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Rodriguez de Los Santos M, Kopell BH, Buxbaum Grice A, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. Nat Commun 2024; 15:5366. [PMID: 38926387 PMCID: PMC11208617 DOI: 10.1038/s41467-024-49268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries offer more nuanced and accurate insights into the regulatory mechanisms of RNA editing in the human brain.
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Affiliation(s)
| | - Brian H Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Chen HW, Ma CP, Chin E, Chen YT, Wang TC, Kuo YP, Su CH, Huang PJ, Tan BCM. Imbalance in Unc80 RNA Editing Disrupts Dynamic Neuronal Activity and Olfactory Perception. Int J Mol Sci 2024; 25:5985. [PMID: 38892173 PMCID: PMC11172567 DOI: 10.3390/ijms25115985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
A-to-I RNA editing, catalyzed by the ADAR protein family, significantly contributes to the diversity and adaptability of mammalian RNA signatures, aligning with developmental and physiological needs. Yet, the functions of many editing sites are still to be defined. The Unc80 gene stands out in this context due to its brain-specific expression and the evolutionary conservation of its codon-altering editing event. The precise biological functions of Unc80 and its editing, however, are still largely undefined. In this study, we first demonstrated that Unc80 editing occurs in an ADAR2-dependent manner and is exclusive to the brain. By employing the CRISPR/Cas9 system to generate Unc80 knock-in mouse models that replicate the natural editing variations, our findings revealed that mice with the "gain-of-editing" variant (Unc80G/G) exhibit heightened basal neuronal activity in critical olfactory regions, compared to the "loss-of-editing" (Unc80S/S) counterparts. Moreover, an increase in glutamate levels was observed in the olfactory bulbs of Unc80G/G mice, indicating altered neurotransmitter dynamics. Behavioral analysis of odor detection revealed distinctive responses to novel odors-both Unc80 deficient (Unc80+/-) and Unc80S/S mice demonstrated prolonged exploration times and heightened dishabituation responses. Further elucidating the olfactory connection of Unc80 editing, transcriptomic analysis of the olfactory bulb identified significant alterations in gene expression that corroborate the behavioral and physiological findings. Collectively, our research advances the understanding of Unc80's neurophysiological functions and the impact of its editing on the olfactory sensory system, shedding light on the intricate molecular underpinnings of olfactory perception and neuronal activity.
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Affiliation(s)
- Hui-Wen Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chung-Pei Ma
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
| | - En Chin
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan;
| | - Teh-Cheng Wang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Yu-Ping Kuo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hao Su
- Center for General Education, Chang Gung University, Taoyuan 333, Taiwan;
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Genomic Medicine Core Laboratory, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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Belur NR, Bustos BI, Lubbe SJ, Mazzulli JR. Nuclear aggregates of NONO/SFPQ and A-to-I-edited RNA in Parkinson's disease and dementia with Lewy bodies. Neuron 2024:S0896-6273(24)00328-3. [PMID: 38761794 DOI: 10.1016/j.neuron.2024.05.003] [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: 05/27/2023] [Revised: 03/06/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
Neurodegenerative diseases are commonly classified as proteinopathies that are defined by the aggregation of a specific protein. Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are classified as synucleinopathies since α-synuclein (α-syn)-containing inclusions histopathologically define these diseases. Unbiased biochemical analysis of PD and DLB patient material unexpectedly revealed novel pathological inclusions in the nucleus comprising adenosine-to-inosine (A-to-I)-edited mRNAs and NONO and SFPQ proteins. These inclusions showed no colocalization with Lewy bodies and accumulated at levels comparable to α-syn. NONO and SFPQ aggregates reduced the expression of the editing inhibitor ADAR3, increasing A-to-I editing mainly within human-specific, Alu-repeat regions of axon, synaptic, and mitochondrial transcripts. Inosine-containing transcripts aberrantly accumulated in the nucleus, bound tighter to recombinant purified SFPQ in vitro, and potentiated SFPQ aggregation in human dopamine neurons, resulting in a self-propagating pathological state. Our data offer new insight into the inclusion composition and pathophysiology of PD and DLB.
