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Ibraheem Shelash Al-Hawari S, Abdalkareem Jasim S, M A Altalbawy F, Bansal P, Kaur H, Hjazi A, Sani Mohammed J, Deorari M, Alsaadi SB, Hussein Zwamel A. An overview of lncRNA NEAT1 contribution in the pathogenesis of female cancers; from diagnosis to therapy resistance. Gene 2024; 933:148975. [PMID: 39353536 DOI: 10.1016/j.gene.2024.148975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/25/2024] [Accepted: 09/27/2024] [Indexed: 10/04/2024]
Abstract
Despite the ongoing progress in detecting and treating cancer, there is still a need for extensive research into the molecular mechanisms involved in the emergence, progression, and resistance to recurrence of female reproductive tissue-specific cancers such as ovarian, breast, cervical, and endometrial cancers. The nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) that exhibits increased expression in female tumors. Moreover, elevated levels of NEAT1 have been associated with poorer survival outcomes in cancer patients. NEAT1 plays a pivotal role in driving tumor initiation through modulating the expression of genes involved in various aspects of tumor cell proliferation, epithelial-to-mesenchymal transition (EMT), metastasis, chemoresistance, and radio-resistance. Mechanistically, NEAT1 acts as a scaffold RNA molecule via interacting with EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit), thereby influencing the expression of downstream effectors of EZH2. Additionally, NEAT1 functions as a competing endogenous RNA (ceRNA) by microRNAs (miRNAs) sponging, consequently altering the expression levels of their target genes during the development of female cancers. This comprehensive review aims to shed light on the latest insights regarding the expression pattern, biological functions, and underlying mechanisms governing the function and regulation of NEAT1 in tumors. Furthermore, particular emphasis is placed on its clinical significance as a novel diagnostic biomarker and a promising therapeutic target for female cancers.
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Affiliation(s)
- Sulieman Ibraheem Shelash Al-Hawari
- Electronic Marketing and Social Media, Economic and Administrative Sciences Zarqa University, Jordan; Research follower, INTI International University, 71800 Negeri Sembilan, Malaysia
| | - Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, College of Health and Medical Technology, University of Al-maarif, Anbar, Iraq.
| | - Farag M A Altalbawy
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh 247341, India; Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand 831001, India
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Jaafaru Sani Mohammed
- Medical Analysis Department, Faculty of Applied Science, Tishk International University, Erbil, Iraq
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Salim B Alsaadi
- Department of Pharmaceutics/ Al-Hadi University College, Baghdad 10011, Iraq
| | - Ahmed Hussein Zwamel
- Department of Medical Laboratory Technology, College of Medical Technology, The Islamic University, Najaf, Iraq
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2
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Noches V, Campos-Melo D, Droppelmann CA, Strong MJ. Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis. Front Mol Neurosci 2024; 17:1417961. [PMID: 39290830 PMCID: PMC11405384 DOI: 10.3389/fnmol.2024.1417961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.
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Affiliation(s)
- Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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3
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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024; 52:1809-1825. [PMID: 38958608 DOI: 10.1042/bst20231447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
TDP-43 is an abundant and ubiquitously expressed nuclear protein that becomes dysfunctional in a spectrum of neurodegenerative diseases. TDP-43's ability to phase separate and form/enter biomolecular condensates of varying size and composition is critical for its functionality. Despite the high density of phase-separated assemblies in the nucleus and the nuclear abundance of TDP-43, our understanding of the condensate-TDP-43 relationship in this cellular compartment is only emerging. Recent studies have also suggested that misregulation of nuclear TDP-43 condensation is an early event in the neurodegenerative disease amyotrophic lateral sclerosis. This review aims to draw attention to the nuclear facet of functional and aberrant TDP-43 condensation. We will summarise the current knowledge on how TDP-43 containing nuclear condensates form and function and how their homeostasis is affected in disease.
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Affiliation(s)
- Ruaridh Lang
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
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Fan Z, Yin B, Chen X, Yang G, Zhang W, Ye X, Han H, Li M, Shu M, Liu R. Comprehensive analysis of paraspeckle-associated gene modules unveils prognostic signatures and immunological relevance in multi-cancers. Discov Oncol 2024; 15:345. [PMID: 39133261 PMCID: PMC11319543 DOI: 10.1007/s12672-024-01188-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, characterized by high rates of angiogenesis and immune evasion. Paraspeckle genes, involved in gene regulation and RNA metabolism, have recently been linked to tumor progression. This study aims to elucidate the relationship between paraspeckle genes and HCC prognosis, focusing on SFPQ, DDX39B, and UBAP2. METHODS We analyzed HCC (LIHC) and prostate cancer (PRAD) samples from the TCGA database to explore the correlation between paraspeckle genes and angiogenesis. We conducted unsupervised clustering, risk scoring, and survival analysis to identify distinct patient groups and their clinical outcomes. Gene expression data were used to perform differential analysis and Gene Ontology (GO) enrichment. RESULTS Our analysis identified significant correlations between paraspeckle genes and angiogenesis across multiple cancer types. Elevated expression levels of SFPQ, DDX39B, and UBAP2 were associated with poor prognosis in HCC patients, and all of them has statistical significance. Unsupervised clustering of HCC samples based on paraspeckle gene expression revealed two distinct clusters, with high-risk patients exhibiting stronger immune suppression and tumor immune evasion. GO enrichment highlighted critical pathways related to angiogenesis and immune regulation. Additionally, a risk scoring model based on these genes effectively distinguished high-risk and low-risk patient groups, providing valuable prognostic insights. CONCLUSION This study demonstrates that SFPQ, DDX39B, and UBAP2 are significantly associated with poor prognosis in HCC, likely due to their roles in promoting angiogenesis and immune suppression. These findings highlight the potential of paraspeckle genes as prognostic biomarkers and therapeutic targets, offering new avenues for personalized treatment strategies in HCC. Further research into their functional mechanisms and clinical applicability is crucial for advancing HCC treatment and improving patient outcomes.
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Affiliation(s)
- Zhuoyang Fan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bowen Yin
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology, (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaochen Chen
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guowei Yang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Zhang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodan Ye
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hong Han
- Department of Ultrasound, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Minfeng Shu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
- Key Laboratory of Medical Molecular Virology, (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Rong Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Interventional Radiology, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, 361015, China.
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Valizadeh M, Derafsh E, Abdi Abyaneh F, Parsamatin SK, Noshabad FZR, Alinaghipour A, Yaghoobi Z, Taheri AT, Dadgostar E, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. Non-Coding RNAs and Neurodegenerative Diseases: Information of their Roles in Apoptosis. Mol Neurobiol 2024; 61:4508-4537. [PMID: 38102518 DOI: 10.1007/s12035-023-03849-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Apoptosis can be known as a key factor in the pathogenesis of neurodegenerative disorders. In disease conditions, the rate of apoptosis expands and tissue damage may become apparent. Recently, the scientific studies of the non-coding RNAs (ncRNAs) has provided new information of the molecular mechanisms that contribute to neurodegenerative disorders. Numerous reports have documented that ncRNAs have important contributions to several biological processes associated with the increase of neurodegenerative disorders. In addition, microRNAs (miRNAs), circular RNAs (circRNAs), as well as, long ncRNAs (lncRNAs) represent ncRNAs subtypes with the usual dysregulation in neurodegenerative disorders. Dysregulating ncRNAs has been associated with inhibiting or stimulating apoptosis in neurodegenerative disorders. Therefore, this review highlighted several ncRNAs linked to apoptosis in neurodegenerative disorders. CircRNAs, lncRNAs, and miRNAs were also illustrated completely regarding the respective signaling pathways of apoptosis.
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Affiliation(s)
| | - Ehsan Derafsh
- Windsor University School of Medicine, Cayon, Canada
| | | | - Sayedeh Kiana Parsamatin
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Azam Alinaghipour
- School of Medical Sciences, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Zahra Yaghoobi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
| | - Abdolkarim Talebi Taheri
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, IR, Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, IR, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, IR, Iran.
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran.
| | - Fatemeh Nabavizadeh
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
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Sarangi P, Senthilkumar MB, Amit S, Kumar N, Jayandharan GR. AAV mediated repression of Neat1 lncRNA combined with F8 gene augmentation mitigates pathological mediators of joint disease in haemophilia. J Cell Mol Med 2024; 28:e18460. [PMID: 38864710 PMCID: PMC11167708 DOI: 10.1111/jcmm.18460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/24/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
Haemophilic arthropathy (HA), a common comorbidity in haemophilic patients leads to joint pain, deformity and reduced quality of life. We have recently demonstrated that a long non-coding RNA, Neat1 as a primary regulator of matrix metalloproteinase (MMP) 3 and MMP13 activity, and its induction in the target joint has a deteriorating effect on articular cartilage. In the present study, we administered an Adeno-associated virus (AAV) 5 vector carrying an short hairpin (sh)RNA to Neat1 via intra-articular injection alone or in conjunction with systemic administration of a capsid-modified AAV8 (K31Q) vector carrying F8 gene (F8-BDD-V3) to study its impact on HA. AAV8K31Q-F8 vector administration at low dose, led to an increase in FVIII activity (16%-28%) in treated mice. We further observed a significant knockdown of Neat1 (~40 fold vs. untreated injured joint, p = 0.005) in joint tissue of treated mice and a downregulation of chondrodegenerative enzymes, MMP3, MMP13 and the inflammatory mediator- cPLA2, in mice receiving combination therapy. These data demonstrate that AAV mediated Neat1 knockdown in combination with F8 gene augmentation can potentially impact mediators of haemophilic joint disease.
