1
|
Pigoń-Zając D, Mazurek M, Maziarz M, Ochieng’ Otieno M, Martinez-Useros J, Małecka-Massalska T, Powrózek T. Characterization of Undiscovered miRNA Involved in Tumor Necrosis Factor Alpha-Induced Atrophy in Mouse Skeletal Muscle Cell Line. Int J Mol Sci 2024; 25:6064. [PMID: 38892252 PMCID: PMC11172509 DOI: 10.3390/ijms25116064] [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: 04/23/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Muscular atrophy is a complex catabolic condition that develops due to several inflammatory-related disorders, resulting in muscle loss. Tumor necrosis factor alpha (TNF-α) is believed to be one of the leading factors that drive inflammatory response and its progression. Until now, the link between inflammation and muscle wasting has been thoroughly investigated, and the non-coding RNA machinery is a potential connection between the candidates. This study aimed to identify specific miRNAs for muscular atrophy induced by TNF-α in the C2C12 murine myotube model. The difference in expression of fourteen known miRNAs and two newly identified miRNAs was recorded by next-generation sequencing between normal muscle cells and treated myotubes. After validation, we confirmed the difference in the expression of one novel murine miRNA (nov-mmu-miRNA-1) under different TNF-α-inducing conditions. Functional bioinformatic analyses of nov-mmu-miRNA-1 revealed the potential association with inflammation and muscle atrophy. Our results suggest that nov-mmu-miRNA-1 may trigger inflammation and muscle wasting by the downregulation of LIN28A/B, an anti-inflammatory factor in the let-7 family. Therefore, TNF-α is involved in muscle atrophy through the modulation of the miRNA cellular machinery. Here, we describe for the first time and propose a mechanism for the newly discovered miRNA, nov-mmu-miRNA-1, which may regulate inflammation and promote muscle atrophy.
Collapse
Affiliation(s)
- Dominika Pigoń-Zając
- Department of Human Physiology of the Chair of Preclinical Sciences, Medical University in Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (M.M.); (T.M.-M.)
| | - Marcin Mazurek
- Department of Human Physiology of the Chair of Preclinical Sciences, Medical University in Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (M.M.); (T.M.-M.)
| | - Mirosław Maziarz
- Department of Human Physiology of the Chair of Preclinical Sciences, Medical University in Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (M.M.); (T.M.-M.)
| | - Michael Ochieng’ Otieno
- Translational Oncology Division, Oncohealth Institute, Fundacion Jiménez Díaz University Hospital, 28040 Madrid, Spain; (M.O.O.); (J.M.-U.)
| | - Javier Martinez-Useros
- Translational Oncology Division, Oncohealth Institute, Fundacion Jiménez Díaz University Hospital, 28040 Madrid, Spain; (M.O.O.); (J.M.-U.)
- Area of Physiology, Department of Basic Health Sciences, Faculty of Health Sciences, Rey Juan Carlos University, 28922 Madrid, Spain
| | - Teresa Małecka-Massalska
- Department of Human Physiology of the Chair of Preclinical Sciences, Medical University in Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (M.M.); (T.M.-M.)
| | - Tomasz Powrózek
- Department of Human Physiology of the Chair of Preclinical Sciences, Medical University in Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (M.M.); (T.M.-M.)
