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Xia W, Shi N, Li C, Tang A. RNA-Seq and miRNA-Seq data from Epstein-Barr virus-infected tree shrews reveal a ceRNA network contributing to immune microenvironment regulation. Virulence 2024; 15:2306795. [PMID: 38251668 PMCID: PMC10826628 DOI: 10.1080/21505594.2024.2306795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Epstein-Barr virus (EBV) infection in humans is ubiquitous and associated with various diseases. Remodeling of the immune microenvironment is the primary cause of EBV infection and pathogenesis; however, the underlying mechanism has not been fully elucidated. In this study, we used whole-transcriptome RNA-Seq to detect mRNAs, long non-coding RNAs (lncRNA), and microRNA (miRNA) profiles in the control group, 3 days, and 28 days after EBV infection, based on the tree shrew model that we reported previously. First, we estimated the proportion of 22 cell types in each sample using CIBERSORT software and identified 18 high-confidence DElncRNAs related to immune microenvironment regulation after EBV infection. Functional enrichment analysis of these differentially expressed lncRNAs primarily focused on the autophagy, endocytosis, and ferroptosis signalling pathways. Moreover, EBV infection affects miRNA expression patterns, and many miRNAs are silenced. Finally, three competing endogenous RNA regulatory networks were built using lncRNAs that significantly correlated with immune cell types, miRNAs that responded to EBV infection, and potentially targeted the mRNA of the miRNAs. Among them, MRPL42-AS-5 might act as an hsa-miR-296-5p "sponge" and compete with target mRNAs, thus increasing mRNA expression level, which could induce immune cell infiltration through the cellular senescence signalling pathway against EBV infection. Overall, we conducted a complete transcriptomic analysis of EBV infection in vivo for the first time and provided a novel perspective for further investigation of EBV-host interactions.
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Affiliation(s)
- Wei Xia
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Nan Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Chaoqian Li
- Department of Emergency, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Anzhou Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
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2
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Yilihamu Y, Xu R, Jia W, Kukun H, Aihemaiti D, Chang Y, Ding S, Wang Y. Role of long non-coding RNA TCONS_02443383 in regulating cell adhesion and peroxisome proliferator-activated receptor (PPAR) signaling genes in atherosclerosis: A New Zealand white rabbit model study. Gene 2024; 927:148694. [PMID: 38878987 DOI: 10.1016/j.gene.2024.148694] [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: 03/19/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
OBJECTIVE In this study, we performed RNA sequencing (RNA-seq) on the abdominal aorta tissue of New Zealand rabbits and investigated the potential association of lncRNA TCONS_02443383 with the development of AS through bioinformatics analysis of the sequencing data. The obtained results were further validated using quantitative real-time polymerase chain reaction (qRT-PCR). METHOD We induced an AS model in New Zealand rabbits by causing balloon injury to the abdominal aorta vascular wall and administering a high-fat diet. We then upregulated the expression level of the lncRNA TCONS_02443383 by injecting lentiviral plasmids through the ear vein. RNA sequencing (RNA-seq) was performed on the abdominal aorta tissues. We conducted Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway and Gene Ontology (GO) analyses. RESULT The overexpression of the lncRNA TCONS_02443383 led to an upregulation of peroxisome proliferator-activated receptor (PPAR) signaling pathways as well as genes related to cell adhesion. CONCLUSION The overexpression of the lncRNA TCONS_02443383 can inhibit the occurrence and development of AS by upregulating peroxisome proliferator-activated receptor (PPAR) signaling pathways and genes related to cell adhesion.
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Affiliation(s)
- Yilinuer Yilihamu
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Rui Xu
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Wenxiao Jia
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Hanjiaerbieke Kukun
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Dilinuerkezi Aihemaiti
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Yifan Chang
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Shuang Ding
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China.
| | - Yunling Wang
- Department of Radiology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China.
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Zhao X, Zhao F, Yan L, Wu J, Fang Y, Wang C, Xin Z, Yang X. Long non-coding ribonucleic acid SNHG18 induced human granulosa cell apoptosis via disruption of glycolysis in ovarian aging. J Ovarian Res 2024; 17:185. [PMID: 39272131 PMCID: PMC11395969 DOI: 10.1186/s13048-024-01510-4] [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: 03/13/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND In-depth understanding of dynamic expression profiles of human granulosa cells (GCs) during follicular development will contribute to the diagnostic and targeted interventions for female infertility. However, genome-scale analysis of long non-coding ribonucleic acid (lncRNA) in GCs across diverse developmental stages is challenging. Meanwhile, further research is needed to determine how aberrant lncRNA expression participates in ovarian diseases. METHODS Granulosa cell-related lncRNAs data spanning five follicular development stages were retrieved and filtered from the NCBI dataset (GSE107746). Stage-specific lncRNA expression patterns and mRNA-lncRNA co-expression networks were identified with bioinformatic approaches. Subsequently, the expression pattern of SNHG18 was detected in GCs during ovarian aging. And SNHG18 siRNA or overexpression plasmids were transfected to SVOG cells in examining the regulatory roles of SNHG18 in GC proliferation and apoptosis. Moreover, whether PKCɛ/SNHG18 signaling take part in GC glycolysis via ENO1 were verified in SVOG cells. RESULTS We demonstrated that GC-related lncRNAs were specifically expressed across different developmental stages, and coordinated crucial biological functions like mitotic cell cycle and metabolic processes in the folliculogenesis. Thereafter, we noticed a strong correlation of PRKCE and SNHG18 expression in our analysis. With downregulated SNHG18 of GCs identified in the context of ovarian aging, SNHG18 knockdown could further induce cell apoptosis, retard cell proliferation and exacerbate DNA damage in SVOG cell. Moreover, downregulated PKCɛ/SNHG18 pathway interrupted the SVOG cell glycolysis by lowering the ENO1 expression. CONCLUSIONS Altogether, our results revealed that folliculogenesis-related lncRNA SNHG18 participated in the pathogenesis of ovarian aging, which may provide novel biomarkers for ovarian function and new insights for the infertility treatment.
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Affiliation(s)
- Xuehan Zhao
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feiyan Zhao
- Department of Obstetrics and Gynecology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Long Yan
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiaqi Wu
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Fang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Cong Wang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Zhimin Xin
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
| | - Xiaokui Yang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
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4
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Wang B, Liu X, Li C, Yang N. LncRNA (BCO1-AS) regulate inflammatory responses in bacterial infection through caspase-1 in turbot (Scophthalmus maximus). Int J Biol Macromol 2024; 279:135131. [PMID: 39208888 DOI: 10.1016/j.ijbiomac.2024.135131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
LncRNA plays key role in several biological processes, including transcriptional regulation, post transcriptional control and epigenetic regulation. However, research on the functional roles of lncRNAs in teleost species remains limited. Here, we discovered a lncRNA (BCO1-AS) with a critical role in antibacterial responses. Briefly, the full length of BCO1-AS was 2005 bp. Subsequently, BCO1-AS was distributed throughout the nucleus, where it may either trans- or cis-regulate the nearby genes. In addition, BCO1-AS was widely expressed in all the examined tissues with the highest expression level in intestine, while the lowest expression level was detected in muscle. Moreover, following Vibrio anguillarum challenge, BCO1-AS was significantly down-regulated in intestine, and up-regulated in gill and skin. In CHIRP experiment, BCO1-AS could effectively enrich RNA and might interact with several immune-related genes. Furthermore, we found that LPS could induce the expression of BCO1-AS. Finally, BCO1-AS could positively regulate caspase-1 at the mRNA and protein level. The BCO1-AS was speculated to inhibit the synthesis of inflammatory components. In summary, these results showed the roles of BCO1-AS in the regulation of inflammatory in turbot, which provided valuable information for further understanding the immune regulation network of lncRNA in teleost fish.
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Affiliation(s)
- Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoli Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
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DeCasien AR, Chiou KL, Testard C, Mercer A, Negrón-Del Valle JE, Bauman Surratt SE, González O, Stock MK, Ruiz-Lambides AV, Martínez MI, Antón SC, Walker CS, Sallet J, Wilson MA, Brent LJN, Montague MJ, Sherwood CC, Platt ML, Higham JP, Snyder-Mackler N. Evolutionary and biomedical implications of sex differences in the primate brain transcriptome. CELL GENOMICS 2024; 4:100589. [PMID: 38942023 PMCID: PMC11293591 DOI: 10.1016/j.xgen.2024.100589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/28/2023] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Abstract
Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.
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Affiliation(s)
- Alex R DeCasien
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA; Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA.
| | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Department of Psychology, University of Washington, Seattle, WA, USA; Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Washington, Seattle, WA, USA.
| | - Camille Testard
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Arianne Mercer
- Department of Psychology, University of Washington, Seattle, WA, USA
| | | | | | - Olga González
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | | | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
| | - Susan C Antón
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Christopher S Walker
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jérôme Sallet
- Stem Cell and Brain Research Institute, Université Lyon, Lyon, France
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behavior, University of Exeter, Exeter, UK
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA; Department of Marketing, University of Pennsylvania, Philadelphia, PA, USA
| | - James P Higham
- Department of Anthropology, New York University, New York, NY, USA; New York Consortium in Evolutionary Primatology, New York, NY, USA.
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Department of Psychology, University of Washington, Seattle, WA, USA; Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Washington, Seattle, WA, USA; ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA.
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6
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Liu Y, Lu S, Yang J, Yang Y, Jiao L, Hu J, Li Y, Yang F, Pang Y, Zhao Y, Gao Y, Liu W, Shu P, Ge W, He Z, Peng X. Analysis of the aging-related biomarker in a nonhuman primate model using multilayer omics. BMC Genomics 2024; 25:639. [PMID: 38926642 PMCID: PMC11209966 DOI: 10.1186/s12864-024-10556-z] [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: 02/09/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Aging is a prominent risk factor for diverse diseases; therefore, an in-depth understanding of its physiological mechanisms is required. Nonhuman primates, which share the closest genetic relationship with humans, serve as an ideal model for exploring the complex aging process. However, the potential of the nonhuman primate animal model in the screening of human aging markers is still not fully exploited. Multiomics analysis of nonhuman primate peripheral blood offers a promising approach to evaluate new therapies and biomarkers. This study explores aging-related biomarker through multilayer omics, including transcriptomics (mRNA, lncRNA, and circRNA) and proteomics (serum and serum-derived exosomes) in rhesus monkeys (Macaca mulatta). RESULTS Our findings reveal that, unlike mRNAs and circRNAs, highly expressed lncRNAs are abundant during the key aging period and are associated with cancer pathways. Comparative analysis highlighted exosomal proteins contain more types of proteins than serum proteins, indicating that serum-derived exosomes primarily regulate aging through metabolic pathways. Finally, eight candidate aging biomarkers were identified, which may serve as blood-based indicators for detecting age-related brain changes. CONCLUSIONS Our results provide a comprehensive understanding of nonhuman primate blood transcriptomes and proteomes, offering novel insights into the aging mechanisms for preventing or treating age-related diseases.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yun Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Jingwen Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanyan Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yunli Pang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yuan Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China
| | - Yanpan Gao
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Liu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Pengcheng Shu
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Wei Ge
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Sciences, CAMS & PUMC, Beijing, 100021, China.
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, 650031, China.
- Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMC, Beijing, 100005, China.
