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Yang L, Xiao Y, Deng S, Yan D, Li Z, Wang Y, Lei C. Signal Transducer and Activator of Transcription 4-Induced Up-Regulated LINC01278 Enhances Proliferation and Invasion of Non-Small Cell Lung Cancer Cells via the MicroRNA-877-5p/Activating Transcription Factor 4 Axis. Tissue Eng Regen Med 2024; 21:595-608. [PMID: 38466361 PMCID: PMC11087432 DOI: 10.1007/s13770-024-00625-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND The purpose of this study was to investigate the specific effects of signal transducer and activator of transcription 4 (STAT4)-induced long intergenic nonprotein coding RNA 1278 (LINC01278) on the growth of non-small cell lung cancer (NSCLC) cells involved in the microRNA (miR)-877-5p/activated transcription factor 4 (ATF4) axis. METHODS NSCLC tumor tissue and adjacent normal tissue were collected. Human normal lung epithelial cell BEAS-2B and human NSCLC cell lines (H1299, H1975, A549, H2228) were collected. The expression levels of STAT4, LINC01278, miR-877-5p, and ATF4 were detected. A549 cells were screened for subsequent experiments. The proliferation ability of cells was detected by colony formation experiment. Cell apoptosis was tested by flow cytometry. Scratch test and transwell assay were used to detect the migration and invasion ability of cells. Biological function of LINC01278 in NSCLC was confirmed by xenograft experiments. RESULTS Low expression miR-877-5p and high expression of STAT4, LINC01278 and ATF4 were detected in NSCLC. Silenced LINC01278 in A549 cell depressed cell proliferation, migration and invasion, but facilitated cell apoptosis. LINC01278 was positively correlated with STAT4 and could directly bind to miR-877-5p. Upregulating miR-877-5p suppressed NSCLC cell progression, while downregulating miR-877-5p had the opposite effect. Upregulating miR-877-5p abrogated the effects of silenced LINC01278 on NSCLC cell progression. MiR-877-5p targeted ATF4. ATF4 upregulation could partly restore the carcinogenic effect of LINC01278 in vitro and in vivo. CONCLUSION Our data supports that STAT4-induced upregulation of LINC01278 promotes NSCLC progression by modulating the miR-877-5p/ATF4 axis, suggesting a novel direction for NSCLC treatment.
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Affiliation(s)
- LinZhu Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, KunMing City, 650032, YunNan Province, China
| | - Yi Xiao
- First Department of Pumonary and Critical Care Medicline, Yan'an Affiliated Hospital of Kunming Medical University, KunMing City, 650051, YunNan Province, China
| | - ShouJun Deng
- Department of Thoracic Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 245 East Renmin Road, Panlong District, KunMing City, 650051, YunNan Province, China
| | - DaiLing Yan
- First Department of Pumonary and Critical Care Medicline, Yan'an Affiliated Hospital of Kunming Medical University, KunMing City, 650051, YunNan Province, China
| | - ZhenHua Li
- Department of Thoracic Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 245 East Renmin Road, Panlong District, KunMing City, 650051, YunNan Province, China
| | - Ying Wang
- Department of Thoracic Surgery, Yan'an Affiliated Hospital of Kunming Medical University, 245 East Renmin Road, Panlong District, KunMing City, 650051, YunNan Province, China.
| | - ChangCheng Lei
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, KunMing City, 650032, YunNan Province, China.
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Lv J, He Q, Yan Z, Xie Y, Wu Y, Li A, Zhang Y, Li J, Huang Z. Inhibitory Impact of Prenatal Exposure to Nano-Polystyrene Particles on the MAP2K6/p38 MAPK Axis Inducing Embryonic Developmental Abnormalities in Mice. TOXICS 2024; 12:370. [PMID: 38787149 PMCID: PMC11125576 DOI: 10.3390/toxics12050370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Nanoplastics, created by the fragmentation of larger plastic debris, are a serious pollutant posing substantial environmental and health risks. Here, we developed a polystyrene nanoparticle (PS-NP) exposure model during mice pregnancy to explore their effects on embryonic development. We found that exposure to 30 nm PS-NPs during pregnancy resulted in reduced mice placental weight and abnormal embryonic development. Subsequently, our transcriptomic dissection unveiled differential expression in 102 genes under PS-NP exposure and the p38 MAPK pathway emerged as being significantly altered in KEGG pathway mapping. Our findings also included a reduction in the thickness of the trophoblastic layer in the placenta, diminished cell invasion capabilities, and an over-abundance of immature red cells in the blood vessels of the mice. In addition, we validated our findings through the human trophoblastic cell line, HTR-8/SVneo (HTR). PS-NPs induced a drop in the vitality and migration capacities of HTR cells and suppressed the p38 MAPK signaling pathway. This research highlights the embryotoxic effects of nanoplastics on mice, while the verification results from the HTR cells suggest that there could also be certain impacts on the human trophoblast layer, indicating a need for further exploration in this area.
