1
|
Yang X, Yu D, Gao F, Yang J, Chen Z, Liu J, Yang X, Li L, Zhang Y, Yan C. Integrative Analysis of Morphine-Induced Differential Circular RNAs and ceRNA Networks in the Medial Prefrontal Cortex. Mol Neurobiol 2024; 61:4602-4618. [PMID: 38109006 DOI: 10.1007/s12035-023-03859-x] [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: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Circular RNAs (circRNAs) are a novel type of non-coding RNAs. Despite the fact that the functional mechanisms of most circRNAs remain unknown, emerging evidence indicates that circRNAs could sponge microRNAs (miRNAs), bind to RNA binding proteins (RBP), and even be translated into protein. Recent research has demonstrated the crucial roles played by circRNAs in neuropsychiatric disorders. The medial prefrontal cortex (mPFC) is a crucial component of drug reward circuitry and exerts top-down control over cognitive functions. However, there is currently limited knowledge about the correlation between circRNAs and morphine-associated contextual memory in the mPFC. Here, we performed morphine-induced conditioned place preference (CPP) in mice and extracted mPFC tissue for RNA-sequencing. Our study represented the first attempt to identify differentially expressed circRNAs (DEcircRNAs) and mRNAs (DEmRNAs) in the mPFC after morphine-induced CPP. We identified 47 significantly up-regulated DEcircRNAs and 429 significantly up-regulated DEmRNAs, along with 74 significantly down-regulated DEcircRNAs and 391 significantly down-regulated DEmRNAs. Functional analysis revealed that both DEcircRNAs and DEmRNAs were closely associated with neuroplasticity. To further validate the DEcircRNAs, we conducted qRT-PCR, Sanger sequencing, and RNase R digestion assays. Additionally, using an integrated bioinformatics approach, we constructed ceRNA networks and identified critical circRNA/miRNA/mRNA axes that contributed to the development of morphine-associated contextual memory. In summary, our study provided novel insights into the role of circRNAs in drug-related memory, specifically from the perspective of ceRNAs.
Collapse
Affiliation(s)
- Xixi Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Dongyu Yu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Feifei Gao
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Jingsi Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Zhennan Chen
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Junlin Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Xiaoyu Yang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Lanjiang Li
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China
| | - Yuxiang Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China.
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China.
| | - Chunxia Yan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
- Key Laboratory of Forensic Medicine, National Health Commission, Xi'an 710061, Shaanxi, China.
- Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi'an Jiaotong University, Xi'an 710100, Shaanxi, China.
| |
Collapse
|
2
|
Goryunov K, Ivanov M, Kulikov A, Shevtsova Y, Burov A, Podurovskaya Y, Zubkov V, Degtyarev D, Sukhikh G, Silachev D. A Review of the Use of Extracellular Vesicles in the Treatment of Neonatal Diseases: Current State and Problems with Translation to the Clinic. Int J Mol Sci 2024; 25:2879. [PMID: 38474125 DOI: 10.3390/ijms25052879] [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: 01/15/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Neonatal disorders, particularly those resulting from prematurity, pose a major challenge in health care and have a significant impact on infant mortality and long-term child health. The limitations of current therapeutic strategies emphasize the need for innovative treatments. New cell-free technologies utilizing extracellular vesicles (EVs) offer a compelling opportunity for neonatal therapy by harnessing the inherent regenerative capabilities of EVs. These nanoscale particles, secreted by a variety of organisms including animals, bacteria, fungi and plants, contain a repertoire of bioactive molecules with therapeutic potential. This review aims to provide a comprehensive assessment of the therapeutic effects of EVs and mechanistic insights into EVs from stem cells, biological fluids and non-animal sources, with a focus on common neonatal conditions such as hypoxic-ischemic encephalopathy, respiratory distress syndrome, bronchopulmonary dysplasia and necrotizing enterocolitis. This review summarizes evidence for the therapeutic potential of EVs, analyzes evidence of their mechanisms of action and discusses the challenges associated with the implementation of EV-based therapies in neonatal clinical practice.
Collapse
Affiliation(s)
- Kirill Goryunov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Mikhail Ivanov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey Kulikov
- Medical Institute, Patrice Lumumba Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Yulia Shevtsova
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Artem Burov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Yulia Podurovskaya
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Victor Zubkov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Dmitry Degtyarev
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Gennady Sukhikh
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
| | - Denis Silachev
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| |
Collapse
|
3
|
Mellios N, Papageorgiou G, Gorgievski V, Maxson G, Hernandez M, Otero M, Varangis M, Dell'Orco M, Perrone-Bizzozero N, Tzavara E. Regulation of neuronal circHomer1 biogenesis by PKA/CREB/ERK-mediated pathways and effects of glutamate and dopamine receptor blockade. RESEARCH SQUARE 2024:rs.3.rs-3547375. [PMID: 38260249 PMCID: PMC10802743 DOI: 10.21203/rs.3.rs-3547375/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
There are currently only very few efficacious drug treatments for SCZ and BD, none of which can significantly ameliorate cognitive symptoms. Thus, further research is needed in elucidating molecular pathways linked to cognitive function and antipsychotic treatment. Circular RNAs (circRNAs) are stable brain-enriched non-coding RNAs, derived from the covalent back-splicing of precursor mRNA molecules. CircHomer1 is a neuronal-enriched, activity-dependent circRNA, derived from the precursor of the long HOMER1B mRNA isoform, which is significantly downregulated in the prefrontal cortex of subjects with psychosis and is able to regulate cognitive function. Even though its relevance to psychiatric disorders and its role in brain function and synaptic plasticity have been well established, little is known about the molecular mechanisms that underlie circHomer1 biogenesis in response to neuronal activity and psychiatric drug treatment. Here we suggest that the RNA-binding protein (RBP) FUS positively regulates neuronal circHomer1 expression. Furthermore, we show that the MEK/ERK and PKA/CREB pathways positively regulate neuronal circHomer1 expression, as well as promote the transcription of Fus and Eif4a3, another RBP previously shown to activate circHomer1 biogenesis. We then demonstrate via both in vitro and in vivo studies that NMDA and mGluR5 receptors are upstream modulators of circHomer1 expression. Lastly, we report that in vivo D2R antagonism increases circHomer1 expression, whereas 5HT2AR blockade reduces circHomer1 levels in multiple brain regions. Taken together, this study allows us to gain novel insights into the molecular circuits that underlie the biogenesis of a psychiatric disease-associated circRNA.
Collapse
|
4
|
Statsenko Y, Kuznetsov NV, Morozova D, Liaonchyk K, Simiyu GL, Smetanina D, Kashapov A, Meribout S, Gorkom KNV, Hamoudi R, Ismail F, Ansari SA, Emerald BS, Ljubisavljevic M. Reappraisal of the Concept of Accelerated Aging in Neurodegeneration and Beyond. Cells 2023; 12:2451. [PMID: 37887295 PMCID: PMC10605227 DOI: 10.3390/cells12202451] [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: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genetic and epigenetic changes, oxidative stress and inflammation influence the rate of aging, which diseases, lifestyle and environmental factors can further accelerate. In accelerated aging (AA), the biological age exceeds the chronological age. OBJECTIVE The objective of this study is to reappraise the AA concept critically, considering its weaknesses and limitations. METHODS We reviewed more than 300 recent articles dealing with the physiology of brain aging and neurodegeneration pathophysiology. RESULTS (1) Application of the AA concept to individual organs outside the brain is challenging as organs of different systems age at different rates. (2) There is a need to consider the deceleration of aging due to the potential use of the individual structure-functional reserves. The latter can be restored by pharmacological and/or cognitive therapy, environment, etc. (3) The AA concept lacks both standardised terminology and methodology. (4) Changes in specific molecular biomarkers (MBM) reflect aging-related processes; however, numerous MBM candidates should be validated to consolidate the AA theory. (5) The exact nature of many potential causal factors, biological outcomes and interactions between the former and the latter remain largely unclear. CONCLUSIONS Although AA is commonly recognised as a perspective theory, it still suffers from a number of gaps and limitations that assume the necessity for an updated AA concept.
Collapse
Affiliation(s)
- Yauhen Statsenko
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Big Data Analytic Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Nik V. Kuznetsov
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Daria Morozova
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Katsiaryna Liaonchyk
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Gillian Lylian Simiyu
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Darya Smetanina
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Aidar Kashapov
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Sarah Meribout
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Klaus Neidl-Van Gorkom
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Rifat Hamoudi
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London NW3 2PS, UK
| | - Fatima Ismail
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Suraiya Anjum Ansari
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Bright Starling Emerald
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Milos Ljubisavljevic
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| |
Collapse
|
5
|
Bai Y, Yao HH. Circular RNAs: Diagnostic and Therapeutic Perspectives in CNS Diseases. Curr Med Sci 2023; 43:879-889. [PMID: 37815742 DOI: 10.1007/s11596-023-2784-8] [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: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023]
Abstract
Circular RNAs (circRNAs) are a class of regulatory non-coding RNAs characterized by the presence of covalently closed ends. A growing body of evidence suggests that circRNAs play important roles in physiology and pathology. In particular, accumulating data on circRNA functions in various central nervous system (CNS) diseases and their correlations indicate that circRNAs are critical contributors to the onset and development of brain disorders. In this review, we focus on the regulatory and functional roles of circRNAs in CNS diseases, highlighting their diagnostic and therapeutic potential, with the aim of providing new insights into CNS diseases.
Collapse
Affiliation(s)
- Ying Bai
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Hong-Hong Yao
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210009, China.
| |
Collapse
|
6
|
Zhou Y, Liu Y, Kang Z, Yao H, Song N, Wang M, Song C, Zhang K, Ding J, Tang J, Hu G, Lu M. CircEPS15, as a sponge of MIR24-3p ameliorates neuronal damage in Parkinson disease through boosting PINK1-PRKN-mediated mitophagy. Autophagy 2023; 19:2520-2537. [PMID: 37014258 PMCID: PMC10392753 DOI: 10.1080/15548627.2023.2196889] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/04/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Despite growing evidence that has declared the importance of circRNAs in neurodegenerative diseases, the clinical significance of circRNAs in dopaminergic (DA) neuronal degeneration in the pathogenesis of Parkinson disease (PD) remains unclear. Here, we performed rRNA-depleted RNA sequencing and detected more than 10,000 circRNAs in the plasma samples of PD patients. In consideration of ROC and the correlation between Hohen-Yahr stage (H-Y stage) and Unified Parkinson Disease Rating Scale-motor score (UPDRS) of 40 PD patients, circEPS15 was selected for further research. Low expression of circEPS15 was found in PD patients and there was a negative positive correlation between the circEPS15 level and severity of PD motor symptoms, while overexpression of circEPS15 protected DA neurons against neurotoxin-induced PD-like neurodegeneration in vitro and in vivo. Mechanistically, circEPS15 acted as a MIR24-3p sponge to promote the stable expression of target gene PINK1, thus enhancing PINK1-PRKN-dependent mitophagy to eliminate damaged mitochondria and maintain mitochondrial homeostasis. Thus, circEPS15 rescued DA neuronal degeneration through the MIR24-3p-PINK1 axis-mediated improvement of mitochondrial function. This study reveals that circEPS15 exerts a critical role in participating in PD pathogenesis, and may give us an insight into the novel avenue to develop potential biomarkers and therapeutic targets for PD.Abbreviations: AAV: adeno-associated virus; DA: dopaminergic; FISH: fluorescence in situ hybridizations; HPLC: high-performance liquid chromatography; H-Y stage: Hohen-Yahr stage; LDH: lactate dehydrogenase; MMP: mitochondrial membrane potential; MPTP/p: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine/probenecid; NC: negative control; PD: Parkinson disease; PINK1: PTEN induced kinase 1; PBS: phosphate-buffered saline; ROS: reactive oxygen species; SNpc: substantia nigra pars compacta; TEM: transmission electron microscopy; UPDRS: Unified Parkinson's Disease Rating Scale-motor score.