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7
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Xiong W, Lu L, Li J. Long non-coding RNAs with essential roles in neurodegenerative disorders. Neural Regen Res 2024; 19:1212-1220. [PMID: 37905867 DOI: 10.4103/1673-5374.385850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/04/2023] [Indexed: 11/02/2023] Open
Abstract
ABSTRACT Recently, with the advent of high-resolution and high-throughput sequencing technologies, an increasing number of long non-coding RNAs (lncRNAs) have been found to be involved in the regulation of neuronal function in the central nervous system with specific spatiotemporal patterns, across different neurodegenerative diseases. However, the underlying mechanisms of lncRNAs during neurodegeneration remain poorly understood. This review provides an overview of the current knowledge of the biology of lncRNAs and focuses on introducing the latest identified roles, regulatory mechanisms, and research status of lncRNAs in Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Finally, this review discusses the potential values of lncRNAs as diagnostic biomarkers and therapeutic targets for neurodegenerative diseases, hoping to provide broader implications for developing effective treatments.
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Affiliation(s)
- Wandi Xiong
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Lin Lu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- National Institute on Drug Dependence, Peking University, Beijing, China
- PKU/McGovern Institute for Brain Research, Peking University, Beijing, China
- Institute of Mental Health, National Clinical Research Center for Mental Disorders, Key Laboratory of Mental Health and Peking University Sixth Hospital, Peking University, Beijing, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan Province, China
- National Institute on Drug Dependence, Peking University, Beijing, China
- PKU/McGovern Institute for Brain Research, Peking University, Beijing, China
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8
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Navandar M, Vennin C, Lutz B, Gerber S. Long non-coding RNAs expression and regulation across different brain regions in primates. Sci Data 2024; 11:545. [PMID: 38806530 PMCID: PMC11133376 DOI: 10.1038/s41597-024-03380-3] [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: 12/22/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Human and non-human primates have strikingly similar genomes, but they strongly differ in many brain-based processes (e.g., behaviour and cognition). While the functions of protein-coding genes have been extensively studied, rather little is known about the role of non-coding RNAs such as long non-coding RNAs (lncRNAs). Here, we predicted lncRNAs and analysed their expression pattern across different brain regions of human and non-human primates (chimpanzee, gorilla, and gibbon). Our analysis identified shared orthologous and non-orthologous lncRNAs, showing striking differences in the genomic features. Differential expression analysis of the shared orthologous lncRNAs from humans and chimpanzees revealed distinct expression patterns in subcortical regions (striatum, hippocampus) and neocortical areas while retaining a homogeneous expression in the cerebellum. Co-expression analysis of lncRNAs and protein-coding genes revealed massive proportions of co-expressed pairs in neocortical regions of humans compared to chimpanzees. Network analysis of co-expressed pairs revealed the distinctive role of the hub-acting orthologous lncRNAs in a region- and species-specific manner. Overall, our study provides novel insight into lncRNA driven gene regulatory landscape, neural regulation, brain evolution, and constitutes a resource for primate's brain lncRNAs.
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Affiliation(s)
- Mohit Navandar
- Institute for Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Constance Vennin
- Leibniz Institute for Resilience Research, 55122, Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research, 55122, Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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9
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Song Y, Shen T, Sun H, Wang X. Genome-wide analyses reveal the regulatory roles of DNA methylation-regulated alternative promoter transcripts in breast cancer. Hum Genet 2024; 143:385-399. [PMID: 38502355 DOI: 10.1007/s00439-024-02653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
A certain proportion of genes are regulated by multiple, distinct promoters, revealing a dynamic landscape of the cancer transcriptome. However, the contribution of alternative promoters (APs) in breast cancer (BRCA) remains largely unexplored. Here, we identified 3654 genes with multiple promoters in BRCA patients, and 53 of them could generate distinct AP transcripts that are dysregulated and prognosis-related in BRCA, namely prognosis-related dysregulated AP (prdeAP) transcripts. Interestingly, when we searched for the genomic signatures of these prdeAP genes, we found that the promoter regions of 92% of the prdeAP genes were enriched with abundant DNA methylation signals. Through further bioinformatic analysis and experimental validation, we showed that AP selections of TANK, UNKL, CCL28, and MAP1LC3A were regulated by DNA methylation upon their corresponding promoter regions. Functionally, by overexpressing AP variants of TANK, we found that TANK|55731 could dramatically suppress MDA-MB-231 cell proliferation and migration. Meanwhile, pan-cancer survival analyses suggested that AP variants of TANK provided more accurate prognostic predictive ability than TANK gene in a variety of tumor types, including BRCA. Together, by uncovering the DNA methylation-regulated AP transcripts with tumor prognostic features, our work revealed a novel layer of regulators in BRCA progression and provided potential targets that served as effective biomarkers for anti-BRCA treatment.
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Affiliation(s)
- Yingdong Song
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tao Shen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu, China.
| | - Huihui Sun
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Anhui Province Key Laboratory of Geriatric Immunology and Nutrition Therapy, Hefei, China.
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10
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Xie T, Huang Q, Huang Q, Huang Y, Liu S, Zeng H, Liu J. Dysregulated lncRNAs regulate human umbilical cord mesenchymal stem cell differentiation into insulin-producing cells by forming a regulatory network with mRNAs. Stem Cell Res Ther 2024; 15:22. [PMID: 38273351 PMCID: PMC10809572 DOI: 10.1186/s13287-023-03572-5] [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: 11/18/2021] [Accepted: 11/16/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE In recent years, cell therapy has emerged as a new research direction in the treatment of diabetes. However, the underlying molecular mechanisms of mesenchymal stem cell (MSC) differentiation necessary to form such treatment have not been clarified. METHODS In this study, human umbilical cord mesenchymal stem cells (HUC-MSCs) isolated from newborns were progressively induced into insulin-producing cells (IPCs) using small molecules. HUC-MSC (S0) and four induced stage (S1-S4) samples were prepared. We then performed transcriptome sequencing experiments to obtain the dynamic expression profiles of both mRNAs and long noncoding RNAs (lncRNAs). RESULTS We found that the number of differentially expressed lncRNAs and mRNAs trended downwards during differentiation. Gene Ontology (GO) analysis showed that the target genes of differentially expressed lncRNAs were associated with translation, cell adhesion, and cell connection. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the NF-KB signalling pathway, MAPK signalling pathway, HIPPO signalling pathway, PI3K-Akt signalling pathway, and p53 signalling pathway were enriched in these differentially expressed lncRNA-targeting genes. We also found that the coexpression of the lncRNA CTBP1-AS2 with PROX1 and the lncRNAs AC009014.3 and GS1-72M22.1 with JARID2 mRNA was related to the development of pancreatic beta cells. Moreover, the coexpression of the lncRNAs: XLOC_ 050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14- AS1, RP11-148K1.12, and CTD2020K17.3 with p53, regulated insulin secretion by pancreatic beta cells. CONCLUSION In this study, HUC-MSCs combined with small molecule compounds were successfully induced into IPCs. Differentially expressed lncRNAs may regulate the insulin secretion of pancreatic beta cells by regulating multiple signalling pathways. The lncRNAs AC009014.3, Gs1-72m21.1, and CTBP1-AS2 may be involved in the development of pancreatic beta cells, and the lncRNAs: XLOC_050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14-AS1, RP11-148K1.12, and CTD2020K17.3 may be involved in regulating the insulin secretion of pancreatic beta cells, thus providing a lncRNA catalogue for future research regarding the mechanism of the transdifferentiation of HUC-MSCs into IPCs. It also provides a new theoretical basis for the transplantation of insulin-producing cells into diabetic patients in the future.
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Affiliation(s)
- Tianqin Xie
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Qiming Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translation Medicine, Nanchang University, Nanchang of Jiangxi, China
| | - Qiulan Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Yanting Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Shuang Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Haixia Zeng
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Jianping Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China.
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11
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Zhang Y, Tang L, Wang Y, Zhu X, Liu L. In-depth analyses of lncRNA and circRNA expression in the hippocampus of LPS-induced AD mice by Byu d Mar 25. Neuroreport 2024; 35:49-60. [PMID: 38051653 PMCID: PMC10702698 DOI: 10.1097/wnr.0000000000001977] [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: 07/19/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023]
Abstract
Byu d Mar 25 (BM25) has been verified to have neuroprotective effects in Alzheimer's disease (AD) mice. However, the molecular mechanism remains unclear. We aimed to investigate the expression profiling of lncRNAs and circRNAs by microarray analysis. Six hippocampus from LPS-mediated AD mice model treated with (normal saline (NS) (n = 3) and AD mice model treated with BM25 (n = 3) were selected. Microarray analysis was performed to detect the expression profiles of lncRNAs and circRNAs in hippocampus. Differentially expressed (DE) lncRNAs, mRNAs and circRNAs were identified through scatter plot and volcano plot filtering with a threshold of fold-change ≥2 and P ≤ 0.05. Co-expression network is analyzed by Circos software. Cis - and Trans - regulation were analyzed using RIsearch-2.0 and FEELNC softwares. LncRNA-transcription factors (TFs) and LncRNA-Target-TFs network were analyzed by Clusterprofiler software. The prediction of miRNAs bind to circRNAs were performed with miRNAbase. A total of 113 DElncRNAs, 117 DEmRNAs, and 4 DEcircRNAs were detected. The pathway analysis showed the mRNAs that correlated with lncRNAs were involved in apoptosis, inflammatory mediator regulation of TRP channels, NF-kappa B and PI3K-Akt signaling pathway. The lncRNA-TFs network analysis suggested the lncRNAs were mostly regulated by Ncoa1, Phf5a, Klf6, Lmx1b, and Pax3. Additionally, lncRNA-target-TFs network analysis indicated the GATA6, Junb, Smad1, Twist1, and Mafb mostly regulate the same lncRNAs: XR_001783430.1 and NR_051982.1. Furthermore, 480 miRNAs were predicted binding to 4 identified circRNAs. The BM25 may affect AD by regulating the expression of lncRNAs and circRNAs, which could regulate the expressions of mRNAs or miRNAs by LncRNA-Target-TFs network.
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Affiliation(s)
| | - Liang Tang
- Department of Basic Medicine, Changsha Medical University
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative Diseases, Changsha Medical University, Changsha, People's Republic of China
| | - Yan Wang
- Department of Basic Medicine, Changsha Medical University
| | - Xiaoyan Zhu
- Medical College, Tibet University, Lhasa, Tibet
| | - Lan Liu
- Medical College, Tibet University, Lhasa, Tibet
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12
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Zeng Y, Xue T, Zhang D, Lv M. Transcriptomic Analysis of lncRNAs and their mRNA Networks in Cerebral Ischemia in Young and Aged Mice. Comb Chem High Throughput Screen 2024; 27:823-833. [PMID: 37340753 DOI: 10.2174/1386207326666230619091603] [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: 08/16/2022] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Ischemic stroke comprises 75% of all strokes and it is associated with a great frailty and casualty rate. Certain data suggest multiple long non-coding Ribonucleic Acids (lncRNAs) assist the transcriptional, post-transcriptional, and epigenetic regulation of genes expressed in the CNS (Central Nervous System). However, these studies generally focus on differences in the expression patterns of lncRNAs and Messenger Ribonucleic Acids (mRNAs) in tissue samples before and after cerebral ischemic injury, ignoring the effects of age. METHODS In this study, differentially expressed lncRNA analysis was performed based on RNAseq data from the transcriptomic analysis of murine brain microglia related to cerebral ischemia injury in mice at different ages (10 weeks and 18 months). RESULTS The results showed that the number of downregulate differentially expressed genes (DEGs) in aged mice was 37 less than in young mice. Among them, lncRNA Gm-15987, RP24- 80F7.5, XLOC_379730, XLOC_379726 were significantly down-regulated. Then, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these specific lncRNAs were mainly related to inflammation. Based on the lncRNA/mRNA coexpression network, the mRNA co-expressed with lncRNA was mainly enriched in pathways, such as immune system progression, immune response, cell adhesion, B cell activation, and T cell differentiation. Our results indicate that the downregulation of lncRNA, such as Gm-15987, RP24- 80F7.5, XLOC_379730, and XLOC_379726 in aged mice may attenuate microglial-induced inflammation via the progress of immune system progression immune response, cell adhesion, B cell activation, and T cell differentiation. CONCLUSION The reported lncRNAs and their target mRNA during this pathology have potentially key regulatory functions in the cerebral ischemia in aged mice while being important for diagnosing and treating cerebral ischemia in the elderly.