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Affiliation(s)
- Junyi Lv
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Qing He
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Zixiang Yan
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Yuan Xie
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Yao Wu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221004, China
| | - Anqi Li
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Yuqing Zhang
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China;
| | - Jing Li
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
| | - Zhenyao Huang
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou 221004, China; (J.L.); (Q.H.); (Z.Y.); (Y.X.); (A.L.); (J.L.)
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Bhardwaj C, Srivastava P. Identification of hub genes in placental dysfunction and recurrent pregnancy loss through transcriptome data mining: A meta-analysis. Taiwan J Obstet Gynecol 2024; 63:297-306. [PMID: 38802191 DOI: 10.1016/j.tjog.2024.01.035] [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] [Accepted: 01/30/2024] [Indexed: 05/29/2024] Open
Abstract
Recurrent pregnancy loss (RPL) is a condition characterized by the loss of two or more pregnancies before 20 weeks of gestation. The causes of RPL are complex and can be due to a variety of factors, including genetic, immunological, hormonal, and environmental factors. This transcriptome data mining study was done to explore the differentially expressed genes (DEGs) and related pathways responsible for pathogenesis of RPL using an Insilco approach. RNAseq datasets from the Gene Expression Omnibus (GEO) database was used to extract RNAseq datasets of RPL. Meta-analysis was done by ExpressAnalyst. The functional and pathway enrichment analysis of DEGs were performed using KEGG and BINGO plugin of Cytoscape software. Protein-protein interaction was done using STRING and hub genes were identified. A total of 91 DEGs were identified, out of which 10 were downregulated and 81 were upregulated. Pathway analysis indicated that majority of DEGs were enriched in immunological pathways (IL-17 signalling pathway, TLR-signalling pathway, autoimmune thyroid disease), angiogenic VEGF-signalling pathway and cell-cycle signalling pathways. Of these, 10 hub genes with high connectivity were selected (CXCL8, CCND1, FOS, PTGS2, CTLA4, THBS1, MMP2, KDR, and CD80). Most of these genes are involved in maintenance of immune response at maternal-fetal interface. Further, in functional enrichment analyses revealed the highest node size in regulation of biological processes followed by cellular processes, their regulation and regulation of multicellular organismal process. This in-silico transcriptomics meta-analysis findings could potentially contribute in identifying novel biomarkers and therapeutic targets for RPL, which could lead to the development of new diagnostic and therapeutic strategies for this condition.
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Affiliation(s)
- Chitra Bhardwaj
- Genetic Metabolic Unit, Department of Paediatrics, Advanced Paediatrics Centre, Post Graduate Institute of Medical Education & Research, Sector-12, Chandigarh, 160012, India
| | - Priyanka Srivastava
- Genetic Metabolic Unit, Department of Paediatrics, Advanced Paediatrics Centre, Post Graduate Institute of Medical Education & Research, Sector-12, Chandigarh, 160012, India.