Collapse
Affiliation(s)
- Yuanzhang Zhou
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Yang Liu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhengwei Kang
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Hang Yao
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Nanshan Song
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Min Wang
- Department of Geriatrics, Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Chenghuan Song
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Kezhong Zhang
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianhua Ding
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Juanjuan Tang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| |
Collapse
|
7
|
Watts ME, Oksanen M, Lejerkrans S, Mastropasqua F, Gorospe M, Tammimies K. Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein. BMC Biol 2023; 21:127. [PMID: 37237280 DOI: 10.1186/s12915-023-01627-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Circular RNA (circRNA) molecules, generated through non-canonical back-splicing of exon-exon junctions, have recently been implicated in diverse biological functions including transcriptional regulation and modulation of protein interactions. CircRNAs are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored. RESULTS Using total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes. CONCLUSIONS Our study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.
Collapse
Affiliation(s)
- Michelle E Watts
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Marika Oksanen
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Francesca Mastropasqua
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD, USA
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
- Karolinska Institutet, BioClinicum J9:30, Visionsgatan 4, 171 56, Solna, Sweden.
| |
Collapse
|
8
|
Wu C, Huang X, Li M, Wang Z, Zhang Y, Tian B. Crosstalk between circRNAs and the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy progression. Future Oncol 2023; 18:4525-4538. [PMID: 36891896 DOI: 10.2217/fon-2022-0429] [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: 03/10/2023] Open
Abstract
Evidence indicates that circular RNAs (circRNAs) may play an important role in regulating gene expression by binding to miRNAs through miRNA response elements. circRNAs are formed by back-splicing and have a covalently closed structure. The biogenesis of circRNAs also appears to be regulated by certain cell-specific and/or gene-specific mechanisms, and thus some circRNAs are tissue specific and tumor-expression specific. Furthermore, the high stability and tissue specificity of circRNAs may be of value for early diagnosis, survival prediction and precision medicine. This review summarizes current knowledge regarding the classification and functions of circRNAs and the role of circRNAs in regulating the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy tumors.
Collapse
Affiliation(s)
- Chao Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Xing Huang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Mao Li
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Zihe Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Yi Zhang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| |
Collapse
|
9
|
Xu X, Li Q, Qian Y, Cai H, Zhang C, Zhao W, Zhu J, Yu Y. Genetic mechanisms underlying gray matter volume changes in patients with drug-naive first-episode schizophrenia. Cereb Cortex 2023; 33:2328-2341. [PMID: 35640648 DOI: 10.1093/cercor/bhac211] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Brain structural damage is a typical feature of schizophrenia. Investigating such disease phenotype in patients with drug-naive first-episode schizophrenia (DFSZ) may exclude the confounds of antipsychotics and illness chronicity. However, small sample sizes and marked clinical heterogeneity have precluded definitive identification of gray matter volume (GMV) changes in DFSZ as well as their underlying genetic mechanisms. Here, GMV changes in DFSZ were assessed using a neuroimaging meta-analysis of 19 original studies, including 605 patients and 637 controls. Gene expression data were derived from the Allen Human Brain Atlas and processed with a newly proposed standardized pipeline. Then, we used transcriptome-neuroimaging spatial correlations to identify genes associated with GMV changes in DFSZ, followed by a set of gene functional feature analyses. Meta-analysis revealed consistent GMV reduction in the right superior temporal gyrus, right insula and left inferior temporal gyrus in DFSZ. Moreover, we found that these GMV changes were spatially correlated with expression levels of 1,201 genes, which exhibited a wide range of functional features. Our findings may provide important insights into the genetic mechanisms underlying brain morphological abnormality in schizophrenia.
Collapse
Affiliation(s)
- Xiaotao Xu
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China.,Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Qian Li
- Department of Radiology, Chaohu Hospital of Anhui Medical University, Hefei 238000, China.,Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Yinfeng Qian
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Huanhuan Cai
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Cun Zhang
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Wenming Zhao
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Jiajia Zhu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.,Research Center of Clinical Medical Imaging, Anhui Province, Hefei, 230032, China.,Anhui Provincial Institute of Translational Medicine, Hefei 230032, China.,Department of Radiology, Chaohu Hospital of Anhui Medical University, Hefei 238000, China.,Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China
| |
Collapse
|
10
|
Yu X, Liu H, Chang N, Fu W, Guo Z, Wang Y. Circular RNAs: New players involved in the regulation of cognition and cognitive diseases. Front Neurosci 2023; 17:1097878. [PMID: 36816112 PMCID: PMC9932922 DOI: 10.3389/fnins.2023.1097878] [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: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.
Collapse
Affiliation(s)
- Xiaohan Yu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haoyu Liu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Chang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Weijia Fu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhiwen Guo
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yue Wang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Yue Wang,
| |
Collapse
|
11
|
Fišar Z. Biological hypotheses, risk factors, and biomarkers of schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2023; 120:110626. [PMID: 36055561 DOI: 10.1016/j.pnpbp.2022.110626] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 12/19/2022]
Abstract
Both the discovery of biomarkers of schizophrenia and the verification of biological hypotheses of schizophrenia are an essential part of the process of understanding the etiology of this mental disorder. Schizophrenia has long been considered a neurodevelopmental disease whose symptoms are caused by impaired synaptic signal transduction and brain neuroplasticity. Both the onset and chronic course of schizophrenia are associated with risk factors-induced disruption of brain function and the establishment of a new homeostatic setpoint characterized by biomarkers. Different risk factors and biomarkers can converge to the same symptoms of schizophrenia, suggesting that the primary cause of the disease can be highly individual. Schizophrenia-related biomarkers include measurable biochemical changes induced by stress (elevated allostatic load), mitochondrial dysfunction, neuroinflammation, oxidative and nitrosative stress, and circadian rhythm disturbances. Here is a summary of selected valid biological hypotheses of schizophrenia formulated based on risk factors and biomarkers, neurodevelopment, neuroplasticity, brain chemistry, and antipsychotic medication. The integrative neurodevelopmental-vulnerability-neurochemical model is based on current knowledge of the neurobiology of the onset and progression of the disease and the effects of antipsychotics and psychotomimetics and reflects the complex and multifactorial nature of schizophrenia.
Collapse
Affiliation(s)
- Zdeněk Fišar
- Charles University and General University Hospital in Prague, First Faculty of Medicine, Department of Psychiatry, Czech Republic.
| |
Collapse
|
12
|
Guo C, Lv H, Bai Y, Guo M, Li P, Tong S, He K. Circular RNAs in extracellular vesicles: Promising candidate biomarkers for schizophrenia. Front Genet 2023; 13:997322. [PMID: 36685830 PMCID: PMC9852742 DOI: 10.3389/fgene.2022.997322] [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: 07/18/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
As one of common and severe mental illnesses, schizophrenia is difficult to be diagnosed exactly. Both its pathogenesis and the causes of its development are still uncertain because of its etiology complexity. At present, the diagnosis of schizophrenia is mainly based on the patient's symptoms and signs, lacking reliable biomarkers that can be used for diagnosis. Circular RNAs in extracellular vesicles (EV circRNAs) can be used as promising candidate biomarkers for schizophrenia and other diseases, for they are not only high stability and disease specificity, but also are rich in contents and easy to be detected. The review is to focus on the research progress of the correlation between circRNAs and schizophrenia, and then to explores the possibility of EV circRNAs as new biomarkers for the schizophrenia diagnosis.
Collapse
Affiliation(s)
- Chuang Guo
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Haibing Lv
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Yulong Bai
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Meng Guo
- Network Center, Inner Mongolia Minzu University, Tongliao, China
| | - Pengfei Li
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Shuping Tong
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Kuanjun He
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China,*Correspondence: Kuanjun He,
| |
Collapse
|
13
|
Lim M, Carollo A, Neoh MJY, Esposito G. Mapping miRNA Research in Schizophrenia: A Scientometric Review. Int J Mol Sci 2022; 24:ijms24010436. [PMID: 36613876 PMCID: PMC9820708 DOI: 10.3390/ijms24010436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Micro RNA (miRNA) research has great implications in uncovering the aetiology of neuropsychiatric conditions due to the role of miRNA in brain development and function. Schizophrenia, a complex yet devastating neuropsychiatric disorder, is one such condition that had been extensively studied in the realm of miRNA. Although a relatively new field of research, this area of study has progressed sufficiently to warrant dozens of reviews summarising findings from past to present. However, as a majority of reviews cannot encapsulate the full body of research, there is still a need to synthesise the diversity of publications made in this area in a systematic but easy-to-understand manner. Therefore, this study adopted bibliometrics and scientometrics, specifically document co-citation analysis (DCA), to review the literature on miRNAs in the context of schizophrenia over the course of history. From a literature search on Scopus, 992 papers were found and analysed with CiteSpace. DCA analysis generated a network of 13 major clusters with different thematic focuses within the subject area. Finally, these clusters are qualitatively discussed. miRNA research has branched into schizophrenia, among other medical and psychiatric conditions, due to previous findings in other forms of non-coding RNA. With the rise of big data, bioinformatics analyses are increasingly common in this field of research. The future of research is projected to rely more heavily on interdisciplinary collaboration. Additionally, it can be expected that there will be more translational studies focusing on the application of these findings to the development of effective treatments.
