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Song Q, Li J, Li S, Cao H, Jin X, Zeng Y, Chen W. Full-Length Transcriptome Analysis of Skeletal Muscle of Jiangquan Black Pig at Different Developmental Stages. Int J Mol Sci 2024; 25:6095. [PMID: 38892283 PMCID: PMC11172715 DOI: 10.3390/ijms25116095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Skeletal muscle grows in response to a combination of genetic and environmental factors, and its growth and development influence the quality of pork. Elucidating the molecular mechanisms regulating the growth and development of skeletal muscle is of great significance to both animal husbandry and farm management. The Jiangquan black pig is an excellent pig breed based on the original Yimeng black pig, importing the genes of the Duroc pig for meat traits, and cultivated through years of scientific selection and breeding. In this study, full-length transcriptome sequencing was performed on three growth stages of Jiangquan black pigs, aiming to study the developmental changes in Jiangquan black pigs at different developmental stages at the molecular level and to screen the key genes affecting the growth of skeletal muscle in Jiangquan black pigs. We performed an enrichment analysis of genes showing differential expression and constructed a protein-protein interaction network with the aim of identifying core genes involved in the development of Jiangquan black pigs. Notably, genes such as TNNI2, TMOD4, PLDIM3, MYOZ1, and MYH1 may be potential regulators of muscle development in Jiangquan black pigs. Our results contribute to the understanding of the molecular mechanisms of skeletal muscle development in this pig breed, which will facilitate molecular breeding efforts and the development of pig breeds to meet the needs of the livestock industry.
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Affiliation(s)
- Qi Song
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Jinbao Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Shiyin Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Hongzhen Cao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Xinlin Jin
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Yongqing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
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Li X, Yang Y, Li L, Ren M, Zhou M, Li S. Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs. Genes (Basel) 2023; 14:genes14040903. [PMID: 37107661 PMCID: PMC10137702 DOI: 10.3390/genes14040903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Intramuscular fat (IMF) is a key index to measure the tenderness and flavor of pork. Wannanhua pig, a famous indigenous pig breed in Anhui Province, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model for investigating the lipid position trait mechanisms in pigs. However, the regulatory mechanisms of lipid deposition and development in pigs remain unclear. Furthermore, the temporal differences in gene regulation are based on muscle growth and IMF deposition. The purpose of this study was to study the expression changes of longissimus dorsi (LD) at different growth stages of WH pigs at the molecular level, to screen the candidate genes and signaling pathways related to IMF during development by transcriptome sequencing technology, and to explore the transcriptional regulation mechanism of IMF deposition-related genes at different development stages. In total, 616, 485, and 1487 genes were differentially expressed between LD60 and LD120, LD120 and LD240, and LD60 and LD240, respectively. Numerous differentially expressed genes (DEGs) associated with lipid metabolism and muscle development were identified, and most of them were involved in IMF deposition and were significantly up-regulated in LD120 and LD240 compared to LD60. STEM (Short Time-series Expression Miner) analysis indicated significant variations in the mRNA expression across distinct muscle development stages. The differential expression of 12 selected DEGs was confirmed by RT-qPCR. The results of this study contribute to our understanding of the molecular mechanism of IMF deposition and provide a new way to accelerate the genetic improvement of pork quality.