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Huang Z, Chen X, Wang Y, Yuan J, Li J, Hang W, Meng H. SLC7A11 inhibits ferroptosis and downregulates PD-L1 levels in lung adenocarcinoma. Front Immunol 2024; 15:1372215. [PMID: 38655266 PMCID: PMC11035808 DOI: 10.3389/fimmu.2024.1372215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Lung adenocarcinoma (LUAD) is a prevalent form of lung cancer originating from lung glandular cells with low survival rates despite recent therapeutic advances due to its diverse and complex nature. Recent evidence suggests a link between ferroptosis and the effectiveness of anti-PD-L1 therapy, with potential synergistic effects. Methods Our study comprehensively analyzed the expression patterns of ferroptosis regulators in LUAD and their association with prognosis and PD-L1 expression. Furthermore, we identified two distinct subtypes of LUAD through consensus clustering of ferroptosis regulators, revealing significant tumor heterogeneity, divergent PD-L1 expression, and varying prognoses between the subtypes. Results Among the selected ferroptosis regulators, SLC7A11 emerged as an independent prognostic marker for LUAD patients and exhibited a negative correlation with PD-L1 expression. Subsequent investigations revealed high expression of SLC7A11 in the LUAD population. In vitro experiments demonstrated that overexpression of SLC7A11 led to reduced PD-L1 expression and inhibited ferroptosis in A549 cells, underscoring the significant role of SLC7A11 in LUAD. Additionally, pan-cancer analyses indicated an association between SLC7A11 and the expression of immune checkpoint genes across multiple cancer types with poor prognoses. Discussion From a clinical standpoint, these findings offer a foundation for identifying and optimizing potential combination strategies to enhance the therapeutic effectiveness of immune checkpoint inhibitors and improve the prognosis of patients with LUAD.
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Affiliation(s)
- Zhenyao Huang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Xia Chen
- Department of Respiratory Medicine, Xuyi People’s Hospital, Huai’an, Jiangsu, China
| | - Yun Wang
- Department of Dermatology, the Affiliated Huai'an Hospital of Xuzhou Medical University, the Second People's Hospital of Huai’an, Huai’an, China
| | - Jiali Yuan
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Jing Li
- Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Wenlu Hang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hao Meng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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Hou Y, Li Y, Xiang JF, Tilahun K, Jiang J, Corces VG, Yao B. TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep 2024; 43:113662. [PMID: 38184854 PMCID: PMC10857847 DOI: 10.1016/j.celrep.2023.113662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders.
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Affiliation(s)
- Yingzi Hou
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Wang S, Wang H, Liu J, Zhang X, Yang Y, Lu C, Cai C, Zhao Y, Liang G, Guo X, Li B, Cao G, Gao P. Expression patterns and functional analysis of porcine lnc-34015. Anim Biotechnol 2023; 34:2251-2261. [PMID: 35714975 DOI: 10.1080/10495398.2022.2085112] [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
Long noncoding RNAs (lncRNAs) play important roles in immune regulation in humans and animals. The lnc-34015 was discovered to be critical for the development of muscles, based on the muscle transcriptome of pigs; however, the underlying molecular mechanism requires better understanding. Here, the sequence characteristics of lnc-34015 were analyzed and a competitive endogenous RNA regulatory network of lncRNA was predicted. The developmental expression trend and tissue expression profiles of lnc-34015 were investigated using quantitative polymerase chain reaction. The lnc-34015 sequence is overlapped with introns 11 and 12 of CWF19L1, while CWF19L1, PKD2L1, and CHUK were identified as cis-regulatory genes of lnc-34015. Bioinformatics analyses revealed that lnc-34015 binds to 15 microRNAs (miRNAs), including miR-3646, miR-377-3p, and miR-190b-3p, to regulate downstream gene expression. GO and KEGG enrichment results show that lnc-34015 was mainly involved in cell proliferation, stress response, transcriptional regulation, and alternative splicing. The expression trend of lnc-34015 in muscle was similar to that of target genes and opposite to that of miRNAs. The expression of lnc-34015 was significantly higher in the porcine small intestine and IPEC-J2 cells. Our findings suggest that lnc-34015 regulates CHUK, ZBTB20, and XIAP gene expression by competing with endogenous RNAs to regulate porcine inflammatory responses.
