1
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Gurung R, Masood M, Singh P, Jha P, Sinha A, Ajmeriya S, Sharma M, Dohare R, Haque MM. Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach. J Appl Genet 2024:10.1007/s13353-024-00843-6. [PMID: 38358594 DOI: 10.1007/s13353-024-00843-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with [Formula: see text] T cells, positively with [Formula: see text] T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with [Formula: see text] T cells, negatively with [Formula: see text] T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.
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Affiliation(s)
- Rishabh Gurung
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Mohammad Masood
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, 110007, India
| | - Anuradha Sinha
- Department of Preventive Oncology, Homi Bhabha Cancer Hospital and Research Centre, Muzaffarpur, 842004, India
| | - Swati Ajmeriya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Milin Sharma
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Mohammad Mahfuzul Haque
- Department of Biotechnology, Faculty of Life Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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2
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Wijayanti D, Zhang S, Bai Y, Pan C, Chen H, Qu L, Guo Z, Lan X. Investigation on mRNA expression and genetic variation within goat SMAD2 gene and its association with litter size. Anim Biotechnol 2023; 34:2111-2119. [PMID: 35584800 DOI: 10.1080/10495398.2022.2077214] [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: 11/01/2022]
Abstract
The SMAD family member 2 (SMAD2), a member of the TGF-beta superfamily, executes a significant part in the oogenesis and ovulation process. A genome-wide selective sweep analysis also found SMAD2 was different in the fertility groups of Laoshan dairy goats; whether this gene was linked to litter size was unknown. Therefore, SMAD2 was chosen to study its effects on Shaanbei white cashmere goat reproduction and mRNA expression profile. Herein, the mRNA expression level of SMAD2 was firstly determined in female goat tissues, revealing significant differences in mRNA levels of different tissues (p < 0.05), including ovary tissue, indicating a potential role for SMAD2 in goat prolificacy. Then, using six pairs of primers, only one indel locus (P3-Del-12-bp) was found to be polymorphic in goat SMAD2 (n = 501). ANOVA also revealed that a P3-Del-12-bp deletion was significantly related to first-born litter size (p = 0.037). The Chi-square (χ2) test revealed that the ID genotype was significantly more prevalent in mothers with multiple lambs (p = 0.01), indicating that heterozygous individuals (ID) are more likely to produce multiple lambs. Our findings suggest that the SMAD2 gene's P3-Del-12-bp deletion could be used to improve goat breeds by assisting with litter size selection.
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Affiliation(s)
- Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, Indonesia
| | - Sihuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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3
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Li BZ, Lin CY, Xu WB, Zhang YM, Shao QJ, Dong WR, Shu MA. The first identification and functional analysis of two drosophila mothers against decapentaplegic protein genes (SpSmad1 and SpSmad2/3) and their involvement in the innate immune response in Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109183. [PMID: 37884105 DOI: 10.1016/j.fsi.2023.109183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Smad,a member of the TGF-β superfamily,controls cell proliferation,growth and guiding cell differentiation, thus playing a crucial role in diseases. However, the presence as well as specific function of Smad in crabs is still unknown. In this study, two Smads (Smad1 and Smad2/3) were identified for the first time from the mud crab Scylla paramamosain. The complete open reading frames of SpSmad1 and SpSmad2/3 were 1,497bp and 1,338bp, encoding deduced proteins of 498 and 445 amino acids respectively. Moreover, under the administration of Vibrio alginolyticus and WSSV, the relative expression levels of SpSmad1 and SpSmad2/3 were significantly increased, indicating their involvement in the innate immune response of mud crabs. Knockdown of SpSmad1 and SpSmad2/3 in vivo not only led to the increasement of the expressions of NF-κB signaling genes and antimicrobial peptides genes, but also significantly affected the bacterial clearance process of mud crabs. Additionally, overexpression of SpSmad1 and SpSmad2/3 in HEK293T cells could markedly activate NF-κB signaling. These results indicated that Smad1 and Smad2/3 participated in the innate immunity of Scylla paramamosain, and might provide a better understanding of the presence and immune regulatory functions of Smad1 and Smad2/3 in crabs and even invertebrates.
