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Chen S, Zhao Q, Zhang R, Liu J, Peng W, Xu H, Li X, Wang X, Wu S, Li G, Nan A. A transcribed ultraconserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation through dual targeting of CDC42 by directly binding mRNA and protein. Transl Res 2024; 270:52-65. [PMID: 38552953 DOI: 10.1016/j.trsl.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/12/2024]
Abstract
The transcribed ultraconserved region (T-UCR) belongs to a new type of lncRNAs that are conserved in homologous regions of the rat, mouse and human genomes. A lot of research has reported that differential expression of T-UCRs can influence the development of various cancers, revealing the ability of T-UCRs as new therapeutic targets or potential cancer biomarkers. Most studies on the molecular mechanisms of T-UCRs in cancer have focused on ceRNA regulatory networks and interactions with target proteins, but the present study reveals an innovative dual-targeted regulatory approach in which T-UCRs bind directly to mRNAs and directly to proteins. We screened T-UCRs that may be related to colorectal cancer (CRC) by performing a whole-genome T-UCR gene microarray and further studied the functional mechanism of T-UCR uc.285+ in the development of CRC. Modulation of uc.285+ affected the proliferation of CRC cell lines and influenced the expression of the CDC42 gene. We also found that uc.285+ promoted the proliferation of CRC cells by directly binding to CDC42 mRNA and enhancing its stability while directly binding to CDC42 protein and affecting its stability. In short, our research on the characteristics of cell proliferation found that uc.285+ has a biological function in promoting CRC proliferation. uc.285+ may have considerable potential as a new diagnostic biomarker for CRC.
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Affiliation(s)
- Sixian Chen
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Qingyun Zhao
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Jungang Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, PR China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Haotian Xu
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xiaofei Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xin Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Shuilian Wu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Gang Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China.
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China.
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Carrese AM, Vitale R, Turco M, Masola V, Aniello F, Vitale E, Donizetti A. Sustained Depolarization Induces Gene Expression Pattern Changes Related to Synaptic Plasticity in a Human Cholinergic Cellular Model. Mol Neurobiol 2024:10.1007/s12035-024-04262-w. [PMID: 38941065 DOI: 10.1007/s12035-024-04262-w] [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: 03/04/2024] [Accepted: 05/25/2024] [Indexed: 06/29/2024]
Abstract
Neuronal gene expression in the brain dynamically responds to synaptic activity. The interplay among synaptic activity, gene expression, and synaptic plasticity has crucial implications for understanding the pathophysiology of diseases such as Alzheimer's disease and epilepsy. These diseases are marked by synaptic dysfunction that affects the expression patterns of neuroprotective genes that are incompletely understood. In our study, we developed a cellular model of synaptic activity using human cholinergic neurons derived from SH-SY5Y cell differentiation. Depolarization induction modulates the expression of neurotrophic genes and synaptic markers, indicating a potential role in synaptic plasticity regulation. This hypothesis is further supported by the induction kinetics of various long non-coding RNAs, including primate-specific ones. Our experimental model showcases the utility of SH-SY5Y cells in elucidating the molecular mechanisms underlying synaptic plasticity in human cellular systems.
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Affiliation(s)
- Anna Maria Carrese
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | - Rossella Vitale
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | - Manuela Turco
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, 80131, Italy
| | - Valeria Masola
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
- Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, 80138, Italy
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | - Emilia Vitale
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, 80131, Italy.
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy.
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Yang H, Zhang X, Zhang M, Lu Y, Xie B, Sun S, Yu H, Cong B, Luo Y, Ma C, Wen D. Roles of lncLingo2 and its derived miR-876-5p in the acquisition of opioid reinforcement. Addict Biol 2024; 29:e13375. [PMID: 38380802 PMCID: PMC10898844 DOI: 10.1111/adb.13375] [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: 11/14/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/22/2024]
Abstract
Recent studies found that non-coding RNAs (ncRNAs) played crucial roles in drug addiction through epigenetic regulation of gene expression and underlying drug-induced neuroadaptations. In this study, we characterized lncRNA transcriptome profiles in the nucleus accumbens (NAc) of mice exhibiting morphine-conditioned place preference (CPP) and explored the prospective roles of novel differentially expressed lncRNA, lncLingo2 and its derived miR-876-5p in the acquisition of opioids-associated behaviours. We found that the lncLingo2 was downregulated within the NAc core (NAcC) but not in the NAc shell (NAcS). This downregulation was found to be associated with the development of morphine CPP and heroin intravenous self-administration (IVSA). As Mfold software revealed that the secondary structures of lncLingo2 contained the sequence of pre-miR-876, transfection of LV-lncLingo2 into HEK293 cells significantly upregulated miR-876 expression and the changes of mature miR-876 are positively correlated with lncLingo2 expression in NAcC of morphine CPP trained mice. Delivering miR-876-5p mimics into NAcC also inhibited the acquisition of morphine CPP. Furthermore, bioinformatics analysis and dual-luciferase assay confirmed that miR-876-5p binds to its target gene, Kcnn3, selectively and regulates morphine CPP training-induced alteration of Kcnn3 expression. Lastly, the electrophysiological analysis indicated that the currents of small conductance calcium-activated potassium (SK) channel was increased, which led to low neuronal excitability in NAcC after CPP training, and these changes were reversed by lncLingo2 overexpression. Collectively, lncLingo2 may function as a precursor of miR-876-5p in NAcC, hence modulating the development of opioid-associated behaviours in mice, which may serve as an underlying biomarker and therapeutic target of opioid addiction.
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Affiliation(s)
- Hongyu Yang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Xiuning Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Minglong Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
- Department of GeneticsQiqihar Medical UniversityQiqiharHeilongjiang ProvinceChina
| | - Yun Lu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Bing Xie
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Shaoguang Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei ProvinceHebei Medical UniversityShijiazhuangChina
- Key Laboratory of Neural and Vascular BiologyMinistry of EducationShijiazhuangHebei ProvinceChina
| | - Hailei Yu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
| | - Yixiao Luo
- Hunan Province People's HospitalThe First‐Affiliated Hospital of Hunan Normal UniversityChangshaChina
| | - Chunling Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
- Key Laboratory of Neural and Vascular BiologyMinistry of EducationShijiazhuangHebei ProvinceChina
| | - Di Wen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and ToxicologyChinese Academy of Medical SciencesShijiazhuangHebei ProvinceChina
- Key Laboratory of Neural and Vascular BiologyMinistry of EducationShijiazhuangHebei ProvinceChina
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He C, Li Z, Yang M, Yu W, Luo R, Zhou J, He J, Chen Q, Song Z, Cheng S. Non-Coding RNA in Microglia Activation and Neuroinflammation in Alzheimer's Disease. J Inflamm Res 2023; 16:4165-4211. [PMID: 37753266 PMCID: PMC10519213 DOI: 10.2147/jir.s422114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by complex pathophysiological features. Amyloid plaques resulting from extracellular amyloid deposition and neurofibrillary tangles formed by intracellular hyperphosphorylated tau accumulation serve as primary neuropathological criteria for AD diagnosis. The activation of microglia has been closely associated with these pathological manifestations. Non-coding RNA (ncRNA), a versatile molecule involved in various cellular functions such as genetic information storage and transport, as well as catalysis of biochemical reactions, plays a crucial role in microglial activation. This review aims to investigate the regulatory role of ncRNAs in protein expression by directly targeting genes, proteins, and interactions. Furthermore, it explores the ability of ncRNAs to modulate inflammatory pathways, influence the expression of inflammatory factors, and regulate microglia activation, all of which contribute to neuroinflammation and AD. However, there are still significant controversies surrounding microglial activation and polarization. The categorization into M1 and M2 phenotypes may oversimplify the intricate and multifaceted regulatory processes in microglial response to neuroinflammation. Limited research has been conducted on the role of ncRNAs in regulating microglial activation and inducing distinct polarization states in the context of neuroinflammation. Moreover, the regulatory mechanisms through which ncRNAs govern microglial function continue to be refined. The current understanding of ncRNA regulatory pathways involved in microglial activation remains incomplete and may be influenced by spatial, temporal, and tissue-specific factors. Therefore, further in-depth investigations are warranted. In conclusion, there are ongoing debates and uncertainties regarding the activation and polarization of microglial cells, particularly concerning the categorization into M1 and M2 phenotypes. The study of ncRNA regulation in microglial activation and polarization, as well as its mechanisms, is still in its early stages and requires further investigation. However, this review offers new insights and opportunities for therapeutic approaches in AD. The development of ncRNA-based drugs may hold promise as a new direction in AD treatment.
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Affiliation(s)
- Chunxiang He
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Ze Li
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Miao Yang
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Wenjing Yu
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Rongsiqing Luo
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Jinyong Zhou
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Jiawei He
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Qi Chen
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Zhenyan Song
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
| | - Shaowu Cheng
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
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Zhao X, Sun X, Chen Y, Wu H, Liu Y, Jiang Y, Xie F, Chen Y. Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1158035. [PMID: 37229126 PMCID: PMC10204806 DOI: 10.3389/fpls.2023.1158035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 05/27/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant-pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.
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Affiliation(s)
- Xueying Zhao
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xiaoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yang Chen
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Hanfu Wu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yujiao Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Fuchun Xie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- College of Horticulture, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Jiang B, Yuan Y, Yi T, Dang W. The Roles of Antisense Long Noncoding RNAs in Tumorigenesis and Development through Cis-Regulation of Neighbouring Genes. Biomolecules 2023; 13:684. [PMID: 37189431 PMCID: PMC10135817 DOI: 10.3390/biom13040684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antisense long noncoding RNA (as-lncRNA) is a lncRNA transcribed in reverse orientation that is partially or completely complementary to the corresponding sense protein-coding or noncoding genes. As-lncRNAs, one of the natural antisense transcripts (NATs), can regulate the expression of their adjacent sense genes through a variety of mechanisms, affect the biological activities of cells, and further participate in the occurrence and development of a variety of tumours. This study explores the functional roles of as-lncRNAs, which can cis-regulate protein-coding sense genes, in tumour aetiology to understand the occurrence and development of malignant tumours in depth and provide a better theoretical basis for tumour therapy targeting lncRNAs.
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Affiliation(s)
- Binyuan Jiang
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Yeqin Yuan
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Ting Yi
- Department of Science and Education, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
| | - Wei Dang
- Department of Clinical Laboratory, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Medical Research Center, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
- Department of Science and Education, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha 410004, China
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Akkaya C, Karadag M, Hangul Z, Sahin E, Isbilen E. Evaluation of the Regulatory Role of Circadian Rhythm Related Long Non-Coding RNAs in ADHD Etiogenesis. J Atten Disord 2023; 27:201-213. [PMID: 36254757 DOI: 10.1177/10870547221130113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE ADHD is associated with increased sleep problems and circadian rhythm disturbances. This study aimed to examine ADHD patients and healthy controls in terms of chronotypic features and expression levels of CLOCK, PER1, lncRNA HULC, lncRNA UCA1. METHOD Eighty-three children were included (43 ADHD). Conner's Parent Rating Scale-Revised Short Form, Childhood Chronotype Questionnaire, Children's Sleep Disorders Scale were administered. Gene expression levels were studied from peripheral blood. RESULTS Evening chronotype, sleep initiation/maintenance disorder, sleep-wake transition disorder, excessive sleepiness disorder were higher in the ADHD group compared to the controls in the scales reported by the parents. Expression levels of all examined genes were statistically significantly higher in the ADHD group. There was no significant relationship between genes and sleep parameters in the ADHD group. CONCLUSION Our study provides the first evidence that lncRNA HULC and lncRNA UCA1 might have a role in the etiology of ADHD.