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Affiliation(s)
- Shu Wang
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Haizhen Wang
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Juan Liu
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Xiaona Zhang
- Beijing Allwegene Technology Company, Transcriptional Regulation Division, Beijing, China
| | - Yang Yang
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Chang Lu
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Chunbo Cai
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Yan Zhao
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Guoming Liang
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Xiaohong Guo
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Bugao Li
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Guoqing Cao
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
| | - Pengfei Gao
- Department of Animal Sciences, Shanxi Agricultural University, Taigu, China
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孙 建, 张 逸, 杨 丽, 周 立, 卢 喜, 李 久, 陈 萍. [High expression of long noncoding RNA UCA1 promotes invasion, migration and epithelial-mesenchymal transition of trophoblasts in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:1984-1988. [PMID: 38081619 PMCID: PMC10713461 DOI: 10.12122/j.issn.1673-4254.2023.11.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Indexed: 12/18/2023]
Abstract
OBJECTIVE To investigate the role of urothelial carcinoma antigen 1 (UCA1) in regulation of invasion, migration and epithelial-mesenchymal transition (EMT) of trophoblast HTR-8/SVneo cells and its association with tubal pregnancy. METHODS Cultured HTR- 8/SVneo cells stimulated with interleukin-6 (IL-6) were examined for changes in UCA1 expression and cell migration ability using qRT-PCR and scratch assay, respectively. A HTR-8/SVneo cell model with UCA1 silencing was constructed by transient transfection, and the migration and invasion abilities of the cells were assessed using Scratch assay and Transwell assay; qRT-PCR and Western blotting were performed to detect the mRNA and protein expression levels of EMT markers. RESULTS HTR-8/SVneo cells stimulated with IL-6 exhibited significantly increased migration ability and up-regulated expression of UCA1 (P < 0.01). UCA1 silencing obviously suppressed migration and invasion abilities of HTR-8/SVneo cells (P < 0.01), significantly up-regulated the mRNA and protein expressions of EMT epithelial marker E-cadherin (P < 0.01), and down-regulated the expressions of the mesenchymal markers integrin β3, vimentin and N-cadherin (P < 0.05). CONCLUSION UCA1 may be a key gene that promotes the occurrence of tubal pregnancy and thus provides a new therapeutic target for tubal pregnancy.
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Affiliation(s)
- 建华 孙
- 河南中医药大学第一临床医学院,河南 郑州 450046First Clinical College of Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
- 河南中医药大学第一附属医院妇产科,河南 郑州 450099Department of Obstetrics and Gynecology, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450099, China
| | - 逸 张
- 河南中医药大学第一临床医学院,河南 郑州 450046First Clinical College of Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
| | - 丽萍 杨
- 河南中医药大学第一临床医学院,河南 郑州 450046First Clinical College of Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
| | - 立 周
- 河南中医药大学第一临床医学院,河南 郑州 450046First Clinical College of Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
- 河南中医药大学第一附属医院妇产科,河南 郑州 450099Department of Obstetrics and Gynecology, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450099, China
| | - 喜洋 卢
- 河南中医药大学第一附属医院妇产科,河南 郑州 450099Department of Obstetrics and Gynecology, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450099, China
| | - 久现 李
- 河南中医药大学第一附属医院妇产科,河南 郑州 450099Department of Obstetrics and Gynecology, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou 450099, China
| | - 萍 陈
- 河南中医药大学第一临床医学院,河南 郑州 450046First Clinical College of Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
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Lei S, Li C, She Y, Zhou S, Shi H, Chen R. Roles of super enhancers and enhancer RNAs in skeletal muscle development and disease. Cell Cycle 2023; 22:495-505. [PMID: 36184878 PMCID: PMC9928468 DOI: 10.1080/15384101.2022.2129240] [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: 07/28/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022] Open
Abstract
Skeletal muscle development is a multistep biological process regulated by a variety of myogenic regulatory factors, including MyoG, MyoD, Myf5, and Myf6 (also known as MRF4), as well as members of the FoxO subfamily. Differentiation and regeneration during skeletal muscle myogenesis contribute to the physiological function of muscles. Super enhancers (SEs) and enhancer RNAs (eRNAs) are involved in the regulation of development and diseases. Few studies have identified the roles of SEs and eRNAs in muscle development and pathophysiology. To develop approaches to enhance skeletal muscle mass and function, a more comprehensive understanding of the key processes underlying muscular diseases is needed. In this review, we summarize the roles of SEs and eRNAs in muscle development and disease through affecting of DNA methylation, FoxO subfamily, RAS-MEK signaling, chromatin modifications and accessibility, MyoD and cis regulating target genes. The summary could inform strategies to increase muscle mass and treat muscle-related diseases.