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Affiliation(s)
- Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Yanan Yang
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Lei Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Mei Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230041, China
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
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Jing J, Jiang X, Zhu C, Zheng Q, Ji Q, Yin H, Huang J, Zhu Y, Wang J, Qin S, Ling Y. Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits. BMC Genomics 2021; 22:577. [PMID: 34315409 PMCID: PMC8314457 DOI: 10.1186/s12864-021-07896-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND miRNA is one of the crucial roles in the complex and dynamic network that regulates the development of skeletal muscle. The landscape of skeletal muscle miRNAs from fetus to adult in New Zealand rabbits has not been revealed yet. RESULTS In this study, nine RNA-seq libraries of fetus, child and adult rabbits' leg muscles were constructed. A total of 278 differentially expressed miRNAs (DEmiRNAs) were identified. In the fetus vs. child group, the main functional enrichments were involved in membrane and transport. Pathway enriched terms of up-regulated DEmiRNAs were connected with the differentiation and hypertrophy of skeletal muscle, and down-regulated ones were related to muscle structure and metabolic capacity. In the child vs. adult group, functions were associated to positioning and transportation, and pathways were relevant to ECM, muscle structure and hypertrophy. Finally, ocu-miR-185-3p and ocu-miR-370-3p, which had the most target genes, were identified as hub-miRNAs in these two groups. CONCLUSIONS In short, we summarized the highly expressed and uniquely expressed DEmiRNAs of fetus, child and adult rabbits' leg muscles. Besides, the potential functional changes of miRNAs in two consecutive stages have been explored. Among them, the ocu-miR-185-3p and ocu-miR-370-3p with the most target genes were selected as hub-miRNAs. These data improved the understanding of the regulatory molecules of meat rabbit development, and provided a novel perspective for molecular breeding of meat rabbits.
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Affiliation(s)
- Jing Jing
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Xichun Jiang
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui, 230031, Hefei, People's Republic of China
| | - Cuiyun Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Qianyun Ji
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Huiqun Yin
- Reproductive Medicine Center, The 901st Hospital, Anhui, 230031, Hefei, People's Republic of China
| | - Jingtong Huang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Yixiao Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Jiao Wang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Shuaiqi Qin
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China. .,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.
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Wang X, Yan P, Feng S, Luo Y, Liang J, Zhao L, Liu H, Tang Q, Long K, Jin L, Ma J, Jiang A, Shuai S, Li M. Identification and expression pattern analysis of miRNAs in pectoral muscle during pigeon ( Columba livia) development. PeerJ 2021; 9:e11438. [PMID: 34221709 PMCID: PMC8234919 DOI: 10.7717/peerj.11438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of crucial regulators in the process of animal growth and development. However, little is known about the expression and function of miRNAs in pigeon muscles. To identify the miRNAs participating in the rapid development of pigeon pectoral muscles and quantitate their expression levels of pectoral muscles in different age stages, we performed miRNA transcriptome analysis in pigeon pectoral muscles by sequencing small RNAs over three different age stages (1-day old, 28 days old, and 2 years old). Dual-luciferase reporter assay was applied to validate the interaction between miRNA and its target gene. We identified 304 known miRNAs, 201 conserved miRNAs, and 86 novel miRNAs in pigeon pectoral muscles. 189 differentially expressed (DE) miRNAs were screened out during pigeon development. A short time-series expression miner (STEM) analysis indicated 89 DE miRNAs were significantly clustered in a progressively decreasing expression profile, and mainly enriched in biosynthesis-related GO categories and signaling pathways for MAPK and TGF-β. Dual-luciferase reporter assay indicated that a progressively down-regulated miRNA (miR-20b-5p) could directly target Krüppel-like factor 3 (KLF3) gene. To sum-up, our data expand the repertoire of pigeon miRNAs and enhance understanding of the mechanisms underlying rapid development in squabs.
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Affiliation(s)
- Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peiqi Yan
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Siyuan Feng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiyuan Liang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ling Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haifeng Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Surong Shuai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
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Daza KR, Velez-Irizarry D, Casiró S, Steibel JP, Raney NE, Bates RO, Ernst CW. Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle. Front Genet 2021; 12:644091. [PMID: 33859669 PMCID: PMC8042294 DOI: 10.3389/fgene.2021.644091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/24/2021] [Indexed: 01/19/2023] Open
Abstract
Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry.