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Zakutansky PM, Feng Y. The Long Non-Coding RNA GOMAFU in Schizophrenia: Function, Disease Risk, and Beyond. Cells 2022; 11:1949. [PMID: 35741078 PMCID: PMC9221589 DOI: 10.3390/cells11121949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Neuropsychiatric diseases are among the most common brain developmental disorders, represented by schizophrenia (SZ). The complex multifactorial etiology of SZ remains poorly understood, which reflects genetic vulnerabilities and environmental risks that affect numerous genes and biological pathways. Besides the dysregulation of protein-coding genes, recent discoveries demonstrate that abnormalities associated with non-coding RNAs, including microRNAs and long non-coding RNAs (lncRNAs), also contribute to the pathogenesis of SZ. lncRNAs are an actively evolving family of non-coding RNAs that harbor greater than 200 nucleotides but do not encode for proteins. In general, lncRNA genes are poorly conserved. The large number of lncRNAs specifically expressed in the human brain, together with the genetic alterations and dysregulation of lncRNA genes in the SZ brain, suggests a critical role in normal cognitive function and the pathogenesis of neuropsychiatric diseases. A particular lncRNA of interest is GOMAFU, also known as MIAT and RNCR2. Growing evidence suggests the function of GOMAFU in governing neuronal development and its potential roles as a risk factor and biomarker for SZ, which will be reviewed in this article. Moreover, we discuss the potential mechanisms through which GOMAFU regulates molecular pathways, including its subcellular localization and interaction with RNA-binding proteins, and how interruption to GOMAFU pathways may contribute to the pathogenesis of SZ.
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Affiliation(s)
- Paul M. Zakutansky
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA;
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yue Feng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Liu Y, Cheng L, Zhan H, Li H, Li X, Huang Y, Li Y. The Roles of Noncoding RNAs in Systemic Sclerosis. Front Immunol 2022; 13:856036. [PMID: 35464474 PMCID: PMC9024074 DOI: 10.3389/fimmu.2022.856036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Noncoding RNAs (ncRNAs) constitute more than 90% of the RNAs in the human genome. In the past decades, studies have changed our perception of ncRNAs from “junk” transcriptional products to functional regulatory molecules that mediate critical processes, including chromosomal modifications, mRNA splicing and stability, and translation, as well as key signaling pathways. Emerging evidence suggests that ncRNAs are abnormally expressed in not only cancer but also autoimmune diseases, such as systemic sclerosis (SSc), and may serve as novel biomarkers and therapeutic targets for the diagnosis and treatment of SSc. However, the functions and underlying mechanisms of ncRNAs in SSc remain incompletely understood. In this review, we discuss the current findings on the biogenetic processes and functions of ncRNAs, including microRNAs and long noncoding RNAs, as well as explore emerging ncRNA-based diagnostics and therapies for SSc.
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Affiliation(s)
- Yongmei Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linlin Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haoting Zhan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaomeng Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Yongzhe Li,
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10
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Far from the nuclear crowd: Cytoplasmic lncRNA and their implications in synaptic plasticity and memory. Neurobiol Learn Mem 2021; 185:107522. [PMID: 34547434 DOI: 10.1016/j.nlm.2021.107522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/20/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022]
Abstract
A striking proportion of long non-coding RNAs are expressed specifically in the mammalian brain. Advances in genome-wide sequencing detected widespread diversity in neuronal lncRNAs based on their expression pattern, localization and function. A growing body of literature proposes that localization of lncRNAs is a critical determinant of their function. A rising number of recent findings documented distinct cytoplasmic functions of lncRNAs that are linked to activity-induced control of synaptic plasticity. However, the comprehensive role of cytoplasmic lncRNAs in neuronal functions is less understood. This review surveys our current understanding of lncRNAs that regulate the cytoplasmic life of mRNAs. We discuss the necessity of subcellular localization of lncRNAs in neuronal dendrites and the impact of their compartmentalized positioning on localized translation at the synapse. We have highlighted how lncRNAs modify a functional compartment to meet the demand for input-specific control of synaptic plasticity and memory.
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11
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Zhang Z, Wu H, Peng Q, Xie Z, Chen F, Ma Y, Zhang Y, Zhou Y, Yang J, Chen C, Li S, Zhang Y, Tian W, Wang Y, Xu Y, Luo H, Zhu M, Kuang YQ, Yu J, Wang K. Integration of Molecular Inflammatory Interactome Analyses Reveals Dynamics of Circulating Cytokines and Extracellular Vesicle Long Non-Coding RNAs and mRNAs in Heroin Addicts During Acute and Protracted Withdrawal. Front Immunol 2021; 12:730300. [PMID: 34489980 PMCID: PMC8416766 DOI: 10.3389/fimmu.2021.730300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/04/2021] [Indexed: 01/01/2023] Open
Abstract
Heroin addiction and withdrawal influence multiple physiological functions, including immune responses, but the mechanism remains largely elusive. The objective of this study was to investigate the molecular inflammatory interactome, particularly the cytokines and transcriptome regulatory network in heroin addicts undergoing withdrawal, compared to healthy controls (HCs). Twenty-seven cytokines were simultaneously assessed in 41 heroin addicts, including 20 at the acute withdrawal (AW) stage and 21 at the protracted withdrawal (PW) stage, and 38 age- and gender-matched HCs. Disturbed T-helper(Th)1/Th2, Th1/Th17, and Th2/Th17 balances, characterized by reduced interleukin (IL)-2, elevated IL-4, IL-10, and IL-17A, but normal TNF-α, were present in the AW subjects. These imbalances were mostly restored to the baseline at the PW stage. However, the cytokines TNF-α, IL-2, IL-7, IL-10, and IL-17A remained dysregulated. This study also profiled exosomal long non-coding RNA (lncRNA) and mRNA in the plasma of heroin addicts, constructed co-expression gene regulation networks, and identified lncRNA-mRNA-pathway pairs specifically associated with alterations in cytokine profiles and Th1/Th2/Th17 imbalances. Altogether, a large amount of cytokine and exosomal lncRNA/mRNA expression profiling data relating to heroin withdrawal was obtained, providing a useful experimental and theoretical basis for further understanding of the pathogenic mechanisms of withdrawal symptoms in heroin addicts.
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Affiliation(s)
- Zunyue Zhang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hongjin Wu
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qingyan Peng
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhenrong Xie
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fengrong Chen
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuru Ma
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yizhi Zhang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yong Zhou
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiqing Yang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Cheng Chen
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shaoyou Li
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yongjin Zhang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Weiwei Tian
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuan Wang
- Department of Research and Development, Echo Biotech Co., Ltd, Beijing, China
| | - Yu Xu
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Huayou Luo
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Mei Zhu
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yi-Qun Kuang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juehua Yu
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Kunhua Wang
- National Health Commission (NHC) Key Laboratory of Drug Addiction Medicine (Kunming Medical University), The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan University, Kunming, China
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12
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Nishimoto Y, Nakagawa S, Okano H. NEAT1 lncRNA and amyotrophic lateral sclerosis. Neurochem Int 2021; 150:105175. [PMID: 34481908 DOI: 10.1016/j.neuint.2021.105175] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/14/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a representative neurological disease that is known to devastate entire motor neurons within a period of just a few years. Discoveries of the specific pathologies of relevant RNA-binding proteins, including TAR DNA-binding protein-43 (TDP-43) and fused in sarcoma/translocated in liposarcoma (FUS/TLS), and the causative genes of both familial and sporadic ALS have provided crucial information that could lead to a cure. In recent ALS research the GGGGCC-repeat expansion in the C9orf72 gene was identified as one of the most important pathological findings, suggesting the significance of both nuclear dysfunction due to dipeptide repeat proteins (DPRs) and RNA toxicity (such as pathological alterations of non-coding RNAs). In research on model animals carrying ALS-related molecules, the determination of whether a factor is protective or toxic has been controversial. Herein, we review the findings regarding NEAT1 RNA and C9orf72 GGGGCC repeats associated with ALS, from the viewpoint of conversion from the protective stage in the nucleus in early-phase ALS to late-phase induction of cell death. This review will provide insights for the development of RNA effectors as novel ALS treatments.
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Affiliation(s)
- Yoshinori Nishimoto
- Department of Neurology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan.
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan.
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13
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Deng L, Guo Y, Liu J, Chen S, Wang X, Zhao H, Zuo T, Hu Q, Dong Z. Long noncoding RNA ANRIL knockdown attenuates neuroinflammation following ischemic stroke via suppressing the expression of NF-κB in vitro and in vivo. Neurol Res 2021; 43:767-777. [PMID: 34080525 DOI: 10.1080/01616412.2021.1934317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Increasing evidence suggests that long-noncoding RNAs can exert neuroprotective effects in cerebral ischemia-reperfusion injury. Levels of the long noncoding RNA ANRIL (ANRIL) are reportedly altered in ischemic stroke (IS) patients, but its role in IS requires further clarification. This study was designed to explore the mechanistic function of ANRIL in IS. METHODS In vitro, HT22 cells was treated with an oxygen-glucose deprivation/reperfusion (OGD/R). In vivo, brain ischemia/reperfusion was induced by 60-minute transient middle cerebral artery occlusion/reperfusion (MCAO/R) IS model in C57/BL6 mice. Additionally, cells were transfected with si-ANRIL, pcDNA3.1-ANRIL, pcDNA3.1-NF-κB, or appropriate negative controls, and si-ANRIL and pcDNA3.1-NF-κB were administered into the lateral ventricles in MCAO/R model mice. Cell viability and apoptosis were detected via MTT and flow cytometry assays. mRNA and protein expression of NF-κB were detected via qRT-PCR and Western blotting. IL-1β, IL-6, TNF-a, and iNOS levels were detected via ELISA. In addition, infarcted area and neuronal injury were evaluated via TTC, Nissl, and immunofluorescent staining. RESULTS We found that ANRIL knockdown increased cell viability and reduced apoptosis in vitro. Additionally, we found that ANRIL knockdown decreased p-P65, P65, IL-1β, IL-6, TNF-a, and iNOS levels, whereas these effects were reversed by NF-κB overexpression both in vitro and in vivo. CONCLUSION our results suggest that ANRIL knockdown attenuates neuroinflammation by suppressing the expression of NF-κB both in vitro and vivo model of IS, sugguesting that ANRIL might be a potentially viable therapeutictarget to diminish neuroinflammation in IS patients.