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Affiliation(s)
- Bang-Ze Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chen-Yang Lin
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wen-Bin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan-Mei Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qing-Jun Shao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Ren Dong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Miao-An Shu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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4
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Wang X, Song C, Ye Y, Gu Y, Li X, Chen P, Leng D, Xiao J, Wu H, Xie S, Liu W, Zhao Q, Chen D, Chen X, Wu Q, Chen G, Zhang W. BRD9-mediated control of the TGF-β/Activin/Nodal pathway regulates self-renewal and differentiation of human embryonic stem cells and progression of cancer cells. Nucleic Acids Res 2023; 51:11634-11651. [PMID: 37870468 PMCID: PMC10681724 DOI: 10.1093/nar/gkad907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a specific subunit of the non-canonical SWI/SNF (ncBAF) chromatin-remodeling complex, whose function in human embryonic stem cells (hESCs) remains unclear. Here, we demonstrate that impaired BRD9 function reduces the self-renewal capacity of hESCs and alters their differentiation potential. Specifically, BRD9 depletion inhibits meso-endoderm differentiation while promoting neural ectoderm differentiation. Notably, supplementation of NODAL, TGF-β, Activin A or WNT3A rescues the differentiation defects caused by BRD9 loss. Mechanistically, BRD9 forms a complex with BRD4, SMAD2/3, β-CATENIN and P300, which regulates the expression of pluripotency genes and the activity of TGF-β/Nodal/Activin and Wnt signaling pathways. This is achieved by regulating the deposition of H3K27ac on associated genes, thus maintaining and directing hESC differentiation. BRD9-mediated regulation of the TGF-β/Activin/Nodal pathway is also demonstrated in the development of pancreatic and breast cancer cells. In summary, our study highlights the crucial role of BRD9 in the regulation of hESC self-renewal and differentiation, as well as its participation in the progression of pancreatic and breast cancers.
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Affiliation(s)
- Xuepeng Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Chengcheng Song
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Ying Ye
- Medical College of Soochow University, Suzhou 215123, China
| | - Yashi Gu
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Xuemei Li
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Peixin Chen
- Medical College of Soochow University, Suzhou 215123, China
| | - Dongliang Leng
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Jing Xiao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hao Wu
- Medical College of Soochow University, Suzhou 215123, China
| | - Sisi Xie
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Qi Zhao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Di Chen
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518000, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
- The Precision Regenerative Medicine Centre, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Wensheng Zhang
- Medical College of Soochow University, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China
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5
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Yavuz BR, Arici MK, Demirel HC, Tsai CJ, Jang H, Nussinov R, Tuncbag N. Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome. NPJ Genom Med 2023; 8:37. [PMID: 37925498 PMCID: PMC10625621 DOI: 10.1038/s41525-023-00377-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/02/2023] [Indexed: 11/06/2023] Open
Abstract
Epidemiological studies suggest that individuals with neurodevelopmental disorders (NDDs) are more prone to develop certain types of cancer. Notably, however, the case statistics can be impacted by late discovery of cancer in individuals afflicted with NDDs, such as intellectual disorders, autism, and schizophrenia, which may bias the numbers. As to NDD-associated mutations, in most cases, they are germline while cancer mutations are sporadic, emerging during life. However, somatic mosaicism can spur NDDs, and cancer-related mutations can be germline. NDDs and cancer share proteins, pathways, and mutations. Here we ask (i) exactly which features they share, and (ii) how, despite their commonalities, they differ in clinical outcomes. To tackle these questions, we employed a statistical framework followed by network analysis. Our thorough exploration of the mutations, reconstructed disease-specific networks, pathways, and transcriptome levels and profiles of autism spectrum disorder (ASD) and cancers, point to signaling strength as the key factor: strong signaling promotes cell proliferation in cancer, and weaker (moderate) signaling impacts differentiation in ASD. Thus, we suggest that signaling strength, not activating mutations, can decide clinical outcome.
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Affiliation(s)
- Bengi Ruken Yavuz
- Graduate School of Informatics, Middle East Technical University, Ankara, 06800, Turkey
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - M Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, 06800, Turkey
| | - Habibe Cansu Demirel
- Graduate School of Sciences and Engineering, Koc University, Istanbul, 34450, Turkey
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Nurcan Tuncbag
- Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.
- School of Medicine, Koc University, Istanbul, 34450, Turkey.
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey.