| |
Collapse
|
2
|
Livshits G, Kalinkovich A. Restoration of epigenetic impairment in the skeletal muscle and chronic inflammation resolution as a therapeutic approach in sarcopenia. Ageing Res Rev 2024; 96:102267. [PMID: 38462046 DOI: 10.1016/j.arr.2024.102267] [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: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Sarcopenia is an age-associated loss of skeletal muscle mass, strength, and function, accompanied by severe adverse health outcomes, such as falls and fractures, functional decline, high health costs, and mortality. Hence, its prevention and treatment have become increasingly urgent. However, despite the wide prevalence and extensive research on sarcopenia, no FDA-approved disease-modifying drugs exist. This is probably due to a poor understanding of the mechanisms underlying its pathophysiology. Recent evidence demonstrate that sarcopenia development is characterized by two key elements: (i) epigenetic dysregulation of multiple molecular pathways associated with sarcopenia pathogenesis, such as protein remodeling, insulin resistance, mitochondria impairments, and (ii) the creation of a systemic, chronic, low-grade inflammation (SCLGI). In this review, we focus on the epigenetic regulators that have been implicated in skeletal muscle deterioration, their individual roles, and possible crosstalk. We also discuss epidrugs, which are the pharmaceuticals with the potential to restore the epigenetic mechanisms deregulated in sarcopenia. In addition, we discuss the mechanisms underlying failed SCLGI resolution in sarcopenia and the potential application of pro-resolving molecules, comprising specialized pro-resolving mediators (SPMs) and their stable mimetics and receptor agonists. These compounds, as well as epidrugs, reveal beneficial effects in preclinical studies related to sarcopenia. Based on these encouraging observations, we propose the combination of epidrugs with SCLI-resolving agents as a new therapeutic approach for sarcopenia that can effectively attenuate of its manifestations.
Collapse
Affiliation(s)
- Gregory Livshits
- Department of Morphological Sciences, Adelson School of Medicine, Ariel University, Ariel 4077625, Israel; Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel.
| | - Alexander Kalinkovich
- Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel
| |
Collapse
|
3
|
Cai B, Ma M, Yuan R, Zhou Z, Zhang J, Kong S, Lin D, Lian L, Li J, Zhang X, Nie Q. MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken. Cell Mol Biol Lett 2024; 29:9. [PMID: 38177995 PMCID: PMC10765903 DOI: 10.1186/s11658-023-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Skeletal muscle development is pivotal for animal growth and health. Recently, long noncoding RNAs (lncRNAs) were found to interact with chromatin through diverse roles. However, little is known about how lncRNAs act as chromatin-associated RNAs to regulate skeletal muscle development. Here, we aim to investigate the regulation of chromatin-associated RNA (MYH1G-AS) during skeletal muscle development. METHODS We provided comprehensive insight into the RNA profile and chromatin accessibility of different myofibers, combining RNA sequencing (RNA-seq) with an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). The dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to analyze the transcriptional regulation mechanism of MYH1G-AS. ALKBH5-mediated MYH1G-AS N6-methyladenosine (m6A) demethylation was assessed by a single-base elongation and ligation-based qPCR amplification method (SELECT) assay. Functions of MYH1G-AS were investigated through a primary myoblast and lentivirus/cholesterol-modified antisense oligonucleotide (ASO)-mediated animal model. To validate the interaction of MYH1G-AS with fibroblast growth factor 18 (FGF18) protein, RNA pull down and an RNA immunoprecipitation (RIP) assay were performed. Specifically, the interaction between FGF18 and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5) protein was analyzed by coimmunoprecipitation (Co-IP) and a yeast two-hybrid assay. RESULTS A total of 45 differentially expressed (DE) lncRNAs, with DE ATAC-seq peaks in their promoter region, were classified as open chromatin-associated lncRNAs. A skeletal muscle-specific lncRNA (MSTRG.15576.9; MYH1G-AS), which is one of the open chromatin-associated lncRNA, was identified. MYH1G-AS transcription is coordinately regulated by transcription factors (TF) SMAD3 and SP2. Moreover, SP2 represses ALKBH5 transcription to weaken ALKBH5-mediated m6A demethylation of MYH1G-AS, thus destroying MYH1G-AS RNA stability. MYH1G-AS accelerates myoblast proliferation but restrains myoblast differentiation. Moreover, MYH1G-AS drives a switch from slow-twitch to fast-twitch fibers and causes muscle atrophy. Mechanistically, MYH1G-AS inhibits FGF18 protein stabilization to reduce the interaction of FGF18 to SMARCA5, thus repressing chromatin accessibility of the SMAD4 promoter to activate the SMAD4-dependent pathway. CONCLUSIONS Our results reveal a new pattern of the regulation of lncRNA expression at diverse levels and help expound the regulation of m6A methylation on chromatin status.
