyes Fernandez PC, Replogle RA, Wang L, Zhang M, Fleet JC. Novel Genetic Loci Control Calcium Absorption and Femur Bone Mass as Well as Their Response to Low Calcium Intake in Male BXD Recombinant Inbred Mice. J Bone Miner Res 2016; 31:994-1002. [PMID: 26636428 PMCID: PMC4862900 DOI: 10.1002/jbmr.2760] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/24/2015] [Accepted: 12/02/2015] [Indexed: 12/30/2022]
Abstract
Low dietary calcium (Ca) intake during growth limits peak bone mass but physiological adaptation can prevent this adverse effect. To assess the genetic control on the physiologic response to dietary Ca restriction (RCR), we conducted a study in 51 BXD lines fed either 0.5% (basal) or 0.25% (low) Ca diets from ages 4 to 12 weeks (n = 8/line/diet). Ca absorption (CaAbs), femur bone mineral density (BMD), and bone mineral content (BMC) were examined. ANCOVA with body size as covariate was used to detect significant line and diet main effects, and line-by-diet interactions. Body size-corrected residuals were used for linkage mapping and to estimate heritability (h(2) ). Loci controlling the phenotypes were identified using composite interval mapping on each diet and for the RCR. h(2) of basal phenotypes (0.37-0.43) and their RCR (0.32-0.38) was moderate. For each phenotype, we identified multiple quantitative trait loci (QTL) on each diet and for the RCR. Several loci affected multiple traits: Chr 1 (88.3-90.6 cM, CaAbs, BMC), Chr 4 (45.8-49.2 cM, CaAbs, BMD, BMC), Chr 8 (28.6-31.6 cM, CaAbs, BMD, RCR), and Chr 15 (13.6-24 cM, BMD, BMC; 32.3-36 cM, CaAbs RCR, BMD). This suggests that gene clusters may regulate interdependent bone-related phenotypes. Using in silico expression QTL (eQTL) mapping and bioinformatic tools, we identified novel candidates for the regulation of bone under Ca stress (Ext1, Deptor), and for the first time, we report genes modulating Ca absorption (Inadl, Sc4mol, Sh3rf1, and Dennd3), and both Ca and bone metabolism (Tceanc2, Tll1, and Aadat). Our data reveal gene-by-diet interactions and the existence of novel relationships between bone and Ca metabolism during growth. © 2015 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Rebecca A Replogle
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Libo Wang
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - James C Fleet
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
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Bamunusinghe D, Naghashfar Z, Buckler-White A, Plishka R, Baliji S, Liu Q, Kassner J, Oler AJ, Hartley J, Kozak CA. Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice. J Virol 2016; 90:4186-98. [PMID: 26865715 DOI: 10.1128/JVI.03186-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/03/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Mouse leukemia viruses (MLVs) are found in the common inbred strains of laboratory mice and in the house mouse subspecies ofMus musculus Receptor usage and envelope (env) sequence variation define three MLV host range subgroups in laboratory mice: ecotropic, polytropic, and xenotropic MLVs (E-, P-, and X-MLVs, respectively). These exogenous MLVs derive from endogenous retroviruses (ERVs) that were acquired by the wild mouse progenitors of laboratory mice about 1 million years ago. We analyzed the genomes of seven MLVs isolated from Eurasian and American wild mice and three previously sequenced MLVs to describe their relationships and identify their possible ERV progenitors. The phylogenetic tree based on the receptor-determining regions ofenvproduced expected host range clusters, but these clusters are not maintained in trees generated from other virus regions. Colinear alignments of the viral genomes identified segmental homologies to ERVs of different host range subgroups. Six MLVs show close relationships to a small xenotropic ERV subgroup largely confined to the inbred mouse Y chromosome.envvariations define three E-MLV subtypes, one of which carries duplications of various sizes, sequences, and locations in the proline-rich region ofenv Outside theenvregion, all E-MLVs are related to different nonecotropic MLVs. These results document the diversity in gammaretroviruses isolated from globally distributedMussubspecies, provide insight into their origins and relationships, and indicate that recombination has had an important role in the evolution of these mutagenic and pathogenic agents. IMPORTANCE Laboratory mice carry mouse leukemia viruses (MLVs) of three host range groups which were acquired from their wild mouse progenitors. We sequenced the complete genomes of seven infectious MLVs isolated from geographically separated Eurasian and American wild mice and compared them with endogenous germ line retroviruses (ERVs) acquired early in house mouse evolution. We did this because the laboratory mouse viruses derive directly from specific ERVs or arise by recombination between different ERVs. The six distinctively different wild mouse viruses appear to be recombinants, often involving different host range subgroups, and most are related to a distinctive, largely Y-chromosome-linked MLV ERV subtype. MLVs with ecotropic host ranges show the greatest variability with extensive inter- and intrasubtype envelope differences and with homologies to other host range subgroups outside the envelope. The sequence diversity among these wild mouse isolates helps define their relationships and origins and emphasizes the importance of recombination in their evolution.