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Affiliation(s)
- Yuanyuan Zeng
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Tengteng Xue
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Dayong Zhang
- Department of New Media and Arts, Harbin Institute of Technology, Harbin, 150001, China
| | - Manhua Lv
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
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13
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Zhou Y, Huang Y, Chen X, Chen T, Hu W, Hou W, Zhang Q, Xiong Y. Transcriptomic study reveals changes of lncRNAs in PBMCs from HIV-1 patients before and after ART. Sci Rep 2023; 13:22493. [PMID: 38110484 PMCID: PMC10728114 DOI: 10.1038/s41598-023-49595-z] [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: 05/21/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play important roles in regulating HIV-1 infection and virus-host interactions. However, it is unclear whether and how ART alters lncRNAs in HIV-infected patients. In the present study, we investigated changes of lncRNAs in PBMCs from HIV-1 patients pre- and post-ART. We identified a total of 974 lncRNAs whose expression was restored to normal levels after ART. Cis-acting analysis showed that six lncRNAs have cis-regulated target genes, among which RP11-290F5.1 and interferon regulatory factor 2 (IRF2) were reported to promote HIV replication. Furthermore, we found that lncRNA CTB-119C2.1, which regulates most mRNAs with differential expression in PBMCs from HIV-1 infected patients after ART, was significantly upregulated by RNA-seq and qRT-PCR assays. KEGG analysis of CTB-119C2.1-associated genes revealed that most of the genes are involved in the p53 signaling pathway and pathways related to cell cycle and DNA replication. Our findings thus reveal the dynamic change of lncRNAs in people living with HIV-1 pre- and post-ART and warrant further investigation of the role of lncRNAs in HIV-1 pathogenesis and treatment.
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Affiliation(s)
- Yingying Zhou
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
| | - Yuqing Huang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xiaoping Chen
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
| | - Tielong Chen
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
| | - Wenjia Hu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
| | - Wei Hou
- State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, 185 Donghu Road, Wuhan, 430071, Hubei Province, China.
| | - Qi Zhang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China.
| | - Yong Xiong
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China.
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14
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Zeidan RS, McElroy T, Rathor L, Martenson MS, Lin Y, Mankowski RT. Sex differences in frailty among older adults. Exp Gerontol 2023; 184:112333. [PMID: 37993077 DOI: 10.1016/j.exger.2023.112333] [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: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
By definition, aging is a natural, gradual and continuous process. On the other hand, frailty reflects the increase in vulnerability to stressors and shortens the time without disease (health span) while longevity refers to the length of life (lifespan). The average life expectancy has significantly increased during the last few decades. A longer lifespan has been accompanied by an increase in frailty and decreased independence in older adults, with major differences existing between men and women. For example, women tend to live longer than men but also experience higher rates of frailty and disability. Sex differences prevent optimization of lifestyle interventions and therapies to effectively prevent frailty. Sex differences in frailty and aging are rooted in a complex interplay between uncontrollable (genetic, epigenetic, physiological), and controllable factors (psychosocial and lifestyle factors). Thus, understanding the underlying causes of sex differences in frailty and aging is essential for developing personalized interventions to promote healthy aging and improve quality of life in older men and women. In this review, we have discussed the key contributors and knowledge gaps related to sex differences in aging and frailty.
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Affiliation(s)
- Rola S Zeidan
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Taylor McElroy
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Laxmi Rathor
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Matthew S Martenson
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Yi Lin
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Robert T Mankowski
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
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15
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Wang W, Bo T, Zhang G, Li J, Ma J, Ma L, Hu G, Tong H, Lv Q, Araujo DJ, Luo D, Chen Y, Wang M, Wang Z, Wang GZ. Noncoding transcripts are linked to brain resting-state activity in non-human primates. Cell Rep 2023; 42:112652. [PMID: 37335775 DOI: 10.1016/j.celrep.2023.112652] [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: 09/21/2022] [Revised: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Brain-derived transcriptomes are known to correlate with resting-state brain activity in humans. Whether this association holds in nonhuman primates remains uncertain. Here, we search for such molecular correlates by integrating 757 transcriptomes derived from 100 macaque cortical regions with resting-state activity in separate conspecifics. We observe that 150 noncoding genes explain variations in resting-state activity at a comparable level with protein-coding genes. In-depth analysis of these noncoding genes reveals that they are connected to the function of nonneuronal cells such as oligodendrocytes. Co-expression network analysis finds that the modules of noncoding genes are linked to both autism and schizophrenia risk genes. Moreover, genes associated with resting-state noncoding genes are highly enriched in human resting-state functional genes and memory-effect genes, and their links with resting-state functional magnetic resonance imaging (fMRI) signals are altered in the brains of patients with autism. Our results highlight the potential for noncoding RNAs to explain resting-state activity in the nonhuman primate brain.
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Affiliation(s)
- Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tingting Bo
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Clinical Neuroscience Center, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ge Zhang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liangxiao Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ganlu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Lv
- School of Psychological and Cognitive Sciences, Beijing Key Laboratory of Behavior and Mental Health, IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Daniel J Araujo
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Dong Luo
- School of Biomedical Engineering, Hainan University, Haikou, Hainan, China
| | - Yuejun Chen
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Meiyun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, China
| | - Zheng Wang
- School of Psychological and Cognitive Sciences, Beijing Key Laboratory of Behavior and Mental Health, IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; School of Biomedical Engineering, Hainan University, Haikou, Hainan, China.
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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16
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Yang N, Zhang N, Wang Z, Cao W, He X, Zhang W, Xing Y. Galectin-1-dependent ceRNA network in HRMECs revealed its association with retinal neovascularization. BMC Genomics 2023; 24:327. [PMID: 37322431 DOI: 10.1186/s12864-023-09352-y] [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: 11/25/2022] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Retinal neovascularization (RNV) is a leading cause of blindness worldwide. Long non-coding RNA (lncRNA) and competing endogenous RNA (ceRNA) regulatory networks play vital roles in angiogenesis. The RNA-binding protein galectin-1 (Gal-1) participates in pathological RNV in oxygen-induced retinopathy mouse models. However, the molecular associations between Gal-1 and lncRNAs remain unclear. Herein, we aimed to explore the potential mechanism of action of Gal-1 as an RNA-binding protein. RESULTS A comprehensive network of Gal-1, ceRNAs, and neovascularization-related genes was constructed based on transcriptome chip data and bioinformatics analysis of human retinal microvascular endothelial cells (HRMECs). We also conducted functional enrichment and pathway enrichment analyses. Fourteen lncRNAs, twenty-nine miRNAs, and eleven differentially expressed angiogenic genes were included in the Gal-1/ceRNA network. Additionally, the expression of six lncRNAs and eleven differentially expressed angiogenic genes were validated by qPCR in HRMECs with or without siLGALS1. Several hub genes, such as NRIR, ZFPM2-AS1, LINC0121, apelin, claudin-5, and C-X-C motif chemokine ligand 10, were found to potentially interact with Gal-1 via the ceRNA axis. Furthermore, Gal-1 may be involved in regulating biological processes related to chemotaxis, chemokine-mediated signaling, the immune response, and the inflammatory response. CONCLUSIONS The Gal-1/ceRNA axis identified in this study may play a vital role in RNV. This study provides a foundation for the continued exploration of therapeutic targets and biomarkers associated with RNV.
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Affiliation(s)
- Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Zhiyi Wang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Wenye Cao
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Xuejun He
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Wenxi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
- Department of Ophthalmology, Aier Eye Hospital of Wuhan University, Wuhan, China.
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17
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Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs. Int J Mol Sci 2023; 24:ijms24043947. [PMID: 36835359 PMCID: PMC9960057 DOI: 10.3390/ijms24043947] [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: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.
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18
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Zhao L, Xin S, Wu Y, Huang S, Xu K, Xu Y, Ruan D, Wu B, Chen D, He X. Global DNA and protein interactomes of FLT1P1 (Fms-related tyrosine kinase 1 pseudogene 1) revealed its molecular regulatory functions associated with preeclampsia. Mol Biol Rep 2023; 50:1267-1279. [PMID: 36451001 DOI: 10.1007/s11033-022-08070-0] [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: 07/21/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Preeclampsia (PE) is one of the most serious pregnancy complications with unknown pathogenesis. Emerging evidence has demonstrated that Fms-related tyrosine kinase 1 (FLT1) is highly involved in PE development. As a pseudogene of FLT1, FLT1P1 increased in PE samples. However, its functions remain largely unknown. METHODS AND RESULTS In this study, co-expression analysis was performed to identify the potential target genes of FTL1P1. Then chromatin isolation using RNA purification (ChIRP) method was employed to explore the interactomes of FLT1P1, including interacting with DNA fragments and proteins. We found that in PE samples, both FLT1P1 and FLT1 were highly expressed and closely correlated. ChIRP-protein data revealed that FLT1P1 interacts with translation- and transcription-related proteins, including 4 transcription factors (TFs). ChIRP-DNA analysis revealed that FLT1P1 preferentially interacted with DNA fragments downstream of transcription start sites (TSSs). Functional analysis of its interacting genes revealed that they were enriched in transcriptional regulation and apoptosis-related pathways. Twenty-six TFs, including CREB1 and SRF, were extracted from the potential FLT1P1-interacting gene sets and were potential targets of FLT1P1. CREB1 could bind to FLT1 promoter, and was negatively correlated with FLT1 at the expression level, making it a potential regulator of FLT1. CONCLUSIONS Our study extensively investigated the interactome profiles of FLT1P1, especially the prompter region of TF gene CREB1, and revealed the potential molecular regulatory mechanisms of FLT1 expression in PE samples. Our results provide a novel view of PE pathogenesis, and suggest that FLT1P1 could serve as a potential therapeutic target in PE diagnosis and treatment.
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Affiliation(s)
- Lu Zhao
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Siming Xin
- Department of Obstetrics, Maternal, Child Health Hospital Afflicted to Nanchang University, Nanchang, People's Republic of China
| | - Yunfei Wu
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, People's Republic of China
| | - Shaofang Huang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Kangxiang Xu
- Second Clinical Medical College, Nanchang University, Nanchang, People's Republic of China
| | - Yuqi Xu
- Second Clinical Medical College, Nanchang University, Nanchang, People's Republic of China
| | - Dong Ruan
- Second Clinical Medical College, Nanchang University, Nanchang, People's Republic of China
| | - Bingqi Wu
- Second Clinical Medical College, Nanchang University, Nanchang, People's Republic of China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, People's Republic of China
| | - Xiaoju He
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.