Collapse
Affiliation(s)
- Bolin Cai
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Manting Ma
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Rongshuai Yuan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Zhen Zhou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Jing Zhang
- Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, New Hunt's House, King's College London, Guy's Campus, London, UK
| | - Shaofen Kong
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Duo Lin
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
| |
Collapse
|
4
|
Li L, Qin C, Chen Y, Zhao W, Zhu Q, Dai D, Zhan S, Guo J, Zhong T, Wang L, Cao J, Zhang H. The novel RNA-RNA activation of H19 on MyoD transcripts promoting myogenic differentiation of goat muscle satellite cells. Int J Biol Macromol 2023; 253:127341. [PMID: 37852400 DOI: 10.1016/j.ijbiomac.2023.127341] [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: 01/31/2023] [Revised: 10/01/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
The elaborate interplay of coding and noncoding factors governs muscle growth and development. Here, we reported a mutual activation between long noncoding RNA (lncRNA) H19 and MyoD (myogenic determination gene number 1) in the muscle process. We successfully cloned the two isoforms of goat H19, which were significantly enriched and positively correlated with MyoD transcripts in skeletal muscles or differentiating muscle satellite cells (MuSCs). To systematically screen genes altered by H19, we performed RNA-seq using cDNA libraries of differentiating H19-deficiency MuSCs and consequently anchored MyoD as the critical genes in mediating H19 function. Intriguingly, some transcripts of MyoD and H19 overlapped in the cytoplasm, which was dramatically damaged when the core complementary nucleotides were mutated. Meanwhile, MyoD RNA successfully pulled down H19 in MS2-RIP experiments. Furthermore, HuR could bind both H19 and MyoD transcripts, while H19 or its truncated mutants successfully stabilized MyoD mRNA, with or without HuR deficiency. In turn, novel functional MyoD protein-binding sites were identified in the promoter and exons of the H19 gene. Our results suggest that MyoD activates H19 transcriptionally, and RNA-RNA hybridization is critical for H19-promoted MyoD expression, which extends our knowledge of the hierarchy of regulatory networks in muscle growth.
Collapse
Affiliation(s)
- Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Chenyu Qin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Yuan Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Qi Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Dinghui Dai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, 211# Huimin Rd., Wenjiang District, Chengdu 611130, China.
| |
Collapse
|
5
|
Yu M, He X, Liu T, Li J. lncRNA GPRC5D-AS1 as a ceRNA inhibits skeletal muscle aging by regulating miR-520d-5p. Aging (Albany NY) 2023; 15:13980-13997. [PMID: 38100482 PMCID: PMC10756129 DOI: 10.18632/aging.205279] [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: 05/01/2023] [Accepted: 10/23/2023] [Indexed: 12/17/2023]
Abstract
Sarcopenia induced by muscle aging is associated with negative outcomes in a variety of diseases. Long non-coding RNAs are a class of RNAs longer than 200 nucleotides with lower protein coding potential. An increasing number of studies have shown that lncRNAs play a vital role in skeletal muscle development. According to our previous research, lncRNA GPRC5D-AS1 is selected in the present study as the target gene to further study its effect on skeletal muscle aging in a dexamethasone-induced human muscle atrophy cell model. As a result, GPRC5D-AS1 functions as a ceRNA of miR-520d-5p to repress cell apoptosis and regulate the expression of muscle regulatory factors, including MyoD, MyoG, Mef2c and Myf5, thus accelerating myoblast proliferation and differentiation, facilitating development of skeletal muscle. In conclusion, lncRNA GPRC5D-AS1 could be a novel therapeutic target for treating sarcopenia.