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Affiliation(s)
- Ling Deng
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
- Library, Southwest Medical University, Luzhou, Sichuan, China
| | - Yi Guo
- Department of Radiology, Chongqing University Central Hospital, Chongqing, China
| | - Jingdong Liu
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Sha Chen
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Xuan Wang
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Hongxia Zhao
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Tianrui Zuo
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Qingwen Hu
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Zhi Dong
- College of Pharmacology, the Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
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14
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Wang J, Fu Z, Wang M, Lu J, Yang H, Lu H. Knockdown of XIST Attenuates Cerebral Ischemia/Reperfusion Injury Through Regulation of miR-362/ROCK2 Axis. Neurochem Res 2021; 46:2167-2180. [PMID: 34037903 DOI: 10.1007/s11064-021-03354-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
Long non-coding RNAs (lncRNAs) are considered as critical regulators in the pathogenesis of cerebral ischemia. In this present study, we aimed to investigate the impact and underlying mechanism of lncRNA X-inactive specific transcript (XIST) in cerebral ischemia/reperfusion (I/R) injury. An oxygen-glucose deprivation/reperfusion (OGD/R) model in PC12 cells was applied to mimic cerebral I/R injury in vitro and middle cerebral artery occlusion/reperfusion (MCAO/R) model was performed in mice to mimic cerebral I/R injury in vivo. Real-time PCR, fluorescence in situ hybridization (FISH) assay, and western blotting assay were carried out to detect the expression levels of XIST, miR-362, and Rho-related coiled-coil containing protein kinase 2 (ROCK2). The functional experiments were measured by CCK-8 assay, immumofluorescence assay, ELISA assay, TUNEL, and TTC staining. Results displayed that XIST was elevated in PC12 cells with OGD/R, as well as in the ischemic penumbra of mice with MCAO/R. In vitro, knockdown of XIST facilitated cell survival, inhibited apoptosis, and alleviated inflammation injury in OGDR PC12 cells. In vivo, inhibition of XIST remarkably reduced the neurological impairments, promoted neuron proliferation, and suppressed apoptosis in MCAO mice. Mechanistically, XIST acted as a competing endogenous RNA of miR-362 to regulate the downstream gene ROCK2. In conclusion, depletion of XIST attenuated I/R-induced neurological impairment and inflammatory response via the miR-362/ROCK2 axis. These findings offer a potential novel strategy for ischemic stroke therapy.
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Affiliation(s)
- Jingtao Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Zhenqiang Fu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Menghan Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Jingjing Lu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Hecheng Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Hong Lu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan, China.
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15
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Shen B, Wang L, Xu Y, Wang H, He S. Long non-coding RNA ZFAS1 exerts a protective role to alleviate oxygen and glucose deprivation-mediated injury in ischemic stroke cell model through targeting miR-186-5p/MCL1 axis. Cytotechnology 2021; 73:605-617. [PMID: 34349350 DOI: 10.1007/s10616-021-00481-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years, accumulating articles have revealed that long non-coding RNAs (lncRNAs) play crucial roles in ischemic stroke (IS). A previous study found that lncRNA zinc finger antisense 1 (ZFAS1) was down-regulated in IS patients compared with healthy controls. However, the precise function of ZFAS1 in IS and its associated mechanism remain unclear. Cell viability was assessed by cell counting kit-8 (CCK8) assay. Cell apoptosis was analyzed by flow cytometry. Western blot assay and quantitative real-time polymerase chain reaction (qRT-PCR) were conducted to measure protein and RNA expression. The interaction between microRNA-186-5p (miR-186-5p) and ZFAS1 or MCL1 apoptosis regulator, BCL2 family member (MCL1) was confirmed by dual-luciferase reporter assay, RNA-pull down assay and RNA immunoprecipitation (RIP) assay. IS cell model was established through exposing N2a cells to oxygen and glucose deprivation (OGD). OGD exposure restrained the viability and induced the apoptosis of N2a cells. OGD exposure down-regulated the expression of ZFAS1 and up-regulated the level of miR-186-5p in a time-dependent manner. ZFAS1 overexpression alleviated OGD-mediated injury in IS cell model. MiR-186-5p was identified as a direct target of ZFAS1, and OGD-induced injury in IS cell model was attenuated by the silence of miR-186-5p. MiR-186-5p interacted with the 3' untranslated region (3'UTR) of MCL1 messenger RNA (mRNA). ZFAS1 positively regulated MCL1 mRNA expression by sequestering miR-186-5p in N2a cells. ZFAS1 overexpression-mediated protective effects in IS cell model were partly overturned by the overexpression of miR-186-5p. MCL1 silencing partly counteracted the protective effects mediated by miR-186-5p silencing in IS cell model. In conclusion, ZFAS1 overexpression exerted a protective role in IS cell model to attenuate OGD-induced injury through targeting miR-186-5p/MCL1 axis. ZFAS1/miR-186-5p/MCL1 signaling might be a novel diagnostic marker and promising treatment target for IS patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-021-00481-4.
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Affiliation(s)
- Bin Shen
- Jiangsu Vocational College of Medicine, Jinhua Garden, Chaosheng Road, Tinghu District, Yancheng, 224005 Jiangsu China
| | - Lan Wang
- Hubei University of Chinese Medicine, Wuhan, 430065 Hubei China
| | - Yuejun Xu
- Wuchang University of Technology, Wuhan, 430223 Hubei China
| | - Hongwei Wang
- Jiangsu Vocational College of Medicine, Jinhua Garden, Chaosheng Road, Tinghu District, Yancheng, 224005 Jiangsu China
| | - Shiyi He
- Jiangsu Vocational College of Medicine, Jinhua Garden, Chaosheng Road, Tinghu District, Yancheng, 224005 Jiangsu China
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16
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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17
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Tamizkar KH, Ghafouri-Fard S, Omrani MD, Pouresmaeili F, Arsang-Jang S, Taheri M. Altered expression of lncRNAs in autism spectrum disorder. Metab Brain Dis 2021; 36:983-990. [PMID: 33587235 DOI: 10.1007/s11011-021-00681-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been recognized as an important epigenetic factor in the evolution of neuropsychiatric conditions. We have selected five lncRNAs (DISC2, PRKAR2A-AS1, LOC105375675, LRRC2-AS1, and LOC101928237) to measure their expression in blood samples of children with autism spectrum disorder (ASD) versus children with normal development. Expressions of DISC2, PRKAR2A-AS1 and LOC101928237 have been enhanced in ASD cases compared with healthy children (Posterior Beta = 2.508, P value<0.0001; Posterior Beta = 2.793, P value = 0.014 and Posterior Beta = 1.646, P value <0.0001, respectively). On the other hand, expression of LRRC2-AS1 has been lower in ASD patients compared with controls (Posterior Beta = -3.781, P value<0.0001). Remarkably, expression of DISC2 and PRKAR2A-AS1 have been lower in girls compared with boys (Posterior Beta = -0.982, P value<0.0001 and Posterior Beta = -0.135, P value<0.0001, respectively). In addition, expression of DISC2 has been lower in ASD cases aged more than 6 compared with those aged less than 6 years (Posterior Beta = -0.876, P value = 0.003). DISC2, LOC101928237, LRRC2-AS1, and PRKAR2A-AS1 had the area under curve (AUC) values of 0.76, 0.90, 0.92, and 0.79 in distinguishing between ASD and healthy children. Expression levels of none of DISC2, LOC101928237, LOC105375675, LRRC2-AS1, and PRKAR2A-AS1 were correlated with age of ASD cases or healthy controls. A significant correlation was detected between expressions of DISC2 and PRKAR2A-AS1. There were inverse correlations between the following pairs of lncRNAs: DISC2/LRRC2-AS1, DISC2/LOC101928237, LRRC2-AS1/PRKAR2A-AS1, LOC101928237/LRRC2-AS1, and LOC101928237 /LOC105375675. We conclude that DISC2, LOC101928237, LRRC2-AS1, and PRKAR2A-AS1 might be used as potential markers for this condition.
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Affiliation(s)
| | - Soudeh Ghafouri-Fard
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mir Davood Omrani
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahram Arsang-Jang
- Department of Biostatistics and Epidemiology, Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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18
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Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR). Cells 2021; 10:cells10040921. [PMID: 33923632 PMCID: PMC8072961 DOI: 10.3390/cells10040921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Impaired fetal growth is one of the most important causes of prematurity, stillbirth and infant mortality. The pathogenesis of idiopathic fetal growth restriction (FGR) is poorly understood but is thought to be multifactorial and comprise a range of genetic causes. This research aimed to investigate non-coding RNAs (lncRNAs) in the placentas of male and female fetuses affected by FGR. RNA-Seq data were analyzed to detect lncRNAs, their potential target genes and circular RNAs (circRNAs); a differential analysis was also performed. The multilevel bioinformatic analysis enabled the detection of 23,137 placental lncRNAs and 4263 of them were classified as novel. In FGR-affected female fetuses’ placentas (ff-FGR), among 19 transcriptionally active regions (TARs), five differentially expressed lncRNAs (DELs) and 12 differentially expressed protein-coding genes (DEGs) were identified. Within 232 differentially expressed TARs identified in male fetuses (mf-FGR), 33 encompassed novel and 176 known lncRNAs, and 52 DEGs were upregulated, while 180 revealed decreased expression. In ff-FGR ACTA2-AS1, lncRNA expression was significantly correlated with five DEGs, and in mf-FGR, 25 TARs were associated with DELs correlated with 157 unique DEGs. Backsplicing circRNA processes were detected in the range of H19 lncRNA, in both ff- and mf-FGR placentas. The performed global lncRNAs characteristics in terms of fetal sex showed dysregulation of DELs, DEGs and circRNAs that may affect fetus growth and pregnancy outcomes. In female placentas, DELs and DEGs were associated mainly with the vasculature, while in male placentas, disturbed expression predominantly affected immune processes.