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Affiliation(s)
- Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Steven J Lubbe
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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Li W, Wu H, Li J, Wang Z, Cai M, Liu X, Liu G. Transcriptomic analysis reveals associations of blood-based A-to-I editing with Parkinson's disease. J Neurol 2024; 271:976-985. [PMID: 37902879 DOI: 10.1007/s00415-023-12053-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: 04/17/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Adenosine-to-inosine (A-to-I) editing is the most common type of RNA editing in humans and the role of A-to-I RNA editing remains unclear in Parkinson's disease (PD). OBJECTIVE We aimed to explore the potential causal association between A-to-I editing and PD, and to assess whether changes in A-to-I editing were associated with cognitive progression in PD. METHODS The RNA-seq data from 380 PD patients and 178 healthy controls in the Parkinson's Progression Marker Initiative cohort was used to quantify A-to-I editing sites. We performed cis-RNA editing quantitative trait loci analysis and a two-sample Mendelian Randomization (MR) study by integrating genome-wide association studies to infer the potential causality between A-to-I editing and PD pathogenesis. The potential causal A-to-I editing sites were further confirmed by Summary-data-based MR analysis. Spearman's correlation analysis was performed to characterize the association between longitudinal A-to-I editing and cognitive progression in patients with PD. RESULTS We identified 17 potential causal A-to-I editing sites for PD and indicated that genetic risk variants may contribute to the risk of PD through A-to-I editing. These A-to-I editing sites were located in genes NCOR1, KANSL1 and BST1. Moreover, we observed 57 sites whose longitudinal A-to-I editing levels correlated with cognitive progression in PD. CONCLUSIONS We found potential causal A-to-I editing sites for PD onset and longitudinal changes of A-to-I editing were associated with cognitive progression in PD. We anticipate this study will provide new biological insights and drive the discovery of the epitranscriptomic role underlying Parkinson's disease.
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Affiliation(s)
- Weimin Li
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Hao Wu
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Jinxia Li
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Zhuo Wang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, People's Republic of China
| | - Miao Cai
- Neurology Department, Zhejiang Hospital, Hangzhou, 310013, People's Republic of China
| | - Xiaoli Liu
- Neurology Department, Zhejiang Hospital, Hangzhou, 310013, People's Republic of China
| | - Ganqiang Liu
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China.
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China.
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Mercer HM, Nair AM, Ridgel A, Piontkivska H. Alterations in RNA editing in skeletal muscle following exercise training in individuals with Parkinson's disease. PLoS One 2023; 18:e0287078. [PMID: 38134032 PMCID: PMC10745226 DOI: 10.1371/journal.pone.0287078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/01/2023] [Indexed: 12/24/2023] Open
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disease behind Alzheimer's Disease, currently affecting more than 10 million people worldwide and 1.5 times more males than females. The progression of PD results in the loss of function due to neurodegeneration and neuroinflammation. The etiology of PD is multifactorial, including both genetic and environmental origins. Here we explored changes in RNA editing, specifically editing through the actions of the Adenosine Deaminases Acting on RNA (ADARs), in the progression of PD. Analysis of ADAR editing of skeletal muscle transcriptomes from PD patients and controls, including those that engaged in a rehabilitative exercise training program revealed significant differences in ADAR editing patterns based on age, disease status, and following rehabilitative exercise. Further, deleterious editing events in protein coding regions were identified in multiple genes with known associations to PD pathogenesis. Our findings of differential ADAR editing complement findings of changes in transcriptional networks identified by a recent study and offer insights into dynamic ADAR editing changes associated with PD pathogenesis.