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Affiliation(s)
- Si Lei
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Cheng Li
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Yanling She
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Shanyao Zhou
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Huacai Shi
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Rui Chen
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
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Wang L, Deng Z, Yang J, Zhao Y, Zhou L, Diao L, Li L, Cheng Y. Epigenetic and transcriptomic characterization of maternal-fetal interface in patients with recurrent miscarriage via an integrated multi-omics approach. J Reprod Immunol 2022; 154:103754. [PMID: 36206604 DOI: 10.1016/j.jri.2022.103754] [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: 03/08/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Recurrent miscarriage (RM) occurs in 2.5 % of women aiming at childbirth, with unknown etiology in half of the cases. To identify the molecular features, an integrative study combining bioinformatics and multi-omics from GEO database was performed in these patients. Two datasets (GSE43256 and GSE73025) were integrated to indicate 1657 differentially expressed genes (DE-genes) in villus of females with RM. DE-genes in villus of females with RM mainly focused on cell growth and development. On the other hand, 230 DE-genes in decidua of RM patients were retrieved from GSE113790, and the DE-genes were involved in diverse functions, including transport of nutrients, immune response, extracellular matrix remodeling, and angiogenesis. Additionally, the results of immunologic signatures indicated that immune regulation played roles in both decidua and villus of RM. Interestingly, C1q and TNF related 7 (C1QTNF7), acquired from the intersection of decidua and villus datasets, is crucial in maintaining immune homeostasis, so is its upstream miRNA (miR-149-3p). The enhanced expression of C1QTNF7 in macrophages might inhibit the proliferation and migration of trophoblasts, and further result in pregnancy loss. The present study suggests C1QTNF7 might be a new target for the diagnosis and treatment of RM, but more basic researches are further required to illustrate its mechanism in RM.
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Affiliation(s)
- Linlin Wang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong 518045, PR China
| | - Zhimin Deng
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Jing Yang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Yulin Zhao
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong 518045, PR China
| | - Linyan Zhou
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong 518045, PR China
| | - Lianghui Diao
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong 518045, PR China
| | - Longfei Li
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, Guangdong 518045, PR China.
| | - Yanxiang Cheng
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China.
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Li J, Wang L, Ding J, Cheng Y, Diao L, Li L, Zhang Y, Yin T. Multiomics Studies Investigating Recurrent Pregnancy Loss: An Effective Tool for Mechanism Exploration. Front Immunol 2022; 13:826198. [PMID: 35572542 PMCID: PMC9094436 DOI: 10.3389/fimmu.2022.826198] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
Patients with recurrent pregnancy loss (RPL) account for approximately 1%-5% of women aiming to achieve childbirth. Although studies have shown that RPL is associated with failure of endometrial decidualization, placental dysfunction, and immune microenvironment disorder at the maternal-fetal interface, the exact pathogenesis remains unknown. With the development of high-throughput technology, more studies have focused on the genomics, transcriptomics, proteomics and metabolomics of RPL, and new gene mutations and new biomarkers of RPL have been discovered, providing an opportunity to explore the pathogenesis of RPL from different biological processes. Bioinformatics analyses of these differentially expressed genes, proteins and metabolites also reflect the biological pathways involved in RPL, laying a foundation for further research. In this review, we summarize the findings of omics studies investigating decidual tissue, villous tissue and blood from patients with RPL and identify some possible limitations of current studies.
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Affiliation(s)
- Jianan Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Linlin Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China.,Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Jinli Ding
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanxiang Cheng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lianghui Diao
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Longfei Li
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tailang Yin
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
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11
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Circulating Long Non-Coding RNAs as Novel Potential Biomarkers for Osteogenic Sarcoma. Cancers (Basel) 2021; 13:cancers13164214. [PMID: 34439367 PMCID: PMC8392488 DOI: 10.3390/cancers13164214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022] Open
Abstract
Circulating cell-free nucleic acids recently became attractive targets to develop non-invasive diagnostic tools for cancer detection. Along with DNA and mRNAs, transcripts lacking coding potential (non-coding RNAs, ncRNAs) directly involved in the process of tumor pathogenesis have been recently detected in liquid biopsies. Interestingly, circulating ncRNAs exhibit specific expression patterns associated with cancer and suggest their role as novel biomarkers. However, the potential of circulating long ncRNAs (c-lncRNAs) to be markers in osteosarcoma (OS) is still elusive. In this study we performed a systematic review to identify thirteen c-lncRNAs whose altered expression in blood associate with OS. We herein discuss the potential impact that these c-lncRNAs may have on clinical decision-making in the management of OS. Overall, we aimed to provide novel insights that can contribute to the development of future precision medicine in oncology.