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Affiliation(s)
- Pratiksha Sarangi
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Mohankumar B. Senthilkumar
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Sonal Amit
- Department of PathologyAutonomous State Medical CollegeKanpurUttar PradeshIndia
| | - Narendra Kumar
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Giridhara R. Jayandharan
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
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Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
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Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Dayal S, Chaubey D, Joshi DC, Ranmale S, Pillai B. Noncoding RNAs: Emerging regulators of behavioral complexity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1847. [PMID: 38702948 DOI: 10.1002/wrna.1847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/06/2024]
Abstract
The mammalian genome encodes thousands of non-coding RNAs (ncRNAs), ranging in size from about 20 nucleotides (microRNAs or miRNAs) to kilobases (long non-coding RNAs or lncRNAs). ncRNAs contribute to a layer of gene regulation that could explain the evolution of massive phenotypic complexity even as the number of protein-coding genes remains unaltered. We propose that low conservation, poor expression, and highly restricted spatiotemporal expression patterns-conventionally considered ncRNAs may affect behavior through direct, rapid, and often sustained regulation of gene expression at the transcriptional, post-transcriptional, or translational levels. Besides these direct roles, their effect during neurodevelopment may manifest as behavioral changes later in the organism's life, especially when exposed to environmental cues like stress and seasonal changes. The lncRNAs affect behavior through diverse mechanisms like sponging of miRNAs, recruitment of chromatin modifiers, and regulation of alternative splicing. We highlight the need for synthesis between rigorously designed behavioral paradigms in model organisms and the wide diversity of behaviors documented by ethologists through field studies on organisms exquisitely adapted to their environmental niche. Comparative genomics and the latest advancements in transcriptomics provide an unprecedented scope for merging field and lab studies on model and non-model organisms to shed light on the role of ncRNAs in driving the behavioral responses of individuals and groups. We touch upon the technical challenges and contentious issues that must be resolved to fully understand the role of ncRNAs in regulating complex behavioral traits. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sanovar Dayal
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Divya Chaubey
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samruddhi Ranmale
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Beena Pillai
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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9
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Yucel-Polat A, Campos-Melo D, Alikhah A, Strong MJ. Dynamic Localization of Paraspeckle Components under Osmotic Stress. Noncoding RNA 2024; 10:23. [PMID: 38668381 PMCID: PMC11053584 DOI: 10.3390/ncrna10020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
Paraspeckles are nuclear condensates formed by NEAT1_2 lncRNA and different RNA-binding proteins. In general, these membraneless organelles function in the regulation of gene expression and translation and in miRNA processing, and in doing this, they regulate cellular homeostasis and mediate pro-survival in the cell. Despite evidence showing the importance of paraspeckles in the stress response, the dynamics of paraspeckles and their components under conditions of osmotic stress remain unknown. We exposed HEK293T cells to sorbitol and examined NEAT1_2 expression using real-time PCR. Localization and quantification of the main paraspeckle components, NEAT1_2, PSPC1, NONO, and SFPQ, in different cellular compartments was performed using smFISH and immunofluorescence. Our findings showed a significant decrease in total NEAT1_2 expression in cells after osmotic stress. Sorbitol shifted the subcellular localization of NEAT1_2, PSPC1, NONO, and SFPQ from the nucleus to the cytoplasm and decreased the number and size of NEAT1_2 foci in the nucleus. PSPC1 formed immunoreactive cytoplasmic fibrils under conditions of osmotic stress, which slowly disassembled under recovery. Our study deepens the paraspeckle dynamics in response to stress, suggesting a novel role for NEAT1_2 in the cytoplasm in osmotic stress and physiological conditions.
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Affiliation(s)
- Aysegul Yucel-Polat
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Danae Campos-Melo
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Asieh Alikhah
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Michael J. Strong
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
- Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
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10
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Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2024; 29:874-890. [PMID: 38145986 PMCID: PMC11176085 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
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11
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Gandhi P, Wang Y, Li G, Wang S. The role of long noncoding RNAs in ocular angiogenesis and vascular oculopathy. Cell Biosci 2024; 14:39. [PMID: 38521951 PMCID: PMC10961000 DOI: 10.1186/s13578-024-01217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are RNA transcripts over 200 nucleotides in length that do not code for proteins. Initially considered a genomic mystery, an increasing number of lncRNAs have been shown to have vital roles in physiological and pathological conditions by regulating gene expression through diverse mechanisms depending on their subcellular localization. Dysregulated angiogenesis is responsible for various vascular oculopathies, including diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration, and corneal neovascularization. While anti-VEGF treatment is available, it is not curative, and long-term outcomes are suboptimal, and some patients are unresponsive. To better understand these diseases, researchers have investigated the role of lncRNAs in regulating angiogenesis and models of vascular oculopathies. This review summarizes recent research on lncRNAs in ocular angiogenesis, including the pro-angiogenic lncRNAs ANRIL, HOTAIR, HOTTIP, H19, IPW, MALAT1, MIAT, NEAT1, and TUG1, the anti-angiogenic lncRNAs MEG3 and PKNY, and the human/primate specific lncRNAs lncEGFL7OS, discussing their functions and mechanisms of action in vascular oculopathies.
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Affiliation(s)
- Pranali Gandhi
- Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yuzhi Wang
- Louisiana State University School of Medicine, New Orleans, LA, 70112, USA
| | - Guigang Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, P.R. China.
| | - Shusheng Wang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, 70118, USA.
- Department of Ophthalmology, Tulane University, New Orleans, LA, 70112, USA.
- Tulane Personalized Health Institute, Tulane University, New Orleans, LA, 70112, USA.
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12
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Babington S, Tilbrook AJ, Maloney SK, Fernandes JN, Crowley TM, Ding L, Fox AH, Zhang S, Kho EA, Cozzolino D, Mahony TJ, Blache D. Finding biomarkers of experience in animals. J Anim Sci Biotechnol 2024; 15:28. [PMID: 38374201 PMCID: PMC10877933 DOI: 10.1186/s40104-023-00989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/28/2023] [Indexed: 02/21/2024] Open
Abstract
At a time when there is a growing public interest in animal welfare, it is critical to have objective means to assess the way that an animal experiences a situation. Objectivity is critical to ensure appropriate animal welfare outcomes. Existing behavioural, physiological, and neurobiological indicators that are used to assess animal welfare can verify the absence of extremely negative outcomes. But welfare is more than an absence of negative outcomes and an appropriate indicator should reflect the full spectrum of experience of an animal, from negative to positive. In this review, we draw from the knowledge of human biomedical science to propose a list of candidate biological markers (biomarkers) that should reflect the experiential state of non-human animals. The proposed biomarkers can be classified on their main function as endocrine, oxidative stress, non-coding molecular, and thermobiological markers. We also discuss practical challenges that must be addressed before any of these biomarkers can become useful to assess the experience of an animal in real-life.
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Affiliation(s)
- Sarah Babington
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Alan J Tilbrook
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Shane K Maloney
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Jill N Fernandes
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Tamsyn M Crowley
- School of Medicine, Deakin University, Geelong, VIC, 3217, Australia
- Poultry Hub Australia, University of New England, Armidale, NSW, 2350, Australia
| | - Luoyang Ding
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Song Zhang
- School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Elise A Kho
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Daniel Cozzolino
- Centre for Nutrition and Food Sciences, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Timothy J Mahony
- Centre for Animal Science, The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dominique Blache
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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13
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Anilkumar AK, Vij P, Lopez S, Leslie SM, Doxtater K, Khan MM, Yallapu MM, Chauhan SC, Maestre GE, Tripathi MK. Long Non-Coding RNAs: New Insights in Neurodegenerative Diseases. Int J Mol Sci 2024; 25:2268. [PMID: 38396946 PMCID: PMC10889599 DOI: 10.3390/ijms25042268] [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: 01/03/2024] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of NDDs are related to mitochondrial dysfunction, oxidative stress, and inflammation, which further stimulate the progression of NDDs. Recently, long non-coding RNAs (lncRNAs) have attracted ample attention as critical mediators in the pathology of NDDs. However, there is a significant gap in understanding the biological function, molecular mechanisms, and potential importance of lncRNAs in NDDs. This review documents the current research on lncRNAs and their implications in NDDs. We further summarize the potential implication of lncRNAs to serve as novel therapeutic targets and biomarkers for patients with NDDs.
