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Workman AM, Heaton MP, Vander Ley BL, Webster DA, Sherry L, Bostrom JR, Larson S, Kalbfleisch TS, Harhay GP, Jobman EE, Carlson DF, Sonstegard TS. First gene-edited calf with reduced susceptibility to a major viral pathogen. PNAS NEXUS 2023; 2:pgad125. [PMID: 37181049 PMCID: PMC10167990 DOI: 10.1093/pnasnexus/pgad125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023]
Abstract
Bovine viral diarrhea virus (BVDV) is one of the most important viruses affecting the health and well-being of bovine species throughout the world. Here, we used CRISPR-mediated homology-directed repair and somatic cell nuclear transfer to produce a live calf with a six amino acid substitution in the BVDV binding domain of bovine CD46. The result was a gene-edited calf with dramatically reduced susceptibility to infection as measured by reduced clinical signs and the lack of viral infection in white blood cells. The edited calf has no off-target edits and appears normal and healthy at 20 months of age without obvious adverse effects from the on-target edit. This precision bred, proof-of-concept animal provides the first evidence that intentional genome alterations in the CD46 gene may reduce the burden of BVDV-associated diseases in cattle and is consistent with our stepwise, in vitro and ex vivo experiments with cell lines and matched fetal clones.
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Affiliation(s)
- Aspen M Workman
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Michael P Heaton
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska–Lincoln, 820 Road 313 Clay Center, NE 68933, USA
| | - Dennis A Webster
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | - Luke Sherry
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | | | - Sabreena Larson
- Acceligen Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | - Theodore S Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd Lexington, KY 40546, USA
| | - Gregory P Harhay
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Erin E Jobman
- Great Plains Veterinary Educational Center, University of Nebraska–Lincoln, 820 Road 313 Clay Center, NE 68933, USA
| | - Daniel F Carlson
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
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Petersen JL, Kalbfleisch TS, Parris M, Tietze SM, Cruickshank J. MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens). J Hered 2020; 111:182-193. [PMID: 31714577 PMCID: PMC7530542 DOI: 10.1093/jhered/esz070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Small numbers of domestic yak (Bos grunniens) were imported to North America in the late 19th century indirectly from the Qinghai-Tibetan Plateau. Coat color of yak is of interest for fiber production, aesthetics, and as a potential indicator of recent hybridization with cattle. North American yak are classified into 3 major coat color patterns depending upon the presence and extent of white markings. They are further classified by nose pigmentation (black or gray). The aim of this study was to identify loci involved in white patterning and nose pigmentation of North American yak. Genotyping by mass spectrometry of markers identified through Sanger and whole-genome sequencing revealed a 388 kb haplotype of KIT associated in a semi-dominant manner with white coloration in this population of yak. This KIT haplotype is similar to both a haplotype found in white-faced Chinese yak and to haplotypes found in cattle but is divergent from other Bos species such as bison, gaur, and banteng. Melanocortin 1 receptor (MC1R) was implicated as a dominant determinant of black nose color with a single haplotype containing 2 missense mutations perfectly associated with the phenotype. The MC1R haplotype associated with black nose pigment is also similar to cattle haplotypes. No cattle studied, however, shared either of the 2 haplotypes associated with color in yak, suggesting these alleles were introgressed into yak before they were imported to North America. These results provide molecular insight into the history of North American yak and information from which breeders can determine possible color outcomes of matings.
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Affiliation(s)
- Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE
| | - Theodore S Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY
| | - Morgan Parris
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE
| | - Shauna M Tietze
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE
| | - Jenifer Cruickshank
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR
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Kim AS, Zimmerman O, Fox JM, Nelson CA, Basore K, Zhang R, Durnell L, Desai C, Bullock C, Deem SL, Oppenheimer J, Shapiro B, Wang T, Cherry S, Coyne CB, Handley SA, Landis MJ, Fremont DH, Diamond MS. An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. Cell Host Microbe 2020; 27:428-440.e9. [PMID: 32075743 DOI: 10.1016/j.chom.2020.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Accepted: 01/14/2020] [Indexed: 01/08/2023]
Abstract
Alphaviruses are emerging, mosquito-transmitted RNA viruses with poorly understood cellular tropism and species selectivity. Mxra8 is a receptor for multiple alphaviruses including chikungunya virus (CHIKV). We discovered that while expression of mouse, rat, chimpanzee, dog, horse, goat, sheep, and human Mxra8 enables alphavirus infection in cell culture, cattle Mxra8 does not. Cattle Mxra8 encodes a 15-amino acid insertion in its ectodomain that prevents Mxra8 binding to CHIKV. Identical insertions are present in zebu, yak, and the extinct auroch. As other Bovinae lineages contain related Mxra8 sequences, this insertion likely occurred at least 5 million years ago. Removing the Mxra8 insertion in Bovinae enhances alphavirus binding and infection, while introducing the insertion into mouse Mxra8 blocks CHIKV binding, prevents infection by multiple alphaviruses in cells, and mitigates CHIKV-induced pathogenesis in mice. Our studies on how this insertion provides resistance to CHIKV infection could facilitate countermeasures that disrupt Mxra8 interactions with alphaviruses.