Collapse
Affiliation(s)
- Miao Yu
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiuting He
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Ting Liu
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Jie Li
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| |
Collapse
|
6
|
Rizavi HS, Gavin HE, Krishnan HR, Gavin DP, Sharma RP. Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons. Noncoding RNA 2023; 9:72. [PMID: 37987368 PMCID: PMC10661276 DOI: 10.3390/ncrna9060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Although, by definition, long noncoding RNAs (lncRNAs) are not translated, they are sometimes associated with ribosomes. In fact, some estimates suggest the existence of more than 50 K lncRNA molecules that could encode for small peptides. We examined the effects of an ethanol and Poly-ADP Ribose Polymerase (PARP) inhibitor (ABT-888) on ribosome-bound lncRNAs. Mice were administered via intraperitoneal injection (i.p.) either normal saline (CTL) or ethanol (EtOH) twice a day for four consecutive days. On the fourth day, a sub-group of mice administered with ethanol also received ABT-888 (EtOH+ABT). Ribosome-bound lncRNAs in CaMKIIα-expressing pyramidal neurons were measured using the Translating Ribosome Affinity Purification (TRAP) technique. Our findings show that EtOH altered the attachment of 107 lncRNA transcripts, while EtOH+ABT altered 60 lncRNAs. Among these 60 lncRNAs, 49 were altered by both conditions, while EtOH+ABT uniquely altered the attachment of 11 lncRNA transcripts that EtOH alone did not affect. To validate these results, we selected eight lncRNAs (Mir124-2hg, 5430416N02Rik, Snhg17, Snhg12, Snhg1, Mir9-3hg, Gas5, and 1110038B12Rik) for qRT-PCR analysis. The current study demonstrates that ethanol-induced changes in lncRNA attachment to ribosomes can be mitigated by the addition of the PARP inhibitor ABT-888.
Collapse
Affiliation(s)
- Hooriyah S. Rizavi
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Hannah E. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Harish R. Krishnan
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - David P. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Rajiv P. Sharma
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| |
Collapse
|
7
|
Liu S, Wu J, Zhang W, Jiang H, Zhou Y, Liu J, Mao H, Liu S, Chen B. Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis. Int J Mol Sci 2023; 24:16387. [PMID: 38003577 PMCID: PMC10671564 DOI: 10.3390/ijms242216387] [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: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Duck meat is pivotal in providing high-quality protein for human nutrition, underscoring the importance of studying duck myogenesis. The regulatory mechanisms governing duck myogenesis involve both coding and non-coding RNAs, yet their specific expression patterns and molecular mechanisms remain elusive. To address this knowledge gap, we performed expression profiling analyses of mRNAs, lncRNAs, circRNAs, and miRNAs involved in duck myogenesis using whole-transcriptome RNA-seq. Our analysis identified 1733 differentially expressed (DE)-mRNAs, 1116 DE-lncRNAs, 54 DE-circRNAs, and 174 DE-miRNAs when comparing myoblasts and myotubes. A GO analysis highlighted the enrichment of DE molecules in the extracellular region, protein binding, and exocyst. A KEGG analysis pinpointed pathways related to ferroptosis, PPAR signaling, nitrogen metabolism, cell cycle, cardiac muscle contraction, glycerolipid metabolism, and actin cytoskeleton. A total of 51 trans-acting lncRNAs, including ENSAPLT00020002101 and ENSAPLT00020012069, were predicted to participate in regulating myoblast proliferation and differentiation. Based on the ceRNAs, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks involving five miRNAs (miR-129-5p, miR-133a-5p, miR-22-3p, miR-27b-3p, and let-7b-5p) that are relevant to myogenesis. Furthermore, the GO and KEGG analyses of the DE-mRNAs within the ceRNA network underscored the significant enrichment of the glycerolipid metabolism pathway. We identified five different DE-mRNAs, specifically ENSAPLG00020001677, ENSAPLG00020002183, ENSAPLG00020005019, ENSAPLG00020010497, and ENSAPLG00020017682, as potential target genes that are crucial for myogenesis in the context of glycerolipid metabolism. These five mRNAs are integral to ceRNA networks, with miR-107_R-2 and miR-1260 emerging as key regulators. In summary, this study provides a valuable resource elucidating the intricate interplay of mRNA-lncRNA-circRNA-miRNA in duck myogenesis, shedding light on the molecular mechanisms that govern this critical biological process.