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Affiliation(s)
- Adithya K. Anilkumar
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Puneet Vij
- Department of Pharmaceutical Sciences, St. John’s University, Queens, NY 11439, USA
| | - Samantha Lopez
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Sophia M. Leslie
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Kyle Doxtater
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Murali M. Yallapu
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Gladys E. Maestre
- Department of Neurosciences, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78550, USA
- South Texas Alzheimer’s Disease Research Center, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX 78550, USA
| | - Manish K. Tripathi
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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14
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Hussain MS, Gupta G, Afzal M, Alqahtani SM, Samuel VP, Hassan Almalki W, Kazmi I, Alzarea SI, Saleem S, Dureja H, Singh SK, Dua K, Thangavelu L. Exploring the role of lncrna neat1 knockdown in regulating apoptosis across multiple cancer types: A review. Pathol Res Pract 2023; 252:154908. [PMID: 37950931 DOI: 10.1016/j.prp.2023.154908] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression, contributing significantly to a diverse range of cellular processes, including apoptosis. One such lncRNA is NEAT1, which is elevated in several types of cancer and aid in cancer growth. However, recent studies have also demonstrated that the knockdown of NEAT1 can inhibit cancer cells proliferation, movement, and infiltration while enhancing apoptosis. This article explores the function of lncRNA NEAT1 knockdown in regulating apoptosis across multiple cancer types. We explore the existing understanding of NEAT1's involvement in the progression of malignant conditions, including its structure and functions. Additionally, we investigate the molecular mechanisms by which NEAT1 modulates the cell cycle, cellular proliferation, apoptosis, movement, and infiltration in diverse cancer types, including acute myeloid leukemia, breast cancer, cervical cancer, colorectal cancer, esophageal squamous cell carcinoma, glioma, non-small cell lung cancer, ovarian cancer, prostate cancer, and retinoblastoma. Furthermore, we review the recent studies investigating the therapeutic potential of NEAT1 knockdown in cancer treatment. Targeting the lncRNA NEAT1 presents a promising therapeutic approach for treating cancer. It has shown the ability to suppress cancer cell proliferation, migration, and invasion while promoting apoptosis in various cancer types.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | - Gaurav Gupta
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Safar M Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Vijaya Paul Samuel
- Department of Anatomy, RAK Medical & Health Sciences University, Ras Al Khaimah College of Medical Sciences, Ras Al Khaimah, United Arab Emirates
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - Kamal Dua
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
| | - Lakshmi Thangavelu
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
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15
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Cao T, Zhang S, Chen Q, Zeng C, Wang L, Jiao S, Chen H, Zhang B, Cai H. Long non-coding RNAs in schizophrenia: Genetic variations, treatment markers and potential targeted signaling pathways. Schizophr Res 2023; 260:12-22. [PMID: 37543007 DOI: 10.1016/j.schres.2023.07.027] [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: 04/29/2022] [Revised: 05/19/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
Schizophrenia (SZ), a complex and debilitating spectrum of psychiatric disorders, is now mainly attributed to multifactorial etiology that includes genetic and environmental factors. Long non-coding RNAs (lncRNAs) are gaining popularity as a way to better understand the comprehensive mechanisms beneath the clinical manifestation of SZ. Only in recent years has it been elucidated that mammalian genomes encode thousands of lncRNAs. Strikingly, roughly 30-40% of these lncRNAs are extensively expressed in different regions across the brain, which may be closely associated with SZ. The therapeutic and adverse effects of atypical antipsychotic drugs (AAPDs) are partially reflected by their role in the regulation of lncRNAs. This begs the question directly, do any lncRNAs exist as biomarkers for AAPDs treatment? Furthermore, we comprehend a range of mechanistic investigations that have revealed the regulatory roles for lncRNAs both involved in the brain and the periphery of SZ. More crucially, we also combine insights from a variety of signaling pathways to argue that lncRNAs probably play critical roles in SZ via their interactive downstream factors. This review provides a thorough understanding regarding dysregulation of lncRNAs, corresponding genetic alternations, as well as their potential regulatory roles in the pathology of SZ, which might help reveal useful therapeutic targets in SZ.
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Affiliation(s)
- Ting Cao
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - ShuangYang Zhang
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Chen
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - CuiRong Zeng
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - LiWei Wang
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - ShiMeng Jiao
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Chen
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - BiKui Zhang
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - HuaLin Cai
- Department of Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Institute of Clinical Pharmacy, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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16
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Maruyama M, Sakai A, Fukunaga T, Miyagawa Y, Okada T, Hamada M, Suzuki H. Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury. Front Immunol 2023; 14:1185322. [PMID: 37614230 PMCID: PMC10442554 DOI: 10.3389/fimmu.2023.1185322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Primary sensory neurons regulate inflammatory processes in innervated regions through neuro-immune communication. However, how their immune-modulating functions are regulated in concert remains largely unknown. Here, we show that Neat1 long non-coding RNA (lncRNA) organizes the proinflammatory gene expressions in the dorsal root ganglion (DRG) in chronic intractable neuropathic pain in rats. Neat1 was abundantly expressed in the DRG and was upregulated after peripheral nerve injury. Neat1 overexpression in primary sensory neurons caused mechanical and thermal hypersensitivity, whereas its knockdown alleviated neuropathic pain. Bioinformatics analysis of comprehensive transcriptome changes indicated the inflammatory response was the most relevant function of genes upregulated through Neat1. Consistent with this, upregulation of proinflammatory genes in the DRG following nerve injury was suppressed by Neat1 knockdown. Expression changes of these proinflammatory genes were regulated through Neat1-mRNA interaction-dependent and -independent mechanisms. Notably, Neat1 increased proinflammatory genes by stabilizing its interacting mRNAs in neuropathic pain. Finally, Neat1 in primary sensory neurons contributed to spinal inflammatory processes that mediated peripheral neuropathic pain. These findings demonstrate that Neat1 lncRNA is a key regulator of neuro-immune communication in neuropathic pain.
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Affiliation(s)
- Motoyo Maruyama
- Department of Pharmacology, Nippon Medical School, Bunkyo-ku, Japan
- Division of Laboratory Animal Science, Nippon Medical School, Bunkyo-ku, Japan
| | - Atsushi Sakai
- Department of Pharmacology, Nippon Medical School, Bunkyo-ku, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Shinjuku-ku, Japan
- Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Japan
| | - Yoshitaka Miyagawa
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Bunkyo-ku, Japan
| | - Takashi Okada
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Bunkyo-ku, Japan
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Shinjuku-ku, Japan
- Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Japan
| | - Hidenori Suzuki
- Department of Pharmacology, Nippon Medical School, Bunkyo-ku, Japan
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17
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Tokunaga M, Imamura T. Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans. Front Cell Dev Biol 2023; 11:1168072. [PMID: 37408531 PMCID: PMC10318543 DOI: 10.3389/fcell.2023.1168072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Microcephaly is characterized as a small head circumference, and is often accompanied by developmental disorders. Several candidate risk genes for this disease have been described, and mutations in non-coding regions are occasionally found in patients with microcephaly. Various non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), SINEUPs, telomerase RNA component (TERC), and promoter-associated lncRNAs (pancRNAs) are now being characterized. These ncRNAs regulate gene expression, enzyme activity, telomere length, and chromatin structure through RNA binding proteins (RBPs)-RNA interaction. Elucidating the potential roles of ncRNA-protein coordination in microcephaly pathogenesis might contribute to its prevention or recovery. Here, we introduce several syndromes whose clinical features include microcephaly. In particular, we focus on syndromes for which ncRNAs or genes that interact with ncRNAs may play roles. We discuss the possibility that the huge ncRNA field will provide possible new therapeutic approaches for microcephaly and also reveal clues about the factors enabling the evolutionary acquisition of the human-specific "large brain."
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18
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Srinivas T, Mathias C, Oliveira-Mateos C, Guil S. Roles of lncRNAs in brain development and pathogenesis: Emerging therapeutic opportunities. Mol Ther 2023; 31:1550-1561. [PMID: 36793211 PMCID: PMC10277896 DOI: 10.1016/j.ymthe.2023.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The human genome is pervasively transcribed, producing a majority of short and long noncoding RNAs (lncRNAs) that can influence cellular programs through a variety of transcriptional and post-transcriptional regulatory mechanisms. The brain houses the richest repertoire of long noncoding transcripts, which function at every stage during central nervous system development and homeostasis. An example of functionally relevant lncRNAs is species involved in spatiotemporal organization of gene expression in different brain regions, which play roles at the nuclear level and in transport, translation, and decay of other transcripts in specific neuronal sites. Research in the field has enabled identification of the contributions of specific lncRNAs to certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders, resulting in notions of potential therapeutic strategies that target these RNAs to recover the normal phenotype. Here, we summarize the latest mechanistic findings associated with lncRNAs in the brain, focusing on their dysregulation in neurodevelopmental or neurodegenerative disorders, their use as biomarkers for central nervous system (CNS) diseases in vitro and in vivo, and their potential utility for therapeutic strategies.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain
| | - Carolina Mathias
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, PR, Brazil; Laboratory of Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, PR, Brazil
| | | | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Catalonia, Spain; Germans Trias i Pujol Health Science Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain.