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19
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Shirokova O, Zaborskaya O, Pchelin P, Kozliaeva E, Pershin V, Mukhina I. Genetic and Epigenetic Sexual Dimorphism of Brain Cells during Aging. Brain Sci 2023; 13:brainsci13020195. [PMID: 36831738 PMCID: PMC9954625 DOI: 10.3390/brainsci13020195] [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: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
In recent years, much of the attention paid to theoretical and applied biomedicine, as well as neurobiology, has been drawn to various aspects of sexual dimorphism due to the differences that male and female brain cells demonstrate during aging: (a) a dimorphic pattern of response to therapy for neurodegenerative disorders, (b) different age of onset and different degrees of the prevalence of such disorders, and (c) differences in their symptomatic manifestations in men and women. The purpose of this review is to outline the genetic and epigenetic differences in brain cells during aging in males and females. As a result, we hereby show that the presence of brain aging patterns in males and females is due to a complex of factors associated with the effects of sex chromosomes, which subsequently entails a change in signal cascades in somatic cells.
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Affiliation(s)
- Olesya Shirokova
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Correspondence:
| | - Olga Zaborskaya
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Pavel Pchelin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Elizaveta Kozliaeva
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Vladimir Pershin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Irina Mukhina
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
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Yang J, Yang M, Sheng G. Dysregulated lncRNAs are involved in the progress of myocardial infarction by constructing regulatory networks. Open Med (Wars) 2023; 18:20230657. [PMID: 36910851 PMCID: PMC9999115 DOI: 10.1515/med-2023-0657] [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: 09/25/2022] [Revised: 01/08/2023] [Accepted: 02/07/2023] [Indexed: 03/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes. However, the effect of all dysregulated lncRNAs in myocardial infarction (MI) is not clear. Whole transcriptome sequencing analysis was used to characterize the dynamic changes in lncRNA and mRNA expression. A gene network was constructed, and genes were classified into different modules using WGCNA. In addition, for all dysregulated lncRNAs, gene ontology analysis and cis-regulatory analysis were applied. The results demonstrated that a large number of the differentially co-expressed genes were primarily linked to the immune system process, inflammatory response, and innate immune response. The functional pathway analysis of the MEblue module included immune system process and apoptosis, and MEbrown included the T-cell receptor signal pathway by WGCNA. In addition, through cis-acting analysis of lncRNA regulation, the cis-regulated mRNAs were mainly enriched in immune system processes, innate immune responses, and VEGF signal pathways. We found that lncRNA regulation of mRNAs plays an important role in immune and inflammatory pathways. Our study provides a foundation to further understand the role and potential mechanism of dysregulated lncRNAs in the regulation of MI, in which many of them could be potential targets for MI.
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Affiliation(s)
- Jingqi Yang
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
| | - Ming Yang
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
| | - Guotai Sheng
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
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Wu S, Cheng C, Zhu W, Yang J, He BB, Li S, Wang X, Guo H, Chen D, Guo YM. Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation. Front Immunol 2023; 14:1152742. [PMID: 37081883 PMCID: PMC10110847 DOI: 10.3389/fimmu.2023.1152742] [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: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 04/22/2023] Open
Abstract
Introduction In most instances, liver transplantation (LT) is the only available treatment for end-stage liver diseases. However, LT could also induce serious liver diseases or injury, and the underlying mechanisms of LT-induced complications remain largely unknown, especially the mechanisms of the dysfunction of the immune system mediated by long noncoding RNAs (lncRNAs). Methods In this study, we globally analyzed the proportion of immune cells by using the transcriptome sequencing data (RNA-seq) of needle-core liver biopsies from pre- and post-transplantation recipients. Dysregulated lncRNAs were found to be correlated with the altered fractions of immune cells. We finally explored the potential targets of dysregulated lncRNAs and analyzed their functions in LT. Results We found that in the samples, some immune cells changed significantly after LT, including CD4 T cells, NK cells and mast cells. The proportion of macrophages in different polarization states also changed significantly, with M0 macrophages increasing and M2 macrophages decreasing. Through weighted gene co-expression network analysis (WGCNA), 7 gene expression modules related to LT were identified. These modules were related to changes in the proportion of different immune cells. The functions of these modules represent the response modes of different functional genes after LT. Among these modules, MEtan and MEyellow modules were primarily enriched in apoptosis and inflammatory pathways. Twelve immunity-related lncRNAs were identified for the first time, and the regulatory network co-changing with immune cells was also identified. The co-expressed genes of these lncRNAs were highly enriched in apoptosis-related pathways. Many apoptosis-related genes were found to be up-regulated after LT. Discussion In summary, we speculated that the expression and regulation of these apoptotic genes may be related to the changes in the proportion of immune cells. Some of these lncRNAs and apoptosis-related genes have been reported to be related to cell proliferation and apoptosis. They are also potential biomarkers or therapeutic targets.
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Affiliation(s)
- Shile Wu
- Soochow University, Suzhou, Jiangsu, China
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Chao Cheng
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, China
| | - Wenjun Zhu
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Jinyu Yang
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Bei-bei He
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Song Li
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Xinsheng Wang
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
| | - Hao Guo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, China
- *Correspondence: Ya-min Guo, ; Dong Chen,
| | - Ya-min Guo
- General Surgery Department, Qinghai Provincial People’s Hospital, Xining, Qinghai, China
- *Correspondence: Ya-min Guo, ; Dong Chen,
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22
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Cheng Y, Xu L, Wang J, Cao X, Chen D, Zhang P, Yang L, Qin L. Analysis of bulk RNA-seq data from sepsis patients reveals sepsis-associated lncRNAs and targeted cell death-related genes contributing to immune microenvironment regulation. Front Immunol 2023; 14:1026086. [PMID: 36817490 PMCID: PMC9932711 DOI: 10.3389/fimmu.2023.1026086] [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: 08/23/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Background Sepsis is a life-threatening organ dysfunction syndrome that leads to the massive death of immune cells. Long non-coding RNAs (lncRNAs) have been reported to exert key regulatory roles in cells. However, it is unclear how lncRNAs regulate the survival of immune cells in the occurrence and development of sepsis. Methods In this study, we used blood whole transcriptome sequencing data (RNA-seq) from normal controls (Hlty) and patients with uncomplicated infection (Inf1 P), sepsis (Seps P), and septic shock (Shock P), to investigate the fraction changes of immune cell types, expression pattern of cell death-related genes, as well as differentially expressed lncRNAs. Association network among these factors was constructed to screen out essential immune cell types, lncRNAs and their potential targets. Finally, the expression of lncRNAs and cell death genes in sepsis patients were validated by qRT-PCR. Results In this study, we found fifteen immune cell types showed significant fraction difference between Hlty and three patient groups. The expression pattern of cell death-related genes was also dysregulated in Hlty compared with patient groups. Co-expression network analysis identified a key turquoise module that was associated with the fraction changes of immune cells. We then identified differentially expressed lncRNAs and their potential targets that were tightly associated with the immune cell dysregulation in sepsis. Seven lncRNAs, including LINC00861, LINC01278, RARA-AS1, RP11-156P1.3, RP11-264B17.3, RP11-284N8.3 and XLOC_011309, as well as their co-expressed cell death genes, were finally identified, and we validated two lncRNAs (LINC00861 and LINC01278) and four mRNA targets using qRT-PCR in sepsis samples. Conclusion The global analysis of cell death-related genes in the occurrence and development of sepsis was carried out for the first time, and its expression regulation mode was displayed. The expression pattern of sepsis-associated lncRNAs were analyzed and identified, and the lncRNAs were significantly related to the change of immune cell proportion. We highlight the important roles of lncRNAs and their potential targets in the regulation of immune cell fraction changes during sepsis progression. The identified lncRNAs and their target genes may become new biomarkers and therapeutic targets of sepsis.
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Affiliation(s)
- Yanwei Cheng
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijun Xu
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Jiaoyang Wang
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xue Cao
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, China
| | - Peirong Zhang
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lei Yang
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijie Qin
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
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Lei L, Bai YH, Wang JP, Li YL. Association of the expression pattern and functions of long non-coding RNA with the progression of diabetic nephropathy. Asian J Surg 2022; 45:2752-2754. [PMID: 35718604 DOI: 10.1016/j.asjsur.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Lei Lei
- Department of Nephrology, The Second Hospital Affiliated to Kunming Medical University, Yunnan, 650101, China
| | - Yi-Hua Bai
- Department of Nephrology, The Second Hospital Affiliated to Kunming Medical University, Yunnan, 650101, China.
| | - Jia-Ping Wang
- Department of Radiology, The Second Hospital Affiliated to Kunming Medical University, Yunnan, 650101, China
| | - Ya-Ling Li
- Department of Nephrology, The Second Hospital Affiliated to Kunming Medical University, Yunnan, 650101, China
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Quan C, Li Y, Chen G, Tian X, Jia Z, Tu J, Shen J, Yi B, Fu T, Ma C, Dai C. The dynamics of lncRNAs transcription in interspecific F 1 allotriploid hybrids between Brassica species. Genomics 2022; 114:110505. [PMID: 36265744 DOI: 10.1016/j.ygeno.2022.110505] [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: 08/04/2022] [Revised: 10/05/2022] [Accepted: 10/15/2022] [Indexed: 01/15/2023]
Abstract
Interspecific hybridization is the intrinsic forces behind genome evolution. Long non-coding RNAs (lncRNAs) are important for plant biological processes regulation. However, it is unclear that these non-coding fractions are impacted by interspecific hybridization. Here we examined the profiles of lncRNAs by comparing them with coding genes in Brassica napus, three accessions of Brassica rapa, and their F1 hybrids. 6206 high-confidential lncRNAs were identified in F 1 hybrids and their parentals, and the lncRNAs transcriptome in the F1 hybrids was reprogrammed by the genome shock. Notably, genome-wide unbalanced of lncRNAs were observed between An and Ar subgenomes, ELD (Expression Level Dominance) was biased toward the An -genome in F1 hybrids, and ELD of non-conserved lncRNAs was more than conserved lncRNAs. Our findings demonstrate that the reprogramed lncRNAs acts as important role in enhancing plant plasticity, leading to the acquisition of desirable traits in polyploid Brassica species.
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Affiliation(s)
- Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuanyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Guoting Chen
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhibao Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Zheng J, Wang J, Qin X, Li K, Gao Q, Yang M, Liu H, Li S, Chang X, Sun Y. LncRNA HOTAIRM1 Involved in Nano NiO-Induced Pulmonary Fibrosis via Regulating PRKCB DNA Methylation-Mediated JNK/c-Jun Pathway. Toxicol Sci 2022; 190:64-78. [PMID: 36066426 DOI: 10.1093/toxsci/kfac092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nickel oxide nanoparticles (Nano NiO) lead to pulmonary fibrosis, and the mechanisms are associated with epigenetics. This study aimed to clarify the regulatory relationship among long noncoding RNA HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1), DNA methylation and expression of protein kinase C beta (PRKCB), and JNK/c-Jun pathway in Nano NiO-induced pulmonary fibrosis. Therefore, we constructed the rat pulmonary fibrosis model by intratracheal instillation of Nano NiO twice a week for 9 weeks and established the collagen deposition model by treating BEAS-2B cells with Nano NiO for 24 h. Here, the DNA methylation pattern was analyzed by whole-genome bisulfite sequencing in rat fibrotic lung tissues. Then, we integrated mRNA transcriptome data and found 93 DNA methylation genes with transcriptional significance. Meanwhile, the data showed that Nano NiO caused the down-regulation of lncRNA HOTAIRM1, the hypomethylation, and up-regulation of PRKCB2, JNK/c-Jun pathway activation, and collagen deposition (the up-regulated Col-I and α-SMA) both in vivo and in vitro. DNMTs inhibitor 5-AZDC attenuated Nano NiO-induced PRKCB2 expression, JNK/c-Jun pathway activation, and collagen deposition, but overexpression of PRKCB2 aggravated the changes mentioned indicators in Nano NiO-induced BEAS-2B cells. Furthermore, JNK/c-Jun pathway inhibitor (SP600125) alleviated Nano NiO-induced excessive collagen formation. Additionally, overexpression of HOTAIRM1 restrained the PRKCB hypomethylation, the activation of JNK/c-Jun pathway, and collagen formation induced by Nano NiO in BEAS-2B cells. In conclusion, these findings demonstrated that HOTAIRM1 could arrest Nano NiO-induced pulmonary fibrosis by suppressing the PRKCB DNA methylation-mediated JNK/c-Jun pathway.