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6
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Li B, Jin X, Chan HM. Effects of low doses of methylmercury (MeHg) exposure on definitive endoderm cell differentiation in human embryonic stem cells. Arch Toxicol 2023; 97:2625-2641. [PMID: 37612375 PMCID: PMC10475006 DOI: 10.1007/s00204-023-03580-7] [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: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023]
Abstract
Fetal development is one of the most sensitive windows to methylmercury (MeHg) toxicity. Laboratory and epidemiological studies have shown a dose-response relationship between fetal MeHg exposure and neuro performance in different life stages from infants to adults. In addition, MeHg exposure has been reported to be associated with disorders in endoderm-derived organs, such as morphological changes in liver cells and pancreatic cell dysfunctions. However, the mechanisms of the effects of MeHg on non-neuronal organs or systems, especially during the early development of endoderm-derived organs, remain unclear. Here we determined the effects of low concentrations of MeHg exposure during the differentiation of definitive endoderm (DE) cells from human embryonic stem cells (hESCs). hESCs were exposed to MeHg (0, 10, 100, and 200 nM) that covers the range of Hg concentrations typically found in human maternal blood during DE cell induction. Transcriptomic analysis showed that sub-lethal doses of MeHg exposure could alter global gene expression patterns during hESC to DE cell differentiation, leading to increased expression of endodermal genes/proteins and the over-promotion of endodermal fate, mainly through disrupting calcium homeostasis and generating ROS. Bioinformatic analysis results suggested that MeHg exerts its developmental toxicity mainly by disrupting ribosome biogenesis during early cell lineage differentiation. This disruption could lead to aberrant growth or dysfunctions of the developing endoderm-derived organs, and it may be the underlying mechanism for the observed congenital diseases later in life. Based on the results, we proposed an adverse outcome pathway for the effects of MeHg exposure during human embryonic stem cells to definitive endoderm differentiation.
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Affiliation(s)
- Bai Li
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Xiaolei Jin
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, HPFB, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Hing Man Chan
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
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7
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Yi Y, Lan X, Li Y, Yan C, Lv J, Zhang T, Jiang W. Fatty acid synthesis and oxidation regulate human endoderm differentiation by mediating SMAD3 nuclear localization via acetylation. Dev Cell 2023; 58:1670-1687.e4. [PMID: 37516106 DOI: 10.1016/j.devcel.2023.07.005] [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: 12/08/2022] [Revised: 05/02/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
Metabolic remodeling is one of the earliest events that occur during cell differentiation. Here, we define fatty acid metabolism as a key player in definitive endoderm differentiation from human embryonic stem cells. Fatty acid β-oxidation is enhanced while lipogenesis is decreased, and this is due to the phosphorylation of lipogenic enzyme acetyl-CoA carboxylase by AMPK. More importantly, inhibition of fatty acid synthesis by either its inhibitors or AMPK agonist significantly promotes human endoderm differentiation, while blockade of fatty acid oxidation impairs differentiation. Mechanistically, reduced de novo fatty acid synthesis and enhanced fatty acid β-oxidation both contribute to the accumulation of intracellular acetyl-CoA, which guarantees the acetylation of SMAD3 and further causes nuclear localization to promote endoderm differentiation. Thus, our current study identifies a fatty acid synthesis/oxidation shift during early differentiation and presents an instructive role for fatty acid metabolism in regulating human endoderm differentiation.
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Affiliation(s)
- Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yinglei Li
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jing Lv
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; College of Life Science, Cangzhou Normal University, Cangzhou 061000, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China.
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8
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Zhang W, Wei C, Wang L. Identification of Key lncRNAs, circRNAs, and mRNAs in Osteoarthritis via Bioinformatics Analysis. Mol Biotechnol 2023:10.1007/s12033-023-00790-3. [PMID: 37382793 DOI: 10.1007/s12033-023-00790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
Osteoarthritis (OA) is a common degenerative joint disorder that adversely affects the quality of life of patients. Identification of novel diagnostic biomarkers is pivotal for the early detection and prevention of OA. Dataset GSE185059 was selected from Gene Expression Omnibus database to obtain differentially expressed lncRNAs (DE-lncRNAs), mRNAs (DE-mRNAs), and circRNAs (DE-circRNAs) between OA and normal samples. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as protein-protein interaction (PPI) network construction of DE-mRNAs were conducted. Hub genes were identified from PPI networks and validated by RT-qPCR. starBase database was utilized for predicting miRNAs binding with hub genes, selected DE-lncRNAs and DE-circRNAs, respectively. The competing endogenous RNA (ceRNA) networks were constructed. A total of 818 DE-mRNAs, 191 DE-lncRNAs, and 2053 DE-circRNAs were identified. The DE-mRNAs were significantly enriched in several inflammation-related GO terms and KEGG pathways such as positive regulation of cell-cell adhesion, TNF-alpha signaling pathway and NF-kappa B signaling pathway. Thirteen hub genes were identified, which were CFTR, GART, SMAD2, NCK1, TJP1, UBE2D1, EFTUD2, PRKACB, IL10, SNRPG, CHD4, RPS24, and SRSF6. OA-related DE-lncRNA/circRNA-miRNA-hub gene networks were constructed. We identified 13 hub genes and constructed the ceRNA networks related to OA, providing a theoretical basis for further research.