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19
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Irwin AB, Martina V, Jago SCS, Bahabry R, Schreiber AM, Lubin FD. The lncRNA Neat1 is associated with astrocyte reactivity and memory deficits in a mouse model of Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539260. [PMID: 37205548 PMCID: PMC10187170 DOI: 10.1101/2023.05.03.539260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Dysregulation of long non-coding RNAs (lncRNAs) have been associated with Alzheimer's disease (AD). However, the functional role of lncRNAs in AD remains unclear. Here, we report a crucial role for the lncRNA Neat1 in astrocyte dysfunction and memory deficits associated with AD. Transcriptomics analysis show abnormally high expression levels of NEAT1 in the brains of AD patients relative to aged-matched healthy controls, with the most significantly elevated levels in glial cells. In a human transgenic APP-J20 (J20) mouse model of AD, RNA-fluorescent in situ hybridization characterization of Neat1 expression in hippocampal astrocyte versus non-astrocyte cell populations revealed a significant increase in Neat1 expression in astrocytes of male, but not female, mice. This corresponded with increased seizure susceptibility in J20 male mice. Interestingly, Neat1 deficiency in the dCA1 in J20 male mice did not alter seizure threshold. Mechanistically, Neat1 deficiency in the dorsal area CA1 of the hippocampus (dCA1) J20 male mice significantly improved hippocampus-dependent memory. Neat1 deficiency also remarkably reduced astrocyte reactivity markers suggesting that Neat1 overexpression is associated with astrocyte dysfunction induced by hAPP/Aβ in the J20 mice. Together, these findings indicate that abnormal Neat1 overexpression may contribute to memory deficits in the J20 AD model not through altered neuronal activity, but through astrocyte dysfunction.
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Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Verdion Martina
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Silvienne C Sint Jago
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Anna Maria Schreiber
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Farah D. Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
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20
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Hassani SS, Karamali N, Rajabinejad M, Ashjari D, Afshar Hezarkhani L, Gorgin Karaji A, Salari F, Rezaiemanesh A. Dysregulation of Long Noncoding RNA NEAT1/miR-199a-5/BiP Axis in Patients with Diabetic Neuropathy. Lab Med 2023; 54:160-165. [PMID: 36166353 DOI: 10.1093/labmed/lmac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE Diabetic neuropathy (DN) is a type of nerve damage and the most common complication of diabetes. Regarding the association between endoplasmic reticulum (ER) stress with the pathogenesis of neuropathy, this study aims to examine binding immunoglobulin protein (BiP) gene expression and long noncoding RNA nuclear enriched abundant transcript 1 (NEAT1), miR-199a-5 as its regulator in the peripheral blood of DN patients compared to diabetic patients without neuropathy. METHODS Peripheral blood samples were obtained from DN (n = 20) patients and diabetic patients without neuropathy (non-DN) (n = 20). After RNA extraction from peripheral blood mononuclear cells, reverse transcription-quantitative polymerase chain reaction was performed to evaluate RNA expression. RESULTS The results showed that the expression level of NEAT1 and BiP genes in the DN group increased significantly compared to the non-DN group. Also, the expression level of miR-199a-5p in the DN group was significantly downregulated. CONCLUSION As a result, the axis of NEAT1, miR-199a-5p, and BiP may have a role in the DN pathogenesis.
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Affiliation(s)
- Seyedeh Sara Hassani
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Negin Karamali
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Misagh Rajabinejad
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Donya Ashjari
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Leila Afshar Hezarkhani
- Department of Neurology, School of Medicine, Farabi Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Gorgin Karaji
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farhad Salari
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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21
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Merjane J, Chung R, Patani R, Lisowski L. Molecular mechanisms of amyotrophic lateral sclerosis as broad therapeutic targets for gene therapy applications utilizing adeno-associated viral vectors. Med Res Rev 2023. [PMID: 36786126 DOI: 10.1002/med.21937] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 08/19/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Despite the devastating clinical outcome of the neurodegenerative disease, amyotrophic lateral sclerosis (ALS), its etiology remains mysterious. Approximately 90% of ALS is characterized as sporadic, signifying that the patient has no family history of the disease. The development of an impactful disease modifying therapy across the ALS spectrum has remained out of grasp, largely due to the poorly understood mechanisms of disease onset and progression. Currently, ALS is invariably fatal and rapidly progressive. It is hypothesized that multiple factors can lead to the development of ALS, however, treatments are often focused on targeting specific familial forms of the disease (10% of total cases). There is a strong need to develop disease modifying treatments for ALS that can be effective across the full ALS spectrum of familial and sporadic cases. Although the onset of disease varies significantly between patients, there are general disease mechanisms and progressions that can be seen broadly across ALS patients. Therefore, this review explores the targeting of these widespread disease mechanisms as possible areas for therapeutic intervention to treat ALS broadly. In particular, this review will focus on targeting mechanisms of defective protein homeostasis and RNA processing, which are both increasingly recognized as design principles of ALS pathogenesis. Additionally, this review will explore the benefits of gene therapy as an approach to treating ALS, specifically focusing on the use of adeno-associated virus (AAV) as a vector for gene delivery to the CNS and recent advances in the field.
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Affiliation(s)
- Jessica Merjane
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Roger Chung
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rickie Patani
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK.,The Francis Crick Institute, London, UK
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia.,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
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22
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Li X, Li J, Shan G, Wang X. Identification of long non-coding RNA and circular RNA associated networks in cellular stress responses. Front Genet 2023; 14:1097571. [PMID: 36845400 PMCID: PMC9953141 DOI: 10.3389/fgene.2023.1097571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Mammalian cells employ various adaptive responses to cope with multiple stresses to maintain homeostasis. Functional roles of non-coding RNAs (ncRNAs) in response to cellular stresses have been proposed, and systematical investigations about the crosstalk among distinct types of RNAs are required. Here, we challenged HeLa cells with thapsigargin (TG) and glucose deprivation (GD) treatments to induce endoplasmic reticulum (ER) and metabolic stresses, respectively. Ribosomal RNA (rRNA)-depleted RNA sequencing (RNA-seq) was then performed. Characterization of the RNA-seq data revealed a series of differentially expressed long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) with parallel changes responsive to both stimuli. We further constructed the lncRNA/circRNA-mRNA co-expressing network, competing endogenous RNA (ceRNA) network in the lncRNA/circRNA-miRNA-mRNA axis, and lncRNA/circRNA-RNA binding protein (RBP) interactome map. These networks indicated the potential cis and/or trans regulatory roles of lncRNAs and circRNAs. Moreover, Gene Ontology analysis demonstrated that these identified ncRNAs were associated with several essential biological processes known to be related to cellular stress responses. In conclusion, we systematically established functional regulatory networks of lncRNA/circRNA-mRNA, lncRNA/circRNA-miRNA-mRNA and lncRNA/circRNA-RBP to perceive the potential interactions and biological processes during cellular stresses. These results provided insights in ncRNA regulatory networks of stress responses and the basis for further identification of pivotal factors involved in cellular stress responses.
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Affiliation(s)
- Xiuzhi Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, Anhui, China
| | - Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, Anhui, China
| | - Ge Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, Anhui, China,Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China,*Correspondence: Xiaolin Wang, ; Ge Shan,
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, Anhui, China,*Correspondence: Xiaolin Wang, ; Ge Shan,
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23
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Ünal İ, Cansız D, Sürmen MG, Sürmen S, Sezer Z, Beler M, Üstündağ ÜV, Güzel E, Alturfan AA, Emekli-Alturfan E. Identification of molecular network of gut-brain axis associated with neuroprotective effects of PPARδ-ligand erucic acid in rotenone-induced Parkinson's disease model in zebrafish. Eur J Neurosci 2023; 57:585-606. [PMID: 36564343 DOI: 10.1111/ejn.15904] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Disruption of the gut-brain axis in Parkinson's disease (PD) may lead to motor symptoms and PD pathogenesis. Recently, the neuroprotective potential of different PPARδ-agonists has been shown. We aimed to reveal the effects of erucic acid, peroxisome proliferator-activated receptors (PPARs)-ligand in rotenone-induced PD model in zebrafish, focusing on the gut-brain axis. Adult zebrafish were exposed to rotenone and erucic acid for 30 days. Liquid chromatography-mass spectrometry and tandem mass spectrometry (LC-MS/MS) analysis was performed. Raw files were analysed by Proteome Discoverer 2.4 software; peptide lists were searched against Danio rerio proteins. STRING database was used for protein annotations or interactions. Lipid peroxidation (LPO), nitric oxide (No), alkaline phosphatase, superoxide dismutase, glutathione S-transferase (GST), acetylcholinesterase and the expressions of PD-related genes were determined. Immunohistochemical tyrosine hydroxylase (TH) staining was performed. LC-MS/MS analyses allowed identification of over 2000 proteins in each sample. The 2502 and 2707 proteins overlapped for intestine and brain. The 196 and 243 significantly dysregulated proteins in the brain and intestines were found in rotenone groups. Erucic acid treatment corrected the changes in the expression of proteins associated with cytoskeletal organisation, transport and localisation and improved locomotor activity, expressions of TH, PD-related genes (lrrk2, park2, park7, pink1) and oxidant-damage in brain and intestines in the rotenone group as evidenced by decreased LPO, No and increased GST. Our results showed beneficial effects of erucic acid as a PPARδ-ligand in neurotoxin-induced PD model in zebrafish. We believe that our study will shed light on the mechanism of the effects of PPARδ agonists and ω9-fatty acids in the gut-brain axis of PD.