Collapse
Affiliation(s)
- Mengyu Lim
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Alessandro Carollo
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
| | - Michelle Jin Yee Neoh
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Gianluca Esposito
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
- Correspondence:
| |
Collapse
|
14
|
Choudhary A, Peles D, Nayak R, Mizrahi L, Stern S. Current progress in understanding schizophrenia using genomics and pluripotent stem cells: A meta-analytical overview. Schizophr Res 2022:S0920-9964(22)00406-6. [PMID: 36443183 DOI: 10.1016/j.schres.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/16/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022]
Abstract
Schizophrenia (SCZ) is a complex, heritable and polygenic neuropsychiatric disease, which disables the patients as well as decreases their life expectancy and quality of life. Common and rare variants studies on SCZ subjects have provided >100 genomic loci that hold importance in the context of SCZ pathophysiology. Transcriptomic studies from clinical samples have informed about the differentially expressed genes (DEGs) and non-coding RNAs in SCZ patients. Despite these advancements, no causative genes for SCZ were found and hence SCZ is difficult to recapitulate in animal models. In the last decade, induced Pluripotent Stem Cells (iPSCs)-based models have helped in understanding the neural phenotypes of SCZ by studying patient iPSC-derived 2D neuronal cultures and 3D brain organoids. Here, we have aimed to provide a simplistic overview of the current progress and advancements after synthesizing the enormous literature on SCZ genetics and SCZ iPSC-based models. Although further understanding of SCZ genetics and pathophysiological mechanisms using these technological advancements is required, the recent approaches have allowed to delineate important cellular mechanisms and biological pathways affected in SCZ.
Collapse
Affiliation(s)
- Ashwani Choudhary
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - David Peles
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Ritu Nayak
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Liron Mizrahi
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel.
| |
Collapse
|
15
|
Wang J, Liu Y, Gao Y, Liang J, Wang B, Xia Q, Xie Y, Shan F, Xia Q. Comprehensive bioinformatics analysis and molecular validation of lncRNAs-mediated ceRNAs network in schizophrenia. Life Sci 2022; 312:121205. [PMID: 36410410 DOI: 10.1016/j.lfs.2022.121205] [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: 06/27/2022] [Revised: 10/31/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
AIMS The present study aimed to investigate how Schizophrenia (SCZ)-specific long non-coding RNAs (lncRNAs) served as competing endogenous RNAs (ceRNAs) to modulate the biological functions and pathways involved in the pathogenesis of SCZ. MAIN METHODS Microarray dataset (GSE54913) was obtained from Gene Expression Omnibus (GEO) database. Differently expressed (DE) lncRNAs and mRNAs were identified by "limma" package. The binding miRNAs of lncRNAs and target mRNAs of shared miRNAs were predicted by miRcode, miRDB, miRTarbase and targetscan databases. Following the ceRNAs theory, interaction network was established and visualized with the cytoscape. Functional enrichment analysis uncovered the concentrated functions and signaling pathways that may be associated with SCZ progression. Protein-protein interaction (PPI) analysis was utilized to determine hub genes. Quantitative real-time PCR (qRT-PCR) and receiver operating characteristic curve (ROC) were performed to evaluate the expression and diagnostic value of ceRNAs members, respectively. KEY FINDINGS DElncRNAs and DEmRNAs were initially screened from GSE54913 to construct the SCZ-related ceRNAs network with 42 nodes and 53 edges. Functional enrichment analysis revealed that ceRNAs members appeared to be highly correlated with transcription factor activation, cell replication and tumor-related pathways. Once validated, a significant ceRNAs subnetwork was proposed as being implicated in the pathogenesis of SCZ. ROC analysis indicated that SCZ-related ceRNAs members may be sensitive diagnostic biomarkers for SCZ. SIGNIFICANCE The significant SCZ-related ceRNAs subnetworks (lncRNA-C2orf48A/hsa-miR-20b-5p,-17-5p/KIF23, FOXJ2) may represent promising predictive and diagnostic biomarkers and provide novel insights into the mechanism by which lncRNAs act as microRNA sponges and contribute to the pathogenesis of SCZ.
Collapse
Affiliation(s)
- Jiequan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Yaru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China
| | - Yejun Gao
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jun Liang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Baoshi Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China
| | - Yawen Xie
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui 230022, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, China
| | - Feng Shan
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China
| | - Qingrong Xia
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui 230000, China.
| |
Collapse
|
16
|
Bao N, Liu J, Peng Z, Zhang R, Ni R, Li R, Wu J, Liu Z, Pan B. Identification of circRNA-miRNA-mRNA networks to explore the molecular mechanism and immune regulation of postoperative neurocognitive disorder. Aging (Albany NY) 2022; 14:8374-8393. [PMID: 36279395 PMCID: PMC9648807 DOI: 10.18632/aging.204348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022]
Abstract
Postoperative neurocognitive disorder (PND) is a common complication in older patients. However, its pathogenesis has still remained elusive. Recent studies have shown that circular RNA (circRNA) plays an important role in the development of neurodegenerative diseases, such as PND after surgery. CircRNA, as a competitive endogenous RNA (ceRNA), mainly acts as a molecular sponge for miRNA to "adsorb" microRNA (miRNA) and to reduce the inhibitory effects of miRNAs on target mRNA. The sequencing data of circRNA were obtained from the Gene Expression Omnibus (GEO) database. By bioinformatic methods, circAtlas, miRDB, miRTarBase and miRwalk databases were applied to construct circRNA-miRNA-mRNA networks and screen differentially expressed mRNAs. To improve the accuracy of the data, we randomly divided aging mice into control (non-PND group) and PND groups, and used high-throughput sequencing to analyze their brain hippocampal tissue for analysis. Three key genes were cross-detected in the data of both groups, which were Unc13c, Tbx20 and St8sia2 (as hub genes), providing new targets for PND treatment. According to the results of the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, immune cell infiltration analysis, gene set enrichment analysis (GSEA), Connectivity Map (CMap) analysis, quantitative real-time polymerase chain reaction (qRT-PCR), the genes that were not related to the central nervous system were removed, and finally, mmu_circ_0000331/miR-1224-3p/Unc13c and mmu_circ_0000406/miR-24-3p/St8sia2 ceRNA networks were identified. In addition, the CMap method was used to select the top 4 active compounds with the largest negative correlation absolute values, including cimaterol, Rucaparib, FG-7142, and Hydrocortisone.
Collapse
Affiliation(s)
- Ning Bao
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
- Department of Anesthesiology, Shenyang Women’s and Children’s Hospital, Shenyang, Liaoning, China
| | - Jiping Liu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Zhe Peng
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Rong Zhang
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Rufei Ni
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Runzuan Li
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Jian Wu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Zhenhua Liu
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Botao Pan
- Department of Anesthesiology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| |
Collapse
|
17
|
Gong Z, Rong X, Li X, Wang H, Liu D, He L, Pan J, Shen Q, Peng Y. Male mice exposed to chronic intermittent ethanol exposure exhibit significant upregulation or downregulation of circular RNAs. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2022; 48:562-572. [PMID: 35838410 DOI: 10.1080/00952990.2022.2073449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
B a ckground: Circular RNAs (circRNAs) have been crucially implicated in various diseases, however, their involvement in chronic intermittent ethanol (CIE) exposure remains unclear.O bjective: The present study was conducted to evaluate the circular RNA expression alteration in brain samples and to identify the molecular mechanisms underlying chronic intermittent ethanol exposure.M ethods: Male C57BL/6J mice (10 for each group) were given 4 weeks of chronic intermittent ethanol exposure. Whole brain samples were collected for high-throughput sequencing and circRNA bioinformatic analysis. Real-time quantitative PCR (RI-qPCR) and agarose electrophoresis were used to validate the differentially expressed circRNAs. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were performed. A p level < 0.05 was considered statistically significant.R esults: Compared with the control group and baseline values, the CIE group showed a significant increase in ethanol intake. High-throughput sequencing revealed 399 significantly different circRNAs in CIE mice, including 150 up-regulated circRNAs and 249 down-regulated circRNAs. GO analysis showed that the most significantly enriched term for biological process, cellular component, and molecular function were GO:0050885, GO:0016020 and GO:0005515, respectively. The most enriched pathways in KEGG analysis were GABAergic synapse (mmu04727), followed by retrograde endocannabinoid (eCB) signaling (mmu04723) and morphine addiction (mmu05032). Among the circRNAs, RT-qPCR confirmed 14 upregulated and 13 downregulated circRNAs in the brain tissues with 9 upregulated and 10 downregulated circRNAs being observed in blood samples.C onclusions: Our study suggests that chronic ethanol exposure upregulates or downregulates circRNAs in the brain, which, in turn, could alter neurotransmitter release and signal transduction.
Collapse
Affiliation(s)
- Zhe Gong
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China.,Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoming Rong
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Xiangpen Li
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Hongxuan Wang
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Dandan Liu
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Lei He
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Jingrui Pan
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Qingyu Shen
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China
| | - Ying Peng
- Memorial Hospital, Sun Yat-sen UniversityDepartment of Neurology, Sun Yat-sen, Guangzhou, China.,Memorial Hospital, Sun Yat-sen UniversityGuangdong Provincial Key Laboratory of Malignant Tumour Epigenetics and Gene Regulation, Sun Yat-sen, Guangzhou, China
| |
Collapse
|
18
|
Singh M, Dwibedy SLL, Biswal SR, Muthuswamy S, Kumar A, Kumar S. Circular RNA: A novel and potential regulator in pathophysiology of schizophrenia. Metab Brain Dis 2022; 37:1309-1316. [PMID: 35435609 DOI: 10.1007/s11011-022-00978-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Circular RNAs (CircRNAs) are a sub-class of non-coding RNA, which are covalently closed at the ends through a non-canonical process called, backsplicing from the precursor linear RNAs. These molecules are involved in several biological phenomena including regulation of gene expression, synaptic plasticity, and cognition. Several studies have shown that circRNA are present abundantly inside the mammalian brain and they are believed to be associated with the development of neurons and neuronal functions. It is also evident that alterations in intracellular and extracellular levels of circRNAs are linked with various neurological and neuropsychiatric disorders including schizophrenia (SZ). Detailed studies of circRNAs are required to decode the molecular mechanism behind the onset of SZ and the related biological activities during disease progression. This can help unravel their role in this neurobehavioral disorder and develop effective therapeutics against the disease. The present review mainly focuses on the expression and activities of the circRNAs in the post-mortem brain, peripheral blood, and exosomes. It also gives an insight into the role of circRNA interaction with RNA binding proteins (RBPs) and nucleotide modification and their therapeutic potential in the context of schizophrenia.