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Affiliation(s)
- Wenjing Zhang
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China
| | - Chun Wei
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China
| | - Ling Wang
- Department of Rheumatic Immunity, Changzhi People's Hospital, No. 502, Changxing Middle Road, Luzhou District, Changzhi, 046099, Shanxi, China.
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9
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Zare M, Mirhoseini SZ, Ghovvati S, Yakhkeshi S, Hesaraki M, Barati M, Sayyahpour FA, Baharvand H, Hassani SN. The constitutively active pSMAD2/3 relatively improves the proliferation of chicken primordial germ cells. Mol Reprod Dev 2023. [PMID: 37379342 DOI: 10.1002/mrd.23689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 05/06/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023]
Abstract
In many multicellular organisms, mature gametes originate from primordial germ cells (PGCs). Improvements in the culture of PGCs are important not only for developmental biology research, but also for preserving endangered species, and for genome editing and transgenic animal technologies. SMAD2/3 appear to be powerful regulators of gene expression; however, their potential positive impact on the regulation of PGC proliferation has not been taken into consideration. Here, the effect of TGF-β signaling as the upstream activator of SMAD2/3 transcription factors was evaluated on chicken PGCs' proliferation. For this, chicken PGCs at stages 26-28 Hamburger-Hamilton were obtained from the embryonic gonadal regions and cultured on different feeders or feeder-free substrates. The results showed that TGF-β signaling agonists (IDE1 and Activin-A) improved PGC proliferation to some extent while treatment with SB431542, the antagonist of TGF-β, disrupted PGCs' proliferation. However, the transfection of PGCs with constitutively active SMAD2/3 (SMAD2/3CA) resulted in improved PGC proliferation for more than 5 weeks. The results confirmed the interactions between overexpressed SMAD2/3CA and pluripotency-associated genes NANOG, OCT4, and SOX2. According to the results, the application of SMAD2/3CA could represent a step toward achieving an efficient expansion of avian PGCs.
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Affiliation(s)
- Masumeh Zare
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
| | | | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht, Guilan, Iran
| | - Saeed Yakhkeshi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahdi Hesaraki
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mojgan Barati
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Forough Azam Sayyahpour
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Seyedeh-Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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10
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Zhang D, Hua M, Zhang N. LINC01232 promotes lung squamous cell carcinoma progression through modulating miR-181a-5p/SMAD2 axis. Am J Med Sci 2023; 365:386-395. [PMID: 36543302 DOI: 10.1016/j.amjms.2022.12.014] [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: 06/21/2021] [Revised: 07/21/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND LINC01232 has been implicated in the progression of multiple malignancies. Yet, the function of LINC01232 in the carcinogenesis of lung squamous cell carcinoma (LUSC) remains unclear. This study aims to examine the role LINC01232 plays in LUSC progression. METHODS mRNA and protein levels were assessed using qRT-PCR and western blot, respectively. Cell proliferation was assessed by CCK-8 and colony formation assays. Cell migration and invasion were evaluated by transwell assay. The interactions between LINC01232, miR-181a-5p, and SMAD2 were assessed using luciferase reporter, RNA pull-down, and RNA immunoprecipitation (RIP) assays. The subcellular distribution of LINC01232 was examined by cytosolic/nuclear fractionation assay RESULTS: LINC01232 was upregulated in both LUSC tissues and cell lines. Knockdown of LINC01232 impaired cell proliferation, migration and invasion capability in H1229 and A549 cells, a phenotype that could be reversed by miR-181a-5p silencing. In addition, LINC01232 silencing reduced levels of N-cadherin, Vimentin, and Snail in H1229 and A549 cells, but increased the level of E-cadherin, which can be abrogated by miR-181a-5p inhibitors. CONCLUSIONS In summary, our study demonstrates that LINC01232 expression increases in LUSC tissues and cell lines and promotes LUSC progression by modulating the miR-181a-5p/SMAD2 signaling, providing new potential drug targets for LUSC treatment.