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Affiliation(s)
- İsmail Ünal
- Institute of Health Sciences, Department of Biochemistry, Marmara University, Istanbul, Turkey
| | - Derya Cansız
- Faculty of Medicine, Department of Medical Biochemistry, Istanbul Medipol University, Istanbul, Turkey
| | - Mustafa Gani Sürmen
- Hamidiye Institute of Health Sciences, Department of Molecular Medicine, University of Health Sciences, Istanbul, Turkey
| | - Saime Sürmen
- Hamidiye Institute of Health Sciences, Department of Molecular Medicine, University of Health Sciences, Istanbul, Turkey
| | - Zehra Sezer
- Cerrahpasa Faculty of Medicine, Department of Histology and Embryology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Merih Beler
- Institute of Health Sciences, Department of Biochemistry, Marmara University, Istanbul, Turkey
| | - Ünsal Veli Üstündağ
- Faculty of Medicine, Department of Medical Biochemistry, Istanbul Medipol University, Istanbul, Turkey
| | - Elif Güzel
- Cerrahpasa Faculty of Medicine, Department of Histology and Embryology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - A Ata Alturfan
- Faculty of Medicine, Department of Biochemistry, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Faculty of Dentistry, Department of Basic Medical Sciences, Marmara University, Istanbul, Turkey
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24
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Reviewing the Potential Links between Viral Infections and TDP-43 Proteinopathies. Int J Mol Sci 2023; 24:ijms24021581. [PMID: 36675095 PMCID: PMC9867397 DOI: 10.3390/ijms24021581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Transactive response DNA binding protein 43 kDa (TDP-43) was discovered in 2001 as a cellular factor capable to inhibit HIV-1 gene expression. Successively, it was brought to new life as the most prevalent RNA-binding protein involved in several neurological disorders, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite the fact that these two research areas could be considered very distant from each other, in recent years an increasing number of publications pointed out the existence of a potentially important connection. Indeed, the ability of TDP-43 to act as an important regulator of all aspects of RNA metabolism makes this protein also a critical factor during expression of viral RNAs. Here, we summarize all recent observations regarding the involvement of TDP-43 in viral entry, replication and latency in several viruses that include enteroviruses (EVs), Theiler's murine encephalomyelitis virus (TMEV), human immunodeficiency virus (HIV), human endogenous retroviruses (HERVs), hepatitis B virus (HBV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), West Nile virus (WNV), and herpes simplex virus-2 (HSV). In particular, in this work, we aimed to highlight the presence of similarities with the most commonly studied TDP-43 related neuronal dysfunctions.
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25
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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26
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Singh AK. Hsrω and Other lncRNAs in Neuronal Functions and Disorders in Drosophila. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010017. [PMID: 36675966 PMCID: PMC9865238 DOI: 10.3390/life13010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/27/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) have a crucial role in epigenetic, transcriptional and posttranscriptional regulation of gene expression. Many of these regulatory lncRNAs, such as MALAT1, NEAT1, HOTAIR, etc., are associated with different neurodegenerative diseases in humans. The lncRNAs produced by the hsrω gene are known to modulate neurotoxicity in polyQ and amyotrophic lateral sclerosis disease models of Drosophila. Elevated expression of hsrω lncRNAs exaggerates, while their genetic depletion through hsrω-RNAi or in an hsrω-null mutant background suppresses, the disease pathogenicity. This review discusses the possible mechanistic details and implications of the functions of hsrω lncRNAs in the modulation of neurodegenerative diseases.
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Affiliation(s)
- Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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27
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An H, Elvers KT, Gillespie JA, Jones K, Atack JR, Grubisha O, Shelkovnikova TA. A toolkit for the identification of NEAT1_2/paraspeckle modulators. Nucleic Acids Res 2022; 50:e119. [PMID: 36099417 PMCID: PMC9723620 DOI: 10.1093/nar/gkac771] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
Paraspeckles are ribonucleoprotein granules assembled by NEAT1_2 lncRNA, an isoform of Nuclear Paraspeckle Assembly Transcript 1 (NEAT1). Dysregulation of NEAT1_2/paraspeckles has been linked to multiple human diseases making them an attractive drug target. However currently NEAT1_2/paraspeckle-focused translational research and drug discovery are hindered by a limited toolkit. To fill this gap, we developed and validated a set of tools for the identification of NEAT1_2 binders and modulators comprised of biochemical and cell-based assays. The NEAT1_2 triple helix stability element was utilized as the target in the biochemical assays, and the cellular assay ('ParaQuant') was based on high-content imaging of NEAT1_2 in fixed cells. As a proof of principle, these assays were used to screen a 1,200-compound FDA-approved drug library and a 170-compound kinase inhibitor library and to confirm the screening hits. The assays are simple to establish, use only commercially-available reagents and are scalable for higher throughput. In particular, ParaQuant is a cost-efficient assay suitable for any cells growing in adherent culture and amenable to multiplexing. Using ParaQuant, we identified dual PI3K/mTOR inhibitors as potent negative modulators of paraspeckles. The tools we describe herein should boost paraspeckle studies and help guide the search, validation and optimization of NEAT1_2/paraspeckle-targeted small molecules.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Karen T Elvers
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Jason A Gillespie
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Kimberley Jones
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - John R Atack
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Olivera Grubisha
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK.,Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
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28
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Sekar D, Tusubira D, Ross K. TDP-43 and NEAT long non-coding RNA: Roles in neurodegenerative disease. Front Cell Neurosci 2022; 16:954912. [PMID: 36385948 PMCID: PMC9650703 DOI: 10.3389/fncel.2022.954912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/11/2022] [Indexed: 01/03/2023] Open
Abstract
Understanding and ameliorating neurodegenerative diseases represents a key challenge for supporting the health span of the aging population. Diverse protein aggregates have been implicated in such neurodegenerative disorders, including amyloid-β, α-synuclein, tau, fused in sarcoma (FUS), and transactivation response element (TAR) DNA-binding protein 43 (TDP-43). Recent years have seen significant growth in our mechanistic knowledge of relationships between these proteins and some of the membrane-less nuclear structures that fulfill key roles in the cell function. These include the nucleolus, nuclear speckles, and paraspeckles. The ability of macromolecular protein:RNA complexes to partition these nuclear condensates through biophysical processes that involve liquid-liquid phase separation (LLPS) has also gained attention recently. The paraspeckle, which is scaffolded by the architectural long-non-coding RNA nuclear enriched abundant transcript 1 (NEAT1) plays central roles in RNA processing and metabolism and has been linked dynamically to TDP-43. In this mini-review, we outline essential early and recent insights in relation to TDP-43 proteinopathies. We then appraise the relationships between TDP-43 and NEAT1 in the context of neuronal paraspeckles and neuronal stress. We highlight key areas for investigation based on recent advances in our understanding of how TDP-43 affects neuronal function, especially in relation to messenger ribosomal nucleic acid (mRNA) splicing. Finally, we offer perspectives that should be considered for translational pipelines in order to improve health outcomes for the management of neurodegenerative diseases.
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Affiliation(s)
- Durairaj Sekar
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Deusdedit Tusubira
- Department of Biochemistry, Mbarara University of Science and Technology, Mbarara, Uganda,*Correspondence: Deusdedit Tusubira, ; orcid.org/0000-0002-4698-424X
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom,Institute for Health Research, Liverpool John Moores University, Liverpool, United Kingdom,Kehinde Ross, ; orcid.org/0000-0003-0252-1152
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29
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Qi L, Li X, Liu SM, Jiao DL, Hu D, Ju XY, Zhao SY, Si SH, Hu L, Li GN, Ma BZ, Zhou S, Zhao C. Identification of a hippocampal lncRNA-regulating network in a natural aging rat model. BMC Neurosci 2022; 23:56. [PMID: 36171542 PMCID: PMC9520886 DOI: 10.1186/s12868-022-00743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/15/2022] [Indexed: 11/14/2022] Open
Abstract
Background Dysregulation of long noncoding RNA (lncRNA) expression is related to aging and age-associated neurodegenerative diseases, and the lncRNA expression profile in the aging hippocampus is not well characterized. In the present investigation, the changed mRNAs and lncRNAs were confirmed via deep RNA sequencing. GO and KEGG pathway analyses were conducted to investigate the principal roles of the clearly dysregulated mRNAs and lncRNAs. Subsequently, through the prediction of miRNAs via which mRNAs and lncRNAs bind together, a competitive endogenous RNA network was constructed. Results A total of 447 lncRNAs and 182 mRNAs were upregulated, and 385 lncRNAs and 144 mRNAs were downregulated. Real-time reverse transcription-polymerase chain reaction validated the reliability of mRNA and lncRNA sequencing. KEGG pathway and GO analyses revealed that differentially expressed (DE) mRNAs were associated with cell adhesion molecules (CAMs), the p53 signaling pathway (SP), phagosomes, PPAR SP and ECM—receptor interactions. KEGG pathway and GO analyses showed that the target genes of the DE lncRNAs were related to cellular senescence, the p53 signaling pathway, leukocyte transendothelial migration and tyrosine metabolism. Coexpression analyses showed that 561 DE lncRNAs were associated with DE mRNAs. A total of 58 lncRNA–miRNA–mRNA target pairs were confirmed in this lncRNA‒miRNA‒mRNA network, comprising 10 mRNAs, 13 miRNAs and 38 lncRNAs. Conclusions We found specific lncRNAs and mRNAs in the hippocampus of natural aging model rats, as well as abnormal regulatory ceRNA networks. Our outcomes help explain the pathogenesis of brain aging and provide direction for further research. Supplementary Information The online version contains supplementary material available at 10.1186/s12868-022-00743-7.