Collapse
Affiliation(s)
- Mandakini Singh
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | | | - Smruti Rekha Biswal
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | - Srinivasan Muthuswamy
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India
| | - Ajay Kumar
- Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology (NIT) Rourkela, Odisha, 769008, India.
| |
Collapse
|
19
|
Peng L, Yang C, Huang L, Chen X, Fu X, Liu W. RNMFLP: Predicting circRNA-disease associations based on robust nonnegative matrix factorization and label propagation. Brief Bioinform 2022; 23:6582881. [PMID: 35534179 DOI: 10.1093/bib/bbac155] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/09/2022] [Accepted: 04/06/2022] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of structurally stable endogenous noncoding RNA molecules. Increasing studies indicate that circRNAs play vital roles in human diseases. However, validating disease-related circRNAs in vivo is costly and time-consuming. A reliable and effective computational method to identify circRNA-disease associations deserves further studies. In this study, we propose a computational method called RNMFLP that combines robust nonnegative matrix factorization (RNMF) and label propagation algorithm (LP) to predict circRNA-disease associations. First, to reduce the impact of false negative data, the original circRNA-disease adjacency matrix is updated by matrix multiplication using the integrated circRNA similarity and the disease similarity information. Subsequently, the RNMF algorithm is used to obtain the restricted latent space to capture potential circRNA-disease pairs from the association matrix. Finally, the LP algorithm is utilized to predict more accurate circRNA-disease associations from the integrated circRNA similarity network and integrated disease similarity network, respectively. Fivefold cross-validation of four datasets shows that RNMFLP is superior to the state-of-the-art methods. In addition, case studies on lung cancer, hepatocellular carcinoma and colorectal cancer further demonstrate the reliability of our method to discover disease-related circRNAs.
Collapse
Affiliation(s)
- Li Peng
- School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.,Hunan Key Laboratory for Service computing and Novel Software Technology
| | - Cheng Yang
- School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, 10084, Beijing, China.,The Future Laboratory, Tsinghua University, 10084, Beijing, China
| | - Xiang Chen
- School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Xiangzheng Fu
- College of Information Science and Engineering, Hunan University, Changsha, 410082, Hunan, China
| | - Wei Liu
- College of Information Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
| |
Collapse
|
20
|
Chen Y, Li X, Meng S, Huang S, Chang S, Shi J. Identification of Functional CircRNA–miRNA–mRNA Regulatory Network in Dorsolateral Prefrontal Cortex Neurons of Patients With Cocaine Use Disorder. Front Mol Neurosci 2022; 15:839233. [PMID: 35493321 PMCID: PMC9048414 DOI: 10.3389/fnmol.2022.839233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/01/2022] [Indexed: 11/25/2022] Open
Abstract
Increasing evidence has indicated that circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) regulatory network to regulate the expression of target genes by sponging microRNAs (miRNAs), and therefore play an essential role in many neuropsychiatric disorders, including cocaine use disorder. However, the functional roles and regulatory mechanisms of circRNAs as ceRNAs in dorsolateral prefrontal cortex (dlPFC) of patients with cocaine use disorder remain to be determined. In this study, an expression profiling for dlPFC in 19 patients with cocaine use disorder and 17 controls from Gene Expression Omnibus datasets was used for the differentially expressed circRNAs analysis and the differentially expressed mRNAs analysis. Several tools were used to predict the miRNAs targeted by the circRNAs and the miRNAs targeted mRNAs, which then overlapped with the cocaine-associated differentially expressed mRNAs to determine the functional roles of circRNAs. Functional analysis for the obtained mRNAs was performed via Gene Ontology (GO) in Metascape database. Integrated bioinformatics analysis was conducted to further characterize the circRNA–miRNA–mRNA regulatory network and identify the functions of distinct circRNAs. We found a total of 41 differentially expressed circRNAs, and 98 miRNAs were targeted by these circRNAs. The overlapped mRNAs targeted by the miRNAs and the differentially expressed mRNAs constructed a circRNA–miRNA–mRNA regulation network including 24 circRNAs, 43 miRNAs, and 82 mRNAs in the dlPFC of patients with cocaine use disorder. Functional analysis indicated the regulation network mainly participated in cell response-related, receptor signaling-related, protein modification-related and axonogenesis-related pathways, which might be involved with cocaine use disorder. Additionally, we determined four hub genes (HSP90AA1, HSPA1B, YWHAG, and RAB8A) from the protein–protein interaction network and constructed a circRNA–miRNA-hub gene subnetwork based on the four hub genes. In conclusion, our findings provide a deeper understanding of the circRNAs-related ceRNAs regulatory mechanisms in the pathogenesis of cocaine use disorder.
Collapse
Affiliation(s)
- Yun Chen
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory on Drug Dependence Research, National Institute on Drug Dependence, Peking University, Beijing, China
| | - Xianfeng Li
- Department of Gastroenterology of Dapping Hospital, Third Military Medical University, Chongqing, China
| | - Shiqiu Meng
- Beijing Key Laboratory on Drug Dependence Research, National Institute on Drug Dependence, Peking University, Beijing, China
| | - Shihao Huang
- Key Laboratory of Molecular Epidemiology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Suhua Chang
- Institute of Mental Health, National Clinical Research Center for Mental Disorders, Key Laboratory of Mental Health and Peking University Sixth Hospital, Peking University, Beijing, China
- Suhua Chang,
| | - Jie Shi
- Beijing Key Laboratory on Drug Dependence Research, National Institute on Drug Dependence, Peking University, Beijing, China
- Peking University, Shenzhen Hospital, Shenzhen, China
- *Correspondence: Jie Shi,
| |
Collapse
|
21
|
Circ-PKD2 promotes Atg13-mediated autophagy by inhibiting miR-646 to increase the sensitivity of cisplatin in oral squamous cell carcinomas. Cell Death Dis 2022; 13:192. [PMID: 35220397 PMCID: PMC8882170 DOI: 10.1038/s41419-021-04497-8] [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: 06/25/2021] [Revised: 11/03/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022]
Abstract
Autophagy is an evolutionally conserved catabolic process that degrades cells to maintain homeostasis. Cisplatin-activated autophagy promotes the expression of circ-PKD2, which plays a role as a tumor suppressor gene in the proliferation, migration, and invasion in oral squamous cell carcinoma (OSCC). However, the role of circ-PKD2 in regulating the sensitivity of OSCC patients to cisplatin remains to be elucidated. Overexpression of circ-PKD2 increased the formation of autophagosomes in OSCC cells and activation of proteins, such as LC3 II/I. Its activation effect on autophagy was, however, alleviated by 3-MA. Bioinformatics analyses and double luciferases reporter assays conducted in this study confirmed the existence of targeted relationships between circ-PKD2 and miR-646 and miR-646 and Atg13. Functional experiments further revealed that miR-646 reversed the autophagy and apoptosis effects of circ-PKD2 in OSCC cells treated with cisplatin. In addition, circ-PKD2 promoted the expression of ATG13 by adsorption of miR-646. Its interference with Atg13 alleviated the activation effects of circ-PKD2 on autophagy and apoptosis of miR-646. Notably, the in vivo animal experiments also confirmed that circ-PKD2 inhibited tumor proliferation and activated autophagy in OSCC cells. This study provides a theoretical basis for using circ-PKD2 as a target to regulate the sensitivity of OSCC patients to cisplatin, thus increasing its chemotherapeutic effects.
Collapse
|
22
|
Hafez AK, Zimmerman AJ, Papageorgiou G, Chandrasekaran J, Amoah SK, Lin R, Lozano E, Pierotti C, Dell'Orco M, Hartley BJ, Alural B, Lalonde J, Esposito JM, Berretta S, Squassina A, Chillotti C, Voloudakis G, Shao Z, Fullard JF, Brennand KJ, Turecki G, Roussos P, Perlis RH, Haggarty SJ, Perrone-Bizzozero N, Brigman JL, Mellios N. A bidirectional competitive interaction between circHomer1 and Homer1b within the orbitofrontal cortex regulates reversal learning. Cell Rep 2022; 38:110282. [PMID: 35045295 PMCID: PMC8809079 DOI: 10.1016/j.celrep.2021.110282] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/28/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Although circular RNAs (circRNAs) are enriched in the brain, their relevance for brain function and psychiatric disorders is poorly understood. Here, we show that circHomer1 is inversely associated with relative HOMER1B mRNA isoform levels in both the orbitofrontal cortex (OFC) and stem-cell-derived neuronal cultures of subjects with psychiatric disorders. We further demonstrate that in vivo circHomer1 knockdown (KD) within the OFC can inhibit the synaptic expression of Homer1b mRNA. Furthermore, we show that circHomer1 directly binds to Homer1b mRNA and that Homer1b-specific KD increases synaptic circHomer1 levels and improves OFC-mediated behavioral flexibility. Importantly, double circHomer1 and Homer1b in vivo co-KD results in a complete rescue in circHomer1-associated alterations in both chance reversal learning and synaptic gene expression. Lastly, we uncover an RNA-binding protein that can directly bind to circHomer1 and promote its biogenesis. Taken together, our data provide mechanistic insights into the importance of circRNAs in brain function and disease.
Collapse
Affiliation(s)
- Alexander K Hafez
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Amber J Zimmerman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Grigorios Papageorgiou
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | - Stephen K Amoah
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rixing Lin
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Evelyn Lozano
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Caroline Pierotti
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Michela Dell'Orco
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Brigham J Hartley
- Pamela Sklar Division of Psychiatric Genomics, Friedman Brain Institute, Departments of Genetics and Genomic Sciences, Neuroscience, and Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Begüm Alural
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jasmin Lalonde
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Sabina Berretta
- Translational Neuroscience Laboratory, Mclean Hospital, Belmont, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Georgios Voloudakis
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhiping Shao
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Friedman Brain Institute, Departments of Genetics and Genomic Sciences, Neuroscience, and Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Roy H Perlis
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA; Center for Experimental Drugs and Diagnostics, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Haggarty
- Center for Genomic Medicine, Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jonathan L Brigman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA; Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
| |
Collapse
|
23
|
Liu M, Zhang H, Li Y, Wang S. Noncoding RNAs Interplay in Ovarian Cancer Therapy and Drug Resistance. Cancer Biother Radiopharm 2022; 37:186-198. [PMID: 35133881 DOI: 10.1089/cbr.2021.0339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are several types of RNA that do not encode proteins, but are essential for cell regulation. Ovarian cancer (OC) is a type of gynecological cancer with a high mortality rate and a 5-year prognosis. OC is becoming more common with each passing year, and the symptoms of early-stage OC are sometimes undetectable. Meanwhile, early-stage OC has no symptoms and is difficult to diagnose. Because ncRNA has been shown to affect the development of OC and is widely distributed, it could be employed as a new biomarker for early OC. Furthermore, ncRNA has the potential to promote or inhibit drug resistance in OC, potentially giving a solution to multiple drug resistance. Various prior studies have found that different ncRNAs perform differently in OC. This article examines how mainstream ncRNAs have been expressed in OC in recent years, as well as their function in tumor growth.