Collapse
Affiliation(s)
- Shuibing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jintao Wu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wentao Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongxia Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanan Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sanfeng Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Biao Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| |
Collapse
|
8
|
Park J, Cho YE, Kim KH, Shin S, Kim S, Lim CH, Chung SY, Park YG. Correlation Between the Severity of Multifidus Fatty Degeneration and the Size of Ossification of Posterior Longitudinal Ligament at Each Spinal Level. Neurospine 2023; 20:921-930. [PMID: 37798986 PMCID: PMC10562234 DOI: 10.14245/ns.2346506.253] [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: 04/27/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 10/07/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the correlation between ossification of the posterior longitudinal ligament (OPLL) size and multifidus fatty degeneration (MFD), hypothesizing that larger OPLL sizes are associated with worse MFD. METHODS One hundred four patients with cervical OPLL who underwent surgery were screened. OPLL occupying diameter and area ratios, the severity of MFD using the Goutallier classification, and range of motion (ROM) of cervical flexion-extension (ΔCobb) were measured. Correlation analyses between OPLL size, MFD severity, and ΔCobb were conducted. MFD severity was compared for each OPLL type using one-way analysis of variance. RESULTS The final clinical data from 100 patients were analyzed. The average Goutallier grade of C2-7 significantly correlated with the average OPLL diameter and area occupying ratios, and OPLL involved vertebral level (r = 0.58, p < 0.01; r = 0.40, p < 0.01; r = 0.47, p < 0.01, respectively). The OPLL size at each cervical level significantly correlated with MFD of the same or 1-3 adjacent levels. ΔCobb angle was negatively correlated with the average Goutallier grade (r = -0.31, p < 0.01) and average OPLL occupying diameter and area ratios (r = -0.31, p < 0.01; r = -0.35, p < 0.01, respectively). Patients with continuous OPLL exhibited worse MFD than those with segmental OPLL (p < 0.01). CONCLUSION OPLL size is clinically correlated with MFD and cervical ROM. OPLL at one spinal level affects MFD at the same and 1-3 adjacent spinal levels. The worsening severity of MFD is associated with the longitudinal continuity of OPLL.
Collapse
Affiliation(s)
- Jinyoung Park
- Department of Rehabilitation Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Eun Cho
- Department of Neurosurgery, Spine and Spinal Cord Institute, Gangnam Severance Spine Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung Hyun Kim
- Department of Neurosurgery, Spine and Spinal Cord Institute, Gangnam Severance Spine Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sanghoon Shin
- Department of Rehabilitation Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sungjun Kim
- Department of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Chae Hwan Lim
- Department of Rehabilitation Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Young Chung
- Department of Rehabilitation Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yoon Ghil Park
- Department of Rehabilitation Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
9
|
Shen Y, Kim IM, Tang Y. Decoding the Gene Regulatory Network of Muscle Stem Cells in Mouse Duchenne Muscular Dystrophy: Revelations from Single-Nuclei RNA Sequencing Analysis. Int J Mol Sci 2023; 24:12463. [PMID: 37569835 PMCID: PMC10419276 DOI: 10.3390/ijms241512463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The gene dystrophin is responsible for Duchenne muscular dystrophy (DMD), a grave X-linked recessive ailment that results in respiratory and cardiac failure. As the expression of dystrophin in muscle stem cells (MuSCs) is a topic of debate, there exists a limited understanding of its influence on the gene network of MuSCs. This study was conducted with the objective of investigating the effects of dystrophin on the regulatory network of genes in MuSCs. To comprehend the function of dystrophin in MuSCs from DMD, this investigation employed single-nuclei RNA sequencing (snRNA-seq) to appraise the transcriptomic profile of MuSCs obtained from the skeletal muscles of dystrophin mutant mice (DMDmut) and wild-type control mice. The study revealed that the dystrophin mutation caused the disruption of several long non-coding RNAs (lncRNAs), leading to the inhibition of MEG3 and NEAT1 and the upregulation of GM48099, GM19951, and GM15564. The Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the dystrophin mutation activated the cell adhesion pathway in MuSCs, inhibited the circulatory system process, and affected the regulation of binding. The study also revealed that the metabolic pathway activity of MuSCs was altered. The metabolic activities of oxidative phosphorylation (OXPHOS) and glycolysis were elevated in MuSCs from DMDmut. In summary, this research offers novel insights into the disrupted gene regulatory program in MuSCs due to dystrophin mutation at the single-cell level.