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Affiliation(s)
- Jinfa Zheng
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jinyu Wang
- Institute of Anthropotomy and Histoembryology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xin Qin
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Kun Li
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qing Gao
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Mengmeng Yang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Han Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sheng Li
- Department of Public Health, The First People's Hospital of Lanzhou City, Lanzhou 730050, China
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
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Qi L, Li X, Liu SM, Jiao DL, Hu D, Ju XY, Zhao SY, Si SH, Hu L, Li GN, Ma BZ, Zhou S, Zhao C. Identification of a hippocampal lncRNA-regulating network in a natural aging rat model. BMC Neurosci 2022; 23:56. [PMID: 36171542 PMCID: PMC9520886 DOI: 10.1186/s12868-022-00743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/15/2022] [Indexed: 11/14/2022] Open
Abstract
Background Dysregulation of long noncoding RNA (lncRNA) expression is related to aging and age-associated neurodegenerative diseases, and the lncRNA expression profile in the aging hippocampus is not well characterized. In the present investigation, the changed mRNAs and lncRNAs were confirmed via deep RNA sequencing. GO and KEGG pathway analyses were conducted to investigate the principal roles of the clearly dysregulated mRNAs and lncRNAs. Subsequently, through the prediction of miRNAs via which mRNAs and lncRNAs bind together, a competitive endogenous RNA network was constructed. Results A total of 447 lncRNAs and 182 mRNAs were upregulated, and 385 lncRNAs and 144 mRNAs were downregulated. Real-time reverse transcription-polymerase chain reaction validated the reliability of mRNA and lncRNA sequencing. KEGG pathway and GO analyses revealed that differentially expressed (DE) mRNAs were associated with cell adhesion molecules (CAMs), the p53 signaling pathway (SP), phagosomes, PPAR SP and ECM—receptor interactions. KEGG pathway and GO analyses showed that the target genes of the DE lncRNAs were related to cellular senescence, the p53 signaling pathway, leukocyte transendothelial migration and tyrosine metabolism. Coexpression analyses showed that 561 DE lncRNAs were associated with DE mRNAs. A total of 58 lncRNA–miRNA–mRNA target pairs were confirmed in this lncRNA‒miRNA‒mRNA network, comprising 10 mRNAs, 13 miRNAs and 38 lncRNAs. Conclusions We found specific lncRNAs and mRNAs in the hippocampus of natural aging model rats, as well as abnormal regulatory ceRNA networks. Our outcomes help explain the pathogenesis of brain aging and provide direction for further research. Supplementary Information The online version contains supplementary material available at 10.1186/s12868-022-00743-7.
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Affiliation(s)
- Li Qi
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiao Li
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shi-Min Liu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dan-Li Jiao
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dan Hu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xin-Yao Ju
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shu-Yu Zhao
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Shu-Han Si
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Li Hu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guo-Na Li
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Bing-Zhe Ma
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shuang Zhou
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Chen Zhao
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Li M, Jiao L, Shao Y, Li H, Sun L, Yu Q, Gong M, Liu D, Wang Y, Xuan L, Yang X, Qu Y, Wang Y, Jiang L, Han J, Zhang Y, Zhang Y. LncRNA-ZFAS1 Promotes Myocardial Ischemia-Reperfusion Injury Through DNA Methylation-Mediated Notch1 Down-Regulation in Mice. JACC Basic Transl Sci 2022; 7:880-895. [PMID: 36317130 PMCID: PMC9617129 DOI: 10.1016/j.jacbts.2022.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022]
Abstract
The increase of ZFAS1 expression in MIRI is an important cause of cardiomyocyte apoptosis and ROS production. ZFAS1 can directly interact with the promoter region of Notch1, recruit DNMT3b to promote DNA methylation in the promoter region of Notch1, and trigger cardiomyocyte apoptosis and ROS production after MIRI. Nicotinamide mononucleotide has the potential to attenuate the apoptosis of cardiomyocytes after MIRI by competitively binding to DNMT3b and inhibiting the DNA methylation of Notch1.
The most devastating and catastrophic deterioration of myocardial ischemia-reperfusion injury (MIRI) is cardiomyocyte death. Here we aimed to evaluate the role of lncRNA-ZFAS1 in MIRI and delineate its mechanism of action. The level of lncRNA-ZFAS1 was elevated in MIRI hearts, and artificial knockdown of lncRNA-ZFAS1 in mice improved cardiac function. Notch1 is a potential target of lncRNA-ZFAS1, and lncRNA-ZFAS1 could bind to the promoter region of Notch1 and recruit DNMT3b to induce Notch1 methylation. Nicotinamide mononucleotide could promote the expression of Notch1 by competitively inhibiting the expression of DNMT3b and improving the apoptosis of cardiomyocytes and cardiac function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ying Zhang
- Address for correspondence: Dr Yong Zhang or Dr Ying Zhang, Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China.
| | - Yong Zhang
- Address for correspondence: Dr Yong Zhang or Dr Ying Zhang, Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China.
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Sex-Specific Expression of Non-Coding RNA Fragments in Frontal Cortex, Hippocampus and Cerebellum of Rats. EPIGENOMES 2022; 6:epigenomes6020011. [PMID: 35466186 PMCID: PMC9036230 DOI: 10.3390/epigenomes6020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Non-coding RNA fragments (ncRFs) are processed from various non-coding RNAs (ncRNAs), with the most abundant being those produced from tRNAs. ncRFs were reported in many animal and plant species. Many ncRFs exhibit tissue specificity or/and are affected by stress. There is, however, only a handful of reports that describe differential expression of ncRFs in the brain regions. In this work, we analyzed the abundance of ncRFs processed from four major ncRNAs, including tRNA (tRFs), snoRNA (snoRFs), snRNA (snRFs), and rRNA (rRFs) in the frontal cortex (FC), hippocampus (HIP), and cerebellum (CER) of male and female rats. We found brain-specific and sex-specific differences. Reads mapping to lincRNAs were significantly larger in CER as compared to HIP and CER, while those mapping to snRNAs and tRNA were smaller in HIP than in FC and CER. tRF reads were the most abundant among all ncRF reads, and FC had more reads than HIP and CER. Reads mapping to antisense ncRNAs were significantly larger in females than in males in FC. Additionally, males consistently had more tRF, snRF, and snoRF reads in all brain regions. rRFs were more abundant in males in FC and females in HIP. Several tRFs were significantly underrepresented, including tRF-ValCAC, tRF-ValACC, and tRF-LysCTT in all brain regions. We also found brain- and sex-specific differences in the number of brain function-related mRNA targets. To summarize, we found sex-specific differences in the expression of several ncRNA fragments in various brain regions of healthy rats.
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Abstract
Scales, as key structures of fish skin, play an important role in physiological function. The study of fish scale development mechanisms provides a basis for exploring the molecular-level developmental differences between scaled and non-scaled fishes. In this study, alizarin red staining was used to divide the different stages of zebrafish (Danio rerio) scale development. Four developmental stages, namely stage I (~17 dpf, scales have not started to grow), stage II (~33 dpf, the point at which scales start to grow), stage III (~41 dpf, the period in which the scales almost cover the whole body), and stage IV (~3 mpf, scales cover the whole body), were determined and used for subsequent transcriptome analysis. WGCNA (weighted correlation network analysis) and DEG (differentially expressed gene) analysis were used for screening the key genes. Based on the comparison between stage II and stage I, 54 hub-genes were identified by WGCNA analysis. Key genes including the Scpp family (Scpp7, Scpp6, Scpp5, and Scpp8), the Fgf family (Fgfr1b and Fgfr3), Tcf7, Wnt10b, Runx2b, and Il2rb were identified by DEG analysis, which indicated that these genes played important roles in the key nodes of scale development signal pathways. Combined with this analysis, the TGF-β, Wnt/β-catenin, and FGF signaling pathways were suggested to be the most important signal pathways for scales starting to grow. This study laid a foundation for exploring the scale development mechanism of other fishes. The scale development candidate genes identified in the current study will facilitate functional gene identifications in the future.
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Sui B, Zhao J, Zheng J, Zhou M, Chen H, Fu ZF, Zhao L. lncRNA EDAL restricts rabies lyssavirus replication in a cell-specific and infection route-dependent manner. J Gen Virol 2022; 103. [PMID: 35234607 DOI: 10.1099/jgv.0.001725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rabies, caused by rabies lyssavirus (RABV), is a fatal disease among humans and almost all warm-blooded animals. Our previous study showed that the long non-coding RNA (lncRNA) EZH2 degradation-associated lncRNA (EDAL) effectively inhibits RABV infection both in vitro and in vivo by degrading EZH2 and promoting the transcription of an antiviral gene, Pcp4l1. Herein, we found that recombinant RABV expressing EDAL (rRABV-EDAL) restricts RABV replication in primary granule neurons but not in primary cortical neurons or astrocytes. Further study revealed that EDAL induced EZH2 protein degradation and thereby decreased trimethylation of lysine 27 on the histone 3 (H3K27me3) level in granule neuron cells but not in cortical neurons or astrocytes. Furthermore, rRABV-EDAL infection induces more Pcp4l1 mRNA transcription in granule neurons, while there are almost no obvious changes in cortical neurons or astrocytes. Consistently, compared with the parent virus RABV, reduced pathogenicity of rRABV-EDAL was observed in mice post-intranasal infection but not intramuscular infection. These results suggest that the lncRNA EDAL restricts RABV replication in a cell-specific and infection route-dependent manner.
