The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies

Muhammad Abu Talha Safdar Hashmi , Hooriya Fatima , Sadia Ahmad , Amna Rehman , Fiza Safdar

Ibrain ›› 2024, Vol. 10 ›› Issue (4) : 395 -426.

PDF
Ibrain ›› 2024, Vol. 10 ›› Issue (4) :395 -426. DOI: 10.1002/ibra.12183
REVIEW

The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies

Author information +
History +
PDF

Abstract

Neurodegenerative disorders encompass a group of age-related conditions characterized by the gradual decline in both the structure and functionality of the central nervous system (CNS). RNA modifications, arising from the epitranscriptome or RNA-modifying protein mutations, have recently been observed to contribute significantly to neurodegenerative disorders. Specific modifications like N6-methyladenine (m6A), N1-methyladenine (m1A), 5-methylcytosine (m5C), pseudouridine and adenosine-to-inosine (A-to-I) play key roles, with their regulators serving as crucial therapeutic targets. These epitranscriptomic changes intricately control gene expression, influencing cellular functions and contributing to disease pathology. Dysregulation of RNA metabolism, affecting mRNA processing and noncoding RNA biogenesis, is a central factor in these diseases. This review underscores the complex relationship between RNA modifications and neurodegenerative disorders, emphasizing the influence of RNA modification and the epitranscriptome, exploring the function of RNA modification enzymes in neurodegenerative processes, investigating the functional consequences of RNA modifications within neurodegenerative pathways, and evaluating the potential therapeutic advancements derived from assessing the epitranscriptome.

Keywords

Alzheimer’s disease / epitranscriptomics / neurodegeneration / Parkinson's disease / RNA modifications

Cite this article

Download citation ▾
Muhammad Abu Talha Safdar Hashmi, Hooriya Fatima, Sadia Ahmad, Amna Rehman, Fiza Safdar. The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies. Ibrain, 2024, 10(4): 395-426 DOI:10.1002/ibra.12183

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

Nguyen B, Bix G, Yao Y. Basal lamina changes in neurodegenerative disorders. Mol Neurodegener. 2021;16(1):81.

[2]

Qin L, Guo Z, McClure MA, Mu Q. White matter changes from mild cognitive impairment to alzheimer’s disease: a meta-analysis. Acta Neurol Belg. 2021;121(6):1435-1447.

[3]

Masters CL, Bateman R, Blennow K, Rowe CC, Sperling RA, Cummings JL. Alzheimer’s disease. Nat Rev Dis Primers. 2015;1:15056.

[4]

Breijyeh Z, Karaman R. Comprehensive review on alzheimer’s disease: causes and treatment. Molecules. 2020;25(24):5789.

[5]

Mahmood A, Shah AA, Umair M, Wu Y, Khan A. Recalling the pathology of parkinson’s disease;lacking exact figure of prevalence and genetic evidence in Asia with an alarming outcome: A time to step-up. Clin Genet. 2021;100(6):659-677.

[6]

Xu L, Liu T, Liu L, et al. Global variation in prevalence and incidence of amyotrophic lateral sclerosis: a systematic review and meta-analysis. J Neurol. 2020;267:944-953.

[7]

Marangi G, Traynor BJ. Genetic causes of amyotrophic lateral sclerosis: new genetic analysis methodologies entailing new opportunities and challenges. Brain Res. 2015;1607:75-93.

[8]

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Organogenesis and the Patterning of Appendages. Molecular Biology of the Cell. 4th ed. Garland Science;2002.

[9]

Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf. 2000;9

[10]

Liu EY, Cali CP, Lee EB. RNA metabolism in neurodegenerative disease. Dis Models &Mech. 2017;10(5):509-518.

[11]

Prashad S, Gopal PP. RNA-binding proteins in neurological development and disease. RNA Biol. 2021;18(7):972-987.

[12]

Yano M, Hayakawa-Yano Y, Okano H. RNA regulation went wrong in neurodevelopmental disorders: the example of Msi/Elavl RNA binding proteins. Int J Dev Neurosci. 2016;55:124-130.

[13]

Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev. 2021;101(3):1309-1370.

[14]

Boccaletto P, Machnicka MA, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018;46(D1):D303-D307.

[15]

Esteve-Puig R, Bueno-Costa A, Esteller M. Writers, readers and erasers of RNA modifications in cancer. Cancer Lett. 2020;474:127-137.

[16]

Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA. 2017;23(12):1754-1769.

[17]

Chabot B, Shkreta L. Defective control of pre–messenger RNA splicing in human disease. J Cell Biol. 2016;212(1):13-27.

[18]

Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes Dev. 2003;17:419-437.

[19]

Mills JD, Janitz M. Alternative splicing of mRNA in the molecular pathology of neurodegenerative disorders. Neurobiol Aging. 2012;33(5):1012-e11.

[20]

Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017;18(1):18-30.

[21]

Derti A, Garrett-Engele P, MacIsaac KD, et al. A quantitative Atlas of polyadenylation in five mammals. Genome Res. 2012;22(6):1173-1183.

[22]

Hoque M, Ji Z, Zheng D, et al. Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing. Nat Methods. 2013;10(2):133-139.

[23]

Shi Y. Alternative polyadenylation: new insights from global analyses. RNA. 2012;18(12):2105-2117.

[24]

Houseley J, Tollervey D. The many pathways of RNA degradation. Cell. 2009;136(4):763-776.