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19
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Drake J, McMichael GO, Vornholt ES, Cresswell K, Williamson V, Chatzinakos C, Mamdani M, Hariharan S, Kendler KS, Kalsi G, Riley BP, Dozmorov M, Miles MF, Bacanu S, Vladimirov VI. Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence. Alcohol Clin Exp Res 2020; 44:2468-2480. [PMID: 33067813 PMCID: PMC7756309 DOI: 10.1111/acer.14479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Long noncoding RNA (lncRNA) have been implicated in the etiology of alcohol use. Since lncRNA provide another layer of complexity to the transcriptome, assessing their expression in the brain is the first critical step toward understanding lncRNA functions in alcohol use and addiction. Thus, we sought to profile lncRNA expression in the nucleus accumbens (NAc) in a large postmortem alcohol brain sample. METHODS LncRNA and protein-coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL). RESULTS At Bonferroni adj. p-value ≤ 0.05, we identified 19 lncRNA and 5 PCG significant modules, which were enriched for neuronal and immune-related processes. In these modules, we further identified 86 and 315 PCG and lncRNA hubs, respectively. At false discovery rate (FDR) of 10%, the correlation analyses between the lncRNA and PCG hubs revealed 3,125 positive and 1,860 negative correlations. Integration of hubs with genotype data identified 243 eQTLs affecting the expression of 39 and 204 PCG and lncRNA hubs, respectively. CONCLUSIONS Our study identified lncRNA and gene networks significantly associated with AD in the NAc, coordinated lncRNA and mRNA coexpression changes, highlighting potentially regulatory functions for the lncRNA, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
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Affiliation(s)
- John Drake
- From the Center for Integrative Life Sciences Education (JD)Virginia Commonwealth UniversityRichmondVirginia
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Eric Sean Vornholt
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Kellen Cresswell
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Vernell Williamson
- Department of Pathology(VW)Virginia Commonwealth UniversityRichmondVirginia
| | - Chris Chatzinakos
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Siddharth Hariharan
- Summer Research Fellowship(SH)School of MedicineVirginia Commonwealth UniversityRichmondVirginia
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry(GK)Institute of PsychiatryLondonUK
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Mikhail Dozmorov
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Pharmacology and Toxicology(MFM)Virginia Commonwealth UniversityRichmondVirginia
| | - Silviu‐Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Center for Biomarker Research and Personalized Medicine(VIV)Virginia Commonwealth UniversityRichmondVirginia
- Lieber Institute for Brain Development(VIV)Johns Hopkins UniversityBaltimoreMaryland
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20
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Xiong LL, Xue LL, Du RL, Zhou HL, Tan YX, Ma Z, Jin Y, Zhang ZB, Xu Y, Hu Q, Bobrovskaya L, Zhou XF, Liu J, Wang TH. Vi4-miR-185-5p-Igfbp3 Network Protects the Brain From Neonatal Hypoxic Ischemic Injury via Promoting Neuron Survival and Suppressing the Cell Apoptosis. Front Cell Dev Biol 2020; 8:529544. [PMID: 33262982 PMCID: PMC7688014 DOI: 10.3389/fcell.2020.529544] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/14/2020] [Indexed: 02/05/2023] Open
Abstract
Neonatal hypoxic ischemic encephalopathy (HIE) due to birth asphyxia is common and causes severe neurological deficits, without any effective therapies currently available. Neuronal death is an important driving factors of neurological disorders after HIE, but the regulatory mechanisms are still uncertain. Long non-coding RNA (lncRNA) or ceRNA network act as a significant regulator in neuroregeneration and neuronal apoptosis, thus owning a great potential as therapeutic targets in HIE. Here, we found a new lncRNA, is the most functional in targeting the Igfbp3 gene in HIE, which enriched in the cell growth and cell apoptosis processes. In addition, luciferase reporter assay showed competitive regulatory binding sites to the target gene Igfbp3 between TCONS00044054 (Vi4) and miR-185-5p. The change in blood miR-185-5p and Igfbp3 expression is further confirmed in patients with brain ischemia. Moreover, Vi4 overexpression and miR-185-5p knock-out promote the neuron survival and neurite growth, and suppress the cell apoptosis, then further improve the motor and cognitive deficits in rats with HIE, while Igfbp3 interfering got the opposite results. Together, Vi4-miR-185-5p-Igfbp3 regulatory network plays an important role in neuron survival and cell apoptosis and further promote the neuro-functional recovery from HIE, therefore is a likely a drug target for HIE therapy.
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Affiliation(s)
- Liu-Lin Xiong
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,Department of Anesthesiology, The Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia
| | - Lu-Lu Xue
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China
| | - Ruo-Lan Du
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hao-Li Zhou
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ya-Xin Tan
- Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China.,Shijiazhuang Maternity and Child Healthcare Hospital, Shijaizhuang, China
| | - Zheng Ma
- Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China
| | - Yuan Jin
- Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China
| | - Zi-Bin Zhang
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Xu
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiao Hu
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Larisa Bobrovskaya
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia
| | - Xin-Fu Zhou
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia
| | - Jia Liu
- Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China
| | - Ting-Hua Wang
- Institute of Neurological Disease, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,Animal Zoology Department, Institute of Neuroscience, Kunming Medical University, Kunming, China
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21
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Wang Y, Wang X, Wang YX, Ma Y, Di Y. Effect and mechanism of the long noncoding RNA MALAT1 on retinal neovascularization in retinopathy of prematurity. Life Sci 2020; 260:118299. [PMID: 32827542 DOI: 10.1016/j.lfs.2020.118299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/04/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022]
Abstract
AIMS The most typical pathological manifestation of retinopathy of prematurity (ROP) is Retinal neovascularization (RNV). Long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been reported to mediate angiogenesis. Our experiment aimed to research the effect and mechanism of the MALAT1 on RNV in ROP. MAIN METHODS C57 mice was used to establish oxygen-introduced retinopathy (OIR), and divided into control, hyperoxia, hyperoxia control siRNA, and hyperoxia MALAT1 siRNA groups. KEY FINDINGS It was shown that MALAT1 mRNA was high expressed in the retinas of OIR mice. Further studies revealed that after intravitreal injection of MALAT1 siRNA, the degree of retinopathy was significantly reduced compared with OIR group. In addition, the protein and mRNA expression levels of CCN1, AKT and VEGF were significantly decreased. This was accompanied by a decrease in inflammatory genes including IL-1β, IL-6, and TNF-α compared with the hyperoxia control siRNA mice. SIGNIFICANCE The result suggested that MALAT1 may be involved in the process of RNV in ROP and MALAT1 siRNA may be a promising agent for the treatment of ROP by inhibiting RNV.
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Affiliation(s)
- Yue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Xue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yue-Xia Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yuan Ma
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China
| | - Yu Di
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China.
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22
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Abou Alezz M, Celli L, Belotti G, Lisa A, Bione S. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front Genet 2020; 11:488. [PMID: 32499820 PMCID: PMC7242645 DOI: 10.3389/fgene.2020.00488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are recognized as an important class of regulatory molecules involved in a variety of biological functions. However, the regulatory mechanisms of long non-coding genes expression are still poorly understood. The characterization of the genomic features of lncRNAs is crucial to get insight into their function. In this study, we exploited recent annotations by GENCODE to characterize the genomic and splicing features of long non-coding genes in comparison with protein-coding ones, both in human and mouse. Our analysis highlighted differences between the two classes of genes in terms of their gene architecture. Significant differences in the splice sites usage were observed between long non-coding and protein-coding genes (PCG). While the frequency of non-canonical GC-AG splice junctions represents about 0.8% of total splice sites in PCGs, we identified a significant enrichment of the GC-AG splice sites in long non-coding genes, both in human (3.0%) and mouse (1.9%). In addition, we found a positional bias of GC-AG splice sites being enriched in the first intron in both classes of genes. Moreover, a significant shorter length and weaker donor and acceptor sites were found comparing GC-AG introns to GT-AG introns. Genes containing at least one GC-AG intron were found conserved in many species, more prone to alternative splicing and a functional analysis pointed toward their enrichment in specific biological processes such as DNA repair. Our study shows for the first time that GC-AG introns are mainly associated with lncRNAs and are preferentially located in the first intron. Additionally, we discovered their regulatory potential indicating the existence of a new mechanism of non-coding and PCGs expression regulation.
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Affiliation(s)
- Monah Abou Alezz
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
| | - Ludovica Celli
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
| | - Giulia Belotti
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
| | - Antonella Lisa
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
| | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
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23
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Zhang R, Li J, Li G, Jin F, Wang Z, Yue R, Wang Y, Wang X, Sun Y. LncRNA Nron regulates osteoclastogenesis during orthodontic bone resorption. Int J Oral Sci 2020; 12:14. [PMID: 32385254 PMCID: PMC7210890 DOI: 10.1038/s41368-020-0077-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/19/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Activation of osteoclasts during orthodontic tooth treatment is a prerequisite for alveolar bone resorption and tooth movement. However, the key regulatory molecules involved in osteoclastogenesis during this process remain unclear. Long noncoding RNAs (lncRNAs) are a newly identified class of functional RNAs that regulate cellular processes, such as gene expression and translation regulation. Recently, lncRNAs have been reported to be involved in osteogenesis and bone formation. However, as the most abundant noncoding RNAs in vivo, the potential regulatory role of lncRNAs in osteoclast formation and bone resorption urgently needs to be clarified. We recently found that the lncRNA Nron (long noncoding RNA repressor of the nuclear factor of activated T cells) is highly expressed in osteoclast precursors. Nron is downregulated during osteoclastogenesis and bone ageing. To further determine whether Nron regulates osteoclast activity during orthodontic treatment, osteoclastic Nron transgenic (Nron cTG) and osteoclastic knockout (Nron CKO) mouse models were generated. When Nron was overexpressed, the orthodontic tooth movement rate was reduced. In addition, the number of osteoclasts decreased, and the activity of osteoclasts was inhibited. Mechanistically, Nron controlled the maturation of osteoclasts by regulating NFATc1 nuclear translocation. In contrast, by deleting Nron specifically in osteoclasts, tooth movement speed increased in Nron CKO mice. These results indicate that lncRNAs could be potential targets to regulate osteoclastogenesis and orthodontic tooth movement speed in the clinic in the future.
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Affiliation(s)
- Ruilin Zhang
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Junhui Li
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Gongchen Li
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Fujun Jin
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Zuolin Wang
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Rui Yue
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yibin Wang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaogang Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Yao Sun
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China.
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24
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Bobkova NV, Poltavtseva RA, Leonov SV, Sukhikh GT. Neuroregeneration: Regulation in Neurodegenerative Diseases and Aging. BIOCHEMISTRY (MOSCOW) 2020; 85:S108-S130. [PMID: 32087056 DOI: 10.1134/s0006297920140060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It had been commonly believed for a long time, that once established, degeneration of the central nervous system (CNS) is irreparable, and that adult person merely cannot restore dead or injured neurons. The existence of stem cells (SCs) in the mature brain, an organ with minimal regenerative ability, had been ignored for many years. Currently accepted that specific structures of the adult brain contain neural SCs (NSCs) that can self-renew and generate terminally differentiated brain cells, including neurons and glia. However, their contribution to the regulation of brain activity and brain regeneration in natural aging and pathology is still a subject of ongoing studies. Since the 1970s, when Fuad Lechin suggested the existence of repair mechanisms in the brain, new exhilarating data from scientists around the world have expanded our knowledge on the mechanisms implicated in the generation of various cell phenotypes supporting the brain, regulation of brain activity by these newly generated cells, and participation of SCs in brain homeostasis and regeneration. The prospects of the SC research are truthfully infinite and hitherto challenging to forecast. Once researchers resolve the issues regarding SC expansion and maintenance, the implementation of the SC-based platform could help to treat tissues and organs impaired or damaged in many devastating human diseases. Over the past 10 years, the number of studies on SCs has increased exponentially, and we have already become witnesses of crucial discoveries in SC biology. Comprehension of the mechanisms of neurogenesis regulation is essential for the development of new therapeutic approaches for currently incurable neurodegenerative diseases and neuroblastomas. In this review, we present the latest achievements in this fast-moving field and discuss essential aspects of NSC biology, including SC regulation by hormones, neurotransmitters, and transcription factors, along with the achievements of genetic and chemical reprogramming for the safe use of SCs in vitro and in vivo.
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Affiliation(s)
- N V Bobkova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - R A Poltavtseva
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Ministry of Healthcare of Russian Federation, Moscow, 117997, Russia
| | - S V Leonov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Moscow Institute of Physics and Technology (National Research University), The Phystech School of Biological and Medical Physics, Dolgoprudny, Moscow Region, 141700, Russia
| | - G T Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Ministry of Healthcare of Russian Federation, Moscow, 117997, Russia.
