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Li X, Xing SS, Meng SB, Hou ZY, Yu L, Chen MJ, Yuan DD, Xu HF, Cai HF, Li M. SOX6 AU controls myogenesis by cis-modulation of SOX6 in cattle. Epigenetics 2024; 19:2341578. [PMID: 38615330 PMCID: PMC11018032 DOI: 10.1080/15592294.2024.2341578] [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: 10/13/2023] [Accepted: 04/06/2024] [Indexed: 04/16/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to be involved in the regulation of skeletal muscle development through multiple mechanisms. The present study revealed that the lncRNA SOX6 AU (SRY-box transcription factor 6 antisense upstream) is reverse transcribed from upstream of the bovine sex-determining region Y (SRY)-related high-mobility-group box 6 (SOX6) gene. SOX6 AU was significantly differentially expressed in muscle tissue among different developmental stages in Xianan cattle. Subsequently, knockdown and overexpression experiments discovered that SOX6 AU promoted primary skeletal muscle cells proliferation, apoptosis, and differentiation in bovine. The overexpression of SOX6 AU in bovine primary skeletal muscle cells resulted in 483 differentially expressed genes (DEGs), including 224 upregulated DEGs and 259 downregulated DEGs. GO functional annotation analysis showed that muscle development-related biological processes such as muscle structure development and muscle cell proliferation were significantly enriched. KEGG pathway analysis revealed that the PI3K/AKT and MAPK signaling pathways were important pathways for DEG enrichment. Notably, we found that SOX6 AU inhibited the mRNA and protein expression levels of the SOX6 gene. Moreover, knockdown of the SOX6 gene promoted the proliferation and apoptosis of bovine primary skeletal muscle cells. Finally, we showed that SOX6 AU promoted the proliferation and apoptosis of bovine primary skeletal muscle cells by cis-modulation of SOX6 in cattle. This work illustrates our discovery of the molecular mechanisms underlying the regulation of SOX6 AU in the development of beef.
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Affiliation(s)
| | | | - Sheng-Bo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Zhong-Yi Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Lei Yu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Meng-Juan Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Dong-Dong Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Hui-Fen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Han-Fang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
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Tan P, Wang Y, Mei L, Loor JJ, Zhao C, Kong Y, Zeng F, Zhao B, Wang J. Effect of strontium on transcription factors identified by transcriptome analyses of bovine ruminal epithelial cells. BMC Vet Res 2024; 20:88. [PMID: 38459489 PMCID: PMC10921748 DOI: 10.1186/s12917-024-03929-9] [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: 09/21/2023] [Accepted: 02/09/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Strontium (Sr) has similar physicochemical properties as calcium (Ca) and is often used to evaluate the absorption of this mineral. Because the major route of Ca absorption in the bovine occurs in the rumen, it is essential to understand whether Sr impacts the ruminal epithelial cells and to what extent. RESULTS In the present study, RNA sequencing and assembled transcriptome assembly were used to identify transcription factors (TFs), screening and bioinformatics analysis in bovine ruminal epithelial cells treated with Sr. A total of 1405 TFs were identified and classified into 64 families based on an alignment of conserved domains. A total of 174 differently expressed TFs (DE-TFs) were increased and 52 DE-TFs were decreased; the biological process-epithelial cell differentiation was inhibited according to the GSEA-GO analysis of TFs; The GO analysis of DE-TFs was enriched in the DNA binding. Protein-protein interaction network (PPI) found 12 hubs, including SMAD4, SMAD2, SMAD3, SP1, GATA2, NR3C1, PPARG, FOXO1, MEF2A, NCOA2, LEF1, and ETS1, which verified genes expression levels by real-time PCR. CONCLUSIONS In this study, SMAD2, PPARG, LEF1, ETS1, GATA2, MEF2A, and NCOA2 are potential candidates that could be targeted by Sr to mediate cell proliferation and differentiation, as well as lipid metabolism. Hence, these results enhance the comprehension of Sr in the regulation of transcription factors and provide new insight into the study of Sr biological function in ruminant animals.
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Affiliation(s)
- Panpan Tan
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yazhou Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Linshan Mei
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Chenxu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yezi Kong
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangyuan Zeng
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Baoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Jianguo Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Rocks D, Purisic E, Gallo EF, Greally JM, Suzuki M, Kundakovic M. Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572697. [PMID: 38187614 PMCID: PMC10769422 DOI: 10.1101/2023.12.20.572697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Sex differences are found in brain structure and function across species, and across brain disorders in humans1-3. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan4. Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk5-7. However, due to limited molecular studies in female rodents8, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor9, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation1 in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eric Purisic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eduardo F. Gallo
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - John M. Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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4
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Suzuki K, Kwon SJ, Saito D, Atsuta Y. LIN28 is essential for the maintenance of chicken primordial germ cells. Cells Dev 2023; 176:203874. [PMID: 37453484 DOI: 10.1016/j.cdev.2023.203874] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Understanding the mechanism of stem cell maintenance underlies the establishment of long-term and mass culture methods for stem cells that are fundamental for clinical and agricultural applications. In this study, we use chicken primordial germ cell (PGC) as a model to elucidate the molecular mechanisms underlying stem cell maintenance. The PGC is a useful experimental model because it is readily gene-manipulatable and easy to test gene function in vivo using transplantation. Previous studies to establish a long-term culture system have shown that secreted factors such as FGF2 are required to maintain the self-renewal capability of PGC. On the other hand, we know little about intracellular regulators responsible for PGC maintenance. Among representative stem cell factors, we focus on RNA-binding factors LIN28A and LIN28B as possible central regulators for the gene regulatory network essential to PGC maintenance. By taking advantage of the CRISPR/Cas9-mediated gene editing and a clonal culture technique, we find that both LIN28A and LIN28B regulate the proliferation of PGC in vitro. We further showed that colonization efficiency of grafted PGC at the genital ridges, rudiments for the gonads, of chicken embryos were significantly decreased by knockout (KO) of LIN28A or LIN28B. Of note, overexpression of human LIN28 in LIN28-KO PGC was sufficient to restore the low colonization rates, suggesting that LIN28 plays a key role in PGC colonization at the gonads. Transcriptomic analyses of LIN28-KO PGC reveal that several genes related to mesenchymal traits are upregulated, including EGR1, a transcription factor that promotes the differentiation of mesodermal tissues. Finally, we show that the forced expression of human EGR1 deteriorates replication activity and colonization efficiency of PGCs. Taken together, this work demonstrates that LIN28 maintains self-renewal of PGC by suppressing the expression of differentiation genes including EGR1.
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Affiliation(s)
- Katsuya Suzuki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Seung June Kwon
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Saito
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Atsuta
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan.
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Dong Z, Min F, Zhang S, Zhang H, Zeng T. EGR1-Driven METTL3 Activation Curtails VIM-Mediated Neuron Injury in Epilepsy. Neurochem Res 2023; 48:3349-3362. [PMID: 37268752 DOI: 10.1007/s11064-023-03950-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/04/2023]
Abstract
Uncovering mechanisms underlying epileptogenesis aids in preventing further epilepsy progression and to lessen seizure severity and frequency. The purpose of this study is to explore the antiepileptogenic and neuroprotective mechanisms of EGR1 in neuron injuries encountered in epilepsy. Bioinformatics analysis was conducted to identify the key genes related to epilepsy. The mice were rendered epileptic using the kainic acid protocol, followed by measurement of seizure severity, high amplitude and frequency, pathological changes of hippocampal tissues and neuron apoptosis. Furthermore, an in vitro epilepsy model was constructed in the neurons isolated from newborn mice, which was then subjected to loss- and gain-of-function investigations, followed by neuron injury and apoptosis assessment. Interactions among EGR1, METTL3, and VIM were analyzed by a series of mechanistic experiments. In the mouse and cell models of epilepsy, VIM was robustly induced. However, its knockdown reduced hippocampal neuron injury and apoptosis. Meanwhile, VIM knockdown decreased inflammatory response and neuron apoptosis in vivo. Mechanistic investigations indicated that EGR1 transcriptionally activated METTL3, which in turn downregulated VIM expression through m6A modification. EGR1 activated METTL3 and reduced VIM expression, thereby impairing hippocampal neuron injury and apoptosis, preventing epilepsy progression. Taken together, this study demonstrates that EGR1 alleviates neuron injuries in epilepsy by inducing METTL3-mediated inhibition of VIM, which provides clues for the development of novel antiepileptic treatments.
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Affiliation(s)
- Zhaofei Dong
- Department of Neurology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, People's Republic of China
| | - Fuli Min
- Department of Neurology, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510180, Guangdong Province, People's Republic of China
| | - Sai Zhang
- Department of Neurology, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510180, Guangdong Province, People's Republic of China
| | - Huili Zhang
- Department of Neurology, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510180, Guangdong Province, People's Republic of China
| | - Tao Zeng
- Department of Neurology, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, 510180, Guangdong Province, People's Republic of China.