Collapse
Affiliation(s)
- Min Liu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Hui Zhang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yanli Li
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shaojia Wang
- Department of Gynecology, Yunnan Cancer Center, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| |
Collapse
|
24
|
Kuo MC, Liu SCH, Hsu YF, Wu RM. The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways. J Biomed Sci 2021; 28:78. [PMID: 34794432 PMCID: PMC8603508 DOI: 10.1186/s12929-021-00775-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.
Collapse
Affiliation(s)
- Ming-Che Kuo
- Department of Medicine, Section of Neurology, Cancer Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sam Chi-Hao Liu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
25
|
Shi Y, Wang Q, Song R, Kong Y, Zhang Z. Non-coding RNAs in depression: Promising diagnostic and therapeutic biomarkers. EBioMedicine 2021; 71:103569. [PMID: 34521053 PMCID: PMC8441067 DOI: 10.1016/j.ebiom.2021.103569] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/18/2021] [Indexed: 01/18/2023] Open
Abstract
Non-coding RNAs (ncRNAs), including microRNAs, circular RNAs, and long non-coding RNAs, are important regulators of normal biological processes and their abnormal expression may be involved in the pathogenesis of human diseases including depression. Multiple studies have demonstrated a significantly increased or reduced ncRNAs expression in depressed patients compared with healthy subjects and that antidepressant therapy can alter the aberrant expression of ncRNAs in depressed patients. Although the existing evidence is important, it is also mixed and a comprehensive review to guide an effective clinical translation is lacking. Focused on human research, this review summarizes clinical findings of ncRNAs in depression, including those in brain tissues and peripheral samples. We outlined the characteristics and functions of ncRNAs and highlighted their performance in the diagnosis and treatment of depression. Although their precise roles in depression remain uncertain, ncRNAs have shown potential value as biomarkers for diagnosis and therapy in depressed patients.
Collapse
Affiliation(s)
- Yachen Shi
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Institution of Neuropsychiatry, Southeast University, No. 87 Dingjiaqiao Road, Nanjing, Jiangsu 210009, China
| | - Qingyun Wang
- College of Agricultural and Environmental Sciences, University of California, Davis, California 95616, United States
| | - Ruize Song
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Institution of Neuropsychiatry, Southeast University, No. 87 Dingjiaqiao Road, Nanjing, Jiangsu 210009, China
| | - Yan Kong
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, No. 87 Dingjiaqiao Road, Nanjing, Jiangsu 210009, China.
| | - Zhijun Zhang
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Institution of Neuropsychiatry, Southeast University, No. 87 Dingjiaqiao Road, Nanjing, Jiangsu 210009, China; School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu 210096, China; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China; Research Center for Brain Health, Pazhou Lab, Guangzhou, Guangdong 510330, China.
| |
Collapse
|
26
|
Cheng YQ, Wu CR, Du MR, Zhou Q, Wu BY, Fu JYY, Balawi E, Tan WL, Liao ZB. CircLphn3 protects the blood-brain barrier in traumatic brain injury. Neural Regen Res 2021; 17:812-818. [PMID: 34472480 PMCID: PMC8530114 DOI: 10.4103/1673-5374.322467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Circular RNAs (circRNAs) are a new and large group of non-coding RNA molecules that are abundantly expressed in the central nervous system. However, very little is known about their roles in traumatic brain injury. In this study, we firstly screened differentially expressed circRNAs in normal and injured brain tissues of mice after traumatic brain injury. We found that the expression of circLphn3 was substantially decreased in mouse models of traumatic brain injury and in hemin-treated bEnd.3 (mouse brain cell line) cells. After overexpressing circLphn3 in bEnd.3 cells, the expression of the tight junction proteins, ZO-1, ZO-2, and occludin, was upregulated, and the expression of miR-185-5p was decreased. In bEnd.3 cells transfected with miR-185-5p mimics, the expression of ZO-1 was decreased. Dual-luciferase reporter assays showed that circLphn3 bound to miR-185-5p, and that miR-185-5p bound to ZO-1. Additionally, circLphn3 overexpression attenuated the hemin-induced high permeability of the in vitro bEnd.3 cell model of the blood-brain barrier, while miR-185-5p transfection increased the permeability. These findings suggest that circLphn3, as a molecular sponge of miR-185-5p, regulates tight junction proteins' expression after traumatic brain injury, and it thereby improves the permeability of the blood-brain barrier. This study was approved by the Animal Care and Use Committee of Chongqing Medical University of China (approval No. 2021-177) on March 22, 2021.
Collapse
Affiliation(s)
- Yu-Qi Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chen-Rui Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Meng-Ran Du
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiang Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bi-Ying Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia-Yuan-Yuan Fu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ehab Balawi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei-Lin Tan
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng-Bu Liao
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
27
|
Mahmoudi E, Green MJ, Cairns MJ. Dysregulation of circRNA expression in the peripheral blood of individuals with schizophrenia and bipolar disorder. J Mol Med (Berl) 2021; 99:981-991. [PMID: 33782720 DOI: 10.1007/s00109-021-02070-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are head-to-tail back-spliced RNA transcripts that have been linked to several biological processes and their perturbation is evident in human disease, including neurological disorders. There is also emerging research suggesting circRNA expression may also be altered in psychiatric and behavioural syndromes. Here, we provide a comprehensive analysis of circRNA expression in peripheral blood mononuclear cells (PBMCs) from 39 patients with schizophrenia and bipolar disorder as well as 20 healthy individuals using deep RNA-seq. We observed systematic alternative splicing leading to a complex and diverse profile of RNA transcripts including 8762 high confidence circRNAs. More specific scrutiny of the circular transcriptome in schizophrenia and bipolar disorder, compared to a non-psychiatric control group, revealed significant dysregulation of 55 circRNAs with a bias towards downregulation. These molecules were predicted to interact with a large number of miRNAs that target genes enriched in psychiatric disorders. Further replication and cross-validation to determine the specificity of these circRNAs across broader diagnostic groups and subgroups in psychiatry will enable their potential utility as biomarkers to be established. KEY MESSAGES: • We identified 8762 high confidence circRNAs with systematic alternative splicing in human PBMCs. • CircRNAs were dysregulated in schizophrenia and bipolar disorder, compared to a non-psychiatric control group. • The DE circRNAs were predicted to interact with miRNAs with target genes enriched in psychiatric disorders. • Some circRNAs have the potential to serve as biomarkers in psychiatry.
Collapse
Affiliation(s)
- Ebrahim Mahmoudi
- School of Biomedical Sciences and Pharmacy, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales (UNSW), Sydney, NSW, Australia.,Neuroscience Research Australia (NeuRA), Randwick, NSW, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Hunter Medical Research Institute, New Lambton Heights, Australia.
| |
Collapse
|
28
|
Suster I, Feng Y. Multifaceted Regulation of MicroRNA Biogenesis: Essential Roles and Functional Integration in Neuronal and Glial Development. Int J Mol Sci 2021; 22:ijms22136765. [PMID: 34201807 PMCID: PMC8269442 DOI: 10.3390/ijms22136765] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that function as endogenous gene silencers. Soon after the discovery of miRNAs, a subset of brain-enriched and brain-specific miRNAs were identified and significant advancements were made in delineating miRNA function in brain development. However, understanding the molecular mechanisms that regulate miRNA biogenesis in normal and diseased brains has become a prevailing challenge. Besides transcriptional regulation of miRNA host genes, miRNA processing intermediates are subjected to multifaceted regulation by canonical miRNA processing enzymes, RNA binding proteins (RBPs) and epitranscriptomic modifications. Further still, miRNA activity can be regulated by the sponging activity of other non-coding RNA classes, namely circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs). Differential abundance of these factors in neuronal and glial lineages partly underlies the spatiotemporal expression and function of lineage-specific miRNAs. Here, we review the continuously evolving understanding of the regulation of neuronal and glial miRNA biogenesis at the transcriptional and posttranscriptional levels and the cooperativity of miRNA species in targeting key mRNAs to drive lineage-specific development. In addition, we review dysregulation of neuronal and glial miRNAs and the detrimental impacts which contribute to developmental brain disorders.
Collapse
Affiliation(s)
| | - Yue Feng
- Correspondence: ; Tel.: +1-404-727-0351
| |
Collapse
|
29
|
The role of circTmeff-1 in incubation of context-induced morphine craving. Pharmacol Res 2021; 170:105722. [PMID: 34116208 DOI: 10.1016/j.phrs.2021.105722] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/08/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023]
Abstract
A progressive increase in drug craving following drug exposure is an important trigger of relapse. CircularRNAs (CircRNAs), key regulators of gene expression, play an important role in neurological diseases. However, the role of circRNAs in drug craving is unclear. In the present study, we trained mice to morphine conditioned place preference (CPP) and collected the nucleus accumbens (NAc) sections on abstinence day 1 (AD1) and day 14 (AD14) for RNA-sequencing. CircTmeff-1, which was highly expressed in the NAc core, was associated with incubation of context-induced morphine craving. The gain- and loss- of function showed that circTmeff-1 was a positive regulator of incubation. Simultaneously, the expression of miR-541-5p and miR-6934-3p were down-regulated in the NAc core during the incubation period. The dual luciferase reporter, RNA pulldown, and fluorescence insitu hybridization assays confirmed that miR-541-5p and miR-6934-3p bind to circTmeff-1 selectively. Furthermore, bioinformatics and western blot analysis suggested that vesicle-associated membrane protein 1 (VAMP1) and neurofascin (NFASC), both overlapping targets of miR-541-5p and miR-6934-3p, were highly expressed during incubation. Lastly, AAV-induced down-regulation of circTmeff-1 decreased VAMP1 and NFASC expression and incubation of morphine craving. These findings suggested that circTmeff-1, a novel circRNA, promotes incubation of context-induced morphine craving by sponging miR-541/miR-6934 in the NAc core. Thus, circTmeff-1 represents a potential therapeutic target for context-induced opioid craving, following prolonged abstinence.
Collapse
|
30
|
Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
Collapse
Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
| |
Collapse
|
31
|
Xu K, Zhang Y, Li J. Expression and function of circular RNAs in the mammalian brain. Cell Mol Life Sci 2021; 78:4189-4200. [PMID: 33558994 PMCID: PMC11071837 DOI: 10.1007/s00018-021-03780-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/07/2021] [Accepted: 01/27/2021] [Indexed: 01/19/2023]
Abstract
Mammalian brain presents extraordinary complexity reflected in the structure, function, and dynamic changes in the biological and physiological processes of development, maturity, and aging. Recent transcriptomic profiles from the brain tissues of distinct species have described a novel class of transcripts with a covalently closed-loop structure, called circular RNAs (circRNAs), which are produced by alternative back-splicing and derived from genes associated with synaptogenesis and neural activities. Brain is a tightly regulated and largely unexplored organ where circRNAs are highly enriched and expressed in the cell type-, spatiotemporal-specific, sex-biased, and age-related manner. Although the biological functions of most of the circRNAs in the brain remain elusive, increased evidence suggests that dynamic changes in circRNA expression are critical for brain function and the maintenance of physiological homeostasis in the brain. Here, we review the latest immense progresses in the understanding of circRNA expression and function in the mammalian brain. We also discuss possibly biological functions of circRNAs in the brain, which may provide new sights of understanding brain development and aging, as well as the pathogenesis of mental diseases.