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Affiliation(s)
- Baokun Sui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Juanjuan Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jiaxin Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ming Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
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Okabe M, Takarada S, Miyao N, Nakaoka H, Ibuki K, Ozawa S, Watanabe K, Tsuji H, Hashimoto I, Hatasaki K, Hayakawa S, Hamaguchi Y, Hamada M, Ichida F, Hirono K. G0S2 regulates innate immunity in Kawasaki disease via lncRNA HSD11B1-AS1. Pediatr Res 2022; 92:378-387. [PMID: 35292727 PMCID: PMC8922062 DOI: 10.1038/s41390-022-01999-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 11/23/2021] [Accepted: 02/02/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Kawasaki disease (KD) is a systemic vasculitis that is currently the most common cause of acquired heart disease in children. However, its etiology remains unknown. Long non-coding RNAs (lncRNAs) contribute to the pathophysiology of various diseases. Few studies have reported the role of lncRNAs in KD inflammation; thus, we investigated the role of lncRNA in KD inflammation. METHODS A total of 50 patients with KD (median age, 19 months; 29 males and 21 females) were enrolled. We conducted cap analysis gene expression sequencing to determine differentially expressed genes in monocytes of the peripheral blood of the subjects. RESULTS About 21 candidate lncRNA transcripts were identified. The analyses of transcriptome and gene ontology revealed that the immune system was involved in KD. Among these genes, G0/G1 switch gene 2 (G0S2) and its antisense lncRNA, HSD11B1-AS1, were upregulated during the acute phase of KD (P < 0.0001 and <0.0001, respectively). Moreover, G0S2 increased when lipopolysaccharides induced inflammation in THP-1 monocytes, and silencing of G0S2 suppressed the expression of HSD11B1-AS1 and tumor necrosis factor-α. CONCLUSIONS This study uncovered the crucial role of lncRNAs in innate immunity in acute KD. LncRNA may be a novel target for the diagnosis of KD. IMPACT This study revealed the whole aspect of the gene expression profile of monocytes of patients with Kawasaki disease (KD) using cap analysis gene expression sequencing and identified KD-specific molecules: G0/G1 switch gene 2 (G0S2) and long non-coding RNA (lncRNA) HSD11B1-AS1. We demonstrated that G0S2 and its antisense HSD11B1-AS1 were associated with inflammation of innate immunity in KD. lncRNA may be a novel key target for the diagnosis of patients with KD.
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Affiliation(s)
- Mako Okabe
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Shinya Takarada
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Nariaki Miyao
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Hideyuki Nakaoka
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Keijiro Ibuki
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Sayaka Ozawa
- grid.267346.20000 0001 2171 836XDepartment of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan
| | | | - Harue Tsuji
- Department of Pediatrics, Takaoka City Hospital, Toyama, Japan
| | - Ikuo Hashimoto
- grid.417233.00000 0004 1764 0741Department of Pediatrics, Toyama City Hospital, Toyama, Japan
| | - Kiyoshi Hatasaki
- Department of Pediatrics, Toyama Prefectural Hospital, Toyama, Japan
| | - Shotaro Hayakawa
- grid.5290.e0000 0004 1936 9975Department of Electrical Engineering and Bioscience, Waseda University, Tokyo, Japan
| | - Yu Hamaguchi
- grid.5290.e0000 0004 1936 9975Department of Electrical Engineering and Bioscience, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- grid.5290.e0000 0004 1936 9975Department of Electrical Engineering and Bioscience, Waseda University, Tokyo, Japan
| | - Fukiko Ichida
- grid.411731.10000 0004 0531 3030Department of Pediatrics, International University of Health and Welfare, Tokyo, Japan
| | - Keiichi Hirono
- Department of Pediatrics, Faculty of Medicine, University of Toyama, Toyama, Japan.
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32
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Construction and analysis of mRNA, lncRNA, and transcription factor regulatory networks after retinal ganglion cell injury. Exp Eye Res 2021; 215:108915. [PMID: 34971620 DOI: 10.1016/j.exer.2021.108915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/11/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Retinal ganglion cell (RGC) injury is a critical pathological feature of several optic neurodegenerative diseases. The regulatory mechanisms underlying RGC injury remain poorly understood. Recent evidence has highlighted the important roles of long noncoding RNAs (lncRNAs) in degenerative neuropathy but few studies have focused on lncRNAs associated with RGC injury. In this study, we analyzed dysregulated lncRNAs associated with RGC injury, their potential regulatory functions, and the molecular mechanisms underlying the regulation of lncRNAs and transcription factors (TFs). We analyzed lncRNA and mRNA profiles in the GSE142881 dataset associated with RGC injury and identified 1049 differentially expressed genes (DEGs), with 18 differentially expressed (DE) TFs among 883 DE mRNAs and 312 DE lncRNAs. The predicted DE lncRNAs and DE mRNAs were used to construct a lncRNA-mRNA co-expression network. Functional enrichment analysis was performed to explore the functions of the lncRNAs and mRNAs. The co-expression network between DE lncRNAs and DE mRNAs was highly enriched in inflammatory and immune-related pathways, indicating that they play role in the process of RGC injury. Among the DE mRNAs, we screened 18 DE TFs, including activating transcription factor 3 (ATF3), associated with RGC injury. Co-expression analysis predicted that 13 lncRNAs were potential binding targets of ATF3. The screening of the potential targets of these 13 lncRNAs showed that they were also significantly enriched in functional pathways associated with inflammation and apoptosis. After analysis, we constructed the mRNA-ATF3-lncRNA regulatory network after RGCs injury. In summary, we identified the gene module associated with immune and inflammatory responses after optic nerve injury and constructed a regulatory network of lncRNA-TF-mRNA. The results indicate that lncRNAs, by binding to TFs, can regulate downstream genes and function during RGC injury. The results provide a foundation for further studies of the mechanism of RGC injury and provide insight into the clinical diagnosis and investigation direction of neurodegenerative diseases such as traumatic optic neuropathy and glaucoma.
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33
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Irwin AB, Bahabry R, Lubin FD. A putative role for lncRNAs in epigenetic regulation of memory. Neurochem Int 2021; 150:105184. [PMID: 34530054 PMCID: PMC8552959 DOI: 10.1016/j.neuint.2021.105184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
The central dogma of molecular genetics is defined as encoded genetic information within DNA, transcribed into messenger RNA, which contain the instructions for protein synthesis, thus imparting cellular functionality and ultimately life. This molecular genetic theory has given birth to the field of neuroepigenetics, and it is now well established that epigenetic regulation of gene transcription is critical to the learning and memory process. In this review, we address a potential role for a relatively new player in the field of epigenetic crosstalk - long non-coding RNAs (lncRNAs). First, we briefly summarize epigenetic mechanisms in memory formation and examine what little is known about the emerging role of lncRNAs during this process. We then focus discussions on how lncRNAs interact with epigenetic mechanisms to control transcriptional programs under various conditions in the brain, and how this may be applied to regulation of gene expression necessary for memory formation. Next, we explore how epigenetic crosstalk in turn serves to regulate expression of various individual lncRNAs themselves. To highlight the importance of further exploring the role of lncRNA in epigenetic regulation of gene expression, we consider the significant relationship between lncRNA dysregulation and declining memory reserve with aging, Alzheimer's disease, and epilepsy, as well as the promise of novel therapeutic interventions. Finally, we conclude with a discussion of the critical questions that remain to be answered regarding a role for lncRNA in memory.
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Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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34
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Fang Y, Yang Y, Zhang X, Li N, Yuan B, Jin L, Bao S, Li M, Zhao D, Li L, Zeng Z, Huang H. A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma. Front Oncol 2021; 11:745166. [PMID: 34532296 PMCID: PMC8438305 DOI: 10.3389/fonc.2021.745166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background The mechanistic basis for relapsed hepatocellular carcinoma (HCC) remains poorly understood. Recent research has highlighted the important roles of long non-coding RNAs (lncRNAs) in HCC. However, there are only a few studies on the association between lncRNAs and HCC relapse. Methods Differentially expressed lncRNAs and mRNAs between a primary HCC group and relapsed HCC group were identified using the edge R package to analyze the GSE101432 dataset. The differentially expressed lncRNAs and mRNAs were used to construct a lncRNA–mRNA co-expression network. Weighted gene co-expression network analysis followed by Gene Ontology (GO) enrichment analyses were conducted on the database. Furthermore, correlation and survival analyses were performed using The Cancer Genome Atlas database, and expression in the clinical samples was verified by qRT-PCR. Thereafter, we inputted the genes from the two groups into the HCC TNM stage and tumor grade database from TCGA. Finally, we performed Kaplan–Meier survival analysis on the lncRNAs related to relapsed HCC. Results In this study, lncRNAs and mRNAs associated with HCC relapse were identified. Two gene modules were found to be closely linked to this. The GO terms in the yellow and black modules were related to cell proliferation, differentiation, and survival, as well as some transcription-related biological processes. Through qRT-PCR, we found that the expression levels of LINC00941 and LINC00668 in relapsed HCC were higher than those in primary HCC. Further, mRNA levels of LOX, OTX1, MICB, NDUFA4L2, BAIAP2L2, and KCTD17 were changed in relapsed HCC compared to levels in primary HCC. In addition, we verified that these genes could predict the overall survival and recurrence-free survival of HCC. Moreover, we found that LINC00668 and LINC00941 could affect tumor grade and TNM stages. In total, we identified and validated two lncRNAs (LINC00941 and LINC00668) and six mRNAs (LOX, MICB, OTX1, BAIAP2L2, KCTD17, NDUFA4L2) associated with HCC relapse. Conclusion In summary, we identified the key gene modules and central genes associated with relapsed HCC and constructed lncRNA–mRNA networks related to this. These genes are likely to have potential prognostic value for relapsed HCC and might shed new light on novel biomarkers or diagnostic targets for relapsed HCC.
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Affiliation(s)
- Yuan Fang
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yang Yang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - XiaoLi Zhang
- Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Na Li
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Bo Yuan
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Jin
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Sheng Bao
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - MengGe Li
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Zhao
- Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - LingRui Li
- School of Automation Science and Engineering, South China University of Technology, Guangzhou, China
| | - Zhong Zeng
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - HanFei Huang
- Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
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35
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Cheng Y, Cao X, Zhang J, Chen D, Zhu J, Xu L, Qin L. Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells. Front Pharmacol 2021; 12:678256. [PMID: 34483898 PMCID: PMC8416166 DOI: 10.3389/fphar.2021.678256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Sepsis is a highly heterogeneous syndrome that is caused by an unbalanced host response to an infection. Long noncoding RNAs (lncRNAs) have been reported to exert regulatory roles in a variety of biological processes, and became potential biomarkers and therapeutic targets for diverse diseases. However, current understanding on the roles of lncRNAs in sepsis is extremely limited. Herein, to decipher the underlying functions of lncRNAs, we reexplored the 83 transcriptome datasets from specimens with sepsis, no_sepsis by final diagnosis, and control. The results of differentially expressed genes (DEGs), differentially expressed lncRNA (DElncRNA) analysis, and co-expression analysis of lncRNA–mRNA pairs were obtained. We found that the expression pattern of lncRNAs was significantly activated in sepsis specimens, which was clearly distinguished in sepsis from no_sepsis and control specimens. By performing co-expression analysis, we found DElncRNAs were closely related to T-cell activation and immune response–related terms in sepsis by regulating mRNA expression in the trans manner. The lncRNA–mRNA network and the qRT-PCR test revealed that lncRNAs LINC00861, RP11-284N8.3, and CTB-61M7.2 were significantly correlated with the pathogenesis of sepsis. In addition, weighted gene co-expression analysis (WGCNA) and cis-regulation analysis also revealed sepsis-specific lncRNAs were highly associated with important biological processes correlated with sepsis. In summary, the systematic dysregulation of lncRNAs is tightly involved in the remodeling of gene expression regulatory network in sepsis, and the lncRNA–mRNA expression network may be used to refine biomarker predictions for developing novel therapeutic approaches in sepsis.