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Long X, Chen W, Liu G, Hu W, Tan Q. Establishment and characterization of a skeletal myoblast cell line of grass carp (Ctenopharyngodon idellus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1043-1061. [PMID: 37782384 DOI: 10.1007/s10695-023-01246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023]
Abstract
Skeletal muscle myoblastic cell lines can provide a valuable new in vitro model for the exploration of the mechanisms that control skeletal muscle development and its associated molecular regulation. In this study, the skeletal muscle tissues of grass carp were digested with trypsin and collagenase I to obtain the primary myoblast cell culture. Myoblast cells were obtained by differential adherence purification and further analyzed by cryopreservation and resuscitation, chromosome analysis, immunohistochemistry, and immunofluorescence. A continuous grass carp myoblast cell line (named CIM) was established from grass carp (Ctenopharyngodon idellus) muscle and has been subcultured > 100 passages in a year and more. The CIM cells revived at 79.78-95.06% viability after 1-6 months of cryopreservation, and shared a population doubling time of 27.24 h. The number of modal chromosomes of CIM cells was 48, and the mitochondrial 12S rRNA sequence of the CIM cell line shared 99% identity with those of grass carp registered in GenBank. No microorganisms (bacteria, fungi, or mycoplasma) were detected during the whole study. The cell type of CIM cells was proven to be myoblast by immunohistochemistry of specific myogenic protein markers, including CD34, desmin, MyoD, and MyHC, as well as relative expression of key genes. And the myogenic rate and fusion index of this cell line after 10 days of induced differentiation were 8.96 ~ 9.42% and 3-24%, respectively. The telomerase activity and transfection efficiency of CIM cell line were 0.027 IU/mgprot and 23 ~ 24%, respectively. These results suggest that a myoblast cell line named CIM with normal biological function has been successfully established, which may provide a valuable tool for related in vitro studies.
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Affiliation(s)
- Xianmei Long
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Wangwang Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Guoqing Liu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Wenguang Hu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Qingsong Tan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China.
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7
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Shen X, Zhao X, He H, Zhao J, Wei Y, Chen Y, Han S, Zhu Y, Zhang Y, Zhu Q, Yin H. Evolutionary conserved circular MEF2A RNAs regulate myogenic differentiation and skeletal muscle development. PLoS Genet 2023; 19:e1010923. [PMID: 37676887 PMCID: PMC10508632 DOI: 10.1371/journal.pgen.1010923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/19/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Circular RNAs (circRNAs) have been recognized as critical regulators of skeletal muscle development. Myocyte enhancer factor 2A (MEF2A) is an evolutionarily conserved transcriptional factor that regulates myogenesis. However, it remains unclear whether MEF2A produces functional circRNAs. In this study, we identified two evolutionarily conserved circular MEF2A RNAs (circMEF2As), namely circMEF2A1 and circMEF2A2, in chicken and mouse muscle stem cells. Our findings revealed that circMEF2A1 promotes myogenesis by regulating the miR-30a-3p/PPP3CA/NFATC1 axis, whereas circMEF2A2 facilitates myogenic differentiation by targeting the miR-148a-5p/SLIT3/ROBO2/β-catenin signaling pathway. Furthermore, in vivo experiments demonstrated that circMEF2As both promote skeletal muscle growth. We also discovered that the linear MEF2A mRNA-derived MEF2A protein binds to its own promoter region, accelerating the transcription of MEF2A and upregulating the expression of both linear MEF2A and circMEF2As, forming a MEF2A autoregulated positive feedback loop. Moreover, circMEF2As positively regulate the expression of linear MEF2A by adsorbing miR-30a-3p and miR-148a-5p, which directly contribute to the MEF2A autoregulated feedback loop. Importantly, we found that mouse circMEF2As are essential for the myogenic differentiation of C2C12 cells. Collectively, our results demonstrated the evolution, function, and underlying mechanisms of circMEF2As in animal myogenesis, which may provide novel insight for both the farm animal meat industry and human medicine.
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Affiliation(s)
- Xiaoxu Shen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiyu Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haorong He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuanhang Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuqi Chen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shunshun Han
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yifeng Zhu
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yao Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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8
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Shi X, Wang Y, Liu H, Han R. Targeting Hub Genes Involved in Muscle Injury Induced by Jumping Load Based on Transcriptomics. DNA Cell Biol 2023; 42:498-506. [PMID: 37339448 DOI: 10.1089/dna.2022.0285] [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] [Indexed: 06/22/2023] Open
Abstract
The purpose of this study was to find hub genes that may play key roles in skeletal muscle injury induced by jumping load. Twelve female Sprague Dawley rats were divided into the normal control (NC) group and the jumping-induced muscle injury (JI) group. After 6 weeks of jumping, transmission electron microscopy, hematoxylin-eosin staining, transcriptomics sequencing and genes analysis, interaction network prediction of multiple proteins, real-time PCR detection, and Western blotting were performed on gastrocnemius muscles from NC and JI groups. As compared with NC rats, excessive jumping can result in notable structural damage and inflammatory infiltration in JI rats. A total of 112 differentially expressed genes were confirmed in NC rats versus JI rats, with 59 genes upregulated and 53 genes downregulated. Using the online String database, four hub genes in the transcriptional regulatory network were targeted, including FOS, EGR1, ATF3, and NR4A3. All expression levels of FOS, EGR1, ATF3, and NR4A3 mRNAs were decreased in JI rats compared with NC rats (p < 0.05 or p < 0.01). All expression levels of c-Fos, EGR1, ATF3, and NOR1 proteins were upregulated in JI rats (p < 0.01, p < 0.05, p > 0.05, and p < 0.01, respectively). Collectively, these findings indicate that FOS, EGR1, ATF3, and NR4A3 genes may be functionally important in jumping-induced muscle injury.
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Affiliation(s)
- Xiaolan Shi
- Wushu College, Henan University, Kaifeng, China
| | - Yijie Wang
- School of Physical Education and Sport, Henan University, Kaifeng, China
| | - Haitao Liu
- School of Physical Education and Sport, Henan University, Kaifeng, China
- Sports Reform and Development Research Center, Henan University, Kaifeng, China
| | - Rui Han
- School of Physical Education and Sport, Henan University, Kaifeng, China
- Sports Reform and Development Research Center, Henan University, Kaifeng, China
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9
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Kim D, Ban KY, Lee GH, Jun HS. Lysophosphatidic Acid Induces Podocyte Pyroptosis in Diabetic Nephropathy by an Increase of Egr1 Expression via Downregulation of EzH2. Int J Mol Sci 2023; 24:9968. [PMID: 37373116 DOI: 10.3390/ijms24129968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Podocyte damage and renal inflammation are the main features and pathogenesis of diabetic nephropathy (DN). Inhibition of lysophosphatidic acid (LPA) receptor 1 (LPAR1) suppresses glomerular inflammation and improves DN. Herein, we investigated LPA-induced podocyte damage and its underlying mechanisms in DN. We investigated the effects of AM095, a specific LPAR1 inhibitor, on podocytes from streptozotocin (STZ)-induced diabetic mice. E11 cells were treated with LPA in the presence or absence of AM095, and the expression of NLRP3 inflammasome factors and pyroptosis were measured. A chromatin immunoprecipitation assay and Western blotting were performed to elucidate underlying molecular mechanisms. Gene knockdown by transfecting small interfering RNA was used to determine the role of the transcription factor Egr1 (early growth response protein 1) and histone methyltransferase EzH2 (Enhancer of Zeste Homolog 2) in LPA-induced podocyte injury. AM095 administration inhibited podocyte loss, NLRP3 inflammasome factor expression, and cell death in STZ-induced diabetic mice. In E11 cells, LPA increased NLRP3 inflammasome activation and pyroptosis via LPAR1. Egr1 mediated NLRP3 inflammasome activation and pyroptosis in LPA-treated E11 cells. LPA decreased H3K27me3 enrichment at the Egr1 promoter in E11 cells by downregulating EzH2 expression. EzH2 knockdown further increased LPA-induced Egr1 expression. In podocytes from STZ-induced diabetic mice, AM095 suppressed Egr1 expression increase and EzH2/H3K27me3 expression reduction. Collectively, these results demonstrate that LPA induces NLRP3 inflammasome activation by downregulating EzH2/H3K27me3 and upregulating Egr1 expression, resulting in podocyte damage and pyroptosis, which may be a potential mechanism of DN progression.