Collapse
Affiliation(s)
- Kaiyu Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ying Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- National Institute on Drug Dependence, Peking University, Beijing, China.
- PKU/McGovern Institute for Brain Research, Peking University, Beijing, China.
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| |
Collapse
|
32
|
Circular RNAs in depression: Biogenesis, function, expression, and therapeutic potential. Biomed Pharmacother 2021; 137:111244. [DOI: 10.1016/j.biopha.2021.111244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/14/2023] Open
|
33
|
Potential clinical value of circular RNAs as peripheral biomarkers for the diagnosis and treatment of major depressive disorder. EBioMedicine 2021; 66:103337. [PMID: 33862583 PMCID: PMC8054154 DOI: 10.1016/j.ebiom.2021.103337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
Background circular RNAs (circRNAs) are expressed abundantly in the brain and are implicated in the pathophysiology of neuropsychiatric disease. However, the potential clinical value of circRNAs in major depressive disorder (MDD) remains unclear. Methods RNA sequencing was conducted in whole-blood samples in a discovery set (7 highly homogeneous MDD patients and 7 matched healthy controls [HCs]). The differential expression of circRNAs was verified in an independent validation set. The interventional study was conducted to assess the potential effect of the antidepressive treatment on the circRNA expression. Findings in the validation set, compared with 52 HCs, significantly decreased circFKBP8 levels (Diff: -0.24; [95% CI -0.39 ~ -0.09]) and significantly elevated circMBNL1 levels (Diff: 0.37; [95% CI 0.09 ~ 0.64]) were observed in 53 MDD patients. The expression of circMBNL1 was negatively correlated with 24-item Hamilton Depression Scale (HAMD-24) scores in 53 MDD patients. A mediation model indicated that circMBNL1 affected HAMD-24 scores through a mediator, serum brain-derived neurotrophic factor. In 53 MDD patients, the amplitude of low-frequency fluctuations in the right orbital part middle frontal gyrus was positively correlated with circFKBP8 and circMBNL1 expression. Furthermore, the interventional study of 53 MDD patients demonstrated that antidepressive treatment partly increased circFKBP8 expression and the change in expression of circFKBP8 was predictive of further reduced HAMD-24 scores. Interpretation whole-blood circFKBP8 and circMBNL1 may be potential biomarkers for the diagnosis of MDD, respectively, and circFKBP8 may show great potential for the antidepressive treatment.
Collapse
|
34
|
The "missing heritability"-Problem in psychiatry: Is the interaction of genetics, epigenetics and transposable elements a potential solution? Neurosci Biobehav Rev 2021; 126:23-42. [PMID: 33757815 DOI: 10.1016/j.neubiorev.2021.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Psychiatric disorders exhibit an enormous burden on the health care systems worldwide accounting for around one-third of years lost due to disability among adults. Their etiology is largely unknown and diagnostic classification is based on symptomatology and course of illness and not on objective biomarkers. Most psychiatric disorders are moderately to highly heritable. However, it is still unknown what mechanisms may explain the discrepancy between heritability estimates and the present data from genetic analysis. In addition to genetic differences also epigenetic modifications are considered as potentially relevant in the transfer of susceptibility to psychiatric diseases. Though, whether or not epigenetic alterations can be inherited for many generations is highly controversial. In the present article, we will critically summarize both the genetic findings and the results from epigenetic analyses, including also those of noncoding RNAs. We will argue that one possible solution to the "missing heritability" problem in psychiatry is a potential role of retrotransposons, the exploration of which is presently only in its beginnings.
Collapse
|
35
|
Wang J, Yang Z, Chen C, Xu Y, Wang H, Liu B, Zhang W, Jiang Y. Comprehensive circRNA Expression Profile and Construction of circRNAs-Related ceRNA Network in a Mouse Model of Autism. Front Genet 2021; 11:623584. [PMID: 33679870 PMCID: PMC7928284 DOI: 10.3389/fgene.2020.623584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
Autism is a common disease that seriously affects the quality of life. The role of circular RNAs (circRNAs) in autism remains largely unexplored. We aimed to detect the circRNA expression profile and construct a circRNA-based competing endogenous RNA (ceRNA) network in autism. Valproate acid was used to establish an in vivo model of autism in mice. A total of 1,059 differentially expressed circRNAs (477 upregulated and 582 downregulated) in autism group was identified by RNA sequencing. The expression of novel_circ_015779 and novel_circ_035247 were detected by real-time PCR. A ceRNA network based on altered circRNAs was established, with 9,715 nodes and 150,408 edges. Module analysis was conducted followed by GO and KEGG pathway enrichment analysis. The top three modules were all correlated with autism-related pathways involving “TGF-beta signaling pathway,” “Notch signaling pathway,” “MAPK signaling pathway,” “long term depression,” “thyroid hormone signaling pathway,” etc. The present study reveals a novel circRNA involved mechanisms in the pathogenesis of autism.
Collapse
Affiliation(s)
- Ji Wang
- Yangzhou Maternal and Child Health Hospital, Yangzhou, China.,Harbin Children's Hospital, Harbin, China
| | - Zhongxiu Yang
- Xuzhou Children's Hospital, Xuzhou Medical University, Xuzhou, China
| | - Canming Chen
- Yangzhou Maternal and Child Health Hospital, Yangzhou, China
| | - Yang Xu
- Yangzhou Maternal and Child Health Hospital, Yangzhou, China
| | - Hongguang Wang
- School of Civil Engineering, Northeast Forestry University, Harbin, China
| | - Bing Liu
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Wei Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yanan Jiang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| |
Collapse
|
36
|
Ji Y, Zhang X, Wang Z, Qin W, Liu H, Xue K, Tang J, Xu Q, Zhu D, Liu F, Yu C. Genes associated with gray matter volume alterations in schizophrenia. Neuroimage 2020; 225:117526. [PMID: 33147509 DOI: 10.1016/j.neuroimage.2020.117526] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Although both schizophrenia and gray matter volume (GMV) show high heritability, however, genes accounting for GMV alterations in schizophrenia remain largely unknown. Based on risk genes identified in schizophrenia by the genome-wide association study of the Schizophrenia Working Group of the Psychiatric Genomics Consortium, we used transcription-neuroimaging association analysis to test that which of these genes are associated with GMV changes in schizophrenia. For each brain tissue sample, the expression profiles of 196 schizophrenia risk genes were extracted from six donated normal brains of the Allen Human Brain Atlas, and GMV differences between patients with schizophrenia and healthy controls were calculated based on five independent case-control structural MRI datasets (276 patients and 284 controls). Genes associated with GMV changes in schizophrenia were identified by performing cross-sample spatial correlations between expression levels of each gene and case-control GMV difference derived from the five MRI datasets integrated by harmonization and meta-analysis. We found that expression levels of 98 genes consistently showed significant cross-sample spatial correlations with GMV changes in schizophrenia. These genes were functionally enriched for chemical synaptic transmission, central nervous system development, and cell projection. Overall, this study provides a set of genes possibly associated with GMV changes in schizophrenia, which could be used as candidate genes to explore biological mechanisms underlying the structural impairments in schizophrenia.
Collapse
Affiliation(s)
- Yuan Ji
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xue Zhang
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zirui Wang
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Wen Qin
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Huaigui Liu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Kaizhong Xue
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jie Tang
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiang Xu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Dan Zhu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Feng Liu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Chunshui Yu
- Department of Radiology, Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
37
|
Zimmerman AJ, Hafez AK, Amoah SK, Rodriguez BA, Dell'Orco M, Lozano E, Hartley BJ, Alural B, Lalonde J, Chander P, Webster MJ, Perlis RH, Brennand KJ, Haggarty SJ, Weick J, Perrone-Bizzozero N, Brigman JL, Mellios N. A psychiatric disease-related circular RNA controls synaptic gene expression and cognition. Mol Psychiatry 2020; 25:2712-2727. [PMID: 31988434 PMCID: PMC7577899 DOI: 10.1038/s41380-020-0653-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/17/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
Although circular RNAs (circRNAs) are enriched in the mammalian brain, very little is known about their potential involvement in brain function and psychiatric disease. Here, we show that circHomer1a, a neuronal-enriched circRNA abundantly expressed in the frontal cortex, derived from Homer protein homolog 1 (HOMER1), is significantly reduced in both the prefrontal cortex (PFC) and induced pluripotent stem cell-derived neuronal cultures from patients with schizophrenia (SCZ) and bipolar disorder (BD). Moreover, alterations in circHomer1a were positively associated with the age of onset of SCZ in both the dorsolateral prefrontal cortex (DLPFC) and orbitofrontal cortex (OFC). No correlations between the age of onset of SCZ and linear HOMER1 mRNA were observed, whose expression was mostly unaltered in BD and SCZ postmortem brain. Using in vivo circRNA-specific knockdown of circHomer1a in mouse PFC, we show that it modulates the expression of numerous alternative mRNA transcripts from genes involved in synaptic plasticity and psychiatric disease. Intriguingly, in vivo circHomer1a knockdown in mouse OFC resulted in specific deficits in OFC-mediated cognitive flexibility. Lastly, we demonstrate that the neuronal RNA-binding protein HuD binds to circHomer1a and can influence its synaptic expression in the frontal cortex. Collectively, our data uncover a novel psychiatric disease-associated circRNA that regulates synaptic gene expression and cognitive flexibility.
Collapse
Affiliation(s)
- Amber J Zimmerman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Alexander K Hafez
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Stephen K Amoah
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
- Autophagy inflammation and metabolism (AIM) center, Albuquerque, NM, USA
| | - Brian A Rodriguez
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Michela Dell'Orco
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Evelyn Lozano
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Brigham J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Begüm Alural
- Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jasmin Lalonde
- Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Praveen Chander
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, Chevy Chase, MD, USA
| | - Roy H Perlis
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center for Experimental Drugs and Diagnostics, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen J Haggarty
- Departments of Neurology and Psychiatry, Center for Genomic Medicine, Chemical Neurobiology Laboratory, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jason Weick
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jonathan L Brigman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA.