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Fleet JC, Replogle RA, Reyes-Fernandez P, Wang L, Zhang M, Clinkenbeard EL, White KE. Gene-by-Diet Interactions Affect Serum 1,25-Dihydroxyvitamin D Levels in Male BXD Recombinant Inbred Mice. Endocrinology 2016; 157:470-81. [PMID: 26587785 PMCID: PMC4733130 DOI: 10.1210/en.2015-1786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
1,25-Dihydroxyvitamin D (1,25[OH]2D) regulates calcium (Ca), phosphate, and bone metabolism. Serum 1,25(OH)2D levels are reduced by low vitamin D status and high fibroblast growth factor 23 (FGF23) levels and increased by low Ca intake and high PTH levels. Natural genetic variation controls serum 25-hydroxyvitamin D (25[OH]D) levels, but it is unclear how it controls serum 1,25(OH)2D or the response of serum 1,25(OH)2D levels to dietary Ca restriction (RCR). Male mice from 11 inbred lines and from 51 BXD recombinant inbred lines were fed diets with either 0.5% (basal) or 0.25% Ca from 4 to 12 weeks of age (n = 8 per line per diet). Significant variation among the lines was found in basal serum 1,25(OH)2D and in the RCR as well as basal serum 25(OH)D and FGF23 levels. 1,25(OH)2D was not correlated to 25(OH)D but was negatively correlated to FGF23 (r = -0.5). Narrow sense heritability of 1,25(OH)2D was 0.67 on the 0.5% Ca diet, 0.66 on the 0.25% Ca diet, and 0.59 for the RCR, indicating a strong genetic control of serum 1,25(OH)2D. Genetic mapping revealed many loci controlling 1,25(OH)2D (seven loci) and the RCR (three loci) as well as 25(OH)D (four loci) and FGF23 (two loci); a locus on chromosome 18 controlled both 1,25(OH)2D and FGF23. Candidate genes underlying loci include the following: Ets1 (1,25[OH]2D), Elac1 (FGF23 and 1,25[OH]2D), Tbc1d15 (RCR), Plekha8 and Lyplal1 (25[OH]D), and Trim35 (FGF23). This report is the first to reveal that serum 1,25(OH)2D levels are controlled by multiple genetic factors and that some of these genetic loci interact with the dietary environment.
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Affiliation(s)
- James C Fleet
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Rebecca A Replogle
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Perla Reyes-Fernandez
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Libo Wang
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Min Zhang
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Erica L Clinkenbeard
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Kenneth E White
- Departments of Nutrition Science (J.C.F., R.A.R., P.R.-F.) and Statistics (L.W., M.Z.), Purdue University, West Lafayette, Indiana 47907-2059; and Department of Medical and Molecular Genetics (E.L.C., K.E.W.), Indiana University School of Medicine, Indianapolis, Indiana 46202
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Abstract
Motivation: Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational problem is to infer these events in the evolutionary history for given modern genomes, a task for which many algorithms have been proposed under various constraints. Algorithms that can handle both rearrangements and content-modifying events such as duplications and losses remain few and limited in their applicability. Results: We study the comparison of two genomes under a model including general rearrangements (through double-cut-and-join) and segmental duplications. We formulate the comparison as an optimization problem and describe an exact algorithm to solve it by using an integer linear program. We also devise a sufficient condition and an efficient algorithm to identify optimal substructures, which can simplify the problem while preserving optimality. Using the optimal substructures with the integer linear program (ILP) formulation yields a practical and exact algorithm to solve the problem. We then apply our algorithm to assign in-paralogs and orthologs (a necessary step in handling duplications) and compare its performance with that of the state-of-the-art method MSOAR, using both simulations and real data. On simulated datasets, our method outperforms MSOAR by a significant margin, and on five well-annotated species, MSOAR achieves high accuracy, yet our method performs slightly better on each of the 10 pairwise comparisons. Availability and implementation:http://lcbb.epfl.ch/softwares/coser. Contact:mingfu.shao@epfl.ch or bernard.moret@epfl.ch
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Affiliation(s)
- Mingfu Shao
- School of Computer and Communication Sciences, EPFL, CH-1015, Lausanne, Switzerland
| | - Bernard M E Moret
- School of Computer and Communication Sciences, EPFL, CH-1015, Lausanne, Switzerland
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Rutledge H, Baran-Gale J, de Villena FPM, Chesler EJ, Churchill GA, Sethupathy P, Kelada SNP. Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population. BMC Genomics 2015; 16:633. [PMID: 26303911 PMCID: PMC4548451 DOI: 10.1186/s12864-015-1732-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/29/2015] [Indexed: 12/17/2022] Open
Abstract