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Affiliation(s)
- Donghee Kim
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
| | - Ka-Yun Ban
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Geon-Ho Lee
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Hee-Sook Jun
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
- Gachon Medical Research Institute, Gil Hospital, Incheon 21565, Republic of Korea
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10
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Ren Y, Xu YP, Fan XY, Murtaza B, Wang YN, Li Z, Javed MT, Wang ZH, Li Q. Transcriptome analysis reveals key transcription factors and pathways of polian vesicle associated with cell proliferation in Vibrio splendidus-challenged Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101082. [PMID: 37146451 DOI: 10.1016/j.cbd.2023.101082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023]
Abstract
Polian vesicle is thought to produce coelomocytes and contribute to the sea cucumber's immune system. Our previous work has indicated that polian vesicle was responsible for cell proliferation at 72 h post pathogenic challenge. However, the transcription factors related to the activation of effector factors and the molecular process behind this remained unknown. In this study, to reveal the early functions of polian vesicle in response to the microbe, a comparative transcriptome sequencing of polian vesicle in V. splendidus-challenged Apostichopus japonicus, including normal group (PV 0 h), pathogen challenging for 6 h (PV 6 h) and 12 h (PV 12 h) was performed. Compared PV 0 h to PV 6 h, PV 0 h to PV 12 h, and PV 6 h to PV 12 h, we found 69, 211, and 175 differentially expressed genes (DEGs), respectively. KEGG enrichment analysis revealed the DEGs, including several transcription factors such as fos, FOS-FOX, ATF2, egr1, KLF2, and Notch3 between PV 6 h and PV 12 h were consistently enriched in MAPK, Apelin and Notch3 signaling pathways related to cell proliferation compared with that in PV 0 h. Important DEGs involved in cell growth were chosen, and their expression patterns were almost the same as the transcriptome profile analysis by qPCR. Protein interaction network analysis indicated that two DEGs of fos and egr1 were probably significant as key candidate genes controlling cell proliferation and differentiation in polian vesicle after pathogenic infection in A. japonicus. Overall, our analysis demonstrates that polian vesicles may play an essential role in regulating proliferation via transcription factors-mediated signaling pathway in A. japonicus and provide new insights into hematopoietic modulation of polian vesicles in response to pathogen infection.
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Affiliation(s)
- Yuan Ren
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Yong-Ping Xu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xu-Yuan Fan
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yi-Nan Wang
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Zhen Li
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Muhammad Tariq Javed
- Faculty of Veterinary Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Zhen-Hui Wang
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China.
| | - Qiang Li
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, China.
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11
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Feng L, Si J, Yue J, Zhao M, Qi W, Zhu S, Mo J, Wang L, Lan G, Liang J. The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs. Int J Mol Sci 2023; 24:ijms24076413. [PMID: 37047386 PMCID: PMC10094211 DOI: 10.3390/ijms24076413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.
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Affiliation(s)
- Lingli Feng
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jinglei Si
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jingwei Yue
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Mingwei Zhao
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Wenjing Qi
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Siran Zhu
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jiayuan Mo
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Ganqiu Lan
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jing Liang
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
- Correspondence:
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12
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Cai S, Hu B, Wang X, Liu T, Lin Z, Tong X, Xu R, Chen M, Duo T, Zhu Q, Liang Z, Li E, Chen Y, Li J, Liu X, Mo D. Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC Biol 2023; 21:19. [PMID: 36726129 PMCID: PMC9893630 DOI: 10.1186/s12915-023-01519-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Skeletal muscle development is a multistep process whose understanding is central in a broad range of fields and applications, from the potential medical value to human society, to its economic value associated with improvement of agricultural animals. Skeletal muscle initiates in the somites, with muscle precursor cells generated in the dermomyotome and dermomyotome-derived myotome before muscle differentiation ensues, a developmentally regulated process that is well characterized in model organisms. However, the regulation of skeletal muscle ontogeny during embryonic development remains poorly defined in farm animals, for instance in pig. Here, we profiled gene expression and chromatin accessibility in developing pig somites and myotomes at single-cell resolution. RESULTS We identified myogenic cells and other cell types and constructed a differentiation trajectory of pig skeletal muscle ontogeny. Along this trajectory, the dynamic changes in gene expression and chromatin accessibility coincided with the activities of distinct cell type-specific transcription factors. Some novel genes upregulated along the differentiation trajectory showed higher expression levels in muscular dystrophy mice than that in healthy mice, suggesting their involvement in myogenesis. Integrative analysis of chromatin accessibility, gene expression data, and in vitro experiments identified EGR1 and RHOB as critical regulators of pig embryonic myogenesis. CONCLUSIONS Collectively, our results enhance our understanding of the molecular and cellular dynamics in pig embryonic myogenesis and offer a high-quality resource for the further study of pig skeletal muscle development and human muscle disease.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Bin Hu
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tongni Liu
- Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Zhuhu Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Rong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Meilin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Qi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Ziyun Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Enru Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Jianhao Li
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
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13
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Gwynne WD, Suk Y, Custers S, Mikolajewicz N, Chan JK, Zador Z, Chafe SC, Zhai K, Escudero L, Zhang C, Zaslaver O, Chokshi C, Shaikh MV, Bakhshinyan D, Burns I, Chaudhry I, Nachmani O, Mobilio D, Maich WT, Mero P, Brown KR, Quaile AT, Venugopal C, Moffat J, Montenegro-Burke JR, Singh SK. Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma. Cancer Cell 2022; 40:1488-1502.e7. [PMID: 36368321 DOI: 10.1016/j.ccell.2022.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/09/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
MYC-driven medulloblastoma (MB) is an aggressive pediatric brain tumor characterized by therapy resistance and disease recurrence. Here, we integrated data from unbiased genetic screening and metabolomic profiling to identify multiple cancer-selective metabolic vulnerabilities in MYC-driven MB tumor cells, which are amenable to therapeutic targeting. Among these targets, dihydroorotate dehydrogenase (DHODH), an enzyme that catalyzes de novo pyrimidine biosynthesis, emerged as a favorable candidate for therapeutic targeting. Mechanistically, DHODH inhibition acts on target, leading to uridine metabolite scarcity and hyperlipidemia, accompanied by reduced protein O-GlcNAcylation and c-Myc degradation. Pyrimidine starvation evokes a metabolic stress response that leads to cell-cycle arrest and apoptosis. We further show that an orally available small-molecule DHODH inhibitor demonstrates potent mono-therapeutic efficacy against patient-derived MB xenografts in vivo. The reprogramming of pyrimidine metabolism in MYC-driven medulloblastoma represents an unappreciated therapeutic strategy and a potential new class of treatments with stronger cancer selectivity and fewer neurotoxic sequelae.
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Affiliation(s)
- William D Gwynne
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Stefan Custers
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Mikolajewicz
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Jeremy K Chan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zsolt Zador
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Shawn C Chafe
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Kui Zhai
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Laura Escudero
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Cunjie Zhang
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Olga Zaslaver
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chirayu Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Muhammad Vaseem Shaikh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - David Bakhshinyan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Ian Burns
- Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Iqra Chaudhry
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Omri Nachmani
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Daniel Mobilio
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - William T Maich
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Patricia Mero
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kevin R Brown
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Andrew T Quaile
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chitra Venugopal
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jason Moffat
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J Rafael Montenegro-Burke
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Sheila K Singh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
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14
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Single-cell chromatin landscapes of mouse skin development. Sci Data 2022; 9:741. [PMID: 36460683 PMCID: PMC9718782 DOI: 10.1038/s41597-022-01839-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
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15
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Zeng SQ, Liu CL, Huang CN, Si WJ, Liu CB, Ren LX, Zhang WY, He YM, Yuan Y, Zhang HY, Han YG, Na RS, E GX, Huang YF. Identification of the Differential Expression Profile of miRNAs in Longissimus dorsi Muscle of Dazu Black Goat. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542211014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Fu X, Chen W, Pan Y, Liu C, Zhang Z, Shao S, Zhang W. CTPS cytoophidia formation affects cell cycle progression and promotes TSN‑induced apoptosis of MKN45 cells. Mol Med Rep 2022; 26:319. [PMID: 36043523 PMCID: PMC9471557 DOI: 10.3892/mmr.2022.12835] [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: 04/21/2022] [Accepted: 08/03/2022] [Indexed: 11/06/2022] Open
Abstract
Cytidine triphosphate synthase (CTPS) forms filamentous structures termed cytoophidia in numerous types of cell. Toosendanin (TSN) is a tetracyclic triterpenoid and induces CTPS to form cytoophidia in MKN45 cells. However, the effects of CTPS cytoophidia on the proliferation and apoptosis of human gastric cancer cells remain poorly understood. In the present study, CTPS‑overexpression and R294D‑CTPS mutant vectors were generated to assess the effect of CTPS cytoophidia on the proliferation and apoptosis of gastric cancer MKN45 cells. Formation of CTPS cytoophidia significantly inhibited MKN45 cell proliferation (evaluated using EdU incorporation assay), significantly blocked the cell cycle in G1 phase (assessed using flow cytometry) and significantly decreased mRNA and protein expression levels of cyclin D1 (assessed by reverse transcription‑quantitative PCR and western blotting, respectively). Furthermore, the number of apoptotic bodies and apoptosis rate were markedly elevated and mitochondrial membrane potential was markedly decreased. Moreover, mRNA and protein expression levels of Bax increased and Bcl‑2 decreased markedly in MKN45 cells following transfection with the CTPS‑overexpression vector. The proliferation rate increased, percentage of G1/G0‑phase cells decreased and apoptosis was attenuated in cells transfected with the R294D‑CTPS mutant vector and this mutation did not lead to formation of cytoophidia. The results of the present study suggested that formation of CTPS cytoophidia inhibited proliferation and promoted apoptosis in MKN45 cells. These results may provide insights into the role of CTPS cytoophidia in cancer cell proliferation and apoptosis.