- Autophagy inflammation and metabolism (AIM) center, Albuquerque, NM, USA.
| |
Collapse
|
38
|
Abstract
Higher-order organisms possess information processing capabilities that
are only made possible by their biological complexity. Emerging
evidence indicates a critical role for regulatory RNAs in coordinating
many aspects of cellular function that are directly involved in
experience-dependent neural plasticity. Here, we focus on a
structurally distinct class of RNAs known as circular RNAs. These
closed loop, single-stranded RNA molecules are highly stable, enriched
in the brain, and functionally active in both healthy and disease
conditions. Current evidence implicating this ancient class of RNA as
a contributor toward higher-order functions such as cognition and
memory is discussed.
Collapse
Affiliation(s)
- Esmi L. Zajaczkowski
- Cognitive Neuroepigenetics
Laboratory, Queensland Brain Institute, The University of Queensland,
Brisbane, Queensland, Australia
- Esmi L. Zajaczkowski, The University
of Queensland, QBI Building 79, University of Queensland, Saint Lucia,
Queensland 4072, Australia.
| | - Timothy W. Bredy
- Cognitive Neuroepigenetics
Laboratory, Queensland Brain Institute, The University of Queensland,
Brisbane, Queensland, Australia
| |
Collapse
|
39
|
Nedoluzhko A, Gruzdeva N, Sharko F, Rastorguev S, Zakharova N, Kostyuk G, Ushakov V. The Biomarker and Therapeutic Potential of Circular Rnas in Schizophrenia. Cells 2020; 9:E2238. [PMID: 33020462 PMCID: PMC7601372 DOI: 10.3390/cells9102238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are endogenous, single-stranded, most frequently non-coding RNA (ncRNA) molecules that play a significant role in gene expression regulation. Circular RNAs can affect microRNA functionality, interact with RNA-binding proteins (RBPs), translate proteins by themselves, and directly or indirectly modulate gene expression during different cellular processes. The affected expression of circRNAs, as well as their targets, can trigger a cascade of events in the genetic regulatory network causing pathological conditions. Recent studies have shown that altered circular RNA expression patterns could be used as biomarkers in psychiatric diseases, including schizophrenia (SZ); moreover, circular RNAs together with other cell molecules could provide new insight into mechanisms of this disorder. In this review, we focus on the role of circular RNAs in the pathogenesis of SZ and analyze their biomarker and therapeutic potential in this disorder.
Collapse
Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, PB 1490. 8049 Bodø, Norway
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Natalia Gruzdeva
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
| | - Fedor Sharko
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect 33/2, 119071 Moscow, Russia
| | - Sergey Rastorguev
- National Research Center “Kurchatov Institute”, 1st Akademika Kurchatova Square, 123182 Moscow, Russia; (N.G.); (F.S.); (S.R.)
| | - Natalia Zakharova
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Georgy Kostyuk
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
| | - Vadim Ushakov
- Mental-Health Clinic No. 1 Named after N.A. Alexeev, Moscow Healthcare Department, Zagorodnoye Highway, 2, 115191 Moscow, Russia; (N.Z.); (G.K.); (V.U.)
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, Leninskiye Gory, 119899 Moscow, Russia
| |
Collapse
|
40
|
Abstract
Circular RNAs (circRNAs) are covalently circularized RNA moieties that despite being relatively abundant were only recently identified and have only begun to be investigated within the last couple of years. Even though there are many thousands of genes that appear capable of producing circRNAs, and the fact that many circRNAs appear to be highly evolutionarily conserved, the function of all but a few remain to be fully explored. What has been determined, however, is that circRNAs play key regulatory roles in many aspects of biology with focus being given to their function in cancer. Most of the studies to date have found that circRNAs act as master regulator of gene expression most often than not acting to regulate levels though sequestration or "sponging" of other gene expression regulators, particularly miRNAs. They can also function directly modulating transcription, or by interfering with splicing mechanisms. Some circRNAs can also be translated into functional proteins or peptides. A combination of tissue and developmental stage specific expression along with an innate resistance to RNAse activity means that circRNAs show perhaps their greatest potential as novel biomarkers of cancer. In this chapter we consider the current state of knowledge regarding these molecules, their synthesis, function, and association with cancer. We also consider some of the challenges that remain to be overcome to allow this emerging class of RNAs to fulfill their potential in clinical practice.
Collapse
Affiliation(s)
- Carla Solé
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles Henderson Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
41
|
Epigenomic Dysregulation in Schizophrenia: In Search of Disease Etiology and Biomarkers. Cells 2020; 9:cells9081837. [PMID: 32764320 PMCID: PMC7463953 DOI: 10.3390/cells9081837] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
Schizophrenia is a severe psychiatric disorder with a complex array of signs and symptoms that causes very significant disability in young people. While schizophrenia has a strong genetic component, with heritability around 80%, there is also a very significant range of environmental exposures and stressors that have been implicated in disease development and neuropathology, such as maternal immune infection, obstetric complications, childhood trauma and cannabis exposure. It is postulated that epigenetic factors, as well as regulatory non-coding RNAs, mediate the effects of these environmental stressors. In this review, we explore the most well-known epigenetic marks, including DNA methylation and histone modification, along with emerging RNA mediators of epigenomic state, including miRNAs and lncRNAs, and discuss their collective potential for involvement in the pathophysiology of schizophrenia implicated through the postmortem analysis of brain tissue. Given that peripheral tissues, such as blood, saliva, and olfactory epithelium have the same genetic composition and are exposed to many of the same environmental exposures, we also examine some studies supporting the application of peripheral tissues for epigenomic biomarker discovery in schizophrenia. Finally, we provide some perspective on how these biomarkers may be utilized to capture a signature of past events that informs future treatment.
Collapse
|
42
|
Gasparini S, Licursi V, Presutti C, Mannironi C. The Secret Garden of Neuronal circRNAs. Cells 2020; 9:E1815. [PMID: 32751850 PMCID: PMC7463782 DOI: 10.3390/cells9081815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
High-throughput transcriptomic profiling approaches have revealed that circular RNAs (circRNAs) are important transcriptional gene products, identified across a broad range of organisms throughout the eukaryotic tree of life. In the nervous system, they are particularly abundant, developmentally regulated, region-specific, and enriched in genes for neuronal proteins and synaptic factors. These features suggested that circRNAs are key components of an important layer of neuronal gene expression regulation, with known and anticipated functions. Here, we review major recognized aspects of circRNA biogenesis, metabolism and biological activities, examining potential new functions in the context of the nervous system.
Collapse
Affiliation(s)
- Silvia Gasparini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Carlo Presutti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy
| |
Collapse
|
43
|
Zhang Y, Wang M, Zang X, Mao Z, Chen Y, Mao F, Qian H, Xu W, Zhang X. CircHN1 affects cell proliferation and migration in gastric cancer. J Clin Lab Anal 2020; 34:e23433. [PMID: 32608539 PMCID: PMC7595908 DOI: 10.1002/jcla.23433] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/04/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background Increasing evidence indicates that circular RNAs (circRNAs) are dysregulated in human cancers. The biological roles of circRNAs in gastric cancer (GC) have not been well‐characterized. Methods The GEO database was used to analyze circRNA expression profile in GC. The expression level of target circRNA in tumor tissues and adjacent non‐tumor tissues was detected by reverse transcription‐quantitative PCR. Gene transfection was used to manipulate the expression of circRNAs. The biological roles of circRNAs in cell proliferation, migration, and invasion were determined by cell counting, colony formation, transwell migration, Matrigel invasion, and mouse xenograft tumor assays. The interactions between circRNAs and miRNAs were verified by RNA immunoprecipitation and luciferase reporter assays. Results We found that circHN1 was upregulated in GC tissues and cell lines compared to adjacent non‐tumor tissues and normal gastric epithelial cells. Additionally, circHN1 silencing significantly promoted GC cell growth, colony formation, migration, and invasion, whereas circHN1 overexpression had the opposite effects. CircHN1 overexpression also suppressed gastric cancer growth in the mouse xenograft tumor model. CircHN1 was mainly localized in the cytoplasm of GC cells and could bind to AGO2. MiR‐1248 and miR‐375 were predicted to interact with circHN1 by bioinformatic analyses. MiR‐1248 and miR‐375 overexpression inhibited the activity of the circHN1 luciferase reporter. Conclusion CircHN1 is aberrantly expressed in GC and affects the proliferation and migration of gastric cancer cells by acting as miRNA sponge.
Collapse
Affiliation(s)
- Yu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Maoye Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xueyan Zang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zheying Mao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanke Chen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fei Mao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
| |
Collapse
|
44
|
Tan G, Wang L, Liu Y, Zhang H, Feng W, Liu Z. The alterations of circular RNA expression in plasma exosomes from patients with schizophrenia. J Cell Physiol 2020; 236:458-467. [PMID: 32542700 DOI: 10.1002/jcp.29873] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022]
Abstract
Schizophrenia (SZ) is characterized by a high morbidity and disability rate and has gradually increased in rate and caused much burden. However, the pathogenesis of SZ is elusive and may include changes in the biological molecules in exosomes. In this study, we first compared the alterations of plasma exosomal circular RNAs (exo-circRNAs) from SZ patients and matched health controls by high-throughput sequencing. We further explored whether plasma exo-circRNAs can be estimable targets for researching the pathogenesis, potential diagnostic biomarkers, and therapeutic strategy of SZ. A total of 44 plasma exo-circRNAs were differentially expressed between SZ patients and matched Health Controls, including 38 upregulated circRNAs and six downregulated circRNAs (fold change ≥2; p < .05). Eight differentially expressed circRNAs were verified by quantitative real-time polymerase chain reaction, and four out of eight circRNAs were positively confirmed and contained binding sites to many microRNAs. Bioinformatics analysis, including Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, showed that these differentially expressed circRNAs played potential roles in pathogenesis, especially regarding the metabolic process, stress response, and histone ubiquitination. In conclusion, this study supplies a new window for understanding the pathogenesis of SZ at molecular levels, and serves as a tool for better exploring potential diagnostic biomarkers and the therapeutic strategy for SZ.
Collapse
Affiliation(s)
- Guifeng Tan
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Limin Wang
- Department of Neurology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangdong Neuroscience Institute, Guangzhou, Guangdong, China
| | - Yunyun Liu
- Department of Neurology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Han Zhang
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Wenhui Feng
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhonglin Liu
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| |
Collapse
|
45
|
Zhang Y, Lin X, Geng X, Shi L, Li Q, Liu F, Fang C, Wang H. Advances in circular RNAs and their role in glioma (Review). Int J Oncol 2020; 57:67-79. [PMID: 32319596 PMCID: PMC7252450 DOI: 10.3892/ijo.2020.5049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Glioma is the most common primary tumour of the central nervous system, and is associated with a high postoperative recurrence rate and resistance to chemotherapy. High‑grade glioblastoma in particular has a very poor prognosis and poses a serious threat to human health. Related studies have confirmed that the occurrence and development of gliomas are closely associated with the abnormal expression and regulation of genes. Moreover, the number of studies on the association of the expression of non‑coding RNAs [linear RNAs, microRNAs and circular RNAs (circRNAs)] in human cells with glioma has been gradually increasing in recent years. Among those, circRNAs, previously considered to be 'splicing errors', have been shown to be highly expressed in eukaryotic cells and regulate the biological behaviour of gliomas. circRNAs are highly abundant and stable, and have become a research hotspot in the field of glioma molecular biology. The aim of the present review was to focus on the research progress regarding the association between circRNA expression and gliomas, and to provide a theoretical basis according to the currently available literature for further exploring this association. The present study may be of value for the early diagnosis, pathological grading, targeted therapy and prognostic evaluation of gliomas.