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12
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Retis-Resendiz AM, González-García IN, León-Juárez M, Camacho-Arroyo I, Cerbón M, Vázquez-Martínez ER. The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium. Clin Epigenetics 2021; 13:116. [PMID: 34034824 PMCID: PMC8146649 DOI: 10.1186/s13148-021-01103-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The human endometrium is a highly dynamic tissue whose function is mainly regulated by the ovarian steroid hormones estradiol and progesterone. The serum levels of these and other hormones are associated with three specific phases that compose the endometrial cycle: menstrual, proliferative, and secretory. Throughout this cycle, the endometrium exhibits different transcriptional networks according to the genes expressed in each phase. Epigenetic mechanisms are crucial in the fine-tuning of gene expression to generate such transcriptional networks. The present review aims to provide an overview of current research focused on the epigenetic mechanisms that regulate gene expression in the cyclical endometrium and discuss the technical and clinical perspectives regarding this topic. MAIN BODY The main epigenetic mechanisms reported are DNA methylation, histone post-translational modifications, and non-coding RNAs. These epigenetic mechanisms induce the expression of genes associated with transcriptional regulation, endometrial epithelial growth, angiogenesis, and stromal cell proliferation during the proliferative phase. During the secretory phase, epigenetic mechanisms promote the expression of genes associated with hormone response, insulin signaling, decidualization, and embryo implantation. Furthermore, the global content of specific epigenetic modifications and the gene expression of non-coding RNAs and epigenetic modifiers vary according to the menstrual cycle phase. In vitro and cell type-specific studies have demonstrated that epithelial and stromal cells undergo particular epigenetic changes that modulate their transcriptional networks to accomplish their function during decidualization and implantation. CONCLUSION AND PERSPECTIVES Epigenetic mechanisms are emerging as key players in regulating transcriptional networks associated with key processes and functions of the cyclical endometrium. Further studies using next-generation sequencing and single-cell technology are warranted to explore the role of other epigenetic mechanisms in each cell type that composes the endometrium throughout the menstrual cycle. The application of this knowledge will definitively provide essential information to understand the pathological mechanisms of endometrial diseases, such as endometriosis and endometrial cancer, and to identify potential therapeutic targets and improve women's health.
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Affiliation(s)
- Alejandra Monserrat Retis-Resendiz
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Ixchel Nayeli González-García
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Moisés León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Edgar Ricardo Vázquez-Martínez
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico.
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13
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Zhang DD, Shi Y, Liu JB, Yang XL, Xin R, Wang HM, Wang PY, Jia CY, Zhang WJ, Ma YS, Fu D. Construction of a Myc-associated ceRNA network reveals a prognostic signature in hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:1033-1050. [PMID: 34141458 PMCID: PMC8167205 DOI: 10.1016/j.omtn.2021.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) remains an extremely lethal disease worldwide. High-throughput methods have revealed global transcriptome dysregulation; however, a comprehensive investigation of the complexity and behavioral characteristics of the competing endogenous RNA (ceRNA) network in HCC is lacking. In this study, we extracted the transcriptome (RNA) sequencing data of 371 HCC patients from The Cancer Genome Atlas platform. With the comparison of the high Myc expression (Mychigh) tumor and low Myc expression (Myclow) tumor groups in HCC, we identified 1,125 differentially expressed (DE) mRNAs, 589 long non-coding RNAs (lncRNAs), and 93 microRNAs (miRNAs). DE RNAs predicted the interactions necessary to construct an associated Myc ceRNA network, including 19 DE lncRNAs, 5 miRNAs, and 72 mRNAs. We identified a significant signature (long intergenic non-protein-coding [LINC] RNA 2691 [LINC02691] and LINC02499) that effectively predicted overall survival and had protective effects. The target genes of microRNA (miR)-212-3p predicted to intersect with DE mRNAs included SEC14-like protein 2 (SEC14L2) and solute carrier family 6 member 1 (SLC6A1), which were strongly correlated with survival and prognosis. With the use of the lncRNA-miRNA-mRNA axis, we constructed a ceRNA network containing four lncRNAs (LINC02691, LINC02499, LINC01354, and NAV2 antisense RNA 4), one miRNA (miR-212-3p), and two mRNAs (SEC14L2 and SLC6A1). Overall, we successfully constructed a mutually regulated ceRNA network and identified potential precision-targeted therapies and prognostic biomarkers.
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Affiliation(s)
- Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China.,Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yi Shi
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wen-Jie Zhang
- Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China.,The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yu-Shui Ma
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai 200433, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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