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Affiliation(s)
- Xuepeng Fu
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Wen Chen
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Yang Pan
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Chang Liu
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Zhenzhu Zhang
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Shuli Shao
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
| | - Weiwei Zhang
- Department of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang 161006, P.R. China
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17
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Hinkle ER, Blue RE, Tsai YH, Combs M, Davi J, Coffey AR, Boriek AM, Taylor JM, Parker JS, Giudice J. Stretching muscle cells induces transcriptional and splicing transitions and changes in SR proteins. Commun Biol 2022; 5:987. [PMID: 36123433 PMCID: PMC9485123 DOI: 10.1038/s42003-022-03915-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Alternative splicing is an RNA processing mechanism involved in skeletal muscle development and pathology. Muscular diseases exhibit splicing alterations and changes in mechanobiology leading us to investigate the interconnection between mechanical forces and RNA processing. We performed deep RNA-sequencing after stretching muscle cells. First, we uncovered transcriptional changes in genes encoding proteins involved in muscle function and transcription. Second, we observed that numerous mechanosensitive genes were part of the MAPK pathway which was activated in response to stretching. Third, we revealed that stretching skeletal muscle cells increased the proportion of alternatively spliced cassette exons and their inclusion. Fourth, we demonstrated that the serine and arginine-rich proteins exhibited stronger transcriptional changes than other RNA-binding proteins and that SRSF4 phosphorylation is mechanosensitive. Identifying SRSF4 as a mechanosensitive RNA-binding protein that might contribute to crosstalk between mechanotransduction, transcription, and splicing could potentially reveal novel insights into muscular diseases, particularly those with unknown etiologies.
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Affiliation(s)
- Emma R Hinkle
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - R Eric Blue
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Matthew Combs
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Jacquelyn Davi
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Alisha R Coffey
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Aladin M Boriek
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Joan M Taylor
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
- McAllister Heart Institute, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Joel S Parker
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA.
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA.
- McAllister Heart Institute, The University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA.
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18
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EGR1-CCL2 Feedback Loop Maintains Epithelial-Mesenchymal Transition of Cisplatin-Resistant Gastric Cancer Cells and Promotes Tumor Angiogenesis. Dig Dis Sci 2022; 67:3702-3713. [PMID: 34499269 DOI: 10.1007/s10620-021-07250-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/31/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND The mechanism of cisplatin resistance in gastric cancer (GC) is still elusive; several recent evidences proposed that chemoresistant tumor cells acquired aggressive behaviors. AIMS This study was aimed to investigate the mechanism of epithelial-mesenchymal transition (EMT) and angiogenesis in chemoresistant GC. METHODS Bioinformatics analysis and function or mechanism experiments including RT-qPCR, immunofluorescence, Western blot, luciferase reporter assay, Chromatin immunoprecipitation, Chicken chorioallantoic membrane assay and animal experiments were applied to evaluate the role of EGR1-CCL2 feedback loop. RESULTS Compared with the parental cell line SGC7901, cisplatin resistant SGC7901R cells underwent EMT and showed increased angiogenic capabilities. Mechanistically, SGC7901R cells showed increased levels of EGR1, which could transcriptionally activate the angiogenic factor CCL2 and EMT regulator ZEB2. Reciprocally, CCL2 activated the CCR2-ERK-ELK1-EGR1 pathway, thus forming a positive feed-forward loop. Moreover, CCL2 in culture medium of SGC7901R cells promoted angiogenesis of Human Umbilical Vein Endothelial Cells (HUVECs). EGR1 expression was positively correlated with CCL2 and ZEB2 in clinical GC tissues, and the depletion of ERG1 could also decrease microvessel density and ZEB2 expression in metastatic nodules of nude mice. CONCLUSIONS EGR1-CCL2 feedback loop might exert critical roles on EMT and angiogenesis of chemoresistant GC.
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CREB1 promotes proliferation and differentiation by mediating the transcription of CCNA2 and MYOG in bovine myoblasts. Int J Biol Macromol 2022; 216:32-41. [PMID: 35777504 DOI: 10.1016/j.ijbiomac.2022.06.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/17/2022] [Accepted: 06/26/2022] [Indexed: 11/23/2022]
Abstract
The cAMP response element binding protein 1 (CREB1) is an important nuclear transcription factor in eukaryotes. To explore the potential role of CREB1 on Qinchuan bovine skeletal myoblasts, we investigated the function of CREB1 on proliferation and differentiation. In this study, we found that CREB1 promoted cell proliferation by promoting DNA synthesis in S phase and cell division in G2 phase and promoted myogenic differentiation process in bovine myoblasts. Through dual luciferase experiments, we found that CREB1 can bind to the proximal promoter regions of CCNA2 and MyoG, indicating that CREB1 can play a positive regulatory role in the proliferation and differentiation of myoblasts by mediating the transcription of CCNA2 and MyoG. In addition, through downstream target gene analysis and transcriptome sequencing, we found that CREB1 plays a role in cell proliferation, myogenic differentiation, skeletal muscle repair and other related pathways.
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20
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Chiba N, Noguchi Y, Hwan Seong C, Ohnishi T, Matsuguchi T. EGR1 Plays an Important Role in BMP9-Mediated Osteoblast Differentiation by Promoting SMAD1/5 Phosphorylation. FEBS Lett 2022; 596:1720-1732. [PMID: 35594155 DOI: 10.1002/1873-3468.14407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022]
Abstract
Bone morphogenetic proteins (BMPs) are essential regulators of skeletal homeostasis, and BMP9 is the most potently osteogenic among them. Here, we found that BMP9 and BMP2 rapidly induced early growth response 1 (EGR1) protein expression in osteoblasts through MEK/ERK pathway-dependent transcriptional activation. Knockdown of EGR1 using siRNA significantly inhibited BMP9-induced matrix mineralization and osteogenic marker gene expression in osteoblasts. Knockdown of EGR1 significantly reduced SMAD1/5 phosphorylation and inhibited the expression of their transcriptional targets in osteoblasts stimulated by BMP9. In contrast, forced EGR1 overexpression in osteoblasts enhanced BMP9-mediated osteoblast differentiation and SMAD1/5 phosphorylation. An intracellular association between EGR1 and SMAD1/5 was identified using immunoprecipitation assays. These results indicated that EGR1 plays an important role in BMP9-stimulated osteoblast differentiation by enhancing SMAD1/5 phosphorylation.