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25
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Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. Biomolecules 2020; 10:biom10020313. [PMID: 32079202 PMCID: PMC7072442 DOI: 10.3390/biom10020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
Flexibility in signal transmission is essential for high-level brain function. This flexibility is achieved through strict spatial and temporal control of gene expression in neurons. Given the key regulatory roles of a variety of noncoding RNAs (ncRNAs) in neurons, studying neuron-specific ncRNAs provides an important basis for understanding molecular principles of brain function. This approach will have wide use in understanding the pathogenesis of brain diseases and in the development of therapeutic agents in the future. Brain cytoplasmic RNAs (BC RNAs) are a leading paradigm for research on neuronal ncRNAs. Since the first confirmation of brain-specific expression of BC RNAs in 1982, their investigation has been an area of active research. In this review, we summarize key studies on the characteristics and functions of BC RNAs in neurons.
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26
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Liu J, Wang F, Du L, Li J, Yu T, Jin Y, Yan Y, Zhou J, Gu J. Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection. Front Microbiol 2020; 10:3036. [PMID: 32063887 PMCID: PMC6999024 DOI: 10.3389/fmicb.2019.03036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/17/2019] [Indexed: 11/28/2022] Open
Abstract
Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection.
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Affiliation(s)
- Junli Liu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Fangfang Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Liuyang Du
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Juan Li
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Tianqi Yu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Yulan Jin
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
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27
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Gudenas BL, Wang J, Kuang SZ, Wei AQ, Cogill SB, Wang LJ. Genomic data mining for functional annotation of human long noncoding RNAs. J Zhejiang Univ Sci B 2019; 20:476-487. [PMID: 31090273 DOI: 10.1631/jzus.b1900162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Life may have begun in an RNA world, which is supported by increasing evidence of the vital role that RNAs perform in biological systems. In the human genome, most genes actually do not encode proteins; they are noncoding RNA genes. The largest class of noncoding genes is known as long noncoding RNAs (lncRNAs), which are transcripts greater in length than 200 nucleotides, but with no protein-coding capacity. While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization, most lncRNAs are still uncharacterized. We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies. Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Jun Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Shu-Zhen Kuang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - An-Qi Wei
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Steven B Cogill
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Liang-Jiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
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28
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Keihani S, Kluever V, Mandad S, Bansal V, Rahman R, Fritsch E, Gomes LC, Gärtner A, Kügler S, Urlaub H, Wren JD, Bonn S, Rizzoli SO, Fornasiero EF. The long noncoding RNA neuroLNC regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43. SCIENCE ADVANCES 2019; 5:eaay2670. [PMID: 31897430 PMCID: PMC6920028 DOI: 10.1126/sciadv.aay2670] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/23/2019] [Indexed: 05/26/2023]
Abstract
The cellular and the molecular mechanisms by which long noncoding RNAs (lncRNAs) may regulate presynaptic function and neuronal activity are largely unexplored. Here, we established an integrated screening strategy to discover lncRNAs implicated in neurotransmitter and synaptic vesicle release. With this approach, we identified neuroLNC, a neuron-specific nuclear lncRNA conserved from rodents to humans. NeuroLNC is tuned by synaptic activity and influences several other essential aspects of neuronal development including calcium influx, neuritogenesis, and neuronal migration in vivo. We defined the molecular interactors of neuroLNC in detail using chromatin isolation by RNA purification, RNA interactome analysis, and protein mass spectrometry. We found that the effects of neuroLNC on synaptic vesicle release require interaction with the RNA-binding protein TDP-43 (TAR DNA binding protein-43) and the selective stabilization of mRNAs encoding for presynaptic proteins. These results provide the first proof of an lncRNA that orchestrates neuronal excitability by influencing presynaptic function.
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Affiliation(s)
- S. Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - V. Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - S. Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - V. Bansal
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - R. Rahman
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
| | - E. Fritsch
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - L. Caldi Gomes
- Department of Neurology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
| | - A. Gärtner
- VIB Center for the Biology of Disease and Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - S. Kügler
- Department of Neurology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - H. Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - J. D. Wren
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - S. Bonn
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - S. O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
| | - E. F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
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Liu B, Cao W, Xue J. LncRNA ANRIL protects against oxygen and glucose deprivation (OGD)-induced injury in PC-12 cells: potential role in ischaemic stroke. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:1384-1395. [PMID: 31174432 DOI: 10.1080/21691401.2019.1596944] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
lncRNA ANRIL was reported to be closely related to ischaemic stroke (IS). In this study, we used oxygen-glucose deprivation (OGD) to stimulate rat adrenal medulla-derived pheochromocytoma cell line PC-12 to construct an in vitro IS cell model and investigated the role of ANRIL and the underlying mechanism. PC-12 cells were stimulated by OGD and/or transfected with pc-ANRIL, si-ANRIL, miR-127 mimic, miR-127 inhibitor, pEX-Mcl-1, sh-Mcl-1 and their negative controls. Cell viability, apoptosis, mRNA and protein expression was detected using CCK-8 assay, flow cytometry assay, qRT-PCR and western blot, respectively. Results showed that OGD-induced PC-12 cell injury and decreased ANRIL expression. ANRIL overexpression significantly reduced OGD-induced PC-12 cell injury evidenced by increasing cell viability and decreasing apoptosis, while ANRIL silence led to the opposite results. Meanwhile, dysregulation of ANRIL altered the expression of apoptotic proteins. Furthermore, ANRIL negatively regulated miR-127 expression. miR-127 overexpression significantly enhanced OGD-induced PC-12 cell injury. In addition, Mcl-1 expression was negatively regulated by miR-127, besides ANRIL up-regulated Mcl-1 expression by down-regulation of miR-127. Mcl-1 overexpression alleviated cell injury and miR-127 silence up-regulated Mcl-1 expression. In conclusion, lncRNA ANRIL alleviated OGD-induced PC-12 cell injury as evidenced. PI3K/AKT pathway might be involved in this regulating progression.
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Affiliation(s)
- Bin Liu
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Wei Cao
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
| | - Jian Xue
- a Department of Neurosurgery, Jining No.1 People's Hospital , Jining , China
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30
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Cao S, Yuan J, Zhang D, Wen S, Wang J, Li Y, Deng W. Transcriptome Changes In Dorsal Spinal Cord Of Rats With Neuropathic Pain. J Pain Res 2019; 12:3013-3023. [PMID: 31807058 PMCID: PMC6850707 DOI: 10.2147/jpr.s219084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background Mechanisms of neuropathic pain are not fully understood. Molecular changes in spinal dorsal horn take part in the initiation and development of neuropathic pain. Methods To detect the transcriptome changes in the dorsal spinal cord of neuropathic pain rat, sciatic nerve chronic constriction injury (CCI) rats were used. Then, the CCI ipsilateral dorsal spinal cords of lumbar L3-L5 segments were collected at 14th day post-CCI and subjected to microRNA and long non-coding RNA (lncRNA)/mRNA microarray. To evaluate functions of differential mRNAs, bioinformatics methods including gene ontology (GO) and KEGG pathway analysis were conducted for significantly up- and downregulated mRNAs. Results MicroRNA microarrays showed that 13 microRNAs were differently expressed between CCI and sham-operated rats (fold change ≥ 2.0). Six of them were upregulated, and the other seven were downregulated in CCI group. MicroRNA-1b overexpressed 18.7 times after CCI. LncRNA/mRNA microarray detected 876 lncRNAs with significant differential expression (fold change ≥ 2.0). Among them, 339 were significantly upregulated, and 537 were downregulated in CCI group. Sixteen of them differentially expressed more than 10 times and the lncRNA XR_356687 overexpressed as high as 53 times. In addition, 950 mRNAs were differentially expressed (fold change ≥ 2.0), including 405 upregulated and 545 downregulated in CCI group. Ten of these mRNAs with changed expressions of more than 10 times. The Hspa1b (encodes heat shock protein 70) overexpressed 24 times in CCI rats. Gene ontology analysis revealed that hundreds of differentially expressed mRNAs involved in the biological processes, cellular component, and molecular function. In addition, these genes significantly enriched into 32 KEGG pathways, including the TNF, FoxO, cytokine–cytokine receptor interaction, and calcium signaling pathways. Conclusion Neuropathic pain induced comprehensive changes of transcription profile in the dorsal spinal cord. These differentially expressed transcripts in spinal cord could be potential targets in defeating neuropathic pain.
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Affiliation(s)
- Song Cao
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China.,Guizhou Key Laboratory of Anesthesia and Organ Protection, Zunyi Medical University, Zunyi 563003, People's Republic of China
| | - Jie Yuan
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China.,Guizhou Key Laboratory of Anesthesia and Organ Protection, Zunyi Medical University, Zunyi 563003, People's Republic of China
| | - Dexing Zhang
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Song Wen
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Jie Wang
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Ying Li
- Department of Pain Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, People's Republic of China
| | - Wenwen Deng
- Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
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31
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Celik S, Sadegh MK, Morley M, Roselli C, Ellinor PT, Cappola T, Smith JG, Gidlöf O. Antisense regulation of atrial natriuretic peptide expression. JCI Insight 2019; 4:130978. [PMID: 31503546 DOI: 10.1172/jci.insight.130978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
The cardiac hormone atrial natriuretic peptide (ANP) is a central regulator of blood volume and a therapeutic target in hypertension and heart failure. Enhanced ANP activity in such conditions through inhibition of the degradative enzyme neprilysin has shown clinical efficacy but is complicated by consequences of simultaneous accumulation of a heterogeneous array of other hormones. Targets for specific ANP enhancement have not been available. Here, we describe a cis-acting antisense transcript (NPPA-AS1), which negatively regulates ANP expression in human cardiomyocytes. We show that NPPA-AS1 regulates ANP expression via facilitating NPPA repressor RE1-silencing transcription factor (REST) binding to its promoter, rather than forming an RNA duplex with ANP mRNA. Expression of ANP mRNA and NPPA-AS1 was increased and correlated in isolated strained human cardiomyocytes and in hearts from patients with advanced heart failure. Further, inhibition of NPPA-AS1 in vitro and in vivo resulted in increased myocardial expression of ANP, increased circulating ANP, increased renal cGMP, and lower blood pressure. The effects of NPPA-AS1 inhibition on NPPA expression in human cardiomyocytes were further marked under cell-strain conditions. Collectively, these results implicate the antisense transcript NPPA-AS1 as part of a physiologic self-regulatory ANP circuit and a viable target for specific ANP augmentation.
