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Punetha M, Saini S, Choudhary S, Sharma S, Bala R, Kumar P, Sharma RK, Yadav PS, Datta TK, Kumar D. Establishment of CRISPR-Cas9 ribonucleoprotein mediated MSTN gene edited pregnancy in buffalo: Compare cells transfection and zygotes electroporation. Theriogenology 2024; 229:158-168. [PMID: 39178617 DOI: 10.1016/j.theriogenology.2024.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Genome editing is recognized as a powerful tool in agriculture and research, enhancing our understanding of genetic function, diseases, and productivity. However, its progress in buffaloes has lagged behind other mammals due to several challenges, including long gestational periods, single pregnancies, and high raising costs. In this study, we aimed to generate MSTN-edited buffaloes, known for their distinctive double-muscling phenotype, as a proof of concept. To meet our goal, we used somatic cell nuclear transfer (SCNT) and zygotic electroporation (CRISPR-EP) technique. For this, we firstly identified the best transfection method for introduction of RNP complex into fibroblast which was further used for SCNT. For this, we compared the transfection, cleavage efficiency and cell viability of nucleofection and lipofection in adult fibroblasts. The cleavage, transfection efficiency and cell viability of nucleofection group was found to be significantly (P ≤ 0.05) higher than lipofection group. Four MSTN edited colony were generated using nucleofection, out of which three colonies was found to be biallelic and one was monoallelic. Further, we compared the efficacy, embryonic developmental potential and subsequent pregnancy outcome of SCNT and zygotic electroporation. The blastocyst rate of electroporated group was found to be significantly (P ≤ 0.05) higher than SCNT group. However, the zygotic electroporation group resulted into two pregnancies which were confirmed to be MSTN edited. Since, the zygotic electroporation does not require complex micromanipulation techniques associated with SCNT, it has potential for facilitating the genetic modification in large livestock such as buffaloes. The present study lays the basis for inducing genetic alternation with practical or biological significance.
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Affiliation(s)
- Meeti Punetha
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Sheetal Saini
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Suman Choudhary
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Surabhi Sharma
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Renu Bala
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Pradeep Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - R K Sharma
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - P S Yadav
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - T K Datta
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India
| | - Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana, India.
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Li Z, Lan J, Shi X, Lu T, Hu X, Liu X, Chen Y, He Z. Whole-Genome Sequencing Reveals Rare Off-Target Mutations in MC1R-Edited Pigs Generated by Using CRISPR-Cas9 and Somatic Cell Nuclear Transfer. CRISPR J 2024; 7:29-40. [PMID: 38353621 DOI: 10.1089/crispr.2023.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used to create animal models for biomedical and agricultural use owing to its low cost and easy handling. However, the occurrence of erroneous cleavage (off-targeting) may raise certain concerns for the practical application of the CRISPR-Cas9 system. In this study, we created a melanocortin 1 receptor (MC1R)-edited pig model through somatic cell nuclear transfer (SCNT) by using porcine kidney cells modified by the CRISPR-Cas9 system. We then carried out whole-genome sequencing of two MC1R-edited pigs and two cloned wild-type siblings, together with the donor cells, to assess the genome-wide presence of single-nucleotide variants and small insertions and deletions (indels) and found only one candidate off-target indel in both MC1R-edited pigs. In summary, our study indicates that the minimal off-targeting effect induced by CRISPR-Cas9 may not be a major concern in gene-edited pigs created by SCNT.
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Affiliation(s)
- Zhenyang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin Lan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tong Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaoli Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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Petersen-Jones SM, Komáromy AM. Canine and Feline Models of Inherited Retinal Diseases. Cold Spring Harb Perspect Med 2024; 14:a041286. [PMID: 37217283 PMCID: PMC10835616 DOI: 10.1101/cshperspect.a041286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Naturally occurring inherited retinal diseases (IRDs) in cats and dogs provide a rich source of potential models for human IRDs. In many cases, the phenotypes between the species with mutations of the homologous genes are very similar. Both cats and dogs have a high-acuity retinal region, the area centralis, an equivalent to the human macula, with tightly packed photoreceptors and higher cone density. This and the similarity in globe size to that of humans means these large animal models provide information not obtainable from rodent models. The established cat and dog models include those for Leber congenital amaurosis, retinitis pigmentosa (including recessive, dominant, and X-linked forms), achromatopsia, Best disease, congenital stationary night blindness and other synaptic dysfunctions, RDH5-associated retinopathy, and Stargardt disease. Several of these models have proven to be important in the development of translational therapies such as gene-augmentation therapies. Advances have been made in editing the canine genome, which necessitated overcoming challenges presented by the specifics of canine reproduction. Feline genome editing presents fewer challenges. We can anticipate the generation of specific cat and dog IRD models by genome editing in the future.