Background Allergic airway diseases (AADs) such as asthma are characterized in part by granulocytic airway inflammation. The gene regulatory networks that govern granulocyte recruitment are poorly understood, but evidence is accruing that microRNAs (miRNAs) play an important role. To identify miRNAs that may underlie AADs, we used two complementary approaches that leveraged the genotypic and phenotypic diversity of the Collaborative Cross (CC) mouse population. In the first approach, we sought to identify miRNA expression quantitative trait loci (eQTL) that overlap QTL for AAD-related phenotypes. Specifically, CC founder strains and incipient lines of the CC were sensitized and challenged with house dust mite allergen followed by measurement of granulocyte recruitment to the lung. Total lung RNA was isolated and miRNA was measured using arrays for CC founders and qRT-PCR for incipient CC lines. Results Among CC founders, 92 miRNAs were differentially expressed. We measured the expression of 40 of the most highly expressed of these 92 miRNAs in the incipient lines of the CC and identified 18 eQTL corresponding to 14 different miRNAs. Surprisingly, half of these eQTL were distal to the corresponding miRNAs, and even on different chromosomes. One of the largest-effect local miRNA eQTL was for miR-342-3p, for which we identified putative causal variants by bioinformatic analysis of the effects of single nucleotide polymorphisms on RNA structure. None of the miRNA eQTL co-localized with QTL for eosinophil or neutrophil recruitment. In the second approach, we constructed putative miRNA/mRNA regulatory networks and identified three miRNAs (miR-497, miR-351 and miR-31) as candidate master regulators of genes associated with neutrophil recruitment. Analysis of a dataset from human keratinocytes transfected with a miR-31 inhibitor revealed two target genes in common with miR-31 targets correlated with neutrophils, namely Oxsr1 and Nsf. Conclusions miRNA expression in the allergically inflamed murine lung is regulated by genetic loci that are smaller in effect size compared to mRNA eQTL and often act in trans. Thus our results indicate that the genetic architecture of miRNA expression is different from mRNA expression. We identified three miRNAs, miR-497, miR-351 and miR-31, that are candidate master regulators of genes associated with neutrophil recruitment. Because miR-31 is expressed in airway epithelia and is predicted to target genes with known links to neutrophilic inflammation, we suggest that miR-31 is a potentially novel regulator of airway inflammation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1732-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Holly Rutledge
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Jeanette Baran-Gale
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA.
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | | | | | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Samir N P Kelada
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. .,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA.
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31
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Morgan AP, Welsh CE. Informatics resources for the Collaborative Cross and related mouse populations. Mamm Genome 2015; 26:521-39. [PMID: 26135136 DOI: 10.1007/s00335-015-9581-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/23/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Andrew P Morgan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Catherine E Welsh
- Department of Mathematics & Computer Science, Rhodes College, Memphis, TN, USA.
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32
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Frick A, Suzuki OT, Benton C, Parks B, Fedoriw Y, Richards KL, Thomas RS, Wiltshire T. Identifying genes that mediate anthracyline toxicity in immune cells. Front Pharmacol 2015; 6:62. [PMID: 25926793 PMCID: PMC4398020 DOI: 10.3389/fphar.2015.00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The role of the immune system in response to chemotherapeutic agents remains elusive. The interpatient variability observed in immune and chemotherapeutic cytotoxic responses is likely, at least in part, due to complex genetic differences. Through the use of a panel of genetically diverse mouse inbred strains, we developed a drug screening platform aimed at identifying genes underlying these chemotherapeutic cytotoxic effects on immune cells. Using genome-wide association studies (GWAS), we identified four genome-wide significant quantitative trait loci (QTL) that contributed to the sensitivity of doxorubicin and idarubicin in immune cells. Of particular interest, a locus on chromosome 16 was significantly associated with cell viability following idarubicin administration (p = 5.01 × 10(-8)). Within this QTL lies App, which encodes amyloid beta precursor protein. Comparison of dose-response curves verified that T-cells in App knockout mice were more sensitive to idarubicin than those of C57BL/6J control mice (p < 0.05). In conclusion, the cellular screening approach coupled with GWAS led to the identification and subsequent validation of a gene involved in T-cell viability after idarubicin treatment. Previous studies have suggested a role for App in in vitro and in vivo cytotoxicity to anticancer agents; the overexpression of App enhances resistance, while the knockdown of this gene is deleterious to cell viability. Further investigations should include performing mechanistic studies, validating additional genes from the GWAS, including Ppfia1 and Ppfibp1, and ultimately translating the findings to in vivo and human studies.