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Affiliation(s)
- Dongliang Zhang
- Department of Thoracic Surgery, China Coast Guard Hospital of the People's Armed Police Force, Jiaxing, Zhejiang Province, China
| | - Minglei Hua
- Department of Respiratory Medicine, Xincheng Branch of Zaozhuang Municipal Hospital, Zaozhuang, Shandong Province, China
| | - Nan Zhang
- Department of Medical Oncology, China Coast Guard Hospital of the People's Armed Police Force, Jiaxing, Zhejiang Province, China.
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11
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Um SH, Seo Y, Seo H, Lee K, Park SH, Jeon JH, Lim JY, Ok MR, Kim YC, Kim H, Cheon CH, Han HS, Edwards JR, Kim SW, Jeon H. Biomimetic hydrogel blanket for conserving and recovering intrinsic cell properties. Biomater Res 2022; 26:78. [PMID: 36514131 PMCID: PMC9746181 DOI: 10.1186/s40824-022-00327-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cells in the human body experience different growth environments and conditions, such as compressive pressure and oxygen concentrations, depending on the type and location of the tissue. Thus, a culture device that emulates the environment inside the body is required to study cells outside the body. METHODS A blanket-type cell culture device (Direct Contact Pressing: DCP) was fabricated with an alginate-based hydrogel. Changes in cell morphology due to DCP pressure were observed using a phase contrast microscope. The changes in the oxygen permeability and pressure according to the hydrogel concentration of DCP were analyzed. To compare the effects of DCP with normal or artificial hypoxic cultures, cells were divided based on the culture technique: normal culture, DCP culture device, and artificial hypoxic environment. Changes in phenotype, genes, and glycosaminoglycan amounts according to each environment were evaluated. Based on this, the mechanism of each culture environment on the intrinsic properties of conserving chondrocytes was suggested. RESULTS Chondrocytes live under pressure from the surrounding collagen tissue and experience a hypoxic environment because collagen inhibits oxygen permeability. By culturing the chondrocytes in a DCP environment, the capability of DCP to produce a low-oxygen and physical pressure environment was verified. When human primary chondrocytes, which require pressure and a low-oxygen environment during culture to maintain their innate properties, were cultured using the hydrogel blanket, the original shapes and properties of the chondrocytes were maintained. The intrinsic properties could be recovered even in aged cells that had lost their original cell properties. CONCLUSIONS A DCP culture method using a biomimetic hydrogel blanket provides cells with an adjustable physical pressure and a low-oxygen environment. Through this technique, we could maintain the original cellular phenotypes and intrinsic properties of human primary chondrocytes. The results of this study can be applied to other cells that require special pressure and oxygen concentration control to maintain their intrinsic properties. Additionally, this technique has the potential to be applied to the re-differentiation of cells that have lost their original properties.
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Affiliation(s)
- Seung-Hoon Um
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea ,grid.23856.3a0000 0004 1936 8390Laboratory for Biomaterials and Bioengineering, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Laval University, G1V 0A6 Quebec City, Quebec, Canada
| | - Youngmin Seo
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea ,R&D Institute, OID Ltd, Seoul, 06286 Republic of Korea
| | - Hyunseon Seo
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea ,grid.264381.a0000 0001 2181 989XSchool of Medicine, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Kyungwoo Lee
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea
| | - Sun Hwa Park
- grid.23856.3a0000 0004 1936 8390Laboratory for Biomaterials and Bioengineering, Department of Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Laval University, G1V 0A6 Quebec City, Quebec, Canada
| | - Jung Ho Jeon
- grid.411947.e0000 0004 0470 4224Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea ,grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Yeon Lim
- grid.411947.e0000 0004 0470 4224Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myoung-Ryul Ok
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea
| | - Yu-Chan Kim
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Hyunjung Kim
- grid.256753.00000 0004 0470 5964Division of Nursing, Research Institute of Nursing Science, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Cheol-Hong Cheon
- grid.222754.40000 0001 0840 2678Department of Chemistry, Korea University, Seoul, 02841 Republic of Korea
| | - Hyung-Seop Han
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea
| | - James R. Edwards
- grid.4991.50000 0004 1936 8948Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK
| | - Sung Won Kim