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Affiliation(s)
- Heather Milliken Mercer
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
| | - Aiswarya Mukundan Nair
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
| | - Angela Ridgel
- School of Health Sciences, Kent State University, Kent, OH, United States of America
- Brain Health Research Institute, Kent State University, Kent, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, United States of America
- Brain Health Research Institute, Kent State University, Kent, OH, United States of America
- Healthy Communities Research Institute, Kent State University, Kent, OH, United States of America
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Starr LA, McKay LE, Peter KN, Seyfarth LM, Berkowitz LA, Caldwell KA, Caldwell GA. Attenuation of Dopaminergic Neurodegeneration in a C. elegans Parkinson's Model through Regulation of Xanthine Dehydrogenase (XDH-1) Expression by the RNA Editase, ADR-2. J Dev Biol 2023; 11:jdb11020020. [PMID: 37218814 DOI: 10.3390/jdb11020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023] Open
Abstract
Differential RNA editing by adenosine deaminases that act on RNA (ADARs) has been implicated in several neurological disorders, including Parkinson's disease (PD). Here, we report results of a RNAi screen of genes differentially regulated in adr-2 mutants, normally encoding the only catalytically active ADAR in Caenorhabditis elegans, ADR-2. Subsequent analysis of candidate genes that alter the misfolding of human α-synuclein (α-syn) and dopaminergic neurodegeneration, two PD pathologies, reveal that reduced expression of xdh-1, the ortholog of human xanthine dehydrogenase (XDH), is protective against α-synuclein-induced dopaminergic neurodegeneration. Further, RNAi experiments show that WHT-2, the worm ortholog of the human ABCG2 transporter and a predicted interactor of XDH-1, is the rate-limiting factor in the ADR-2, XDH-1, WHT-2 system for dopaminergic neuroprotection. In silico structural modeling of WHT-2 indicates that the editing of one nucleotide in the wht-2 mRNA leads to the substitution of threonine with alanine at residue 124 in the WHT-2 protein, changing hydrogen bonds in this region. Thus, we propose a model where wht-2 is edited by ADR-2, which promotes optimal export of uric acid, a known substrate of WHT-2 and a product of XDH-1 activity. In the absence of editing, uric acid export is limited, provoking a reduction in xdh-1 transcription to limit uric acid production and maintain cellular homeostasis. As a result, elevation of uric acid is protective against dopaminergic neuronal cell death. In turn, increased levels of uric acid are associated with a decrease in ROS production. Further, downregulation of xdh-1 is protective against PD pathologies because decreased levels of XDH-1 correlate to a concomitant reduction in xanthine oxidase (XO), the form of the protein whose by-product is superoxide anion. These data indicate that modifying specific targets of RNA editing may represent a promising therapeutic strategy for PD.
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Affiliation(s)
- Lindsey A Starr
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Luke E McKay
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kylie N Peter
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Lena M Seyfarth
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Laura A Berkowitz
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, Center for Convergent Biomedicine, Alabama Life Research Institute, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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7
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Wu S, Xue Q, Qin X, Wu X, Kim P, Chyr J, Zhou X, Huang L. The Potential Regulation of A-to-I RNA Editing on Genes in Parkinson's Disease. Genes (Basel) 2023; 14:genes14040919. [PMID: 37107677 PMCID: PMC10137963 DOI: 10.3390/genes14040919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Parkinson's disease (PD) is characterized by dopaminergic neurodegeneration and an abnormal accumulation of α-synuclein aggregates. A number of genetic factors have been shown to increase the risk of PD. Exploring the underlying molecular mechanisms that mediate PD's transcriptomic diversity can help us understand neurodegenerative pathogenesis. In this study, we identified 9897 A-to-I RNA editing events associated with 6286 genes across 372 PD patients. Of them, 72 RNA editing events altered miRNA binding sites and this may directly affect miRNA regulations of their host genes. However, RNA editing effects on the miRNA regulation of genes are more complex. They can (1) abolish existing miRNA binding sites, which allows miRNAs to regulate other genes; (2) create new miRNA binding sites that may sequester miRNAs from regulating other genes; or (3) occur in the miRNA seed regions and change their targets. The first two processes are also referred to as miRNA competitive binding. In our study, we found 8 RNA editing events that may alter the expression of 1146 other genes via miRNA competition. We also found one RNA editing event that modified a miRNA seed region, which was predicted to disturb the regulation of four genes. Considering the PD-related functions of the affected genes, 25 A-to-I RNA editing biomarkers for PD are proposed, including the 3 editing events in the EIF2AK2, APOL6, and miR-4477b seed regions. These biomarkers may alter the miRNA regulation of 133 PD-related genes. All these analyses reveal the potential mechanisms and regulations of RNA editing in PD pathogenesis.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Qiuping Xue