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Affiliation(s)
- Li Qi
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiao Li
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shi-Min Liu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dan-Li Jiao
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dan Hu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xin-Yao Ju
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shu-Yu Zhao
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Shu-Han Si
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Li Hu
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guo-Na Li
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Bing-Zhe Ma
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shuang Zhou
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Chen Zhao
- College of Acumox and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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30
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Raskó T, Pande A, Radscheit K, Zink A, Singh M, Sommer C, Wachtl G, Kolacsek O, Inak G, Szvetnik A, Petrakis S, Bunse M, Bansal V, Selbach M, Orbán TI, Prigione A, Hurst LD, Izsvák Z. A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles. Mol Biol Evol 2022; 39:6661922. [PMID: 36205081 PMCID: PMC9538788 DOI: 10.1093/molbev/msac175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1, also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure.
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Affiliation(s)
- Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | | | | | - Annika Zink
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christian Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary,Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Gizem Inak
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Attila Szvetnik
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Mario Bunse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen 72076, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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31
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Recent Advances and the Mechanism of Astaxanthin in Ophthalmological Diseases. J Ophthalmol 2022; 2022:8071406. [PMID: 35646393 PMCID: PMC9142330 DOI: 10.1155/2022/8071406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/13/2022] [Accepted: 03/25/2022] [Indexed: 11/30/2022] Open
Abstract
Astaxanthin (AST) is a naturally occurring carotenoid that has strong antioxidant, anti-inflammatory, and antiapoptosis effects and is used for the prevention of cancer. There is growing evidence that AST has multiple protective effects against various eye diseases. This article reviews the function and the potential mechanism of AST in dry eye syndrome, keratitis, cataract, diabetic retinopathy, age-related macular degeneration, high intraocular pressure, and other ocular diseases. It provides a theoretical basis for the clinical application of AST as a potential nutraceutical.
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32
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Compartment-Specific Proximity Ligation Expands the Toolbox to Assess the Interactome of the Long Non-Coding RNA NEAT1. Int J Mol Sci 2022; 23:ijms23084432. [PMID: 35457249 PMCID: PMC9027746 DOI: 10.3390/ijms23084432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/23/2022] Open
Abstract
The nuclear paraspeckle assembly transcript 1 (NEAT1) locus encodes two long non-coding (lnc)RNA isoforms that are upregulated in many tumours and dynamically expressed in response to stress. NEAT1 transcripts form ribonucleoprotein complexes with numerous RNA-binding proteins (RBPs) to assemble paraspeckles and modulate the localisation and activity of gene regulatory enzymes as well as a subset of messenger (m)RNA transcripts. The investigation of the dynamic composition of NEAT1-associated proteins and mRNAs is critical to understand the function of NEAT1. Interestingly, a growing number of biochemical and genetic tools to assess NEAT1 interactomes has been reported. Here, we discuss the Hybridisation Proximity (HyPro) labeling technique in the context of NEAT1. HyPro labeling is a recently developed method to detect spatially ordered interactions of RNA-containing nuclear compartments in cultured human cells. After introducing NEAT1 and paraspeckles, we describe the advantages of the HyPro technology in the context of other methods to study RNA interactomes, and review the key findings in mapping NEAT1-associated RNA transcripts and protein binding partners. We further discuss the limitations and potential improvements of HyPro labeling, and conclude by delineating its applicability in paraspeckles-related cancer research.
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Ni YQ, Xu H, Liu YS. Roles of Long Non-coding RNAs in the Development of Aging-Related Neurodegenerative Diseases. Front Mol Neurosci 2022; 15:844193. [PMID: 35359573 PMCID: PMC8964039 DOI: 10.3389/fnmol.2022.844193] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
Aging-related neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and amyotrophic lateral sclerosis (ALS), are gradually becoming the primary burden of society and cause significant health-care concerns. Aging is a critical independent risk factor for neurodegenerative diseases. The pathological alterations of neurodegenerative diseases are tightly associated with mitochondrial dysfunction, inflammation, and oxidative stress, which in turn stimulates the further progression of neurodegenerative diseases. Given the potential research value, lncRNAs have attracted considerable attention. LncRNAs play complex and dynamic roles in multiple signal transduction axis of neurodegeneration. Emerging evidence indicates that lncRNAs exert crucial regulatory effects in the initiation and development of aging-related neurodegenerative diseases. This review compiles the underlying pathological mechanisms of aging and related neurodegenerative diseases. Besides, we discuss the roles of lncRNAs in aging. In addition, the crosstalk and network of lncRNAs in neurodegenerative diseases are also explored.
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Affiliation(s)
- Yu-Qing Ni
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - Hui Xu
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
- *Correspondence: You-Shuo Liu,
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Karimi E, Azari H, Tahmasebi A, Nikpoor AR, Negahi AA, Sanadgol N, Shekari M, Mousavi P. LncRNA-miRNA network analysis across the Th17 cell line reveals biomarker potency of lncRNA NEAT1 and KCNQ1OT1 in multiple sclerosis. J Cell Mol Med 2022; 26:2351-2362. [PMID: 35266286 PMCID: PMC8995444 DOI: 10.1111/jcmm.17256] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/11/2022] Open
Abstract
Differentiation of CD4+ T cells into Th17 cells is an important factor in the onset and progression of multiple sclerosis (MS) and Th17/Treg imbalance. Little is known about the role of lncRNAs in the differentiation of CD4+ cells from Th17 cells. This study aimed to analyse the lncRNA‐miRNAs network involved in MS disease and its role in the differentiation of Th17 cells. The lncRNAs in Th17 differentiation were obtained from GSE66261 using the GEO datasets. Differential expression of lncRNAs in Th17 primary cells compared to Th17 effector cells was investigated by RNA‐seq analysis. Next, the most highlighted lncRNAs in autoimmune diseases were downloaded from the lncRNAs disease database, and the most critical miRNA was extracted by literature search. Then, the lncRNA‐miRNA interaction was achieved by the Starbase database, and the ceRNA network was designed by Cytoscape. Finally, using the CytoHubba application, two hub lncRNAs with the most interactions with miRNAs were identified by the MCODE plug‐in. The expression level of genes was measured by qPCR, and the plasma level of cytokines was analysed by ELISA kits. The results showed an increase in the expression of NEAT1, KCNQ1OT1 and RORC and a decrease in the expression of FOXP3. In plasma, an upregulation of IL17 and a downregulation of TGFB inflammatory cytokines were detected. The dysregulated expression of these genes could be attributed to relapsing‐remitting MS (RR‐MS) patients and help us understand MS pathogenesis better.
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Affiliation(s)
- Elham Karimi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hanieh Azari
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Amin Reza Nikpoor
- Sciences Research Center for Molecular Medicine, Hormozgan University of Medical, Hormozgan, Iran
| | - Ahmad Agha Negahi
- Department of Internal Medicine, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Nima Sanadgol
- Institute of Neuroanatomy, RWTH University Hospital Aachen, Aachen, Germany
| | - Mohammad Shekari
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Sciences Research Center for Molecular Medicine, Hormozgan University of Medical, Hormozgan, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Sciences Research Center for Molecular Medicine, Hormozgan University of Medical, Hormozgan, Iran
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Expression and functions of long non-coding RNA NEAT1 and isoforms in breast cancer. Br J Cancer 2022; 126:551-561. [PMID: 34671127 PMCID: PMC8854383 DOI: 10.1038/s41416-021-01588-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/08/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
NEAT1 is a highly abundant nuclear architectural long non-coding RNA. There are two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, of which the latter is an essential scaffold for the assembly of a class of nuclear ribonucleoprotein bodies called paraspeckles. Paraspeckle formation is elevated by a wide variety of cellular stressors and in certain developmental processes, either through transcriptional upregulation of the NEAT1 gene or through a switch from NEAT1_1 to NEAT1_2 isoform production. In such conditions, paraspeckles modulate cellular processes by sequestering proteins or RNA molecules. NEAT1 is abnormally expressed in many cancers and a growing body of evidence suggests that, in many cases, high NEAT1 levels are associated with therapy resistance and poor clinical outcome. Here we review the current knowledge of NEAT1 expression and functions in breast cancer, highlighting its established role in postnatal mammary gland development. We will discuss possible isoform-specific roles of NEAT1_1 and NEAT1_2 in different breast cancer subtypes, which critically needs to be considered when studying NEAT1 and breast cancer.