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Affiliation(s)
- Yanwei Cheng
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xue Cao
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Jiange Zhang
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China
| | - Juan Zhu
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijun Xu
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijie Qin
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
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Shen T, Xia W, Min S, Yang Z, Cheng L, Wang W, Zhan Q, Shao F, Zhang X, Wang Z, Zhang Y, Shen G, Zhang H, Wu LL, Yu GY, Kong QP, Wang X. A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression. BMC Biol 2021; 19:192. [PMID: 34493285 PMCID: PMC8422755 DOI: 10.1186/s12915-021-01112-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are important regulators in tumor progression. However, their biological functions and underlying mechanisms in hypoxia adaptation remain largely unclear. Results Here, we established a correlation between a Chr3q29-derived lncRNA gene and tongue squamous carcinoma (TSCC) by genome-wide analyses. Using RACE, we determined that two novel variants of this lncRNA gene are generated in TSCC, namely LINC00887_TSCC_short (887S) and LINC00887_TSCC_long (887L). RNA-sequencing in 887S or 887L loss-of-function cells identified their common downstream target as Carbonic Anhydrase IX (CA9), a gene known to be upregulated by hypoxia during tumor progression. Mechanistically, our results showed that the hypoxia-augmented 887S and constitutively expressed 887L functioned in opposite directions on tumor progression through the common target CA9. Upon normoxia, 887S and 887L interacted. Upon hypoxia, the two variants were separated. Each RNA recognized and bound to their responsive DNA cis-acting elements on CA9 promoter: 887L activated CA9’s transcription through recruiting HIF1α, while 887S suppressed CA9 through DNMT1-mediated DNA methylation. Conclusions We provided hypoxia-permitted functions of two antagonistic lncRNA variants to fine control the hypoxia adaptation through CA9. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01112-2.
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Affiliation(s)
- Tao Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Wangxiao Xia
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China
| | - Sainan Min
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Zixuan Yang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Lehua Cheng
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China
| | - Wei Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Qianxi Zhan
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Fanghong Shao
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Xuehan Zhang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Zhiyu Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, China
| | - Yan Zhang
- School of Health Services Management, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Guodong Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China
| | - Huafeng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, 100191, China
| | - Guang-Yan Yu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China. .,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
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Wang F, Wang Q, Liu B, Mei L, Ma S, Wang S, Wang R, Zhang Y, Niu C, Xiong Z, Zheng Y, Zhang Z, Shi J, Song X. The long noncoding RNA Synage regulates synapse stability and neuronal function in the cerebellum. Cell Death Differ 2021; 28:2634-2650. [PMID: 33762741 PMCID: PMC8408218 DOI: 10.1038/s41418-021-00774-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
The brain is known to express many long noncoding RNAs (lncRNAs); however, whether and how these lncRNAs function in modulating synaptic stability remains unclear. Here, we report a cerebellum highly expressed lncRNA, Synage, regulating synaptic stability via at least two mechanisms. One is through the function of Synage as a sponge for the microRNA miR-325-3p, to regulate expression of the known cerebellar synapse organizer Cbln1. The other function is to serve as a scaffold for organizing the assembly of the LRP1-HSP90AA1-PSD-95 complex in PF-PC synapses. Although somewhat divergent in its mature mRNA sequence, the locus encoding Synage is positioned adjacent to the Cbln1 loci in mouse, rhesus macaque, and human, and Synage is highly expressed in the cerebella of all three species. Synage deletion causes a full-spectrum cerebellar ablation phenotype that proceeds from cerebellar atrophy, through neuron loss, on to synapse density reduction, synaptic vesicle loss, and finally to a reduction in synaptic activity during cerebellar development; these deficits are accompanied by motor dysfunction in adult mice, which can be rescued by AAV-mediated Synage overexpression from birth. Thus, our study demonstrates roles for the lncRNA Synage in regulating synaptic stability and function during cerebellar development.
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Affiliation(s)
- Fei Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Qianqian Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Baowei Liu
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Lisheng Mei
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Sisi Ma
- grid.506261.60000 0001 0706 7839National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS and PUMC, Beijing, China
| | - Shujuan Wang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Ruoyu Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China ,grid.240145.60000 0001 2291 4776Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX USA
| | - Yan Zhang
- grid.59053.3a0000000121679639Stroke Center & Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Chaoshi Niu
- grid.59053.3a0000000121679639Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Zhiqi Xiong
- grid.9227.e0000000119573309Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yong Zheng
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhi Zhang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Juan Shi
- grid.506261.60000 0001 0706 7839National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS and PUMC, Beijing, China
| | - Xiaoyuan Song
- grid.59053.3a0000000121679639MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. Genes (Basel) 2021; 12:genes12091374. [PMID: 34573356 PMCID: PMC8467702 DOI: 10.3390/genes12091374] [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: 07/14/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (nhigh = 3, nlow = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.
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Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021; 9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic development depends on a highly coordinated shift in transcription programs known as the maternal-to-zygotic transition (MZT). It remains unclear how haploid and diploid embryo coordinate their genomic activation and embryonic development during MZT in haplodiploid animals. Here, we applied a single-embryo RNA-seq approach to characterize the embryonic transcriptome dynamics in haploid males vs. diploid females of the haplodiploid insect honeybee (Apis mellifera). We observed typical zygotic genome activation (ZGA) occurred in three major waves specifically in female honeybee embryos; haploid genome activation was much weaker and occurred later. Strikingly, we also observed three waves of transcriptional activation for thousands of long non-coding transcripts (lncRNA), 73% of which are transcribed from intronic regions and 65% were specific to female honeybee embryos. These findings support a model in which introns encode thousands of lncRNAs that are expressed in a diploid-embryo-specific and ZGA-triggered manner that may have potential functions to regulate gene expression during early embryonic development in the haplodiploid insect honeybee.
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Affiliation(s)
- Miao Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Liuwei Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Yu Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Qingsheng Niu
- Department of Scientific Research, Jilin Province Institute of Apicultural Science, Jilin, China
| | - Shuai Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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40
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Wang A, Shu X, Jing X, Jiao C, Chen L, Zhang J, Ma L, Jiang Y, Yamamoto N, Li S, Deng Q, Wang S, Zhu J, Liang Y, Zou T, Liu H, Wang L, Huang Y, Li P, Zheng A. Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1553-1566. [PMID: 33600077 PMCID: PMC8384605 DOI: 10.1111/pbi.13569] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 02/02/2021] [Accepted: 02/12/2021] [Indexed: 05/05/2023]
Abstract
Rice sheath blight (RSB) is an economically significant disease affecting rice yield worldwide. Genetic resistance to RSB is associated with multiple minor genes, with each providing a minor phenotypic effect, but the underlying dominant resistance genes remain unknown. A genome-wide association study (GWAS) of 259 diverse rice varieties, with genotypes based on a single nucleotide polymorphism (SNP) and haplotype, was conducted to assess their sheath blight reactions at three developmental stages (seedlings, tillering and booting). A total of 653 genes were correlated with sheath blight resistance, of which the disease resistance protein RPM1 (OsRSR1) and protein kinase domain-containing protein (OsRLCK5) were validated by overexpression and knockdown assays. We further found that the coiled-coil (CC) domain of OsRSR1 (OsRSR1-CC) and full-length OsRLCK5 interacted with serine hydroxymethyltransferase 1 (OsSHM1) and glutaredoxin (OsGRX20), respectively. It was found that OsSHM1, which has a role in the reactive oxygen species (ROS) burst, and OsGRX20 enhanced the antioxidation ability of plants. A regulation model of the new RSB resistance though the glutathione (GSH)-ascorbic acid (AsA) antioxidant system was therefore revealed. These results enhance our understanding of RSB resistance mechanisms and provide better gene resources for the breeding of disease resistance in rice.
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Affiliation(s)
- Aijun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Xinyue Shu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Xin Jing
- Novogene Bioinformatics InstituteBeijingChina
| | | | - Lei Chen
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Jinfeng Zhang
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Li Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Yuqi Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Naoki Yamamoto
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Qiming Deng
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Shiquan Wang
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Jun Zhu
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Yueyang Liang
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Huainian Liu
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Lingxia Wang
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
| | - Yubi Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
| | - Ping Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
| | - Aiping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaChengduChina
- Rice Research Institute of Sichuan Agricultural UniversityChengduChina
- Key laboratory of Sichuan Crop Major DiseaseSichuan Agricultural UniversityChengduChina
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41
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LncRNA-AC006129.1 reactivates a SOCS3-mediated anti-inflammatory response through DNA methylation-mediated CIC downregulation in schizophrenia. Mol Psychiatry 2021; 26:4511-4528. [PMID: 32015466 DOI: 10.1038/s41380-020-0662-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/10/2019] [Accepted: 01/23/2020] [Indexed: 01/11/2023]
Abstract
Schizophrenia is a complex genetic disorder, the non-Mendelian features of which are likely complicated by epigenetic factors yet to be elucidated. Here, we performed RNA sequencing of peripheral blood RNA from monozygotic twins discordant for schizophrenia, and identified a schizophrenia-associated upregulated long noncoding RNA (lncRNA, AC006129.1) that participates in the inflammatory response by enhancing SOCS3 and CASP1 expression in schizophrenia patients and further validated this finding in AC006129.1-overexpressing mice showing schizophrenia-related abnormal behaviors. We find that AC006129.1 binds to the promoter region of the transcriptional repressor Capicua (CIC), facilitates the interactions of DNA methyltransferases with the CIC promoter, and promotes DNA methylation-mediated CIC downregulation, thereby ameliorating CIC-induced SOCS3 and CASP1 repression. Derepression of SOCS3 enhances the anti-inflammatory response by inhibiting JAK/STAT-signaling activation. Our findings reveal an epigenetic mechanism with etiological and therapeutic implications for schizophrenia.
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42
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You Y, Zhao X, Wu Y, Mao J, Ge L, Guo J, Zhao C, Chen D, Song Z. Integrated Transcriptome Profiling Revealed That Elevated Long Non-Coding RNA- AC007278.2 Expression Repressed CCR7 Transcription in Systemic Lupus Erythematosus. Front Immunol 2021; 12:615859. [PMID: 34220794 PMCID: PMC8242351 DOI: 10.3389/fimmu.2021.615859] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose Systemic lupus erythematosus (SLE) is a serious autoimmune disease. Its molecular pathogenesis, especially the long non-coding RNA (lncRNA) function, remains unclear. We want to investigate the lncRNA dysregulation profile and their molecular mechanisms in SLE. Methods In this study, we analyzed the transcriptome profiles (RNA-seq) of peripheral blood mononuclear cells (PBMCs) from SLE patients and two published transcriptome datasets to explore lncRNA profiles. The differentially expressed lncRNAs were confirmed by quantitative real-time PCR in another set of female patients. We constructed the lncRNA-mRNA regulatory networks by performing weighted gene co-expression network analysis (WGCNA). Dysregulated lncRNA AC007278.2 was repressed by short hairpin RNA (shRNA) in Jurkat cells. Dual-luciferase reporter gene assay was performed to investigate the regulatory mechanism of AC007278.2 on target gene CCR7. Results We observed dominant up-regulation of transcripts, including mRNAs and lncRNAs, in SLE patients. By WGCNA method, we identified three modules that were highly related to SLE. We then focused on one lncRNA, AC007278.2, with a T-helper 1 lineage-specific expression pattern. We observed consistently higher AC007278.2 expression in SLE patients. Co-expression network revealed that AC007278.2 participated in the innate immune response and inflammatory bowel disease pathways. By knocking down AC007278.2 expression, we found that AC007278.2 could regulate the expression of inflammatory and cytokine stimulus response-related genes, including CCR7, AZU1, and TNIP3. AC007278.2 inhibits the functional CCR7 promoter to repress its transcription, thereby regulating autoimmunity and follicular T-helper cell differentiation. Conclusion In summary, our study indicated the important regulatory role of lncRNAs in SLE. AC007278.2 may be treated as a novel biomarker for SLE diagnosis and treatment.