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Affiliation(s)
- Selvi Celik
- Department of Cardiology, Clinical Sciences.,Wallenberg Center for Molecular Medicine, and.,Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Mardjaneh Karbalaei Sadegh
- Department of Cardiology, Clinical Sciences.,Wallenberg Center for Molecular Medicine, and.,Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Michael Morley
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carolina Roselli
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Cardiovascular Research Center and Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Thomas Cappola
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences.,Wallenberg Center for Molecular Medicine, and.,Lund University Diabetes Center, Lund University, Lund, Sweden.,Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Heart Failure and Valvular Heart Disease, Skane University Hospital, Lund, Sweden
| | - Olof Gidlöf
- Department of Cardiology, Clinical Sciences.,Wallenberg Center for Molecular Medicine, and.,Lund University Diabetes Center, Lund University, Lund, Sweden
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32
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Zhang H, Lu M, Zhang X, Kuai Y, Mei Y, Tan Q, Zhong K, Sun X, Tan W. Isosteviol Sodium Protects against Ischemic Stroke by Modulating Microglia/Macrophage Polarization via Disruption of GAS5/miR-146a-5p sponge. Sci Rep 2019; 9:12221. [PMID: 31434993 PMCID: PMC6704123 DOI: 10.1038/s41598-019-48759-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/07/2019] [Indexed: 01/04/2023] Open
Abstract
Recent studies have shown that transforming microglia phenotype from pro-inflammation of M1 phenotype to anti-inflammation and tissue-repairing M2 phenotype may be an effective therapeutic strategy for preventing ischemic stroke brain injury. Isosteviol Sodium (STV-Na) has shown promise as a neuroprotective agent in cerebral ischemia model, although its effect on microglial polarization and chronic recovery after stroke is not clear. Here, we demonstrated that STV-Na treatment significantly reduced cerebral ischemic damage at both acute and chronic time points. STV-Na has a profound regulatory effect on microglia response after stroke. It can promote M2 polarization and inhibit microglia-mediated inflammation (M1) response following stroke in vivo and in vitro. Furthermore, we also found that Growth Arrest-Specific 5 (GAS5) altered OGD/R-induced microglial activation by increasing Notch1 expression via miR-146a-5p, the mRNA level of GAS5 and the protein level of Notch1 in vivo and in vitro, were discovered that both downgraded with STV-Na. Taken together, the present study demonstrated that STV-Na exerted neuroprotective effects by modulating microglia/macrophage polarization in ischemic stroke via the GAS5/miR-146a-5p sponge. These findings provide new evidence that targeting STV-Na could be a treatment for the prevention of stroke-related brain damage.
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Affiliation(s)
- Hao Zhang
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Minyi Lu
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Xiaofeng Zhang
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yihe Kuai
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Ying Mei
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Qiwen Tan
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Kailun Zhong
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Xiaoou Sun
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
| | - Wen Tan
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
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Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment. Neurobiol Dis 2019; 132:104583. [PMID: 31445158 DOI: 10.1016/j.nbd.2019.104583] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the α-subunit of the neuronal sodium channel Nav1.1. The syndrome is characterized by age-related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Nav1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic inter-neuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Nav1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.
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34
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Teng L, Meng R. Long Non-Coding RNA MALAT1 Promotes Acute Cerebral Infarction Through miRNAs-Mediated hs-CRP Regulation. J Mol Neurosci 2019; 69:494-504. [DOI: 10.1007/s12031-019-01384-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/09/2019] [Indexed: 01/19/2023]
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35
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Takata M, Pachera E, Frank-Bertoncelj M, Kozlova A, Jüngel A, Whitfield ML, Assassi S, Calcagni M, de Vries-Bouwstra J, Huizinga TW, Kurreeman F, Kania G, Distler O. OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis. Front Immunol 2019; 10:1100. [PMID: 31156645 PMCID: PMC6533854 DOI: 10.3389/fimmu.2019.01100] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
Antisense long non-coding RNAs (AS lncRNAs) have increasingly been recognized as important regulators of gene expression and they have been found to play key roles in several diseases. However, very little is known about the role of AS lncRNAs in fibrotic diseases such as systemic sclerosis (SSc). Our recent screening experiments by RNA sequencing showed that ovarian tumor domain containing 6B antisense RNA1 (OTUD6B-AS1) and its sense gene OTUD6B were significantly downregulated in SSc skin biopsies. Therefore, we aimed to identify key regulators of OTUD6B-AS1 and to analyze the functional relevance of OTUD6B-AS1 in SSc. OTUD6B-AS1 and OTUD6B expression in SSc and healthy control (HC) dermal fibroblasts (Fb) after stimulation with transforming growth factor-β (TGFβ), Interleukin (IL)-4, IL-13, and platelet-derived growth factor (PDGF) was analyzed by qPCR. To identify the functional role of OTUD6B-AS1, dermal Fb or human pulmonary artery smooth muscle cells (HPASMC) were transfected with a locked nucleic acid antisense oligonucleotide (ASO) targeting OTUD6B-AS1. Proliferation was measured by BrdU and real-time proliferation assay. Apoptosis was measured by Caspase 3/7 assay and Western blot for cleaved caspase 3. While no difference was recorded at the basal level between HC and SSc dermal Fb, the expression of OTUD6B-AS1 and OTUD6B was significantly downregulated in both SSc and HC dermal Fb after PDGF stimulation in a time-dependent manner. Only mild and inconsistent effects were observed with TGFβ, IL-4, and IL-13. OTUD6B-AS1 knockdown in Fb and HPASMC did not affect extracellular matrix or pro-fibrotic/proinflammatory cytokine production. However, OTUD6B-AS1 knockdown significantly increased Cyclin D1 expression at the mRNA and protein level. Moreover, silencing of OTUD6B-AS1 significantly reduced proliferation and suppressed apoptosis in both dermal Fb and HPASMC. OTUD6B-AS1 knockdown did not affect OTUD6B expression at the mRNA level and protein level. Our data suggest that OTUD6B-AS1 regulates proliferation and apoptosis via cyclin D1 expression in a sense gene independent manner. This is the first report investigating the function of OTUD6B-AS1. Our data shed light on a novel apoptosis resistance mechanism in Fb and vascular smooth muscle cells that might be relevant for pathogenesis of SSc.
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Affiliation(s)
- Miki Takata
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Elena Pachera
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Anastasiia Kozlova
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Astrid Jüngel
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Shervin Assassi
- Department of Internal Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, United States
| | - Maurizio Calcagni
- Department of Plastic Surgery and Hand Surgery, University Hospital Zürich, Zurich, Switzerland
| | | | - Tom W Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Gabriela Kania
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
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36
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Shi HJ, Wang MW, Sun JT, Wang H, Li YF, Chen BR, Fan Y, Wang SB, Wang ZM, Wang QM, Wang LS. A novel long noncoding RNA FAF inhibits apoptosis via upregulating FGF9 through PI3K/AKT signaling pathway in ischemia-hypoxia cardiomyocytes. J Cell Physiol 2019; 234:21973-21987. [PMID: 31093967 DOI: 10.1002/jcp.28760] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 01/03/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been increasingly considered to play an important role in the pathological process of various cardiovascular diseases, which often bind to the proximal promoters of the protein-coding gene to regulate the protein expression. However, the functions and mechanisms of lncRNAs in cardiomyocytes have not been fully elucidated. High-throughput RNA sequencing was performed to identify the differently expressed lncRNAs and messenger RNAs (mRNAs) between acute myocardial infarction (AMI) rats and healthy controls. One novel lncRNA FGF9-associated factor (termed FAF) and mRNAs in AMI rats were verified by bioinformatics, real-time polymerase chain reaction or western blot. Moreover, RNA fluorescence in situ hybridization was performed to determine the location of lncRNA. Subsequently, a series of in vitro assays were used to observe the functions of lncRNA FAF in cardiomyocytes. The expression of lncRNA FAF and FGF9 were remarkably decreased in ischemia-hypoxia cardiomyocytes and heart tissues of AMI rats. Overexpression of FAF could significantly inhibit cardiomyocytes apoptosis induced by ischemia and hypoxia. Conversely, knockdown of lncRNA FAF could promote apoptosis in ischemia-hypoxia cardiomyocytes. Moreover, overexpression of lncRNA FAF could also increase the expression of FGF9. Knockdown of the FGF9 expression could promote apoptosis in cardiomyocytes with the insult of ischemia and hypoxia, which was consistent with the effect of lncRNA FAF overexpression on cardiomyocyte apoptosis. Mechanistically, FGF9 inhibited cardiomyocytes apoptosis through activating signaling tyrosine kinase FGFR2 via phosphoinositide 3-kinase/protein kinase B signaling pathway. Thus, lncRNA FAF plays a protective role in ischemia-hypoxia cardiomyocytes and may serve as a treatment target for AMI.
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Affiliation(s)
- Hao-Jie Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming-Wei Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-Teng Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ya-Fei Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bing-Rui Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Fan
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Si-Bo Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zi-Mu Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi-Ming Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lian-Sheng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Abstract
Background It was shown that the major part of human genome is transcribed and produces a large number of long noncoding RNAs (lncRNAs). Today there are many evidences that lncRNAs play important role in the regulation of gene expression during different cellular processes. Moreover, lncRNAs are involved in the development of various human diseases. However, the function of the major part of annotated transcripts is currently unknown, whereas different lncRNAs annotations tend to have low overlap. Recent studies revealed that some lncRNAs have small open reading frames (smORFs), that produce the functional microproteins. However, the question whether the function of such genes is determined by microprotein or RNA itself or both remains open. Thus, the study of new lncRNA genes is important to understanding the functional role of such a heterogeneous class of genes. Results In the present study, we used reverse transcription PCR and rapid amplification of cDNA ends (RACE) analysis to determine the structure of the LINC01420 transcript. We revealed that LINC01420 has two isoforms that differ in length of the last exon and are localized predominantly in the cytoplasm. We showed that expression of the short isoform is much higher than the long. Besides, MTT and wound-healing assays revealed that LINC01420 inhibited cell migration in human melanoma cell line A375, but does not influence on cell viability. Conclusion During our work, D’Lima et al. found smORF in the first exon of the LINC01420 gene. This smORF produces functional microprotein named non-annotated P-body dissociating polypeptide (NoBody). However, our results provide new facts about LINC01420 transcript and its function.
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Affiliation(s)
- Daria O Konina
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | | | - Mikhail Yu Skoblov
- Research Centre for Medical Genetics, Moscow, Russian Federation, 115522.,Far Eastern Federal University, Vladivostok, 690090, Russian Federation
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Kroeze Y, Oti M, van Beusekom E, Cooijmans RHM, van Bokhoven H, Kolk SM, Homberg JR, Zhou H. Transcriptome Analysis Identifies Multifaceted Regulatory Mechanisms Dictating a Genetic Switch from Neuronal Network Establishment to Maintenance During Postnatal Prefrontal Cortex Development. Cereb Cortex 2019; 28:833-851. [PMID: 28108491 DOI: 10.1093/cercor/bhw407] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Indexed: 12/20/2022] Open
Abstract
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood. We observed 137 differentially expressed lincRNAs and 796 genes showing alternative exon usage during postnatal development. Importantly, we detected a genetic switch from neuronal network establishment in infancy to maintenance of neural networks in adulthood based on gene expression dynamics, involving changes in protein-coding and lincRNA gene expression as well as alternative exon usage. Our gene expression datasets provide insights into the multifaceted transcriptional regulation of the developing PFC. They can be used to study the basic developmental processes of the mPFC and to understand the mechanisms of neurodevelopmental and neuropsychiatric disorders. Our study provides an important contribution to the ongoing efforts to complete the "brain map", and to the understanding of PFC development.