- grid.411947.e0000 0004 0470 4224Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea ,grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hojeong Jeon
- grid.35541.360000000121053345Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 02792 Seoul, Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841 Republic of Korea
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Tsukamoto M, Kimura K, Yoshida T, Sugiura K, Hatoya S. Canine induced pluripotent stem cells efficiently differentiate into definitive endoderm in 3D cell culture conditions using high-dose activin A. Regen Ther 2022; 21:502-510. [DOI: 10.1016/j.reth.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/09/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022] Open
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Hasani Fard AH, Valizadeh M, Mazaheri Z, Hosseini SJ. miR-106b-5p Intensifies the Proliferative Potential of Spermatogonial Stem Cells as a Prerequisite for Male Infertility Treatment. Reprod Sci 2022; 29:3394-3403. [PMID: 35320579 DOI: 10.1007/s43032-022-00884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/09/2022] [Indexed: 12/14/2022]
Abstract
Although numerous studies have investigated the molecular basis of male infertility, various aspects of this area have remained uncovered. Over the past years, researchers have reported the significant potential of miRNAs in posttranscriptional regulatory roles. By targeting mRNAs, these notable molecules can modulate the processes related to male infertility. On the other side, the outstanding potential of male germline stem cells, SSCs, includes their application in infertility treatment. SSCs retain normal spermatogenesis and fertility by adjusting both SSC self-renewal and differentiation. Therefore, for the characterization and manipulation of SSCs, effective and efficient in vitro culture methods are essential in supporting their maintenance and development. In this regard, the present investigation was undertaken to evaluate the impact of one of the recently conspicuous miRNAs, miR-106b, in SSCs enrichment. As a result, we first found that the SSCs induced with miR-106b-5p highly express TGF-β1, which is known as a regulator of epigenetic modifiers and downstream genes. We next sought to show that self-renewal markers, including c-Myc, Oct-4, and Sox2, are increased in the induced SSC group. The intended miRNA also induced the inhibitor of differentiation 4 (ID4) and aided to remain unmethylated in SSCs. Additionally, for the tumorigenicity possibility of the manipulation, we indicated that PTEN, a tumor-suppressor gene, expressed remarkably in the induced SSCs. In conclusion, our findings showed that miR-106b-5p enhances the proliferative potential of SSCs, making it a substantial factor for therapeutic strategies of male infertility.
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Affiliation(s)
- Amir Hossein Hasani Fard
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahmoud Valizadeh
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Mazaheri
- Department of Anatomical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Jalil Hosseini
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Pathophysiology and Emerging Molecular Therapeutic Targets in Heterotopic Ossification. Int J Mol Sci 2022; 23:ijms23136983. [PMID: 35805978 PMCID: PMC9266941 DOI: 10.3390/ijms23136983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/23/2022] Open
Abstract
The term heterotopic ossification (HO) describes bone formation in tissues where bone is normally not present. Musculoskeletal trauma induces signalling events that in turn trigger cells, probably of mesenchymal origin, to differentiate into bone. The aetiology of HO includes extremely rare but severe, generalised and fatal monogenic forms of the disease; and as a common complex disorder in response to musculoskeletal, neurological or burn trauma. The resulting bone forms through a combination of endochondral and intramembranous ossification, depending on the aetiology, initiating stimulus and affected tissue. Given the heterogeneity of the disease, many cell types and biological pathways have been studied in efforts to find effective therapeutic strategies for the disorder. Cells of mesenchymal, haematopoietic and neuroectodermal lineages have all been implicated in the pathogenesis of HO, and the emerging dominant signalling pathways are thought to occur through the bone morphogenetic proteins (BMP), mammalian target of rapamycin (mTOR), and retinoic acid receptor pathways. Increased understanding of these disease mechanisms has resulted in the emergence of several novel investigational therapeutic avenues, including palovarotene and other retinoic acid receptor agonists and activin A inhibitors that target both canonical and non-canonical signalling downstream of the BMP type 1 receptor. In this article we aim to illustrate the key cellular and molecular mechanisms involved in the pathogenesis of HO and outline recent advances in emerging molecular therapies to treat and prevent HO that have had early success in the monogenic disease and are currently being explored in the common complex forms of HO.