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Xinyu Qin
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Xiaoming Wu
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jacqueline Chyr
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
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8
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Wu S, Xue Q, Yang M, Wang Y, Kim P, Zhou X, Huang L. Genetic control of RNA editing in neurodegenerative disease. Brief Bioinform 2023; 24:bbad007. [PMID: 36681936 PMCID: PMC10387301 DOI: 10.1093/bib/bbad007] [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: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/31/2022] [Indexed: 01/23/2023] Open
Abstract
A-to-I RNA editing diversifies human transcriptome to confer its functional effects on the downstream genes or regulations, potentially involving in neurodegenerative pathogenesis. Its variabilities are attributed to multiple regulators, including the key factor of genetic variants. To comprehensively investigate the potentials of neurodegenerative disease-susceptibility variants from the view of A-to-I RNA editing, we analyzed matched genetic and transcriptomic data of 1596 samples across nine brain tissues and whole blood from two large consortiums, Accelerating Medicines Partnership-Alzheimer's Disease and Parkinson's Progression Markers Initiative. The large-scale and genome-wide identification of 95 198 RNA editing quantitative trait loci revealed the preferred genetic effects on adjacent editing events. Furthermore, to explore the underlying mechanisms of the genetic controls of A-to-I RNA editing, several top RNA-binding proteins were pointed out, such as EIF4A3, U2AF2, NOP58, FBL, NOP56 and DHX9, since their regulations on multiple RNA-editing events were probably interfered by these genetic variants. Moreover, these variants may also contribute to the variability of other molecular phenotypes associated with RNA editing, including the functions of 3 proteins, expressions of 277 genes and splicing of 449 events. All the analyses results shown in NeuroEdQTL (https://relab.xidian.edu.cn/NeuroEdQTL/) constituted a unique resource for the understanding of neurodegenerative pathogenesis from genotypes to phenotypes related to A-to-I RNA editing.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Qiuping Xue
- School of Life Science and Technology, Xidian University, Xi’an 710071, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Pora Kim
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
| | - Xiaobo Zhou
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
| | - Liyu Huang
- Corresponding authors: Liyu Huang, School of Life Science and Technology, Xidian University, Xi’an 710071, China. E-mail: ; Xiaobo Zhou, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail: ; Pora Kim, Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. E-mail:
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Advances of Brain Transcriptomics. Genes (Basel) 2022; 13:genes13101831. [PMID: 36292716 PMCID: PMC9601553 DOI: 10.3390/genes13101831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/24/2022] Open
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10
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Zhai J, Koh JH, Soong TW. RNA editing of ion channels and receptors in physiology and neurological disorders. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac010. [PMID: 38596706 PMCID: PMC11003377 DOI: 10.1093/oons/kvac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/14/2022] [Accepted: 05/15/2022] [Indexed: 04/11/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification that diversifies protein functions by recoding RNA or alters protein quantity by regulating mRNA level. A-to-I editing is catalyzed by adenosine deaminases that act on RNA. Millions of editing sites have been reported, but they are mostly found in non-coding sequences. However, there are also several recoding editing sites in transcripts coding for ion channels or transporters that have been shown to play important roles in physiology and changes in editing level are associated with neurological diseases. These editing sites are not only found to be evolutionary conserved across species, but they are also dynamically regulated spatially, developmentally and by environmental factors. In this review, we discuss the current knowledge of A-to-I RNA editing of ion channels and receptors in the context of their roles in physiology and pathological disease. We also discuss the regulation of editing events and site-directed RNA editing approaches for functional study that offer a therapeutic pathway for clinical applications.
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Affiliation(s)
- Jing Zhai
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore,
Singapore 117456, Singapore
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