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Affiliation(s)
- Norika Chiba
- Department of Oral Biochemistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan
| | - Yukie Noguchi
- Department of Oral Biochemistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan
| | - Chang Hwan Seong
- Department of Oral Biochemistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan.,Department of Oral and Maxillofacial Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan
| | - Tomokazu Ohnishi
- Department of Oral Biochemistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan
| | - Tetsuya Matsuguchi
- Department of Oral Biochemistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 8-35-1 Sakuragaoka, 890-8544, Japan
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21
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Liu H, Xu Q, Xi Y, Ma S, Wang J, Bai L, Han C, He H, Li L. Dynamic transcriptome profiling reveals essential roles of the Receptor Tyrosine Kinases (RTK) family in feather development of duck. Br Poult Sci 2022; 63:605-612. [PMID: 35383522 DOI: 10.1080/00071668.2022.2061839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Chicken primary myoblasts (CPMs) are precursors that form muscle fibres. The proliferation and differentiation of CPMs is an essential stage in muscle development. Previous RNA-seq analysis showed that phosphoglycerate dehydrogenase (PHGDH) is a differentially expressed gene in chicken muscle tissue at different growth stages. Therefore, the following study explored the effect of PHGDH on the proliferation and differentiation of CPMs.2. The effect on the proliferation of CPMs by RT-qPCR, CCK-8, and EdU assays after the overexpression and knockdown of PHGDH was evaluated. RT-qPCR, western blotting, and indirect immunofluorescence were used to detect the effect of PHGDH on the differentiation of the CPMs. The expression was observed at different time points for differentiation induced by the CPMs.3. The results showed that PHGDH significantly promoted proliferation and differentiation in CPMs. The results showed that overexpression of PHGDH significantly upregulated CPM proliferation, while knockdown had the opposite effect. Marker genes showed that overexpression of PHGDH significantly upregulated the expression of P21, MYOG and MYOD genes, significantly downregulated the expression of the MSTN gene and promoted the expression of the MYHC protein. In contrast, PHGDH knockdown had the opposite effect.4. Desmin immunofluorescence analysis of myotube differentiation in primary myoblasts showed that overexpression of PHGDH significantly increased the area of myotube differentiation and promoted the proliferation and differentiation of myoblasts. Knockdown of PHGDH had the opposite effect.5. In summary, PHGDH was shown to play a positive role in regulating myoblast proliferation and differentiation. This provided a theoretical basis for further analysis of the regulatory mechanism of the PHGDH gene in chicken muscle development and for improving poultry production.
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Affiliation(s)
| | - Qian Xu
- Sichuan Agricultural University - Chengdu Campus
| | - Yang Xi
- Sichuan Agricultural University - Chengdu Campus
| | - ShengChao Ma
- Sichuan Agricultural University - Chengdu Campus
| | - Jianmei Wang
- Sichuan Agricultural University - Chengdu Campus
| | - Lili Bai
- Sichuan Agricultural University - Chengdu Campus
| | - Chunchun Han
- Sichuan Agricultural University - Chengdu Campus, College of Animal Science and Technology
| | - Hua He
- Sichuan Agricultural University - Chengdu Campus
| | - Liang Li
- Sichuan Agricultural University, College of Animal Sci & Tech
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22
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Chen L, Wu YL, Ding H, Xie KZ, Zhang T, Zhang GX, Wang JY. PHGDH promotes the proliferation and differentiation of primary chicken myoblasts. Br Poult Sci 2022; 63:581-589. [PMID: 35383521 DOI: 10.1080/00071668.2022.2062221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Chicken primary myoblasts (CPMs) are precursors that form muscle fibres. The proliferation and differentiation of CPMs is an essential stage in muscle development. Previous RNA-seq analysis showed that phosphoglycerate dehydrogenase (PHGDH) is a differentially expressed gene in chicken muscle tissue at different growth stages. Therefore, the following study explored the effect of PHGDH on the proliferation and differentiation of CPMs.2. The effect on the proliferation of CPMs by RT-qPCR, CCK-8, and EdU assays after the overexpression and knockdown of PHGDH was evaluated. RT-qPCR, western blotting, and indirect immunofluorescence were used to detect the effect of PHGDH on the differentiation of the CPMs. The expression was observed at different time points for differentiation induced by the CPMs.3. The results showed that PHGDH significantly promoted proliferation and differentiation in CPMs. The results showed that overexpression of PHGDH significantly upregulated CPM proliferation, while knockdown had the opposite effect. Marker genes showed that overexpression of PHGDH significantly upregulated the expression of P21, MYOG and MYOD genes, significantly downregulated the expression of the MSTN gene and promoted the expression of the MYHC protein. In contrast, PHGDH knockdown had the opposite effect.4. Desmin immunofluorescence analysis of myotube differentiation in primary myoblasts showed that overexpression of PHGDH significantly increased the area of myotube differentiation and promoted the proliferation and differentiation of myoblasts. Knockdown of PHGDH had the opposite effect.5. In summary, PHGDH was shown to play a positive role in regulating myoblast proliferation and differentiation. This provided a theoretical basis for further analysis of the regulatory mechanism of the PHGDH gene in chicken muscle development and for improving poultry production.
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Affiliation(s)
- L Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China.,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Y L Wu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - H Ding
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - K Z Xie
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - T Zhang
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - G X Zhang
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - J Y Wang
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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23
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Salguero-Aranda C, Beltran-Povea A, Postigo-Corrales F, Hitos AB, Díaz I, Caballano-Infantes E, Fraga MF, Hmadcha A, Martín F, Soria B, Tapia-Limonchi R, Bedoya FJ, Tejedo JR, Cahuana GM. Pdx1 Is Transcriptionally Regulated by EGR-1 during Nitric Oxide-Induced Endoderm Differentiation of Mouse Embryonic Stem Cells. Int J Mol Sci 2022; 23:ijms23073920. [PMID: 35409280 PMCID: PMC8999925 DOI: 10.3390/ijms23073920] [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: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
The transcription factor, early growth response-1 (EGR-1), is involved in the regulation of cell differentiation, proliferation, and apoptosis in response to different stimuli. EGR-1 is described to be involved in pancreatic endoderm differentiation, but the regulatory mechanisms controlling its action are not fully elucidated. Our previous investigation reported that exposure of mouse embryonic stem cells (mESCs) to the chemical nitric oxide (NO) donor diethylenetriamine nitric oxide adduct (DETA-NO) induces the expression of early differentiation genes such as pancreatic and duodenal homeobox 1 (Pdx1). We have also evidenced that Pdx1 expression is associated with the release of polycomb repressive complex 2 (PRC2) and P300 from the Pdx1 promoter; these events were accompanied by epigenetic changes to histones and site-specific changes in the DNA methylation. Here, we investigate the role of EGR-1 on Pdx1 regulation in mESCs. This study reveals that EGR-1 plays a negative role in Pdx1 expression and shows that the binding capacity of EGR-1 to the Pdx1 promoter depends on the methylation level of its DNA binding site and its acetylation state. These results suggest that targeting EGR-1 at early differentiation stages might be relevant for directing pluripotent cells into Pdx1-dependent cell lineages.
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Affiliation(s)
- Carmen Salguero-Aranda
- Department of Pathology, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, CSIC-University of Seville, 41013 Seville, Spain
- Spanish Biomedical Research Network Centre in Oncology, CIBERONC of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
- Correspondence: (C.S.-A.); (G.M.C.)
| | - Amparo Beltran-Povea
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
| | - Fátima Postigo-Corrales
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
| | - Ana Belén Hitos
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
| | - Irene Díaz
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
- Department of Regeneration and Cell Therapy Andalusian, Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, 41013 Seville, Spain
| | - Estefanía Caballano-Infantes
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Department of Regeneration and Cell Therapy Andalusian, Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, 41013 Seville, Spain
| | - Mario F. Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Cancer Epigenetics and Nanomedicine Laboratory, 33940 El Entrego, Spain;
- Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
| | - Abdelkrim Hmadcha
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Department of Biotechnology, University of Alicante, 03690 Alicante, Spain
| | - Franz Martín
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
- Department of Regeneration and Cell Therapy Andalusian, Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, 41013 Seville, Spain
| | - Bernat Soria
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
- Department of Biotechnology, University of Alicante, 03690 Alicante, Spain
- Health Research Institute-ISABIAL Dr Balmis University Hospital and Institute of Bioengineering, University Miguel Hernández de Elche, 03010 Alicante, Spain
| | - Rafael Tapia-Limonchi
- Tropical Disease Institute, Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas 01001, Peru;
| | - Francisco J. Bedoya
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
| | - Juan R. Tejedo
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
- Tropical Disease Institute, Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas 01001, Peru;
| | - Gladys M. Cahuana
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.B.-P.); (F.P.-C.); (E.C.-I.); (A.H.); (F.M.); (F.J.B.); (J.R.T.)
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-CIBERDEM of the Carlos III Health Institute (ISCIII), 08036 Madrid, Spain; (A.B.H.); (I.D.); (B.S.)
- Correspondence: (C.S.-A.); (G.M.C.)
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Tallafuss A, Stednitz SJ, Voeun M, Levichev A, Larsch J, Eisen J, Washbourne P. Egr1 Is Necessary for Forebrain Dopaminergic Signaling during Social Behavior. eNeuro 2022; 9:ENEURO.0035-22.2022. [PMID: 35346959 PMCID: PMC8994534 DOI: 10.1523/eneuro.0035-22.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/08/2022] [Accepted: 03/12/2022] [Indexed: 12/25/2022] Open
Abstract
Finding the link between behaviors and their regulatory molecular pathways is a major obstacle in treating neuropsychiatric disorders. The immediate early gene (IEG) EGR1 is implicated in the etiology of neuropsychiatric disorders, and is linked to gene pathways associated with social behavior. Despite extensive knowledge of EGR1 gene regulation at the molecular level, it remains unclear how EGR1 deficits might affect the social component of these disorders. Here, we examined the social behavior of zebrafish with a mutation in the homologous gene egr1 Mutant fish exhibited reduced social approach and orienting, whereas other sensorimotor behaviors were unaffected. On a molecular level, expression of the dopaminergic biosynthetic enzyme, tyrosine hydroxylase (TH), was strongly decreased in TH-positive neurons of the anterior parvocellular preoptic nucleus. These neurons are connected with basal forebrain (BF) neurons associated with social behavior. Chemogenetic ablation of around 30% of TH-positive neurons in this preoptic region reduced social attraction to a similar extent as the egr1 mutation. These results demonstrate the requirement of Egr1 and dopamine signaling during social interactions, and identify novel circuitry underlying this behavior.