Collapse
Affiliation(s)
- Yan Shen
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Il-Man Kim
- Anatomy, Cell Biology, and Physiology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Yaoliang Tang
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| |
Collapse
|
10
|
Zhu Y, Chen X, Geng S, Li Q, Li Y, Yuan H, Jiang H. Identification of the cuproptosis-related hub genes and therapeutic agents for sarcopenia. Front Genet 2023; 14:1136763. [PMID: 37007946 PMCID: PMC10063920 DOI: 10.3389/fgene.2023.1136763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Background: Along with acceleration of population aging, the increasing prevalence of sarcopenia has posed a heavy burden on families as well as society. In this context, it is of great significance to diagnose and intervene sarcopenia as early as possible. Recent evidence has indicated the role of cuproptosis in the development of sarcopenia. In this study, we aimed to seek the key cuproptosis-related genes that can be used for identification and intervention of sarcopenia.Methods: The GSE111016 dataset was retrieved from GEO. The 31 cuproptosis-related genes (CRGs) were obtained from previous published studies. The differentially expressed genes (DEGs) and Weighed gene co-expression network analysis (WGCNA) were subsequently analyzed. The core hub genes were acquired by the intersection of DEGs, WGCNA and CRGs. Through logistic regression analysis, we established a diagnostic model of sarcopenia based on the selected biomarkers and was validated in muscle samples from GSE111006 and GSE167186. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis were performed on these genes. Furthermore, the gene set enrichment analysis (GSEA), and immune cell infiltration were also conducted on the identified core genes. Finally, we screened the potential drugs targeting the potential biomarkers of sarcopenia.Results: A total of 902 DEGs and WGCNA containing 1,281 significant genes were preliminarily selected. Intersection of DEGs, WGCNA and CRGs yielded four core genes (PDHA1, DLAT, PDHB, and NDUFC1) as potential biomarkers for the prediction of sarcopenia. The predictive model was established and validated with high AUC values. KEGG pathway and Gene Ontology biological analysis indicated these core genes may play a crucial role in energy metabolism in mitochondria, oxidation process, and aging-related degenerative diseases. In addition, the immune cells may be involved in the development of sarcopenia through mitochondrial metabolism. Finally, metformin was identified as a promising strategy of sarcopenia treatment via targeting NDUFC1.Conclusion: The four cuproptosis-related genes PDHA1, DLAT, PDHB and NDUFC1 may be the diagnostic biomarkers for sarcopenia, and metformin holds great potential to be developed as a therapy for sarcopenia. These outcomes provide new insights for better understanding of sarcopenia and innovative therapeutic approaches.
Collapse
Affiliation(s)
- Yingqian Zhu
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Chen
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shasha Geng
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qingqing Li
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Li
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huixiao Yuan
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hua Jiang
- Department of Geriatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of General Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Hua Jiang,
| |
Collapse
|
11
|
Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs. Genes (Basel) 2023; 14:genes14010197. [PMID: 36672938 PMCID: PMC9858627 DOI: 10.3390/genes14010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.
Collapse
|