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Affiliation(s)
- Amber Frick
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina Chapel Hill, NC, USA
| | - Oscar T Suzuki
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina Chapel Hill, NC, USA
| | - Cristina Benton
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina Chapel Hill, NC, USA
| | - Bethany Parks
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina Chapel Hill, NC, USA ; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina Chapel Hill, NC, USA
| | - Kristy L Richards
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina Chapel Hill, NC, USA ; Department of Genetics, School of Medicine, University of North Carolina Chapel Hill, NC, USA
| | - Russell S Thomas
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA ; National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park NC, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina Chapel Hill, NC, USA ; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina Chapel Hill, NC, USA
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Ishikawa A, Sugiyama M, Hondo E, Kinoshita K, Yamagishi Y. Development of a novel pink-eyed dilution mouse model showing progressive darkening of the eyes and coat hair with aging. Exp Anim 2015; 64:207-20. [PMID: 25739360 PMCID: PMC4427736 DOI: 10.1538/expanim.14-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Oca2p-cas (oculocutaneous albinism II; pink-eyed dilution
castaneus) is a coat color mutant gene on mouse chromosome 7 that arose spontaneously in
wild Mus musculus castaneus mice. Mice homozygous for
Oca2p-cas usually exhibit pink eyes and gray coat hair on
the non-agouti genetic background, and this ordinary phenotype remains unchanged
throughout life. During breeding of a mixed strain carrying this gene on the C57BL/6J
background, we discovered a novel spontaneous mutation that causes darkening of the eyes
and coat hair with aging. In this study, we developed a novel mouse model showing this
unique phenotype. Gross observations revealed that the pink eyes and gray coat hair of the
novel mutant young mice became progressively darker in color by approximately 3 months
after birth. Light and transmission-electron microscopic observations revealed a marked
increase in melanin pigmentation of coat hair shafts and choroid of the eye in the novel
mice compared to that in the ordinary mice. Sequence analysis of
Oca2p-cas revealed a 4.1-kb deletion involving exons 15
and 16 of its wild-type gene. However, there was no sequence difference between the two
types of mutant mice. Mating experiments suggested that the novel mutant phenotype was not
inherited in a simple fashion, due to incomplete penetrance. The novel spontaneous mutant
mouse is the first example of progressive hair darkening animals and is an essential
animal model for understanding of the regulation mechanisms of melanin biosynthesis with
aging.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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Khan RT, Chevenon M, Yuki KE, Malo D. Genetic dissection of the ity3 locus identifies a role for ncf2 co-expression modules and suggests selp as a candidate gene underlying the ity3.2 locus. Front Immunol 2014; 5:375. [PMID: 25161653 PMCID: PMC4129629 DOI: 10.3389/fimmu.2014.00375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/22/2014] [Indexed: 12/19/2022] Open
Abstract
Typhoid fever and salmonellosis, which are caused by Salmonella typhi and typhimurium, respectively, are responsible for significant morbidity and mortality in both developed and developing countries. We model typhoid fever using mice infected with Salmonella typhimurium, which results in a systemic disease, whereby the outcome of infection is variable in different inbred strains of mice. This model recapitulates several clinical aspects of the human disease and allows the study of the host response to Salmonella typhimurium infection in vivo. Previous work in our laboratory has identified three loci (Ity, Ity2, and Ity3) in the wild-derived MOLF/Ei mice influencing survival after infection with Salmonella typhimurium. Fine mapping of the Ity3 locus indicated that two sub-loci contribute collectively to the susceptibility of B6.MOLF-Ity/Ity3 congenic mice to Salmonella infection. In the current paper, we provided further evidence supporting a role for Ncf2 (neutrophil cytosolic factor 2 a subunit of NADPH oxidase) as the gene underlying the Ity3.1 sub-locus. Gene expression profiling indicated that the Ity3.1 sub-locus defined a global gene expression signature with networks articulated around Ncf2. Furthermore, based on differential expression and complementation analysis using Selp (selectin-P) knock-out mice, Selp was identified as a strong candidate gene for the Ity3.2 sub-locus.