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Affiliation(s)
| | | | - Mae Voeun
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403
| | | | - Johannes Larsch
- Max Planck Institut für Neurobiologie, Martinsried, D-82152, Munich Germany
| | - Judith Eisen
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403
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25
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Podgorniak T, Dhanasiri A, Chen X, Ren X, Kuan PF, Fernandes J. Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics 2022; 17:1281-1298. [PMID: 35006036 PMCID: PMC9542679 DOI: 10.1080/15592294.2021.2017554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.
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Affiliation(s)
- Tomasz Podgorniak
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Anusha Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Xianquan Chen
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.,School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Shi J, Zhang Q, Song Y, Lei Z, Fu L, Cheng S. Exploring the effects of different male parent crossings on sheep muscles and related regulatory genes using mRNA-Seq. Anim Biosci 2022; 35:1129-1140. [PMID: 34991197 PMCID: PMC9262716 DOI: 10.5713/ab.21.0463] [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: 10/11/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022] Open
Abstract
Objective With improvements in living standards and increase in population globally, the demand for meat products has been increasing; improved meat production from livestock could effectively meet this demand. In this study, we examined the differences in the muscle traits of different male crossbred sheep and attempted to identify key genes that regulate these traits. Methods Dubo sheep × Small-tailed Han sheep (DP×STH) and Suffolk × Small-tailed Han sheep (SFK×STH) were selected to determine meat quality and production performance by Masson staining. Transcriptome sequencing and bioinformatic analysis were performed to identify differentially expressed genes (DEGs) related to meat quality. The presence of DEGs was confirmed by real-time polymerase chain reaction (qPCR). Results The production performance of SFK×STH sheep was better than that of DP×STH sheep, but the meat quality of DP×STH sheep was better than that of SFK×STH sheep. The muscle fiber diameter of DP×STH sheep was smaller than that of SFK×STH sheep. Twenty-two DEGs were identified. Among them, four Gene Ontology terms were related to muscle traits, and three DEGs were related to muscle or muscle fibers. There were no significant differences in the number of single nucleotide mutations and mutation sites in the different male parent cross combinations. Conclusion This study provides genetic resources for future sheep muscle development and cross-breeding research.
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Affiliation(s)
- Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yali Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhaomin Lei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Lingjuan Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso. PLoS One 2021; 16:e0255089. [PMID: 34351956 PMCID: PMC8341487 DOI: 10.1371/journal.pone.0255089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/09/2021] [Indexed: 11/27/2022] Open
Abstract
In this study, single-SNP GWAS analyses were conducted to find regions affecting tolerance against trypanosomosis and morphometrics traits in purebred and crossbred Baoulé cattle of Burkina Faso. The trypanosomosis status (positive and negative) and a wide set of morphological traits were recorded for purebred Baoulé and crossbred Zebu x Baoulé cattle, and genotyped with the Illumina Bovine SNP50 BeadChip. After quality control, 36,203 SNPs and 619 animals including 343 purebred Baoulé and 279 crossbreds were used for the GWAS analyses. Several important genes were found that can influence morphological parameters. Although there were no genes identified with a reported strong connection to size traits, many of them were previously identified in various growth-related studies. A re-occurring theme for the genes residing in the regions identified by the most significant SNPs was pleiotropic effect on growth of the body and the cardiovascular system. Regarding trypanosomosis tolerance, two potentially important regions were identified in purebred Baoulé on chromosomes 16 and 24, containing the CFH, CRBN, TRNT1 and, IL5RA genes, and one additional genomic region in Baoulé, x Zebu crossbreds on chromosome 5, containing MGAT4C and NTS. Almost all of these regions and genes were previously related to the trait of interest, while the CRBN gene was to our knowledge presented in the context of trypanosomiasis tolerance for the first time.
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28
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Effects of maternal gestational diet, with or without methionine, on muscle transcriptome of Bos indicus-influenced beef calves following a vaccine-induced immunological challenge. PLoS One 2021; 16:e0253810. [PMID: 34166453 PMCID: PMC8224847 DOI: 10.1371/journal.pone.0253810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Maternal nutrition during gestation can cause epigenetic effects that translate to alterations in gene expression in offspring. This 2-year study employed RNA-sequencing technology to evaluate the pre- and post-vaccination muscle transcriptome of early-weaned Bos indicus-influenced beef calves born from dams offered different supplementation strategies from 57 ± 5 d prepartum until 17 ± 5 d postpartum. Seventy-two Brangus heifers (36 heifers/yr) were stratified by body weight and body condition score and assigned to bahiagrass pastures (3 heifers/pasture/yr). Treatments were randomly assigned to pastures and consisted of (i) no pre- or postpartum supplementation (NOSUP), (ii) pre- and postpartum supplementation of protein and energy using 7.2 kg of dry matter/heifer/wk of molasses + urea (MOL), or (iii) MOL fortified with 105 g/heifer/wk of methionine hydroxy analog (MOLMET). Calves were weaned on d 147 of the study. On d 154, 24 calves/yr (8 calves/treatment) were randomly selected and individually limit-fed a high-concentrate diet until d 201. Calves were vaccinated on d 160. Muscle biopsies were collected from the same calves (4 calves/treatment/day/yr) on d 154 (pre-vaccination) and 201 (post-vaccination) for gene expression analysis using RNA sequencing. Molasses maternal supplementation led to a downregulation of genes associated with muscle cell differentiation and development along with intracellular signaling pathways (e.g., Wnt and TGF-β signaling pathway) compared to no maternal supplementation. Maternal fortification with methionine altered functional gene-sets involved in amino acid transport and metabolism and the one-carbon cycle. In addition, muscle transcriptome was impacted by vaccination with a total of 2,396 differentially expressed genes (FDR ≤ 0.05) on d 201 vs. d 154. Genes involved in cell cycle progression, extracellular matrix, and collagen formation were upregulated after vaccination. This study demonstrated that maternal supplementation of energy and protein, with or without, methionine has long-term implications on the muscle transcriptome of offspring and potentially influence postnatal muscle development.
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Shi N, Li Y, Chang L, Zhao G, Jin G, Lyu Y, Genin GM, Ma Y, Xu F. A 3D, Magnetically Actuated, Aligned Collagen Fiber Hydrogel Platform Recapitulates Physical Microenvironment of Myoblasts for Enhancing Myogenesis. SMALL METHODS 2021; 5:e2100276. [PMID: 34927916 DOI: 10.1002/smtd.202100276] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/23/2021] [Indexed: 06/14/2023]
Abstract
Many cell responses that underlie the development, maturation, and function of tissues are guided by the architecture and mechanical loading of the extracellular matrix (ECM). Because mechanical stimulation must be transmitted through the ECM architecture, the synergy between these two factors is important. However, recapitulating the synergy of these physical microenvironmental cues in vitro remains challenging. To address this, a 3D magnetically actuated collagen hydrogel platform is developed that enables combined control of ECM architecture and mechanical stimulation. With this platform, it is demonstrated how these factors synergistically promote cell alignment of C2C12 myoblasts and enhance myogenesis. This promotion is driven in part by the dynamics of Yes-associated protein and structure of cellular microtubule networks. This facile platform holds great promises for regulating cell behavior and fate, generating a broad range of engineered physiologically representative microtissues in vitro, and quantifying the mechanobiology underlying their functions.