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Affiliation(s)
- Yvet Kroeze
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 EZ Nijmegen, The Netherlands.,Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Martin Oti
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands.,Carlos Chagas Filho Biophysics Institute (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
| | - Ellen van Beusekom
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Roel H M Cooijmans
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Sharon M Kolk
- Department of Molecular Animal Physiology, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 EZ Nijmegen, The Netherlands
| | - Huiqing Zhou
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.,Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
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39
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Wu X, Sun L, Wang Z. Identification of lncRNA competitively regulated subpathways in myocardial infarction. Exp Ther Med 2019; 17:3041-3046. [PMID: 30936975 PMCID: PMC6434249 DOI: 10.3892/etm.2019.7320] [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: 06/26/2018] [Accepted: 02/06/2019] [Indexed: 11/05/2022] Open
Abstract
The functions of long non-coding RNAs (lncRNAs) in myocardial infarction (MI) remain largely unknown. Thus, we used the subp athway-LINCE method to characterize the potential roles of lncRNAs in MI. Candidate lncRNA-mRNA interactions were obtained from miRNA-mRNA interactions and lncRNA-miRNA interactions. Then the lncRNA and mRNA co-expression relationship pairs (LncGenePairs) were screened from the lncRNAs and mRNA intersections, which were extracted through candidate lncRNA-mRNA interactions and sample gene expression profiles. The lncRNAs in LncGenePairs were embedded into pathway graphs as nodes through linking to their regulated mRNAs, which resulted in obtaining condition-specific lncRNA competitively regulated signal pathways (csLncRPs). Finally, the csLncRPs were calculated using lenient distance similarity to obtain the lncRNA competitively regulated subpathways. Based on the statistical significance of signal subpathways, lncRNA-mRNA networks were constructed, in which hub lncRNAs were selected. A total of 65 lncRNAs competitively regulated subpathways and 13 hub lncRNAs were obtained, which associated with a risk of MI. Identifying lncRNAs competitively regulated subpathways not only provides potential lncRNA biomarkers for MI, but also helps the understanding of pathogenesis of MI.
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Affiliation(s)
- Xia Wu
- Department of Geriatrics, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163316, P.R. China
| | - Lili Sun
- Department of Geriatrics, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163316, P.R. China
| | - Ziliang Wang
- Department of Cardiovascular Medicine, Daqing People's Hospital, Daqing, Heilongjiang 163316, P.R. China
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Wang C, Qu Y, Suo R, Zhu Y. Long non-coding RNA MALAT1 regulates angiogenesis following oxygen-glucose deprivation/reoxygenation. J Cell Mol Med 2019; 23:2970-2983. [PMID: 30784209 PMCID: PMC6433728 DOI: 10.1111/jcmm.14204] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/17/2018] [Accepted: 01/06/2019] [Indexed: 12/30/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) have been identified as playing critical roles in multiple diseases. However, little is known regarding their roles and mechanisms in post‐stroke angiogenesis. Our studies focused on deciphering the functional roles and the underlying mechanisms of the lncRNA metastasis‐associated lung adenocarcinoma transcript 1 (MALAT1) in the process of angiogenesis following oxygen‐glucose deprivation/reoxygenation (OGD/R). We characterized the up‐regulation of MALAT1 expression in the process of angiogenesis after hypoxic injury in vivo and in vitro. We further showed that compared with the empty vector, MALAT1 knockdown had significantly reduced the capacity for angiogenesis, which was measured by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium (MTT), scratching, cell cycle and immunofluorescent staining. Thus, our findings suggest that MALAT1 may mediate proangiogenic function in OGD/R. To further explore the potential mechanisms, we used lentiviruses expressing shMALAT1 and empty vector; the results revealed that shMALAT1 reduced the expression of 15‐lipoxygenase 1 (15‐LOX1), vascular endothelial growth factor (VEGF) and the phosphorylation of signal transducers and activators of transcription 3 (pSTAT3). Taken together, our results are the first to propose that MALAT1 may regulate angiogenesis through the 15‐LOX1/STAT3 signalling pathway, and they may provide a critical target for the treatment of hypoxic injury and an avenue for therapeutic angiogenesis.
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Affiliation(s)
- Chengya Wang
- Department of Neurology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Youyang Qu
- Department of Neurology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Rui Suo
- Department of Neurology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yulan Zhu
- Department of Neurology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
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41
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Li L, Zhuang Y, Zhao X, Li X. Long Non-coding RNA in Neuronal Development and Neurological Disorders. Front Genet 2019; 9:744. [PMID: 30728830 PMCID: PMC6351443 DOI: 10.3389/fgene.2018.00744] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts which are usually more than 200 nt in length, and which do not have the protein-coding capacity. LncRNAs can be categorized based on their generation from distinct DNA elements, or derived from specific RNA processing pathways. During the past several decades, dramatic progress has been made in understanding the regulatory functions of lncRNAs in diverse biological processes, including RNA processing and editing, cell fate determination, dosage compensation, genomic imprinting and development etc. Dysregulation of lncRNAs is involved in multiple human diseases, especially neurological disorders. In this review, we summarize the recent progress made with regards to the function of lncRNAs and associated molecular mechanisms, focusing on neuronal development and neurological disorders.
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Affiliation(s)
- Ling Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingliang Zhuang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xingsen Zhao
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
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42
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Zhang W, Hu T, Song X. The function of lncRNAs in aging-related diseases and 3D genome. TRANSLATIONAL MEDICINE OF AGING 2019. [DOI: 10.1016/j.tma.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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43
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Expression profile of long non-coding RNAs in rat models of OSA-induced cardiovascular disease: new insight into pathogenesis. Sleep Breath 2018; 23:795-804. [PMID: 30535531 DOI: 10.1007/s11325-018-1753-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 02/01/2023]
Abstract
PURPOSE Long non-coding RNAs (lncRNAs) are a recently identified class of regulatory molecules involved in the regulation of numerous biological processes, but their functions in a rat model of chronic intermittent hypoxia (CIH) remain largely unknown. Therefore, for further investigation, we aimed to explore lncRNA expression profiles and reveal their potential functional roles in rat models of CIH. METHODS We used a well-established CIH rat model and conducted lncRNA microarray experiments on the heart samples of rats with CIH and under normoxia control. Differentially expressed lncRNAs and mRNAs were identified via fold-change filtering and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Bioinformatics analyses were applied to reveal the potential roles of key lncRNAs. Co-expression analysis was conducted to determine the transcriptional regulatory relationship of lncRNAs and mRNAs between the two groups. RESULTS Our data indicated that 157 lncRNAs and 319 mRNAs were upregulated, while 132 lncRNAs and 428 mRNAs were downregulated in the rat model of CIH compared with sham control. Pathway analyses showed that 31 pathways involved in upregulated transcripts and 28 pathways involved in downregulated transcripts. Co-expression networks were also constructed to explore the potential roles of differentially expressed lncRNAs on mRNAs. LncRNAs, namely, XR_596701, XR_344474, XR_600374, ENSRNOT00000065561, XR_590196, and XR_597099, were validated by the use of qRT-PCR. CONCLUSIONS The present study first revealed lncRNAs expression profiles in a rat model of CIH, providing new insight into the pathogenesis of obstructive sleep apnea-induced cardiovascular disease.
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Corney BPA, Widnall CL, Rees DJ, Davies JS, Crunelli V, Carter DA. Regulatory Architecture of the Neuronal Cacng2/Tarpγ2 Gene Promoter: Multiple Repressive Domains, a Polymorphic Regulatory Short Tandem Repeat, and Bidirectional Organization with Co-regulated lncRNAs. J Mol Neurosci 2018; 67:282-294. [PMID: 30478755 PMCID: PMC6373327 DOI: 10.1007/s12031-018-1208-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022]
Abstract
CACNG2 (TARPγ2, Stargazin) is a multi-functional regulator of excitatory neurotransmission and has been implicated in the pathological processes of several brain diseases. Cacng2 function is dependent upon expression level, but currently, little is known about the molecular mechanisms that control expression of this gene. To address this deficit and investigate disease-related gene variants, we have cloned and characterized the rat Cacng2 promoter and have defined three major features: (i) multiple repressive domains that include an array of RE-1 silencing transcription factor (REST) elements, and a calcium regulatory element-binding factor (CaRF) element, (ii) a (poly-GA) short tandem repeat (STR), and (iii) bidirectional organization with expressed lncRNAs. Functional activity of the promoter was demonstrated in transfected neuronal cell lines (HT22 and PC12), but although selective removal of REST and CaRF domains was shown to enhance promoter-driven transcription, the enhanced Cacng2 promoter constructs were still about fivefold weaker than a comparable rat Synapsin-1 promoter sequence. Direct evidence of REST activity at the Cacng2 promoter was obtained through co-transfection with an established dominant-negative REST (DNR) construct. Investigation of the GA-repeat STR revealed polymorphism across both animal strains and species, and size variation was also observed in absence epilepsy disease model cohorts (Genetic Absence Epilepsy Rats, Strasbourg [GAERS] and non-epileptic control [NEC] rats). These data provide evidence of a genotype (STR)-phenotype correlation that may be unique with respect to proximal gene regulatory sequence in the demonstrated absence of other promoter, or 3' UTR variants in GAERS rats. However, although transcriptional regulatory activity of the STR was demonstrated in further transfection studies, we did not find a GAERS vs. NEC difference, indicating that this specific STR length variation may only be relevant in the context of other (Cacna1h and Kcnk9) gene variants in this disease model. Additional studies revealed further (bidirectional) complexity at the Cacng2 promoter, and we identified novel, co-regulated, antisense rat lncRNAs that are paired with Cacng2 mRNA. These studies have provided novel insights into the organization of a synaptic protein gene promoter, describing multiple repressive and modulatory domains that can mediate diverse regulatory inputs.
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Affiliation(s)
- B P A Corney
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - C L Widnall
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - D J Rees
- Molecular Neurobiology, Institute of Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - J S Davies
- Molecular Neurobiology, Institute of Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - V Crunelli
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK
| | - D A Carter
- School of Biosciences, Cardiff University, CF103AX, Cardiff, UK.
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45
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Zhang C, Zhu Y, Liu Y, Zhang X, Yue Q, Li L, Chen Y, Lu S, Teng Z. SEMA3B-AS1-inhibited osteogenic differentiation of human mesenchymal stem cells revealed by quantitative proteomics analysis. J Cell Physiol 2018; 234:2491-2499. [PMID: 30317552 DOI: 10.1002/jcp.26776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/27/2018] [Indexed: 01/27/2023]
Abstract
Human mesenchymal stem cells (hMSCs) are fibroblastoid multipotent adult stem cells with capacities of differentiation into osteoblasts and chondrocytes and show great potential in new bone formation and bone repair-related clinical settings, such as osteoporosis. Long noncoding RNAs (lncRNAs) have been demonstrated to play important roles in various biological processes. Here, we report an antisense lncRNA SEMA3B-AS1 regulating hMSCs osteogenesis. SEMA3B-AS1 is proximal to a member of the semaphorin family Sema3b. Overexpression of SEMA3B-AS1 using the lentivirus system markedly inhibits the proliferation of hMSCs and meanwhile reduces osteogenic differentiation. Using a comprehensive proteomic technique named isobaric tag for relative and absolute quantitation, we found that SEMA3B-AS1 significantly alters the process of osteogenesis through downregulating the expression of proteins involved in actin cytoskeleton, focal adhesion, and extracellular matrix-receptor interaction, while increasing the expression of proteins in the spliceosome. Collectively, we find that SEMA3B-AS1 is a target for controlling osteogenesis of hMSCs.