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Wu Y, Li P, Liu L, Goodwin AJ, Halushka PV, Hirose T, Nakagawa S, Zhou J, Liu M, Fan H. lncRNA Neat1 regulates neuronal dysfunction post sepsis via stabilization of hemoglobin subunit beta. Mol Ther 2022; 30:2618-2632. [PMID: 35331906 PMCID: PMC9263235 DOI: 10.1016/j.ymthe.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022] Open
Abstract
Sepsis-associated encephalopathy (SAE) is characterized by acute and diffuse brain dysfunction and correlates with long-term cognitive impairments with no targeted therapy. We used a mouse model of sepsis-related cognitive impairment to examine the role of lncRNA nuclear enriched abundant transcript 1 (Neat1) in SAE. We observed that Neat1 expression was increased in neuronal cells from septic mice and that it directly interacts with hemoglobin subunit beta (Hbb), preventing its degradation. The Neat1/Hbb axis suppressed postsynaptic density protein 95 (PSD-95) levels and decreased dendritic spine density. Neat1 knockout mice exhibited decreased Hbb levels, which resulted in increased PSD-95 levels, increased neuronal dendritic spine density, and decreased anxiety and memory impairment. Neat1 silencing via the antisense oligonucleotide GapmeR ameliorated anxiety-like behavior and cognitive impairment post-sepsis. In conclusion, we uncovered a previously unknown mechanism of the Neat1/Hbb axis in regulating neuronal dysfunction, which may lead to a novel treatment strategy for SAE.
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Ji X, Meng W, Liu Z, Mu X. Emerging Roles of lncRNAs Regulating RNA-Mediated Type-I Interferon Signaling Pathway. Front Immunol 2022; 13:811122. [PMID: 35280983 PMCID: PMC8914027 DOI: 10.3389/fimmu.2022.811122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The type-I interferon (IFN-I) signaling pathway plays pivot roles in defending against pathogen invasion. Exogenous ssRNA and dsRNA could be immunogenic. RNA-mediated IFN signaling is extensively studied in the field. The incorrect functioning of this pathway leads to either autoimmune diseases or suffering from microorganism invasion. From the discrimination of “self” and “non-self” molecules by receptors to the fine-tune modulations in downstream cascades, all steps are under the surveillance featured by complex feedbacks and regulators. Studies in recent years highlighted the emerging roles of long noncoding RNAs (lncRNAs) as a reservoir for signaling regulation. LncRNAs bind to targets through the structure and sequence, and thus the mechanisms of action can be complex and specific. Here, we summarized lncRNAs modulating the RNA-activated IFN-I signaling pathway according to the event order during the signaling. We hope this review help understand how lncRNAs are participating in the regulation of IFN-I signaling.
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Affiliation(s)
- Xiaoxin Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Wei Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
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Carey JL, Guo L. Liquid-Liquid Phase Separation of TDP-43 and FUS in Physiology and Pathology of Neurodegenerative Diseases. Front Mol Biosci 2022; 9:826719. [PMID: 35187086 PMCID: PMC8847598 DOI: 10.3389/fmolb.2022.826719] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid phase separation of RNA-binding proteins mediates the formation of numerous membraneless organelles with essential cellular function. However, aberrant phase transition of these proteins leads to the formation of insoluble protein aggregates, which are pathological hallmarks of neurodegenerative diseases including ALS and FTD. TDP-43 and FUS are two such RNA-binding proteins that mislocalize and aggregate in patients of ALS and FTD. They have similar domain structures that provide multivalent interactions driving their phase separation in vitro and in the cellular environment. In this article, we review the factors that mediate and regulate phase separation of TDP-43 and FUS. We also review evidences that connect the phase separation property of TDP-43 and FUS to their functional roles in cells. Aberrant phase transition of TDP-43 and FUS leads to protein aggregation and disrupts their regular cell function. Therefore, restoration of functional protein phase of TDP-43 and FUS could be beneficial for neuronal cells. We discuss possible mechanisms for TDP-43 and FUS aberrant phase transition and aggregation while reviewing the methods that are currently being explored as potential therapeutic strategies to mitigate aberrant phase transition and aggregation of TDP-43 and FUS.
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Pan Y, Wang T, Zhao Z, Wei W, Yang X, Wang X, Xin W. Novel Insights into the Emerging Role of Neat1 and Its Effects Downstream in the Regulation of Inflammation. J Inflamm Res 2022; 15:557-571. [PMID: 35115805 PMCID: PMC8802408 DOI: 10.2147/jir.s338162] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yongli Pan
- Department of Neurology, Weifang Medical University, Weifang, Shandong, People’s Republic of China
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Ting Wang
- Department of Radiology, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China
| | - Zhiqiang Zhao
- Department of Neurosurgery, Heji Hospital affiliated Changzhi Medical College, Shanxi, People’s Republic of China
| | - Wei Wei
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
- Department of Neurology, Mianyang Central Hospital, Mianyang, Sichuan, People’s Republic of China
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Xianbin Wang
- Department of Emergency Medicine, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China
- Xianbin Wang, Department of Emergency Medicine, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China, Email
| | - Wenqiang Xin
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Correspondence: Wenqiang Xin, Department of Neurosurgery, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, People’s Republic of China, Tel +86–18526201182, Fax +86–2260362062, Email
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The Role of Long Non-coding RNA, Nuclear Enriched Abundant Transcript 1 (NEAT1) in Cancer and Other Pathologies. Biochem Genet 2021; 60:843-867. [PMID: 34689290 DOI: 10.1007/s10528-021-10138-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023]
Abstract
Nuclear enriched abundant transcript 1 (NEAT1), consisting of two kinds of lncRNAs of 3.7 kB NEAT1-1 and 23 kB NEAT1-2, can be highly expressed in organs and tissues such as the ovary, prostate, colon, and pancreas, and is involved in paraspeckle formation and mRNA editing and gene expression. Therefore, NEAT1 is a potential biomarker for the treatment of a variety of diseases, which may be caused by two factors (isoforms of NEAT1 and NEAT1 sponging miRNA as ceRNA). However, there is still much confusion about the mechanism and downstream effector between the abnormal expression of NEAT1 and various diseases. This review summarizes recent research progress on NEAT1 in cancer and other pathologies and provides a more reliable theoretical basis for the treatment of related diseases.
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41
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Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev 2021; 131:988-1004. [PMID: 34592258 DOI: 10.1016/j.neubiorev.2021.09.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.
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Affiliation(s)
- Manci Li
- University of Minnesota, St. Paul, MN, 55108, United States
| | - Peter A Larsen
- University of Minnesota, St. Paul, MN, 55108, United States.
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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: 14] [Impact Index Per Article: 4.7] [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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Pant T, DiStefano JK, Logan S, Bosnjak ZJ. Emerging Role of Long Noncoding RNAs in Perioperative Neurocognitive Disorders and Anesthetic-Induced Developmental Neurotoxicity. Anesth Analg 2021; 132:1614-1625. [PMID: 33332892 DOI: 10.1213/ane.0000000000005317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Preclinical investigations in animal models have consistently demonstrated neurobiological changes and life-long cognitive deficits following exposure to widely used anesthetics early in life. However, the mechanisms by which these exposures affect brain function remain poorly understood, therefore, limiting the efficacy of current diagnostic and therapeutic options in human studies. The human brain exhibits an abundant expression of long noncoding RNAs (lncRNAs). These biologically active transcripts play critical roles in a diverse array of functions, including epigenetic regulation. Changes in lncRNA expression have been linked with brain development, normal CNS processes, brain injuries, and the development of neurodegenerative diseases, and many lncRNAs are known to have brain-specific expression. Aberrant lncRNA expression has also been implicated in areas of growing importance in anesthesia-related research, including anesthetic-induced developmental neurotoxicity (AIDN), a condition defined by neurological changes occurring in patients repeatedly exposed to anesthesia, and the related condition of perioperative neurocognitive disorder (PND). In this review, we detail recent advances in PND and AIDN research and summarize the evidence supporting roles for lncRNAs in the brain under both normal and pathologic conditions. We also discuss lncRNAs that have been linked with PND and AIDN, and conclude with a discussion of the clinical potential for lncRNAs to serve as diagnostic and therapeutic targets for the prevention of these neurocognitive disorders and the challenges facing the identification and characterization of associated lncRNAs.