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Affiliation(s)
- Nianyuan Shi
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yuhui Li
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Le Chang
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Guoxu Zhao
- School of Material Science and Chemical Engineering, Xi'an Technological University, Xi'an, 710021, China
| | - Guorui Jin
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yi Lyu
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Guy M Genin
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
- NSF Science and Technology Center for Engineering MechanoBiology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Yufei Ma
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, China
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30
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Vettori A, Paolacci S, Maltese PE, Herbst KL, Cestari M, Michelini S, Michelini S, Samaja M, Bertelli M. Genetic Determinants of the Effects of Training on Muscle and Adipose Tissue Homeostasis in Obesity Associated with Lymphedema. Lymphat Res Biol 2020; 19:322-333. [PMID: 33373545 DOI: 10.1089/lrb.2020.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is widely accepted that metabolic changes associated with training are influenced by a person's genetic background. In this review, we explore the polymorphisms underlying interindividual variability in response to training of weight loss and muscle mass increase in obese individuals, with or without lymphedema, and in normal-weight subjects. We searched PubMed for articles in English published up to May 2019 using the following keywords: (((physical training[Title/Abstract] OR sport activity[Title/Abstract]) AND predisposition[Title/Abstract]) AND polymorphism [Title/Abstract]). We identified 38 single-nucleotide polymorphisms that may modulate the genetic adaptive response to training. The identification of genetic marker(s) that improve the beneficial effects of training may in perspective make it possible to assess training programs, which in combination with dietary intervention can optimize body weight reduction in obese subjects, with or without lymphedema. This is particularly important for patients with lymphedema because obesity can worsen the clinical status, and therefore, a personalized approach that could reduce obesity would be fundamental in the clinical management of lymphedema.
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Affiliation(s)
- Andrea Vettori
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | | | - Karen L Herbst
- Department of Medicine, University of Arizona, Tucson, Arizona, USA.,Department of Pharmacy, University of Arizona, Tucson, Arizona, USA.,Department of Medical Imaging, University of Arizona, Tucson, Arizona, USA.,Department of Surgery, University of Arizona, Tucson, Arizona, USA
| | - Marina Cestari
- Study Centre Pianeta Linfedema, Terni, Italy.,Lymphology Sector of the Rehabilitation Service, USLUmbria2, Terni, Italy
| | - Sandro Michelini
- Department of Vascular Rehabilitation, San Giovanni Battista Hospital, Rome, Italy
| | - Serena Michelini
- Unit of Physical Medicine and Rehabilitation, Sant'Andrea Hospital, "Sapienza" University of Rome, Rome, Italy
| | - Michele Samaja
- Department of Health Science, University of Milan-San Paolo Hospital, Milan, Italy
| | - Matteo Bertelli
- MAGI'S Lab, Rovereto, Italy.,MAGI Euregio, Bolzano, Italy.,EBTNA-LAB, Rovereto, Italy
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31
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Zhang X, Yao Y, Han J, Yang Y, Chen Y, Tang Z, Gao F. Longitudinal epitranscriptome profiling reveals the crucial role of N 6-methyladenosine methylation in porcine prenatal skeletal muscle development. J Genet Genomics 2020; 47:466-476. [PMID: 33268291 DOI: 10.1016/j.jgg.2020.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022]
Abstract
N6-methyladenosine (m6A) represents the most abundantly occurring mRNA modification and is involved in the regulation of skeletal muscle development. However, the status and function of m6A methylation in prenatal myogenesis remains unclear. In this study, we first demonstrated that knockdown of METTL14, an m6A methyltransferase, inhibited the differentiation and promoted the proliferation of C2C12 myoblast cells. Then, using a refined m6A-specific methylated RNA immunoprecipitation (RIP) with next generation sequencing (MeRIP-seq) method that is optimal for use with samples containing small amounts of RNA, we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis. The results revealed that, along with a continuous decrease in the mRNA expression of the m6A reader protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), the m6A methylome underwent highly dynamic changes across different development stages, with most of the affected genes being enriched in pathways related to skeletal muscle development. RNA immunoprecipitation confirmed that IGF2BP1 targets 76 genes involved in pathways associated with muscle development, including the key marker genes MYH2 and MyoG. Moreover, small interfering RNA (siRNA)-mediated knockdown of IGF2BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14. In conclusion, we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.
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Affiliation(s)
- Xinxin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jinghua Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yun Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Fei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China; Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, DK-2000, Denmark.
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32
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Cheng J, Cao XK, Peng SJ, Wang XG, Li Z, Elnour IE, Huang YZ, Lan XY, Chen H. Transcriptional regulation of the bovine FGFR1 gene facilitates myoblast proliferation under hypomethylation of the promoter. J Cell Physiol 2020; 235:8667-8678. [PMID: 32324257 DOI: 10.1002/jcp.29711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation, which can affect the expression level of genes, is one of the most vital epigenetic modifications in mammals. Fibroblast growth factor receptor 1 (FGFR1) plays an important role in muscle development; however, DNA methylation of the FGFR1 promoter has not been studied to date in cattle. Our study focused on methylation of the FGFR1 promoter and its effect on bovine myoblast proliferation and differentiation. We identified the FGFR1 core promoter by using luciferase reporter assays; we then studied FGFR1 expression by reverse transcription quantitative polymerase chain reaction, and the methylation pattern in the FGFR1 core promoter by bisulfite sequencing polymerase chain reaction in bovine muscle tissue at three different developmental stages. We used RNAi strategy to investigate the function of FGFR1 in myoblast proliferation and differentiation. Results showed that the FGFR1 core promoters were located at the R2 (-509 to ~-202 bp) and R4 (-1295 to ~-794 bp) regions upstream of the FGFR1 gene. FGFR1 expression level was negatively associated with the degree of methylation of the FGFR1 core promoter during the developmental process. In addition, we found that FGFR1 can promote myoblast proliferation, but had no effect on myoblast differentiation. In conclusion, our results suggest that FGFR1 can promote myoblast proliferation and its transcription can be regulated by the methylation level of the core promoter. Our findings provide a mechanistic basis for the improvement of animal breeding.
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Affiliation(s)
- Jie Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiu-Kai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shu-Jun Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao-Gang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhuang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ibrahim-Elsaeid Elnour
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Faculty of Veterinary Science, University of Nyala, Nyala, Sudan
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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33
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Li J, Wang Y, Wang Y, Yan Y, Tong H, Li S. Fibronectin type III domain containing four promotes differentiation of C2C12 through the Wnt/β-catenin signaling pathway. FASEB J 2020; 34:7759-7772. [PMID: 32298013 DOI: 10.1096/fj.201902860rrr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 01/16/2023]
Abstract
Fibronectin type III domain containing 4 (FNDC4) belongs to the fibronectin type III domain containing protein family. FNDC5, which is highly homologous to FNDC4, can promote the differentiation of cardiac cells. We aimed to investigate the role of FNDC4 in the differentiation of C2C12 mouse skeletal muscle cells. Western blotting and immunofluorescence analysis showed that FNDC4 gradually increased with the differentiation of C2C12. Muscle injury repair experiments indicated that FNDC4 may promote the repair of injured muscles. When FNDC4 was either overexpressed or knocked down, the expression of desmin and myogenin myogenic marker molecules followed that of FNDC4, suggesting that FNDC4 can influence the differentiation of C2C12. In addition, immunoprecipitation results showed that FNDC4 can interact with the Wnt/β-catenin signaling pathway receptor low-density lipoprotein receptor-related protein 6 (LRP6), and that β-catenin levels in the nucleus decreased after knocking down FNDC4. Exogenous addition of FNDC4 protein could not restore the blocking of differentiation due to inhibition of both Wnt/β-catenin signal transduction and LRP6 activity via the β-catenin inhibitor XAV-939. Overall, our findings indicate that FDNC4 can influence the differentiation of C2C12 by activating Wnt/β-catenin signal transduction.
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Affiliation(s)
- Jiwei Li
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
| | - Yanshuang Wang
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
| | - Yan Wang
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
| | - Yunqin Yan
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
| | - Huili Tong
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
| | - Shufeng Li
- The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin, China
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34
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Barruet E, Garcia SM, Striedinger K, Wu J, Lee S, Byrnes L, Wong A, Xuefeng S, Tamaki S, Brack AS, Pomerantz JH. Functionally heterogeneous human satellite cells identified by single cell RNA sequencing. eLife 2020; 9:51576. [PMID: 32234209 PMCID: PMC7164960 DOI: 10.7554/elife.51576] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations.