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Affiliation(s)
- Rabia Tahir Khan
- Department of Human Genetics, McGill University , Montreal, QC , Canada ; Complex Traits Group, McGill University , Montreal, QC , Canada
| | - Marie Chevenon
- Complex Traits Group, McGill University , Montreal, QC , Canada ; Department of Medicine, McGill University , Montreal, QC , Canada
| | - Kyoko E Yuki
- Department of Human Genetics, McGill University , Montreal, QC , Canada ; Complex Traits Group, McGill University , Montreal, QC , Canada
| | - Danielle Malo
- Department of Human Genetics, McGill University , Montreal, QC , Canada ; Complex Traits Group, McGill University , Montreal, QC , Canada ; Department of Medicine, McGill University , Montreal, QC , Canada
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Liu EY, Morgan AP, Chesler EJ, Wang W, Churchill GA, Pardo-Manuel de Villena F. High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics 2014; 197:91-106. [PMID: 24578350 PMCID: PMC4012503 DOI: 10.1534/genetics.114.161653] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/20/2014] [Indexed: 12/31/2022] Open
Abstract
Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these "cold regions" are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants.
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Affiliation(s)
- Eric Yi Liu
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599-3175
| | - Andrew P. Morgan
- Department of Genetics, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | | | - Wei Wang
- Department of Computer Science, University of California, Los Angeles, California 90095-1596
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264
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Kadiyala SB, Papandrea D, Herron BJ, Ferland RJ. Segregation of seizure traits in C57 black mouse substrains using the repeated-flurothyl model. PLoS One 2014; 9:e90506. [PMID: 24594686 PMCID: PMC3940897 DOI: 10.1371/journal.pone.0090506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 02/03/2014] [Indexed: 11/18/2022] Open
Abstract
Identifying the genetic basis of epilepsy in humans is difficult due to its complexity, thereby underlying the need for preclinical models with specific aspects of seizure susceptibility that are tractable to genetic analyses. In the repeated-flurothyl model, mice are given 8 flurothyl-induced seizures, once per day (the induction phase), followed by a 28-day rest period (incubation phase) and final flurothyl challenge. This paradigm allows for the tracking of multiple phenotypes including: initial generalized seizure threshold, decreases in generalized seizure threshold with repeated flurothyl exposures, and changes in the complexity of seizures over time. Given the responses we previously reported in C57BL/6J mice, we analyzed substrains of the C57BL lineage to determine if any of these phenotypes segregated in these substrains. We found that the generalized seizure thresholds of C57BL/10SNJ and C57BL/10J mice were similar to C57BL/6J mice, whereas C57BL/6NJ and C57BLKS/J mice showed lower generalized seizure thresholds. In addition, C57BL/6J mice had the largest decreases in generalized seizure thresholds over the induction phase, while the other substrains were less pronounced. Notably, we observed only clonic seizures during the induction phase in all substrains, but when rechallenged with flurothyl after a 28-day incubation phase, ∼80% of C57BL/6J and 25% of C57BL/10SNJ and C57BL/10J mice expressed more complex seizures with tonic manifestations with none of the C57BL/6NJ and C57BLKS/J mice having complex seizures with tonic manifestations. These data indicate that while closely related, the C57BL lineage has significant diversity in aspects of epilepsy that are genetically controlled. Such differences further highlight the importance of genetic background in assessing the effects of targeted deletions of genes in preclinical epilepsy models.