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Affiliation(s)
- Kaitlyn R Daza
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Deborah Velez-Irizarry
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Sebastian Casiró
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ronald O Bates
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
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Iqbal A, Ping J, Ali S, Zhen G, Juan L, Kang JZ, Ziyi P, Huixian L, Zhihui Z. Role of microRNAs in myogenesis and their effects on meat quality in pig - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1873-1884. [PMID: 32819078 PMCID: PMC7649413 DOI: 10.5713/ajas.20.0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/02/2020] [Accepted: 08/16/2020] [Indexed: 02/02/2023]
Abstract
The demand for food is increasing day by day because of the increasing global population. Therefore, meat, the easiest and largely available source of protein, needs to be produced in large amounts with good quality. The pork industry is a significant shareholder in fulfilling the global meat demands. Notably, myogenesis- development of muscles during embryogenesis- is a complex mechanism which culminates in meat production. But the molecular mechanisms which govern the myogenesis are less known. The involvement of miRNAs in myogenesis and meat quality, which depends on factors such as myofiber composition and intramuscular fat contents which determine the meat color, flavor, juiciness, and water holding capacity, are being extrapolated to increase both the quantity and quality of pork. Various kinds of microRNAs (miRNAs), miR-1, miR-21, miR22, miR-27, miR-34, miR-127, miR-133, miR-143, miR-155, miR-199, miR-206, miR-208, miR-378, and miR-432 play important roles in pig skeletal muscle development. Further, the quality of meat also depends upon myofiber which is developed through the expression of different kinds of miRNAs at different stages. This review will focus on the mechanism of myogenesis, the role of miRNAs in myogenesis, and meat quality with a focus on the pig.
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Affiliation(s)
- Ambreen Iqbal
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jiang Ping
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Shaokat Ali
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Gao Zhen
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Liu Juan
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jin Zi Kang
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Pan Ziyi
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Lu Huixian
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Zhao Zhihui
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
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Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats. Animals (Basel) 2020; 10:ani10111951. [PMID: 33114089 PMCID: PMC7690783 DOI: 10.3390/ani10111951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary In ruminants, the rumen epithelium plays an important role in nutrient absorption, metabolism and transport. MicroRNAs (miRNAs) have been reported to regulate the proliferation of diverse epithelial cells. In this study, we profiled the miRNA transcriptomes of goat rumens at four development stages and screened for candidate miRNAs related to rumen development. MiR-148a-3p was found to be highly expressed in the rumen tissues and induced the proliferation of GES-1 cells by targeting QKI. Our findings provide some insights into the functional roles of miRNAs in rumen growth and functional development in ruminants. Abstract The rumen is an important digestive organ of ruminants. From the fetal to adult stage, the morphology, structure and function of the rumen change significantly. However, the knowledge of the intrinsic genetic regulation of these changes is still limited. We previously reported a genome-wide expression profile of miRNAs in pre-natal goat rumens. In this study, we combined and analyzed the transcriptomes of rumen miRNAs during pre-natal (E60 and E135) and post-natal (D30 and D150) stages. A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the pre-weaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites of miR-148a-3p in the 3′-UTR of QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI through in situ hybridization was observed in the rumen tissues but not in the intestinal tracts. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers of the rumen, suggesting that miR-148a-3p is involved in the development of the rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells. Taken together, our study identified DEMs involved in the development of the rumen and provides insights into the regulation mechanism of rumen development in goats.
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Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages. Animals (Basel) 2020; 10:ani10071198. [PMID: 32679676 PMCID: PMC7401622 DOI: 10.3390/ani10071198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/18/2020] [Accepted: 07/11/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The pigs is the most popular agricultural animal in the world. Muscle growth—which has the highest economic value in pigs—can be regulated by multiple genes and involves complex regulatory mechanisms. It is necessary to understand the dynamics of muscle transcriptome during development to understand the muscle development mechanism. However, the genes and miRNAs that play regulatory roles underlying differences in the meat quality of pigs remain unclear. In the current study, qRT-PCR, miRNA-Seq, and RNA-Seq were applied to analyze and verify muscle tissues of pigs from three different developmental stages and screened genes, miRNAs and pathways related to pig muscle development. This study focused on analyzing the mechanisms of muscle development and uncover the development differences in muscle from embryo to adult. Abstract The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.