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Affiliation(s)
- Emilie Barruet
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven M Garcia
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Katharine Striedinger
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jake Wu
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Solomon Lee
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Lauren Byrnes
- University of California San Francisco, San Francisco, United States
| | - Alvin Wong
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Sun Xuefeng
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Stanley Tamaki
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Andrew S Brack
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jason H Pomerantz
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
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35
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Cui W, Liu CX, Wang J, Zhang YC, Shen Q, Feng ZH, Wu J, Li JX. An oleanolic acid derivative reduces denervation-induced muscle atrophy via activation of CNTF-mediated JAK2/STAT3 signaling pathway. Eur J Pharmacol 2019; 861:172612. [PMID: 31421088 DOI: 10.1016/j.ejphar.2019.172612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/10/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
Abstract
Denervation caused by sciatic nerve injury has brought great harm to the patients, especially denervation-induced muscle atrophy. The body stress produces a large number of Schwann cells when the sciatic nerve is injured, and the cells secrete some cytokines including ciliary neurotrophic factor (CNTF) that not only play a role in promoting the repair of sciatic nerve, but also maintain the normal physiological function of the muscles surrounding the damaged nerves. CNTF upregulates janus kinase 2 (JAK2) and signal transducers and activators of transcription 3 (STAT3) signals in myoblasts, and consequently accelerates the proliferation and differentiation of myoblasts. This effect on myoblasts is the most effective way to relieve muscle atrophy. Therefore, increasing CNTF is a promising direction to improve muscle atrophy. In the present study, an oleanolic acid derivative, HA-19, increased the proliferation of Schwann cells, and elevated CNTF production of the cells. HA-19 up-regulated the phosphorylation of JAK2 and STAT3 not only by directly acting on myoblasts, but also by increasing the secretion of CNTF of Schwann cells; and consequently, promoted the proliferation and differentiation of myoblasts. In denervation-induced muscle atrophy mice model, treatment with HA-19 significantly increased the weights of tibialis anterior (TA), gastrocnemius (Gastroc.), extensor digitorum longus (EDL), soleus and quadriceps (Quad.) under atrophied state. And, very interestingly, these muscles under normal condition were also strengthened by HA-19. Our finding demonstrated that HA-19 has a great potential as a lead compound for the drug discovery of anti-denervation-induced muscle atrophy.
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Affiliation(s)
- Wei Cui
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Chen-Xi Liu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jie Wang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yu-Chao Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qi Shen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhen-Hua Feng
- The Center of Diagnosis and Treatment for Joint Disease, Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, 210008, China
| | - Jing Wu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| | - Jian-Xin Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
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36
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Guanine-rich RNA binding protein GRSF1 inhibits myoblast differentiation through repressing mitochondrial ROS production. Exp Cell Res 2019; 381:139-149. [DOI: 10.1016/j.yexcr.2019.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/23/2022]
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37
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Mahmood N, Rabbani SA. DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications. Front Oncol 2019; 9:489. [PMID: 31245293 PMCID: PMC6579900 DOI: 10.3389/fonc.2019.00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
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38
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Li S, Fu Y, Pang Y, Tong H, Li S, Yan Y. GRP94 promotes muscle differentiation by inhibiting the PI3K/AKT/mTOR signaling pathway. J Cell Physiol 2019; 234:21211-21223. [DOI: 10.1002/jcp.28727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Shuang Li
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
| | - Yuying Fu
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
| | - Yusheng Pang
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
| | - Huili Tong
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
| | - Shufeng Li
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
| | - Yunqin Yan
- The Laboratory of Cell and Development Northeast Agricultural University Harbin Heilongjiang China
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39
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Li Y, Han B, Liu L, Zhao F, Liang W, Jiang J, Yang Y, Ma Z, Sun D. Genetic association of DDIT3, RPL23A, SESN2 and NR4A1 genes with milk yield and composition in dairy cattle. Anim Genet 2019; 50:123-135. [PMID: 30815908 DOI: 10.1111/age.12750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2018] [Indexed: 01/15/2023]
Abstract
Previously, we identified by RNA sequencing that DDIT3, RPL23A, SESN2 and NR4A1 genes were significantly differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentages; thus, these four genes are considered as promising candidates potentially affecting milk yield and composition traits in dairy cattle. In the present study, we further verified whether these genes have genetic effects on milk traits in a Chinese Holstein population. By re-sequencing part of the non-coding and the entire coding regions of the DDIT3, RPL23A, SESN2 and NR4A1 genes, a total of 35 SNPs and three insertions/deletions were identified, of which three were found in DDIT3, 12 in RPL23A, 16 in SESN2 and seven in NR4A1. Moreover, two of the insertions/deletions-g.125714860_125714872del and g.125714806delinsCCCC in SESN2-were novel and have not been reported previously. Subsequent single SNP analyses revealed multiple significant association with all 35 SNPs and three indels regressed against the dairy production traits (P-value = <0.0001-0.0493). In addition, with a linkage disequilibrium analysis, we found one, one, three, and one haplotype blocks in the DDIT3, RPL23A, SESN2 and NR4A1 genes respectively. Haplotype-based association analyses revealed that some haplotypes were also significantly associated with milk production traits (P-value = <0.0001-0.0461). We also found that 12 SNPs and two indels (two in DDIT3, two in RPL23A, nine in SESN2 and one in NR4A1) altered the specific transcription factor binding sites in the promoter, thereby regulating promoter activity, suggesting that they might be promising potential functional variants for milk traits. In summary, our findings first determined the genetic associations of DDIT3, RPL23A, SESN2 and NR4A1 with milk yield and composition traits in dairy cattle and also suggested potentially causal variants, which require in-depth validation.
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Affiliation(s)
- Y Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China.,Beijing Dairy Cattle Center, Beijing, 100192, China
| | - B Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - F Zhao
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - W Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - J Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
| | - Y Yang
- Beijing Municipal Bureau of Agriculture, Beijing, 100101, China
| | - Z Ma
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - D Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, Beijing, 100193, China
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CBP and P300 regulate distinct gene networks required for human primary myoblast differentiation and muscle integrity. Sci Rep 2018; 8:12629. [PMID: 30135524 PMCID: PMC6105712 DOI: 10.1038/s41598-018-31102-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
The acetyltransferases CBP and P300 have been implicated in myogenesis in mouse immortalized cell lines but these studies focused only on the expression of a handful of myogenic factors. Hence, the respective role of these two related cofactors and their impact at global scale on gene expression rewiring during primary myoblast differentiation remain unknown. Here, we characterised the gene networks regulated by these two epigenetic enzymes during human primary myoblast differentiation (HPM). We found that CBP and p300 play a critical role in the activation of the myogenic program and mostly regulate distinct gene sets to control several aspects of HPM biology, even though they also exhibit some degree of redundancy. Moreover, CBP or P300 knockdown strongly impaired muscle cell adhesion and resulted in the activation of inflammation markers, two hallmarks of dystrophic disease. This was further validated in zebrafish where inhibition of CBP and P300 enzymatic activities led to cell adhesion defects and muscle fiber detachment. Our data highlight an unforeseen link between CBP/P300 activity and the emergence of dystrophic phenotypes. They thereby identify CBP and P300 as mediators of adult muscle integrity and suggest a new lead for intervention in muscular dystrophy.
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Jiao Y, Huang B, Chen Y, Hong G, Xu J, Hu C, Wang C. Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells' Proliferation through Regulating the Cell Cycle. Int J Mol Sci 2018; 19:ijms19010271. [PMID: 29337929 PMCID: PMC5796217 DOI: 10.3390/ijms19010271] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/19/2022] Open
Abstract
Notch signaling as a conserved cell fate regulator is involved in the regulation of cell quiescence, proliferation, differentiation and postnatal tissue regeneration. However, how Notch signaling regulates porcine satellite cells (PSCs) has not been elucidated. We stably transfected Notch1 intracellular domain (N1ICD) into PSCs to analyze the gene expression profile and miRNA-seq. The analysis of the gene expression profile identified 295 differentially-expressed genes (DEGs) in proliferating-N1ICD PSCs (P-N1ICD) and nine DEGs on differentiating-N1ICD PSCs (D-N1ICD), compared with that in control groups (P-Control and D-Control, respectively). Analyzing the underlying function of DEGs showed that most of the upregulated DEGs enriched in P-N1ICD PSCs are related to the cell cycle. Forty-four and 12 known differentially-expressed miRNAs (DEMs) were identified in the P-N1ICD PSCs and D-N1ICD PSCs group, respectively. Furthermore, we constructed the gene-miRNA network of the DEGs and DEMs. In P-N1ICD PSCs, miR-125a, miR-125b, miR-10a-5p, ssc-miR-214, miR-423 and miR-149 are downregulated hub miRNAs, whose corresponding hub genes are marker of proliferation Ki-67 (MKI67) and nuclear receptor binding SET domain protein 2 (WHSC1). By contrast, miR-27a, miR-146a-5p and miR-221-3p are upregulated hub miRNAs, whose hub genes are RUNX1 translocation partner 1 (RUNX1T1) and fibroblast growth factor 2 (FGF2). All the hub miRNAs and genes are associated with cell proliferation. Quantitative RT-PCR results are consistent with the gene expression profile and miRNA-seq results. The results of our study provide valuable information for understanding the molecular mechanisms underlying Notch signaling in PSCs and skeletal muscle development.
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Affiliation(s)
- Yiren Jiao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Bo Huang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yu Chen
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Guangliang Hong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jian Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Chingyuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 1955 East-West Road, AgSci. 415J, Honolulu, HI 96822, USA.
| | - Chong Wang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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