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Affiliation(s)
- Arthur S Kim
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ofer Zimmerman
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Julie M Fox
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Christopher A Nelson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katherine Basore
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rong Zhang
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lorellin Durnell
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Christopher Bullock
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sharon L Deem
- Saint Louis Zoo Institute for Conservation Medicine, Saint Louis, MO 63110, USA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Beth Shapiro
- Department Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carolyn B Coyne
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael J Landis
- Department of Biology, Washington University, Saint Louis, MO 63110, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent. Commun Biol 2018; 1:169. [PMID: 30374461 PMCID: PMC6195592 DOI: 10.1038/s42003-018-0176-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/12/2018] [Indexed: 12/30/2022] Open
Abstract
The wisent or European bison is the largest European herbivore and is completely cross-fertile with its American relative. However, mtDNA genome of wisent is similar to that of cattle, which suggests that wisent emerged as a hybrid of bison and an extinct cattle-like species. Here, we analyzed nuclear whole-genome sequences of the bovine species, and found only a minor and recent gene flow between wisent and cattle. Furthermore, we identified an appreciable heterogeneity of the nuclear gene tree topologies of the bovine species. The relative frequencies of various topologies, including the mtDNA topology, were consistent with frequencies of incomplete lineage sorting (ILS) as estimated by tree coalescence analysis. This indicates that ILS has occurred and may well account for the anomalous wisent mtDNA phylogeny as the outcome of a rare event. We propose that ILS is a possible explanation of phylogenomic anomalies among closely related species. Kun Wang et al. present a genomic analysis identifying incomplete lineage sorting and hybridization in the mitochondrial DNA of the European bison (wisent). They find that incomplete lineage sorting is the most feasible explanation for the phylogenetic heterogeneity observed in Bovidae.
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Lee MO, Dobson L, Davis BW, Skow L, Derr J, Womack JE. Genomic Structure and Tissue Expression of the NK-Lysin Gene Family in Bison. J Hered 2018; 109:598-603. [PMID: 29718298 DOI: 10.1093/jhered/esy022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a class of natural peptides with varying numbers of amino acids. They are principal components of innate immunity in vertebrates, encoding natural antibiotics and providing a protective response against a broad range of microbes including those responsible for tuberculosis, an important disease in bison. NK-lysins are AMPs that have been described in various organisms and are coded by a single gene in several mammalian species, including human. Recently, we described a family of 4 NK-lysin genes in cattle. Here, we examined NK-lysin genes in bison and identified 4 bison paralogs (NK1, NK2A, NK2B, and NK2C), although the current bison genome assembly annotates only 2 (NK1 and NK2). Sequence and phylogenetic analysis support the triplication of NK2 prior to the most recent common ancestor of bison and cattle. Comparative mapping of bison and cattle paralogs indicates that the NK-lysin family is located on bison chromosome 11 with well-conserved synteny of flanking genes relative to cattle. The 3 bison NK-lysin2 genes share high sequence similarity with each other. RNA-seq analysis demonstrates that NK2A, NK2B, and NK2C are expressed primarily in the lung, whereas NK1 is expressed at low levels in all tissues studied. This tissue expression pattern differs from that previously reported for cattle, suggesting some divergence in function since the evolutionary separation of the 2 species.
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Affiliation(s)
- Mi Ok Lee
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX
| | - Lauren Dobson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX
| | - Loren Skow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX
| | - James Derr
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX
| | - James E Womack
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A & M University, College Station, TX
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Heaton MP, Smith TPL, Freking BA, Workman AM, Bennett GL, Carnahan JK, Kalbfleisch TS. Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity. F1000Res 2017; 6:1303. [PMID: 28928950 PMCID: PMC5590088 DOI: 10.12688/f1000research.12216.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/20/2022] Open
Abstract
Background: Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals. Methods: A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams. The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line. The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U.S. sheep. Results: The genomes had a combined average read depth of 16, and an average WGS genotype scoring rate and accuracy exceeding 99%. The utility of this resource was illustrated by characterizing three genes with 14 known coding variants affecting litter size in global sheep populations: growth and differentiation factor 9 (
GDF9), bone morphogenetic protein 15 (
BMP15), and bone morphogenetic protein receptor 1B (
BMPR1B). In the 96 U.S. rams, nine missense variants encoding 11 protein variants were identified. However, only one was previously reported to affect litter size (
GDF9 V371M, Finnsheep). Two missense variants in
BMP15 were identified that had not previously been reported: R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in
BMPR1B: M64I in Katahdin, and T345N in Romanov and Finnsheep breeds. Based on the strict conservation of amino acid residues across placental mammals, the four variants encoded by
BMP15 and
BMPR1B are predicted to interfere with their function. However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in
BMP15 and
BMPR1B with daughters of these rams. Conclusions: Collectively, this report describes a new resource for discovering protein variants
in silico and identifies alleles for further testing of their effects on litter size in U.S. breeds.
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Affiliation(s)
- Michael P Heaton
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Bradley A Freking
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Aspen M Workman
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Gary L Bennett
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Jacky K Carnahan
- U.S. Meat Animal Research Center (USMARC), Clay Center, NE, 68933, USA
| | - Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
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