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Affiliation(s)
- Sridhar B. Kadiyala
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York, United States of America
| | - Dominick Papandrea
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York, United States of America
| | - Bruce J. Herron
- Wadsworth Center, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany - State University of New York, Albany, New York, United States of America
| | - Russell J. Ferland
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York, United States of America
- Department of Neurology, Albany Medical College, Albany, New York, United States of America
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Bamunusinghe D, Liu Q, Lu X, Oler A, Kozak CA. Endogenous gammaretrovirus acquisition in Mus musculus subspecies carrying functional variants of the XPR1 virus receptor. J Virol 2013; 87:9845-55. [PMID: 23824809 DOI: 10.1128/JVI.01264-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The xenotropic and polytropic mouse leukemia viruses (X-MLVs and P-MLVs, respectively) have different host ranges but use the same functionally polymorphic receptor, XPR1, for entry. Endogenous retroviruses (ERVs) of these 2 gammaretrovirus subtypes are largely segregated in different house mouse subspecies, but both MLV types are found in the classical strains of laboratory mice, which are genetic mosaics of 3 wild mouse subspecies. To describe the subspecies origins of laboratory mouse XP-MLV ERVs and their coevolutionary trajectory with their XPR1 receptor, we screened the house mouse subspecies for known and novel Xpr1 variants and for the individual full-length XP-MLV ERVs found in the sequenced C57BL mouse genome. The 12 X-MLV ERVs predate the origins of laboratory mice; they were all traced to Japanese wild mice and are embedded in the 5% of the laboratory mouse genome derived from the Asian Mus musculus musculus and, in one case, in the <1% derived from M. m. castaneus. While all 31 P-MLV ERVs map to the 95% of the laboratory mouse genome derived from P-MLV-infected M. m. domesticus, no C57BL P-MLV ERVs were found in wild M. m. domesticus. All M. m. domesticus mice carry the fully permissive XPR1 receptor allele, but all of the various restrictive XPR1 receptors, including the X-MLV-restricting laboratory mouse Xpr1(n) and a novel M. m. castaneus allele, originated in X-MLV-infected Asian mice. Thus, P-MLV ERVs show more insertional polymorphism than X-MLVs, and these differences in ERV acquisition and fixation are linked to subspecies-specific and functionally distinct XPR1 receptor variants.
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Didion JP, de Villena FPM. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome 2013; 24:1-20. [PMID: 23223940 PMCID: PMC4034049 DOI: 10.1007/s00335-012-9441-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/05/2012] [Indexed: 01/26/2023]
Abstract
The laboratory mouse is an artificial construct with a complex relationship to its natural ancestors. In 2002, the mouse became the first mammalian model organism with a reference genome. Importantly, the mouse genome sequence was assembled from data on a single inbred laboratory strain, C57BL/6. Several large-scale genetic variant discovery efforts have been conducted, resulting in a catalog of tens of millions of SNPs and structural variants. High-density genotyping arrays covering a subset of those variants have been used to produce hundreds of millions of genotypes in laboratory stocks and a small number of wild mice. These landmark resources now enable us to determine relationships among laboratory mice, assign local ancestry at fine scale, resolve important controversies, and identify a new set of challenges-most importantly, the troubling scarcity of genetic data on the very natural populations from which the laboratory mouse was derived. Our aim with this review is to provide the reader with an historical context for the mouse as a model organism and to explain how practical decisions made in the past have influenced both the architecture of the laboratory mouse genome and the design and execution of current large-scale resources. We also provide examples on how the accomplishments of the past decade can be used by researchers to streamline the use of mice in their experiments and correctly interpret results. Finally, we propose future steps that will enable the mouse community to extend its successes in the decade to come.
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Affiliation(s)
- John P. Didion
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, de Villena FPM. Status and access to the Collaborative Cross population. Mamm Genome 2012; 23:706-12. [PMID: 22847377 PMCID: PMC3463789 DOI: 10.1007/s00335-012-9410-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/04/2012] [Indexed: 12/03/2022]
Abstract
The Collaborative Cross (CC) is a panel of recombinant inbred lines derived from eight genetically diverse laboratory inbred strains. Recently, the genetic architecture of the CC population was reported based on the genotype of a single male per line, and other publications reported incompletely inbred CC mice that have been used to map a variety of traits. The three breeding sites, in the US, Israel, and Australia, are actively collaborating to accelerate the inbreeding process through marker-assisted inbreeding and to expedite community access of CC lines deemed to have reached defined thresholds of inbreeding. Plans are now being developed to provide access to this novel genetic reference population through distribution centers. Here we provide a description of the distribution efforts by the University of North Carolina Systems Genetics Core, Tel Aviv University, Israel and the University of Western Australia.
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Affiliation(s)
- Catherine E. Welsh
- Department of Computer Science, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Darla R. Miller
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Kenneth F. Manly
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Jeremy Wang
- Department of Computer Science, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Leonard McMillan
- Department of Computer Science, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Grant Morahan
- The Western Australian Institute for Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Fuad A. Iraqi
- Department of Human Microbiology, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - David W. Threadgill
- Department of Genetics, North Carolina State University, Raleigh, NC 27695 USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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