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Affiliation(s)
- Simon M Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA
| | - András M Komáromy
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA
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Pathak J, Singh SP, Kharche SD, Goel A, Soni YK, Kaushik R, Kose M, Kumar A. Cell culture media dependent in vitro dynamics and culture characteristics of adult caprine dermal fibroblast cells. Sci Rep 2023; 13:13716. [PMID: 37607956 PMCID: PMC10444776 DOI: 10.1038/s41598-023-38634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
The enhanced availability of functional fibroblasts from precious tissue samples requires an ideal cell-culture system. Therefore, this study was designed to investigate the performance of caprine adult fibroblast cells (cadFibroblast) when cultivated in different culture media. The cadFibroblast cell lines from adult Barbari (Capra hircus) bucks were established and the effect of different media viz. DMEM/F-12 [with low-glucose (5.5 mM; DL) and high-glucose (30 mM; DH)], α-MEM [with low-glucose (5.5 mM; ML) and with high-glucose (30 mM; MH)], and fibroblast growth medium (FGM) were evaluated. Cells were then compared for growth characteristics and in-vitro dynamics through cellular morphology, proliferation, population-doubling time, double-immunocytochemistry, colony-forming units, wound healing, transwell migration, and differential expression of fibroblast-specific markers (FSP-1 and vimentin). The results of immunocytochemistry, transwell migration/invasion, and wound healing assays showed the superiority of DH over DL and other media tested. Whereas, similar effects of glucose supplementation and expression of FSP-1 were not observed in α-MEM. Transwell migration was significantly (p < 0.05) lower in FGM compared with other media tested. Overall, our results illustrate the media-dependent deviation in in-vitro dynamics and culture characteristics of cadFibroblasts that may be useful to develop strategies to cultivate these cells efficiently for research and downstream applications.
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Affiliation(s)
- Juhi Pathak
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281 406, India
| | - Shiva Pratap Singh
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India.
| | - Suresh Dinkar Kharche
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India.
| | - Anjana Goel
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281 406, India
| | - Yogesh K Soni
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India
| | - Rakesh Kaushik
- Animal Genetics and Breeding Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India
| | - Megha Kose
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India
| | - Ashish Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, Uttar Pradesh, 281 122, India
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Dua S, Bansal S, Gautam D, Jose B, Singh P, Singh MK, De S, Kumar D, Yadav PS, Kues W, Selokar NL. Production of MSTN Gene-Edited Embryos of Buffalo Using the CRISPR/Cas9 System and SCNT. Cell Reprogram 2023; 25:121-127. [PMID: 37042654 DOI: 10.1089/cell.2023.0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system and somatic cell nuclear transfer (SCNT) have been used to produce genome-edited farm animal species for improved production and health traits; however, these tools are rarely used in the buffalo and can play a pivotal role in milk and meat production in tropical and subtropical countries. In this study, we aimed to produce myostatin (MSTN) gene-edited embryos of the Murrah buffalo using the CRISPR/Cas9 system and SCNT. For this, fibroblast cells were electroporated with sgRNAs carrying all-in-one CRISPR/Cas9 plasmids targeting the first exon of the MSTN gene. Following puromycin selection, single-cell clonal populations were established and screened using the TA cloning and Sanger sequencing methods. Of eight single-cell clonal populations, one with a monoallelic and another with a biallelic heterozygous gene editing event were identified. These two gene-edited clonal cell populations were successfully used to produce blastocyst-stage embryos using the handmade cloning method. This work establishes the technical foundation for generation of genome-edited cloned embryos in the buffalo.