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Affiliation(s)
- Tarun Pant
- Department of Diabetes and Fibrotic Disease Unit, Translational Genomic Research Institute, Phoenix, Arizona
| | | | - Sara Logan
- Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Zeljko J Bosnjak
- From the Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin.,Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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RNA Sequencing of CD4 + T Cells in Relapsing-Remitting Multiple Sclerosis Patients at Relapse: Deciphering the Involvement of Novel genes and Pathways. J Mol Neurosci 2021; 71:2628-2645. [PMID: 34286457 DOI: 10.1007/s12031-021-01878-8] [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: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
CD4+ T cells are known as a noteworthy potential modulator of inflammation in multiple sclerosis (MS). In the current study, we investigated the transcriptome profile of CD4+ T cells in patients with relapsing-remitting MS (RRMS) at the relapse phase. We performed RNA sequencing of CD4+ T cells isolated from four relapsing-remitting MS (RRMS) patients at the relapse phase and four age- and sex-matched healthy controls. The edgeR statistical method was employed to determine differentially expressed genes (DEGs). Gene set enrichment analysis was subsequently performed. Applying a physical interaction network, genes with higher degrees were selected as hub genes. A total of 1278 and 1034 genes were defined at significantly higher or lower levels, respectively, in CD4+ T cells of RRMS patients at the relapse phase as compared with healthy controls. The top up- and downregulated genes were JAML and KDM3A. The detected DEGs were remarkable on chromosomes 1 and 2, respectively. The DEGs were mainly enriched in the pathways "regulation of transcription, DNA-templated," "regulation of B cell receptor signaling pathway," "protein phosphorylation," "epidermal growth factor receptor signaling pathway," and "positive regulation of neurogenesis." Moreover, 16 KEGG pathways mostly associated with the immune system and viral infections were enriched. In the constructed physical interaction networks, UBA52 and TP53 were shown to be the most highly ranked hub genes among upregulated and downregulated genes, respectively. By applying global transcriptome profiling of CD4+ T cells, we deciphered the involvement of several novel genes and pathways in MS pathogenesis. The present results must be confirmed by in vivo and in vitro studies.
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Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
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Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
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Landmesser U, Poller W, Tsimikas S, Most P, Paneni F, Lüscher TF. From traditional pharmacological towards nucleic acid-based therapies for cardiovascular diseases. Eur Heart J 2021; 41:3884-3899. [PMID: 32350510 DOI: 10.1093/eurheartj/ehaa229] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/17/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based therapeutics are currently developed at large scale for prevention and management of cardiovascular diseases (CVDs), since: (i) genetic studies have highlighted novel therapeutic targets suggested to be causal for CVD; (ii) there is a substantial recent progress in delivery, efficacy, and safety of nucleic acid-based therapies; (iii) they enable effective modulation of therapeutic targets that cannot be sufficiently or optimally addressed using traditional small molecule drugs or antibodies. Nucleic acid-based therapeutics include (i) RNA-targeted therapeutics for gene silencing; (ii) microRNA-modulating and epigenetic therapies; (iii) gene therapies; and (iv) genome-editing approaches (e.g. CRISPR-Cas-based): (i) RNA-targeted therapeutics: several large-scale clinical development programmes, using antisense oligonucleotides (ASO) or short interfering RNA (siRNA) therapeutics for prevention and management of CVD have been initiated. These include ASO and/or siRNA molecules to lower apolipoprotein (a) [apo(a)], proprotein convertase subtilisin/kexin type 9 (PCSK9), apoCIII, ANGPTL3, or transthyretin (TTR) for prevention and treatment of patients with atherosclerotic CVD or TTR amyloidosis. (ii) MicroRNA-modulating and epigenetic therapies: novel potential therapeutic targets are continually arising from human non-coding genome and epigenetic research. First microRNA-based therapeutics or therapies targeting epigenetic regulatory pathways are in clinical studies. (iii) Gene therapies: EMA/FDA have approved gene therapies for non-cardiac monogenic diseases and LDL receptor gene therapy is currently being examined in patients with homozygous hypercholesterolaemia. In experimental studies, gene therapy has significantly improved cardiac function in heart failure animal models. (iv) Genome editing approaches: these technologies, such as using CRISPR-Cas, have proven powerful in stem cells, however, important challenges are remaining, e.g. low rates of homology-directed repair in somatic cells such as cardiomyocytes. In summary, RNA-targeted therapies (e.g. apo(a)-ASO and PCSK9-siRNA) are now in large-scale clinical outcome trials and will most likely become a novel effective and safe therapeutic option for CVD in the near future. MicroRNA-modulating, epigenetic, and gene therapies are tested in early clinical studies for CVD. CRISPR-Cas-mediated genome editing is highly effective in stem cells, but major challenges are remaining in somatic cells, however, this field is rapidly advancing.
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Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Sotirios Tsimikas
- Division of Cardiovascular Medicine, Sulpizio Cardiovascular Center, University of California San Diego, 9500 Gilman Drive, BSB 1080, La Jolla, CA 92093-0682, USA
| | - Patrick Most
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany.,Center for Translational Medicine, Jefferson Medical College, 1020 Locust Street, Philadelphia, PA 19107, USA.,Molecular and Translational Cardiology, Department of Medicine III, Heidelberg University Hospital, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Rämistrasse 100, MOU2, 8091 Zurich, Switzerland
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Research, Education and Development, Royal Brompton and Harefield Hospital Trust and Imperial College London, National Heart and Lung Institute, Guy Scadding Building, Dovehouse Street, London SW3 6LY, UK
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47
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Shi C, Shen C, Liu G, Yang S, Ye F, Meng J, Pan Y. NEAT1 promotes the repair of abdominal aortic aneurysms of endothelial progenitor cells via regulating miR-204-5p/Ang-1. Am J Transl Res 2021; 13:2111-2126. [PMID: 34017378 PMCID: PMC8129351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
PURPOSE To clarify the regulatory effect of Nuclear-enriched abundant transcript 1 (NEAT1) on abdominal aortic aneurysm (AAA) model rats and isolated endothelial progenitor cells (EPCs). METHODS The AAA rat model was established by CaCl2 stimulation, and overexpressed NEAT1 was injected into rats through tail vein. Abdominal aorta lesions and numbers of EPCs in tissues and peripheral blood were examined by hematoxylin-eosin, immunofluorescence and flow cytometry. The extracted EPCs were identified by microscopy, DiI-ac-LDL staining and flow cytometry. Effect of overexpressed/silencing NEAT1 on the viability, migration, tube formation and VEGF content of EPCs was investigated by MTT-, wound-healing, tube formation assays and ELISA, respectively. The expressions of NEAT1, miR-204-5p, Angiopoietin-1 (Ang-1)/ERK pathway were determined by qRT-PCR and Western blot as needed. The targeting relationships between NEAT1 and miR-204-5p, and miR-204-5p and Ang-1 were predicted on starBase, TargetScan and confirmed by dual-luciferase experiments. The mutual regulation effect was studied through rescue experiments. RESULTS Overexpressed NEAT1 not only reduced inflammatory infiltration and increased the number of EPCs in abdominal aorta and peripheral blood, but also promoted the viability, migration, tube formation of EPCs, increased VEGF content and upregulated the expression of the Ang-1/ERK pathway in EPCs. However, silencing NEAT1 produced opposite results. NEAT1 targeting miR-204-5p inhibited the functional effects of miR-204-5p on of EPCs. Overexpressed/silencing Ang-1 partially reversed the effects of NEAT1 or miR-204-5p on the characteristics of EPCs. CONCLUSION NEAT1 competitively binds with miR-204-5p and up-regulates Ang-1 expression in EPCs to effectively improve the proliferation, migration and angiogenesis of EPCs.
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Affiliation(s)
- Chao Shi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Chongwen Shen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Ge Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Shaofeng Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Fenglin Ye
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Jinjin Meng
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Bengbu Medical CollegeBengbu, China
| | - Youmin Pan
- Department of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, Hubei Province, China
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48
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Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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49
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McCluggage F, Fox AH. Paraspeckle nuclear condensates: Global sensors of cell stress? Bioessays 2021; 43:e2000245. [PMID: 33748979 DOI: 10.1002/bies.202000245] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/31/2022]
Abstract
Paraspeckles are nuclear condensates, or membranelees organelles, that are built on the long noncoding RNA, NEAT1, and have been linked to many diseases. Although originally described as constitutive structures, here, in reviewing this field, we develop the hypothesis that cells increase paraspeckle abundance as part of a general stress response, to aid pro-survival pathways. Paraspeckles increase in many scenarios: when cells transform from one state to another, become infected with viruses and bacteria, begin to degenerate, under inflammation, in aging, and in cancer. Cells increase paraspeckles by increasing transcription of NEAT1 and adjusting its RNA processing. These increases in NEAT1 are driven by numerous stress-sensing signaling pathways, including signaling to mitochondria and stress granules, revealing crosstalk between the cytoplasm and nucleoplasm in the stress response. Thus, paraspeckles are an important piece of the puzzle in cellular homeostasis, and could be considered RNA-scaffolded nuclear equivalents of dynamic stress-induced structures that form in the cytoplasm. We speculate that, in general, cells rely on phase-separated paraspeckles to transiently tweak gene regulation in times of cellular flux.
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Affiliation(s)
- Finn McCluggage
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia.,School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Archa H Fox
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia.,School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
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50
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Pellegrini C, Pirazzini C, Sala C, Sambati L, Yusipov I, Kalyakulina A, Ravaioli F, Kwiatkowska KM, Durso DF, Ivanchenko M, Monti D, Lodi R, Franceschi C, Cortelli P, Garagnani P, Bacalini MG. A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration. Front Aging Neurosci 2021; 13:639428. [PMID: 33790779 PMCID: PMC8006465 DOI: 10.3389/fnagi.2021.639428] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.
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Affiliation(s)
- Camilla Pellegrini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katarzyna M. Kwiatkowska
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Danielle F. Durso
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Raffaele Lodi
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Applied Biomedical Research Center, Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy
- National Research Council of Italy Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” Unit of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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