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15
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Xie Y, Han N, Li F, Wang L, Liu G, Hu M, Wang S, Wei X, Guo J, Jiang H, Wang J, Li X, Wang Y, Wang J, Bian X, Zhu Z, Zhang H, Liu C, Liu X, Liu Z. Melatonin enhances osteoblastogenesis of senescent bone marrow stromal cells through NSD2-mediated chromatin remodelling. Clin Transl Med 2022; 12:e746. [PMID: 35220680 PMCID: PMC8882236 DOI: 10.1002/ctm2.746] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Aging-associated osteoporosis is frequently seen in the elderly in clinic, but efficient managements are limited because of unclear nosogenesis. The current study aims to investigate the role of melatonin on senescent bone marrow stromal cells (BMSCs) and the underlying regulating mechanism. METHODS Melatonin levels were tested by ELISA. Gene expression profiles were performed by RNA-sequencing, enrichment of H3K36me2 on gene promoters was analyzed by Chromatin Immunoprecipitation Sequencing (ChIP-seq), and chromatin accessibility was determined by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). Osteogenesis of BMSCs in vitro was measured by Alizarin Red and Alkaline Phosphatase staining, and in vivo effects of melatonin was assessed by histological staining and micro computed tomography (micro-CT) scan. Correlation of NSD2 expression and severity of senile osteoporosis patients were analyzed by Pearson correlation. RESULTS Melatonin levels were decreased during aging in human bone marrow, accompanied by downregulation of the histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2) expression in the senescent BMSCs. Melatonin stimulated the expression of NSD2 through MT1/2-mediated signaling pathways, resulting in the rebalancing of H3K36me2 and H3K27me3 modifications to increase chromatin accessibility of the osteogenic genes, runt-related transcription factor 2 (RUNX2) and bone gamma-carboxyglutamate protein (BGLAP). Melatonin promoted osteogenesis of BMSCs in vitro, and alleviates osteoporosis progression in the aging mice. In clinic, severity of senile osteoporosis (SOP) was negatively correlated with melatonin level in bone marrow, as well as NSD2 expression in BMSCs. Similarly, melatonin remarkably enhanced osteogenic differentiation of BMSCs derived from SOP patients in vitro. CONCLUSIONS Collectively, our study dissects previously unreported mechanistic insights into the epigenetic regulating machinery of melatonin in meliorating osteogenic differentiation of senescent BMSC, and provides evidence for application of melatonin in preventing aging-associated bone loss.
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Affiliation(s)
- Ying Xie
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Na Han
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's Hospital; National Center for Trauma MedicineBeijingChina
| | - Feng Li
- Department of OrthopaedicsWeifang People's HospitalWeifangChina
| | - Lijuan Wang
- Central Laboratory; Linyi Key Laboratory of Tumor BiologyLinyi People's HospitalLinyiChina
| | - Gerui Liu
- Department of Pharmacology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Meilin Hu
- Tianjin Medical University School of StomatologyHepingChina
| | - Sheng Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Xuelei Wei
- Department of EmergencyTianjin HospitalTianjinChina
| | - Jing Guo
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Hongmei Jiang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Jingjing Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Xin Li
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Yixuan Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Jingya Wang
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
| | - Xiyun Bian
- Central Laboratory; Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm InfantsThe Fifth Central Hospital of TianjinBinhaiTianjinChina
| | - Zhongjiao Zhu
- Department of OrthopaedicsTengzhou Central People's HospitalTenghzouChina
| | - Hui Zhang
- Department of Cardiology, Heart Centre; Ministry of Education Key Laboratory of Child Development and Disorders National Clinical Research Center for Child Health and Disorders; Chongqing Key Laboratory of Pediatrics; China International Science and Technology Cooperation Base of Child Development and DisordersChildren's Hospital of Chongqing Medical UniversityChongqingChina
| | - Chunhua Liu
- Department of PhysiologyShandong First Medical University (Shandong Academy of Medical Sciences)JinanShandongChina
| | - Xiaozhi Liu
- Central Laboratory; Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm InfantsThe Fifth Central Hospital of TianjinBinhaiTianjinChina
| | - Zhiqiang Liu
- The Province and Ministry Co‐Sponsored Collaborative Innovation Center for Medical Epigenetics; Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases; Department of Physiology and Pathophysiology, School of Basic Medical ScienceTianjin Medical UniversityHepingChina
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16
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Adetula AA, Fan X, Zhang Y, Yao Y, Yan J, Chen M, Tang Y, Liu Y, Yi G, Li K, Tang Z. Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ( Sus-scrofa). RNA Biol 2021; 18:439-450. [PMID: 34314293 PMCID: PMC8677025 DOI: 10.1080/15476286.2021.1954380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/08/2022] Open
Abstract
RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function of the differentially edited gene in skeletal muscle was further characterized in pig muscle-derived satellite cells. RNA editome analysis revealed a total of 171,909 A-to-I RNA editing sites (RESs), and examination of its features showed that these A-to-I editing sites were mainly located in SINE retrotransposons PRE-1/Pre0_SS element. Analysis of differentially edited sites (DESs) revealed a total of 4,552 DESs across tissues between Duroc and Luchuan pigs, and functional category enrichment analysis of differentially edited gene (DEG) sets highlighted a significant association and enrichment of tissue-developmental pathways including TGF-beta, PI3K-Akt, AMPK, and Wnt signaling pathways. Moreover, we found that RNA editing events at the miRNA binding sites in the 3'-UTR of HSPA12B mRNA could prevent the miRNA-mediated mRNA downregulation of HSPA12B in the muscle-derived satellite (MDS) cell, consistent with the results obtained from the Luchuan skeletal muscle. This study represents the most systematic attempt to characterize the significance of RNA editing in regulating gene expression, particularly in skeletal muscle, constituting a new layer of regulation to understand the genetic mechanisms behind phenotype variance in animals.Abbreviations: A-to-I: Adenosine-to-inosine; ADAR: Adenosine deaminase acting on RNA; RES: RNA editing site; DEG: Differentially edited gene; DES: Differentially edited site; FDR: False discovery rate; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; MDS cell: musclederived satellite cell; RPKM: Reads per kilobase of exon model in a gene per million mapped reads; UTR: Untranslated coding regions.