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Affiliation(s)
- Seema Dua
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Sonu Bansal
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Devika Gautam
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Bosco Jose
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priyanka Singh
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Manoj Kumar Singh
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Sachinandan De
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Dharmendra Kumar
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Prem Singh Yadav
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Wilfried Kues
- Department of Biotechnology, Stem Cell Physiology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Naresh L Selokar
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, India
- Animal Biotechnology Division, ICAR-National Dairy Research Institute, Karnal, India
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Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses. Genes (Basel) 2023; 14:genes14030638. [PMID: 36980910 PMCID: PMC10048024 DOI: 10.3390/genes14030638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1–31) and X chromosomes, respectively, while 18 INDELs were identified on the mitochondrial genome, totaling 1,566,414 INDELs. Of those, 779,457 loci (49.8%) were novel INDELs, while 786,957 loci (50.2%) were already registered in Ensembl. The sizes of diallelic INDELs ranged from −286 to +476, and the majority, 717,736 (52.14%) and 220,672 (16.03%), were 1-bp and 2-bp variants, respectively. Numerous INDELs were found to have lower frequencies of alternative (Alt) alleles. Many rare variants with low Alt allele frequencies (<0.5%) were also detected. In addition, 5955 loci were genotyped as having a minor allele frequency of 0.5 and being heterogeneous genotypes in all the horses. While short-read sequencing and its mapping to reference genome is a simple way of detecting variants, fake variants may be detected. Therefore, our data help to identify true variants in Thoroughbred horses. The INDEL database we constructed will provide useful information for genetic studies and industrial applications in Thoroughbred horses, including a gene-editing test for gene-doping control and a parentage test using INDELs for horse registration and identification.
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Tozaki T, Ohnuma A, Nakamura K, Hano K, Takasu M, Takahashi Y, Tamura N, Sato F, Shimizu K, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Hamilton NA, Nagata SI. Detection of Indiscriminate Genetic Manipulation in Thoroughbred Racehorses by Targeted Resequencing for Gene-Doping Control. Genes (Basel) 2022; 13:genes13091589. [PMID: 36140757 PMCID: PMC9498419 DOI: 10.3390/genes13091589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
The creation of genetically modified horses is prohibited in horse racing as it falls under the banner of gene doping. In this study, we developed a test to detect gene editing based on amplicon sequencing using next-generation sequencing (NGS). We designed 1012 amplicons to target 52 genes (481 exons) and 147 single-nucleotide variants (SNVs). NGS analyses showed that 97.7% of the targeted exons were sequenced to sufficient coverage (depth > 50) for calling variants. The targets of artificial editing were defined as homozygous alternative (HomoALT) and compound heterozygous alternative (ALT1/ALT2) insertion/deletion (INDEL) mutations in this study. Four models of gene editing (three homoALT with 1-bp insertions, one REF/ALT with 77-bp deletion) were constructed by editing the myostatin gene in horse fibroblasts using CRISPR/Cas9. The edited cells and 101 samples from thoroughbred horses were screened using the developed test, which was capable of identifying the three homoALT cells containing 1-bp insertions. Furthermore, 147 SNVs were investigated for their utility in confirming biological parentage. Of these, 120 SNVs were amenable to consistent and accurate genotyping. Surrogate (nonbiological) dams were excluded by 9.8 SNVs on average, indicating that the 120 SNV could be used to detect foals that have been produced by somatic cloning or embryo transfer, two practices that are prohibited in thoroughbred racing and breeding. These results indicate that gene-editing tests that include variant calling and SNV genotyping are useful to identify genetically modified racehorses.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
- Correspondence:
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
| | - Kotono Nakamura
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan
| | - Kazuki Hano
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan
| | - Yuji Takahashi
- Equine Research Institute, Japan Racing Association, 1400-4, Shiba, Shimotsuke 329-0412, Japan
| | - Norihisa Tamura
- Equine Research Institute, Japan Racing Association, 1400-4, Shiba, Shimotsuke 329-0412, Japan
| | - Fumio Sato
- Equine Research Institute, Japan Racing Association, 1400-4, Shiba, Shimotsuke 329-0412, Japan
| | - Kyo Shimizu
- Registration Department, Japan Association for International Racing and Stud Book, 4-5-4, Shimbashi, Minato, Tokyo 105-0004, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
| | - Taichiro Ishige
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
| | - Kei-ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
| | - Natasha A. Hamilton
- Equine Genetics Research Centre, Racing Australia, 2 Randwick Way, Scone, NSW 2337, Australia
| | - Shun-ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, 1731-2, Tsurutamachi, Utsunomiya 320-0851, Japan
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