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Affiliation(s)
- Yi You
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yaguang Wu
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jiangming Mao
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Lan Ge
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Junkai Guo
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chenglei Zhao
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Wuhan, China.,Science Department, ABLife BioBigData Institute, Wuhan, China
| | - Zhiqiang Song
- Department of Dermatology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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43
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Long noncoding RNA PM maintains cerebellar synaptic integrity and Cbln1 activation via Pax6/Mll1-mediated H3K4me3. PLoS Biol 2021; 19:e3001297. [PMID: 34111112 PMCID: PMC8219131 DOI: 10.1371/journal.pbio.3001297] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/22/2021] [Accepted: 05/24/2021] [Indexed: 01/30/2023] Open
Abstract
Recent studies have shown that long noncoding RNAs (lncRNAs) are critical regulators in the central nervous system (CNS). However, their roles in the cerebellum are currently unclear. In this work, we identified the isoform 204 of lncRNA Gm2694 (designated as lncRNA-Promoting Methylation (lncRNA-PM)) is highly expressed in the cerebellum and derived from the antisense strand of the upstream region of Cerebellin-1 (Cbln1), a well-known critical cerebellar synaptic organizer. LncRNA-PM exhibits similar spatiotemporal expression pattern as Cbln1 in the postnatal mouse cerebellum and activates the transcription of Cbln1 through Pax6/Mll1-mediated H3K4me3. In mouse cerebellum, lncRNA-PM, Pax6/Mll1, and H3K4me3 are all associated with the regulatory regions of Cbln1. Knockdown of lncRNA-PM in cerebellum causes deficiencies in Cbln1 expression, cerebellar synaptic integrity, and motor function. Together, our work reveals an lncRNA-mediated transcriptional activation of Cbln1 through Pax6-Mll1-H3K4me3 and provides novel insights of the essential roles of lncRNA in the cerebellum. The long non-coding RNA lncRNA-PM activates transcription of the cerebellar synaptic organizer Cbln1 by promoting Pax6-Mll1-mediated H3K4me3 methylation, thereby helping to maintain cerebellar synaptic integrity and motor function.
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Li Y, Shen QS, Peng Q, Ding W, Zhang J, Zhong X, An NA, Ji M, Zhou WZ, Li CY. Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. Brief Bioinform 2021; 22:6273384. [PMID: 33973996 PMCID: PMC8574621 DOI: 10.1093/bib/bbab157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/22/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022] Open
Abstract
Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human–macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.
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Affiliation(s)
- Yumei Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Xiaoming Zhong
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
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Pan Y, Lin S, Zhang W. Epigenetic effects of silver nanoparticles and ionic silver in Tetrahymena thermophila. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144659. [PMID: 33736311 DOI: 10.1016/j.scitotenv.2020.144659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/08/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
The widespread use of silver nanoparticles (Ag NPs) has raised substantial health risks, but little is known about the epigenetic toxicity induced by Ag+ and Ag NPs. This study characterized physiological and lncRNA profiles to explore the toxic effects and epigenetic mechanisms in Tetrahymena thermophila on exposure to Ag+ (in the form of AgNO3) and different Ag NPs for 24 h. The Ag NPs studied varied in size (10 nm and 80 nm) and surface coating (citrate and polyvinylpyrrolidone). We found that both Ag+ and Ag NPs elicited strong growth-inhibiting effects on T. thermophila. The toxicity was mainly caused by high reactive oxygen species (ROS) levels, leading to lipid peroxidation and mitochondrial dysfunction. To combat the oxidative stress, the protist activated an antioxidative response, increasing the activity of glutathione peroxidase and other antioxidants. Notably, 1250 lncRNAs were differentially expressed under Ag+ or Ag NPs exposure relative to the non-exposure control, which were clustered into 15 expression modules in weighted gene co-expression network analysis. These gene modules exhibited toxicant-specific expression patterns, potentially playing regulatory roles, via their co-expressed mRNAs, to inhibit cell growth, activate cell membrane cation channel, and promote oxidoreductase activity. This research illuminates how post-transcriptional mechanisms of a ciliated protozoan regulate responses to Ag+ and Ag NPs toxicities.
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Affiliation(s)
- Yongbo Pan
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, and College of Ocean & Earth Sciences, Xiamen University, Xiamen 361005, China; Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361005, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, and College of Ocean & Earth Sciences, Xiamen University, Xiamen 361005, China; Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361005, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Wenjing Zhang
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, and College of Ocean & Earth Sciences, Xiamen University, Xiamen 361005, China; Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361005, China.
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46
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Wen D, Liu WL, Lu ZW, Cao YM, Ji QH, Wei WJ. SNHG9, a Papillary Thyroid Cancer Cell Exosome-Enriched lncRNA, Inhibits Cell Autophagy and Promotes Cell Apoptosis of Normal Thyroid Epithelial Cell Nthy-ori-3 Through YBOX3/P21 Pathway. Front Oncol 2021; 11:647034. [PMID: 34017682 PMCID: PMC8129558 DOI: 10.3389/fonc.2021.647034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/13/2021] [Indexed: 12/13/2022] Open
Abstract
Thyroid cancer is the most common type of endocrine malignancy. Although the general prognosis is good, the treatment of advanced disease is still challenging. Exosomes are vesicle units containing specific components that transmit information between cells. In order to explore its role in papillary thyroid cancer (PTC), our study screened exosome enriched lncRNA SNHG9 by lncRNA chip and explored its biological function. We used lncRNA chips combined with bioinformatics analysis to screen lncRNA SNHG9 enriched in exosomes. GO analysis suggested its relationship with autophagy and apoptosis. Quantitative PCR showed SNHG9 was highly expressed in PTC cells and exosomes and its correlation with PTC tumor size was analyzed by clinical characteristics. SNHG9 could inhibit the protective cell autophagy induced by starvation of human normal thyroid epithelial cell line Nthy-ori-3 and promote its apoptosis through PTC cell exosomes. RNA-pull down combined with protein spectrum showed that SNHG9 could interact with YBOX3. Western blot and RNA immunoprecipitation further confirmed their interaction. Western blot showed that SNHG9 could induce degradation of YBOX3, thus interfering with the stability of P21 mRNA and inducing cell apoptosis. In conclusion, our study identified SNHG9 as a PTC cell exosome-enriched lncRNA. SNHG9 could inhibit cell autophagy and promote apoptosis of Nthy-ori-3 cell through YBOX3/P21 pathway.
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Affiliation(s)
- Duo Wen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wan-Lin Liu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhong-Wu Lu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Ming Cao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing-Hai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Jun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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47
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Xu K, Zhang Y, Li J. Expression and function of circular RNAs in the mammalian brain. Cell Mol Life Sci 2021; 78:4189-4200. [PMID: 33558994 PMCID: PMC11071837 DOI: 10.1007/s00018-021-03780-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/07/2021] [Accepted: 01/27/2021] [Indexed: 01/19/2023]
Abstract
Mammalian brain presents extraordinary complexity reflected in the structure, function, and dynamic changes in the biological and physiological processes of development, maturity, and aging. Recent transcriptomic profiles from the brain tissues of distinct species have described a novel class of transcripts with a covalently closed-loop structure, called circular RNAs (circRNAs), which are produced by alternative back-splicing and derived from genes associated with synaptogenesis and neural activities. Brain is a tightly regulated and largely unexplored organ where circRNAs are highly enriched and expressed in the cell type-, spatiotemporal-specific, sex-biased, and age-related manner. Although the biological functions of most of the circRNAs in the brain remain elusive, increased evidence suggests that dynamic changes in circRNA expression are critical for brain function and the maintenance of physiological homeostasis in the brain. Here, we review the latest immense progresses in the understanding of circRNA expression and function in the mammalian brain. We also discuss possibly biological functions of circRNAs in the brain, which may provide new sights of understanding brain development and aging, as well as the pathogenesis of mental diseases.
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Affiliation(s)
- Kaiyu Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ying Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- National Institute on Drug Dependence, Peking University, Beijing, China.
- PKU/McGovern Institute for Brain Research, Peking University, Beijing, China.
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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48
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Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis. Animals (Basel) 2021; 11:ani11051268. [PMID: 33924848 PMCID: PMC8145500 DOI: 10.3390/ani11051268] [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: 03/17/2021] [Revised: 04/10/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs' quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.
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Pei W, Fu L, Li SQ, Yu Y. Brain transcriptomics of nonhuman primates: A review. Neurosci Lett 2021; 753:135872. [PMID: 33812931 DOI: 10.1016/j.neulet.2021.135872] [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: 02/25/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/12/2022]
Abstract
The brain is one of the most important and intricate organs in our bodies. Interpreting brain function and illustrating the changes and molecular mechanisms during physiological or pathological processes are essential but sometimes difficult to achieve. In addition to histology, ethology and pharmacology, the development of transcriptomics alleviates this condition by enabling high-throughput observation of the brain at various levels of anatomical specificity. Moreover, because human brain samples are scarce, the brains of nonhuman primates are important alternative models. Here in this review, we summarize the applications of transcriptomics in nonhuman primate brain studies, including investigations of brain development, aging, toxic effects and diseases. Overall, as a powerful tool with developmental potential, transcriptomics has been widely utilized in neuroscience.
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Affiliation(s)
- Wendi Pei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China
| | - Lin Fu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China
| | - Shui-Qing Li
- Department of Pain, Peking University Third Hospital, Beijing, 100191, China.
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191, China; Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191, China.
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50
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Bo D, Jiang X, Liu G, Hu R, Chong Y. RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats. Animals (Basel) 2021; 11:ani11030625. [PMID: 33653002 PMCID: PMC7996862 DOI: 10.3390/ani11030625] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 01/09/2023] Open
Abstract
Simple Summary Long intergenic non-coding RNAs (lincRNAs) can regulate testicular development by acting on protein-coding genes. Therefore, it is important to explore the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. In this study, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. Using weighted gene co-expression network analysis, seven time-specifically diverse lincRNA modules and six mRNA modules were identified. Dramatically, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Moreover, potential lincRNA target genes were predicted. Moreover, key lincRNAs in the process of testis development were predicted, such as ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076. In the present study, the divergent regulation patterns of lincRNA on spermatogenesis and testis growth were discovered. This study can improve our understanding of the functions of lincRNAs in the regulation of testis development. Abstract Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to demonstrate the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. Herein, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal (DP) were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. We identified seven time-specifically diverse lincRNA modules and six mRNA modules by weighted gene co-expression network analysis (WGCNA). Interestingly, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Then, potential lincRNA target genes were predicted. Moreover, the co-expression network of lincRNAs demonstrated that ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076 were the key lincRNAs in the process of testis development. Our study discovered the divergent regulation patterns of lincRNA on spermatogenesis and testis growth, providing a fresh insight into age-biased changes in lincRNA expression in the goat testis.
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Affiliation(s)
- Dongdong Bo
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.B.); (X.J.); (R.H.); (Y.C.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan 430070, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.B.); (X.J.); (R.H.); (Y.C.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan 430070, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.B.); (X.J.); (R.H.); (Y.C.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan 430070, China
- Correspondence: ; Tel.: +86-027-87585120
| | - Ruixue Hu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.B.); (X.J.); (R.H.); (Y.C.)
| | - Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (D.B.); (X.J.); (R.H.); (Y.C.)
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