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Affiliation(s)
- Adeyinka A. Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongsheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Muya Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [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: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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Arboretto P, Cillo M, Leonardi A. New Insights into Cancer Targeted Therapy: Nodal and Cripto-1 as Attractive Candidates. Int J Mol Sci 2021; 22:ijms22157838. [PMID: 34360603 PMCID: PMC8345935 DOI: 10.3390/ijms22157838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
The transforming growth factor beta (TGF-β) signaling is fundamental for correct embryonic development. However, alterations of this pathway have been correlated with oncogenesis, tumor progression and sustaining of cancer stem cells (CSCs). Cripto-1 (CR-1) and Nodal are two embryonic proteins involved in TGF-β signaling. Their expression is almost undetectable in terminally differentiated cells, but they are often re-expressed in tumor cells, especially in CSCs. Moreover, cancer cells that show high levels of CR-1 and/or Nodal display more aggressive phenotypes in vitro, while in vivo their expression correlates with a worse prognosis in several human cancers. The ability to target CSCs still represents an unmet medical need for the complete eradication of certain types of tumors. Given the prognostic role and the selective expression of CR-1 and Nodal on cancer cells, they represent archetypes for targeted therapy. The aim of this review is to clarify the role of CR-1 and Nodal in cancer stem populations and to summarize the current therapeutic strategy to target CSCs using monoclonal antibodies (mAbs) or other molecular tools to interfere with these two proteins.
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Niu YT, Xie L, Deng RR, Zhang XY. In the presence of TGF-β1, Asperosaponin VI promotes human mesenchymal stem cell differentiation into nucleus pulposus like- cells. BMC Complement Med Ther 2021; 21:32. [PMID: 33446173 PMCID: PMC7807821 DOI: 10.1186/s12906-020-03169-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/26/2020] [Indexed: 03/15/2023] Open
Abstract
Background The regeneration of nucleus pulposus (NP) cells is an effective method to prevent intervertebral disc degeneration (IVDD). In this study, we investigated the role of Asperosaponin VI (ASA VI), isolated from a traditional Chinese medicine (TCM), the root of Dipsacus asper Wall, in promoting human mesenchymal stem cell (HMSC) proliferation and differentiation into NP-like cells and explored the possible mechanism of action. Methods The effects of ASA VI on HMSC viability and proliferation were determined by the XTT method and EDU staining. Then, Real-time qPCR, immunocytochemistry and immunofluorescence assays were used to measure the effect of ASA VI on the expression of extracellular matrix (ECM) components, such as COL2A1, aggrecan, SOX9, KRT19, PAX1, and glycosaminoglycans (GAGs), in NP cells. In addition, Western blot assay was used to measure the expression of p-ERK1/2 and p-smad2/3. Results ASA VI was able to promote the proliferation and differentiation of HMSCs into NP-like cells, and the optimum concentration was 1 mg/L. Western blot assay indicated that the possible mechanism might be related to the activation of p-ERK1 / 2 and p-Smad2 / 3. Conclusions ASA VI can promote the proliferation and differentiation of HMSCs into NP-like cells, which can potentially be used as a treatment for IVDD. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-020-03169-y.
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Affiliation(s)
- Yong-Tao Niu
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China
| | - Lin Xie
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China.
| | - Rong-Rong Deng
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China
| | - Xiao-Yu Zhang
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China
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