Collapse
Affiliation(s)
- Yuhao Zhang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Xiaomeng Lin
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Xiuchao Geng
- Hebei University of Chinese Medicine, Faculty of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, Hebei 050091, P.R. China
| | - Liang Shi
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Qiang Li
- Hebei University of Chinese Medicine, Faculty of Acupuncture‑Moxibustion and Tuina, Shijiazhuang, Hebei 050200, P.R. China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Hong Wang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| |
Collapse
|
46
|
Mehta SL, Dempsey RJ, Vemuganti R. Role of circular RNAs in brain development and CNS diseases. Prog Neurobiol 2020; 186:101746. [PMID: 31931031 PMCID: PMC7024016 DOI: 10.1016/j.pneurobio.2020.101746] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/13/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
In mammals, many classes of noncoding RNAs (ncRNAs) are expressed at a much higher level in the brain than in other organs. Recent studies have identified a new class of ncRNAs called circular RNAs (circRNAs), which are produced by back-splicing and fusion of either exons, introns, or both exon-intron into covalently closed loops. The circRNAs are also highly enriched in the brain and increase continuously from the embryonic to the adult stage. Although the functional significance and mechanism of action of circRNAs are still being actively explored, they are thought to regulate the transcription of their host genes and sequestration of miRNAs and RNA binding proteins. Some circRNAs are also shown to have translation potential to form peptides. The expression and abundance of circRNAs seem to be spatiotemporally maintained in a normal brain. Altered expression of circRNAs is also thought to mediate several disorders, including brain-tumor growth, and acute and chronic neurodegenerative disorders by affecting mechanisms such as angiogenesis, neuronal plasticity, autophagy, apoptosis, and inflammation. This review discusses the involvement of various circRNAs in brain development and CNS diseases. A better understanding of the circRNA function will help to develop novel therapeutic strategies to treat CNS complications.
Collapse
Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Robert J Dempsey
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States; William S. Middleton Veterans Hospital, Madison, WI, United States.
| |
Collapse
|
47
|
Santarelli DM, Carroll AP, Cairns HM, Tooney PA, Cairns MJ. Schizophrenia-associated MicroRNA-Gene Interactions in the Dorsolateral Prefrontal Cortex. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:623-634. [PMID: 32006661 PMCID: PMC7212302 DOI: 10.1016/j.gpb.2019.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 10/01/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Schizophrenia-associated anomalies in gene expression in postmortem brain can be attributed to a combination of genetic and environmental influences. Given the small effect size of common variants, it is likely that we may only see the combined impact of some of these at the pathway level in small postmortem studies. At the gene level, however, there may be more impact from common environmental exposures mediated by influential epigenomic modifiers, such as microRNA (miRNA). We hypothesise that dysregulation of miRNAs and their alteration of gene expression have significant implications in the pathophysiology of schizophrenia. In this study, we integrate changes in cortical gene and miRNA expression to identify regulatory interactions and networks associated with the disorder. Gene expression analysis in post-mortem prefrontal dorsolateral cortex (BA 46) (n = 74 matched pairs of schizophrenia, schizoaffective, and control samples) was integrated with miRNA expression in the same cohort to identify gene-miRNA regulatory networks. A significant gene-miRNA interaction network was identified, including miR-92a, miR-495, and miR-134, which converged with differentially expressed genes in pathways involved in neurodevelopment and oligodendrocyte function. The capacity for miRNA to directly regulate gene expression through respective binding sites in BCL11A, PLP1, and SYT11 was also confirmed to support the biological relevance of this integrated network model. The observations in this study support the hypothesis that miRNA dysregulation is an important factor in the complex pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Danielle M Santarelli
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Adam P Carroll
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Heath M Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Paul A Tooney
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia; Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia.
| |
Collapse
|
48
|
Li Z, Liu S, Li X, Zhao W, Li J, Xu Y. Circular RNA in Schizophrenia and Depression. Front Psychiatry 2020; 11:392. [PMID: 32457667 PMCID: PMC7221196 DOI: 10.3389/fpsyt.2020.00392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) and depression (DEP) are two common major psychiatric disorders that are associated with high risk of suicide. These disorders affect not only physical and mental health, but they also affect the social function of the individual. However, diagnoses of SZ and DEP are mainly based on symptomatic changes and the clinical experience of psychiatrists. These rather subjective measures can induce misdiagnoses and missed diagnoses. Therefore, it is necessary to further explore objective indexes for improving the early diagnoses and prognoses of SZ and DEP. Current research indicates that non-coding RNA (ncRNA) may play a role in the occurrence and development of SZ and DEP. Circular RNA (circRNA), as an important component of ncRNA, is associated with many biological functions, especially post-transcriptional regulation. Since circRNA is easily detected in peripheral blood and has a high degree of spatiotemporal tissue specificity and stability, these attributes provide us with a new idea to further explore the potential value for the diagnosis and treatment of SZ and DEP. Here, we summarize the classification, characteristics, and biological functions of circRNA and the most significant results of experimental studies, aiming to highlight the involvement of circRNA in SZ and DEP.
Collapse
Affiliation(s)
- Zexuan Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Sha Liu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Xinrong Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Wentao Zhao
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Jing Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Yong Xu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China.,National Key Disciplines, Key Laboratory for Cellular Physiology of Ministry of Education, Department of Neurobiology, Shanxi Medical University, Taiyuan, China.,Department of Humanities and Social Science, Shanxi Medical University, Taiyuan, China
| |
Collapse
|
49
|
Mahmoudi E, Kiltschewskij D, Fitzsimmons C, Cairns MJ. Depolarization-Associated CircRNA Regulate Neural Gene Expression and in Some Cases May Function as Templates for Translation. Cells 2019; 9:cells9010025. [PMID: 31861825 PMCID: PMC7017197 DOI: 10.3390/cells9010025] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
Circular RNAs (circRNAs) are a relatively new class of RNA transcript with high abundance in the mammalian brain. Here, we show that circRNAs expression in differentiated neuroblastoma cells were significantly altered after depolarization with 107 upregulated and 47 downregulated circRNAs. This coincided with a global alteration in the expression of microRNA (miRNA) (n = 269) and mRNA (n = 1511) in depolarized cells, suggesting a regulatory axis of circRNA–miRNA–mRNA is involved in the cellular response to neural activity. In support of this, our in silico analysis revealed that the circular transcripts had the capacity to influence mRNA expression through interaction with common miRNAs. Loss-of-function of a highly expressed circRNA, circ-EXOC6B, resulted in altered expression of numerous mRNAs enriched in processes related to the EXOC6B function, suggesting that circRNAs may specifically regulate the genes acting in relation to their host genes. We also found that a subset of circRNAs, particularly in depolarized cells, were associated with ribosomes, suggesting they may be translated into protein. Overall, these data support a role for circRNAs in the modification of gene regulation associated with neuronal activity.
Collapse
Affiliation(s)
- Ebrahim Mahmoudi
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; (E.M.); (D.K.); (C.F.)
- Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute (HMRI), New Lambton, NSW 2305, Australia
| | - Dylan Kiltschewskij
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; (E.M.); (D.K.); (C.F.)
- Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute (HMRI), New Lambton, NSW 2305, Australia
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; (E.M.); (D.K.); (C.F.)
- Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute (HMRI), New Lambton, NSW 2305, Australia
| | - Murray J. Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; (E.M.); (D.K.); (C.F.)
- Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute (HMRI), New Lambton, NSW 2305, Australia
- Correspondence: ; Tel.: +61-02-4921-8670; Fax: +61-02-4921-7903
| |
Collapse
|
50
|
Pan RY, Zhao CH, Yuan JX, Zhang YJ, Jin JL, Gu MF, Mao ZY, Sun HJ, Jia QW, Ji MY, Zhang J, Wang LS, Ma WZ, Ma WQ, Ding JD, Jia EZ. Circular RNA profile in coronary artery disease. Am J Transl Res 2019; 11:7115-7125. [PMID: 31814914 PMCID: PMC6895512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Circular RNAs (circRNAs) are potential biomarkers and therapeutic targets of coronary artery disease due to their high stability, covalently closed structure. And implied roles in gene regulation. The aim of this study was to identify and characterize circRNAs from human coronary arteries. Epicardial coronary arteries were removed during the autopsy of an 81-year-old man who died from heart attack. The natural history and histological classification of atherosclerotic lesions in coronary artery segments were analyzed by hematoxylin and eosin staining, and their circRNA expression profiles were characterized by RNA sequencing. RNA sequencing identified 1259 annotated and 381 novel circRNAs. Combined with the results of histologic examination, intersection analysis identified 54 upregulated and 12 downregulated circRNAs, representing 4.0% of the total number. Coronary artery segments with or without severe atherosclerosis showed distinctly different circRNA profiles on the basis of hierarchical clustering. Our results suggest that these 66 circRNAs contribute to the pathology underlying coronary artery atherosclerosis and may serve as diagnostic or therapeutic targets in coronary artery disease.
Collapse
Affiliation(s)
- Ren-You Pan
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese MedicineYancheng 224000, Jiangsu Province, China
| | - Chen-Hui Zhao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Jin-Xia Yuan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Yong-Jie Zhang
- Department of Human Anatomy, Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Jian-Liang Jin
- Department of Human Anatomy, Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Mu-Feng Gu
- Department of Human Anatomy, Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Zhi-Yuan Mao
- Department of Human Anatomy, Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Hai-Jian Sun
- Department of Human Anatomy, Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Qiao-Wei Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Ming-Yue Ji
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Jing Zhang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Lian-Sheng Wang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Wen-Zhu Ma
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| | - Wen-Qi Ma
- Department of Cardiovascular Medicine, Zhongda Hospital, School of Medicine, Southeast UniversityNanjing 210029, Jiangsu Province, China
| | - Jian-Dong Ding
- Department of Cardiovascular Medicine, Zhongda Hospital, School of Medicine, Southeast UniversityNanjing 210029, Jiangsu Province, China
| | - En-Zhi Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, Jiangsu Province, China
| |
Collapse
|