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Ma X, Jia C, Chu M, Fu D, Lei Q, Ding X, Wu X, Guo X, Pei J, Bao P, Yan P, Liang C. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes (Basel) 2019; 10:genes10120970. [PMID: 31779203 PMCID: PMC6947547 DOI: 10.3390/genes10120970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 02/04/2023] Open
Abstract
DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Qinhui Lei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
| | - Chunnian Liang
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
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10
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Cheng X, Du J, Shen L, Tan Z, Jiang D, Jiang A, Li Q, Tang G, Jiang Y, Wang J, Li X, Zhang S, Zhu L. MiR-204-5p regulates C2C12 myoblast differentiation by targeting MEF2C and ERRγ. Biomed Pharmacother 2018; 101:528-535. [DOI: 10.1016/j.biopha.2018.02.096] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 11/30/2022] Open
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11
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Jiang L, Wang Q, Yu J, Gowda V, Johnson G, Yang J, Kan X, Yang X. miRNAome expression profiles in the gonads of adult Melopsittacus undulatus. PeerJ 2018; 6:e4615. [PMID: 29666766 PMCID: PMC5896495 DOI: 10.7717/peerj.4615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/22/2018] [Indexed: 01/11/2023] Open
Abstract
The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.
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Affiliation(s)
- Lan Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qingqing Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Jue Yu
- College of Foreign Studies, Anhui Normal University, Wuhu, China
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Jianke Yang
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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12
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He D, Zou T, Gai X, Ma J, Li M, Huang Z, Chen D. MicroRNA expression profiles differ between primary myofiber of lean and obese pig breeds. PLoS One 2017; 12:e0181897. [PMID: 28759650 PMCID: PMC5536276 DOI: 10.1371/journal.pone.0181897] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small miRNAs ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and these differences are programmed during prenatal muscle development. Little research shed light directly on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. Myofiber phenotypes of LW and MS were measured at developmental stages of 35, 55 and 90 days post-conception (dpc), which revealed that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs were identified. Expression analysis of the 10 most abundant miRNAs in every library indicated that functional miRNAome may be a small amount and tend to be greater expressed. These sets of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. Some myogenesis related miRNAs (miR-133, miR-1, miR-206 and miR-148a) are highly abundant in MS, while other miRNAs (let-7 family, miR-214, miR-181) highly expressed in LW. In addition, the expression patterns of miRNAs (miR-1, -133, -206) at three prenatal stages (35, 55 and 90 dpc) were determined using qRT-PCR. Notably, ssc-miR-133 was significantly more highly expressed in LW pigs skeletal muscle at all prenatal stages compared with its expression in LW pigs skeletal muscle. Taken together, the main functional miRNAs during muscle development are different between lean and obese pig breeds. The present study adds new information to existing data on porcine miRNAs and will be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds.
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Affiliation(s)
- Dongting He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Tiande Zou
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Xiangrong Gai
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, People's Republic of China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
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13
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Zhou M, Hara H, Dai Y, Mou L, Cooper DKC, Wu C, Cai Z. Circulating Organ-Specific MicroRNAs Serve as Biomarkers in Organ-Specific Diseases: Implications for Organ Allo- and Xeno-Transplantation. Int J Mol Sci 2016; 17:ijms17081232. [PMID: 27490531 PMCID: PMC5000630 DOI: 10.3390/ijms17081232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/16/2022] Open
Abstract
Different cell types possess different miRNA expression profiles, and cell/tissue/organ-specific miRNAs (or profiles) indicate different diseases. Circulating miRNA is either actively secreted by living cells or passively released during cell death. Circulating cell/tissue/organ-specific miRNA may serve as a non-invasive biomarker for allo- or xeno-transplantation to monitor organ survival and immune rejection. In this review, we summarize the proof of concept that circulating organ-specific miRNAs serve as non-invasive biomarkers for a wide spectrum of clinical organ-specific manifestations such as liver-related disease, heart-related disease, kidney-related disease, and lung-related disease. Furthermore, we summarize how circulating organ-specific miRNAs may have advantages over conventional methods for monitoring immune rejection in organ transplantation. Finally, we discuss the implications and challenges of applying miRNA to monitor organ survival and immune rejection in allo- or xeno-transplantation.
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Affiliation(s)
- Ming Zhou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
- Institute of Immunology, Zhongshan School of Medicine, Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Sun Yat-sen University, Guangzhou 510275, China.
| | - Hidetaka Hara
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Yifan Dai
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 210029, China.
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
| | - David K C Cooper
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Changyou Wu
- Institute of Immunology, Zhongshan School of Medicine, Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhiming Cai
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
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