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Affiliation(s)
- Chen Zhang
- Department of Orthopedic Surgery, The People's Hospital of Yuxi City, The 6th Affiliated Hospital of Kunming Medical University, Yuxi, China
| | - Yun Zhu
- Health Screening Center, The People's Hospital of Yuxi City, The 6th Affiliated Hospital of Kunming Medical University, Yuxi, China
| | - Yugang Liu
- Department of Orthopedics, Affiliated Hospital of Hebei University of Engineering, Handan, China
| | - Xiguang Zhang
- Department of Orthopedic Surgery, The People's Hospital of Yuxi City, The 6th Affiliated Hospital of Kunming Medical University, Yuxi, China
| | - Qiaoning Yue
- Department of Orthopedic Surgery, The People's Hospital of Yuxi City, The 6th Affiliated Hospital of Kunming Medical University, Yuxi, China
| | - Li Li
- Medical Research Center, Wuhan GeneCreate Biological Engineering Co., Ltd., Wuhan, China
| | - Yatang Chen
- Medical Research Center, Wuhan GeneCreate Biological Engineering Co., Ltd., Wuhan, China
| | - Sheng Lu
- Department of Orthopedics, Kunming General Hospital, PLA, Kunming, China
| | - Zhaowei Teng
- Department of Orthopedic Surgery, The People's Hospital of Yuxi City, The 6th Affiliated Hospital of Kunming Medical University, Yuxi, China
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46
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Liu C, Cao Z, Bai Y, Dou C, Gong X, Liang M, Dong R, Quan H, Li J, Dai J, Kang F, Zhao C, Dong S. LncRNA AK077216 promotes RANKL-induced osteoclastogenesis and bone resorption via NFATc1 by inhibition of NIP45. J Cell Physiol 2018; 234:1606-1617. [PMID: 30132869 DOI: 10.1002/jcp.27031] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Osteoclasts derived from the monocyte/macrophage hematopoietic lineage regulate bone resorption, a process balanced by bone formation in the continual renewal of the skeletal system. As dysfunctions of these cells result in bone metabolic diseases such as osteoporosis and osteopetrosis, the exploration of the mechanisms regulating their differentiation is a priority. A potential mechanism may involve long noncoding RNAs (lncRNAs), which are known to regulate various cell biology activities, including proliferation, differentiation, and apoptosis. The expression of the lncRNA AK077216 (Lnc-AK077216) is significantly upregulated during osteoclastogenesis identified by microarray and verified by qPCR. Up- and downregulation of Lnc-AK077216, respectively promotes and inhibits osteoclast differentiation, bone resorption, and the expression of related genes on the basis of tartrate-resistant acid phosphatase staining, qPCR, and western blot results. In addition, Lnc-AK077216 suppresses NIP45 expression and promotes the expression of NFATc1, an essential transcription factor during osteoclastogenesis. Besides, it was found that the expression of Lnc-AK077216 and Nfatc1 is upregulated, whereas Nip45 expression is downregulated in bone marrow and spleen tissues of ovariectomized mice. The results suggest that Lnc-AK077216 regulates NFATc1 expression and promotes osteoclast formation and function, providing a novel mechanism of osteoclastogenesis and a potential biomarker or a new drug target for osteoporosis.
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Affiliation(s)
- Chuan Liu
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China.,Department of Orthopedic, The Army General Hospital, Beijing, China
| | - Zhen Cao
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yun Bai
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ce Dou
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaoshan Gong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Mengmeng Liang
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Rui Dong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hongyu Quan
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jianmei Li
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jingjin Dai
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Fei Kang
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chunrong Zhao
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shiwu Dong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Third Military Medical University (Army Medical University), Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
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Bayyurt B, Arslan S, Engin A, Bakir M. HULC and 7SL RNA expression levels in patients with Crimean-Congo hemorrhagic fever. J Med Virol 2018; 90:1822-1826. [PMID: 30016560 DOI: 10.1002/jmv.25264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease caused by the Crimean-Congo hemorrhagic fever virus. Long non-coding RNAs (lncRNAs) are generally classified as transcripts longer than 200 nucleotides (nt). The various lncRNAs expressed in infected cells are responsible for regulating the expression of viral and host genes. This is the first study to investigate hepatocellular carcinoma upregulated long non-coding RNA (HULC) and 7SL RNA expression levels in patients with CCHF. Blood samples were taken from 100 individuals (60 patients and 40 controls), and total RNA isolation was performed. Quantitative polymerase chain reaction (qPCR) was performed using the SYBR Green method to determine HULC and 7SL RNA expression levels in the study population. Compared the patient and control groups, HULC was upregulated statistically significantly (P = 0.04) and 7SL RNA was downregulated (P = 0.93) in patients. Also, there was a statistically significant difference between fatal cases and surviving patients for HULC and 7SL RNA (P < 0.01 and P = 0.03, respectively). In addition, HULC expression was increased statistically significantly in fatal cases compared with surviving patients in terms of clinical parameters such as aspartate aminotransferase (P < 0.01), alanine aminotransferase (P < 0.01), international normalized ratio (P = 0.05), prothrombin time (P = 0.01), active partial thromboplastin time (P < 0.01), and lactate dehydrogenase (P < 0.01). These findings highlighted that HULC and 7SL RNA could be important mediators for studying the pathogenesis of CCHF and significant therapeutic targets of the disease.
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Affiliation(s)
- Burcu Bayyurt
- Department of Medical Biology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Aynur Engin
- Department of Infectious Diseases, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Mehmet Bakir
- Department of Infectious Diseases, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
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48
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Zhou QZ, Fang SM, Zhang Q, Yu QY, Zhang Z. Identification and comparison of long non-coding RNAs in the silk gland between domestic and wild silkworms. INSECT SCIENCE 2018; 25:604-616. [PMID: 28111905 DOI: 10.1111/1744-7917.12443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/03/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using RNA sequencing technology data of silk gland in domestic and wild silkworms, we identified 599 lncRNAs in the silk gland of the silkworm. Compared with protein-coding genes, the silk gland lncRNA genes tend to have fewer exon numbers, shorter transcript length and lower GC-content. Moreover, we found that three lncRNA genes are significantly and differentially expressed between domestic and wild silkworms. The potential targets of two differentially expressed lncRNAs (DELs) (dw4sg_0040 and dw4sg_0483) and the expression-correlated genes with the two DELs are mainly enriched in the related processes of silk protein translation. This implies that these DELs may affect the phenotypic variation in silk yield between the domestic and wild silkworms through the post-transcriptional regulation of silk protein.
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Affiliation(s)
- Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Shou-Min Fang
- College of Life Science, China West Normal University, Nanchong, Sichuan, China
| | - Qiang Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Quan-You Yu
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing, China
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49
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Pang W, Lian FZ, Leng X, Wang SM, Li YB, Wang ZY, Li KR, Gao ZX, Jiang YG. Microarray expression profiling and co-expression network analysis of circulating LncRNAs and mRNAs associated with neurotoxicity induced by BPA. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:15006-15018. [PMID: 29552716 DOI: 10.1007/s11356-018-1678-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
A growing body of evidence has shown bisphenol A (BPA), an estrogen-like industrial chemical, has adverse effects on the nervous system. In this study, we investigated the transcriptional behavior of long non-coding RNAs (lncRNAs) and mRNAs to provide the information to explore neurotoxic effects induced by BPA. By microarray expression profiling, we discovered 151 differentially expressed lncRNAs and 794 differentially expressed mRNAs in the BPA intervention group compared with the control group. Gene ontology analysis indicated the differentially expressed mRNAs were mainly involved in fundamental metabolic processes and physiological and pathological conditions, such as development, synaptic transmission, homeostasis, injury, and neuroinflammation responses. In the expression network of the BPA-induced group, a great number of nodes and connections were found in comparison to the control-derived network. We identified lncRNAs that were aberrantly expressed in the BPA group, among which, growth arrest specific 5 (GAS5) might participate in the BPA-induced neurotoxicity by regulating Jun, RAS, and other pathways indirectly through these differentially expressed genes. This study provides the first investigation of genome-wide lncRNA expression and correlation between lncRNA and mRNA expression in the BPA-induced neurotoxicity. Our results suggest that the elevated expression of lncRNAs is a major biomarker in the neurotoxicity induced by BPA.
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Affiliation(s)
- Wei Pang
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China
| | - Fu-Zhi Lian
- Department of Preventive Medicine, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xue Leng
- Tianjin Institute of Medical Equipment, Tianjin, 300161, China
| | - Shu-Min Wang
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China
| | - Yi-Bo Li
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China
| | - Zi-Yu Wang
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China
| | - Kai-Ren Li
- Tianjin Institute of Medical Equipment, Tianjin, 300161, China
| | - Zhi-Xian Gao
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China.
| | - Yu-Gang Jiang
- Institute of Environmental and Operational Medicine, Da Li Dao, Tianjin, 300050, China.
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Chen L, Bao Y, Piekos SC, Zhu K, Zhang L, Zhong XB. A Transcriptional Regulatory Network Containing Nuclear Receptors and Long Noncoding RNAs Controls Basal and Drug-Induced Expression of Cytochrome P450s in HepaRG Cells. Mol Pharmacol 2018; 94:749-759. [PMID: 29691280 DOI: 10.1124/mol.118.112235] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are responsible for metabolizing drugs. Expression of P450s can directly affect drug metabolism, resulting in various outcomes in therapeutic efficacy and adverse effects. Several nuclear receptors are transcription factors that can regulate expression of P450s at both basal and drug-induced levels. Some long noncoding RNAs (lncRNAs) near a transcription factor are found to participate in the regulatory functions of the transcription factors. The aim of this study is to determine whether there is a transcriptional regulatory network containing nuclear receptors and lncRNAs controlling both basal and drug-induced expression of P450s in HepaRG cells. Small interfering RNAs or small hairpin RNAs were applied to knock down four nuclear receptors [hepatocyte nuclear factor 1α (HNF1α), hepatocyte nuclear factor 4α (HNF4α), pregnane X receptor (PXR), and constitutive androstane receptor (CAR)] as well as two lncRNAs [HNF1α antisense RNA 1 (HNF1α-AS1) and HNF4α antisense RNA 1 (HNF4α-AS1)] in HepaRG cells with or without treatment of phenobarbital or rifampicin. Expression of eight P450 enzymes was examined in both basal and drug-induced levels. CAR and PXR mainly regulated expression of specific P450s. HNF1α and HNF4α affected expression of a wide range of P450s as well as other transcription factors. HNF1α and HNF4α controlled the expression of their neighborhood lncRNAs, HNF1α-AS1 and HNF4α-AS1, respectively. HNF1α-AS1 and HNF4α-AS1 was also involved in the regulation of P450s and transcription factors in diverse manners. Altogether, our study concludes that a transcription regulatory network containing the nuclear receptors and lncRNAs controls both basal and drug-induced expression of P450s in HepaRG cells.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Stephanie C Piekos
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Kexin Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Lirong Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
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