[25]

Chen CYA, Ezzeddine N, Shyu AB. Messenger RNA half-life measurements in mammalian cells. Methods Enzymol. 2008;448:335-357.

[26]

Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD. Dynamic regulation of mRNA decay during neural development. Neural Dev. 2015;10(1):11.

[27]

Nagano S, Jinno J, Abdelhamid RF, et al. TDP-43 transports ribosomal protein mRNA to regulate axonal local translation in neuronal axons. Acta Neuropathol. 2020;140:695-713.

[28]

Shigeoka T, Koppers M, Wong HH-W. et al. On-site ribosome remodeling by locally synthesized ribosomal proteins in axons. Cell Rep. 2019;29(11):3605-3619.e10.

[29]

Anderson JT, Droogmans L. Biosynthesis and function of 1-methyladenosine in transfer RNA. Fine-tuning of RNA functions by modification and editing. Vol 1, 2005:121-139.

[30]

Zhang C, Jia G. Reversible RNA modification N1-methyladenosine (m1A) in mRNA and tRNA. Genomics Insights. 2018;16(3):155-161.

[31]

Oerum S, Dégut C, Barraud P, Tisné C. m1A Post-Transcriptional modification in tRNAs. Biomolecules. 2017;7(1):20.

[32]

Liu F, Clark W, Luo G, et al. ALKBH1-mediated tRNA demethylation regulates translation. Cell. 2016;167(3):816-828.e16.

[33]

Lin S, Liu Q, Lelyveld VS, Choe J, Szostak JW, Gregory RI. Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation. Mol Cell. 2018;71(2):244-255.e5.

[34]

Tomikawa C. 7-Methylguanosine modifications in transfer RNA (tRNA). Int J Mol Sci. 2018;19(12):4080.

[35]

Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet. 2014;5:1-26.

[36]

Charette M, Gray MW. Pseudouridine in RNA: what, where, how, and why. IUBMB Life. 2000;49(5):341-351.

[37]

Zhao BS, He C. Pseudouridine in a new era of RNA modifications. Cell Res. 2015;25(2):153-154.

[38]

Tuorto F, Liebers R, Musch T, et al. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol. 2012;19(9):900-905.

[39]

Yanas A, Liu KF. RNA modifications and the link to human disease. Methods Enzymol. 2019;626:133-146.

[40]

Jellinger KA. Recent advances in our understanding of neurodegeneration. J Neural Transm. 2009;116(9):1111-1162.

[41]

Skovronsky DM, Lee VMY, Trojanowski JQ. Neurodegenerative diseases: new concepts of pathogenesis and their therapeutic implications. Annu Rev Pathol: Mech Dis. 2006;1:151-170.

[42]

Gibb WR, Lees AJ. The relevance of the lewy body to the pathogenesis of idiopathic Parkinson’s disease. J Neurol Neurosurg Psychiatry. 1988;51(6):745-752.

[43]

Stolp HB, Dziegielewska KM. Review: role of developmental inflammation and blood–brain barrier dysfunction in neurodevelopmental and neurodegenerative diseases. Neuropathol Appl Neurobiol. 2009;35(2):132-146.

[44]

Kell DB. Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics. 2009;2:2.

[45]

Graber JJ, Dhib-Jalbut S. Protective autoimmunity in the nervous system. Pharmacol Ther. 2009;121(2):147-159.

[46]

Ryu JK, McLarnon JG. A leaky blood-brain barrier, fibrinogen infiltration and microglial reactivity in inflamed Alzheimer’s disease brain. J Cell Mol Med. 2009;13(9a):2911-2925.

[47]

Javitch JA, D’Amato RJ, Strittmatter SM, Snyder SH. Parkinsonism-inducing neurotoxin, N-methyl-4-phenyl-1,2,3,6 -tetrahydropyridine: uptake of the metabolite N-methyl-4-phenylpyridine by dopamine neurons explains selective toxicity. Proc Natl Acad Sci. 1985;82(7):2173-2177.

[48]

Langston JW, Ballard P, Tetrud JW, Irwin I. Chronic parkinsonism in humans due to a product of meperidine-analog synthesis. Science. 1983;219(4587):979-980.

[49]

Dubinsky JM. Heterogeneity of nervous system mitochondria: location, location, location! Exp Neurol. 2009;218(2):293-307.

[50]

Chen H, Chan DC. Mitochondrial dynamics-fusion, fission, movement, and mitophagy-in neurodegenerative diseases. Hum Mol Gen. 2009;18(R2):R169-R176.

[51]

Celsi F, Pizzo P, Brini M, et al. Mitochondria, calcium and cell death: a deadly triad in neurodegeneration. Biochim et Biophys Acta -Bioenergetics. 2009;1787(5):335-344.

[52]

Fricker M, Tolkovsky AM, Borutaite V, Coleman M, Brown GC. Neuronal cell death. Physiol Rev. 2018;98(2):813-880.

[53]

Mattson MP, Kroemer G. Mitochondria in cell death: novel targets for neuroprotection and cardioprotection. Trends Mol Med. 2003;9(5):196-205.

[54]

Poewe W, Seppi K, Tanner CM, et al. Parkinson disease. Nat Rev Dis Primers. 2017;3:17013.

[55]

Cunnane SC, Trushina E, Morland C, et al. Brain energy rescue: an emerging therapeutic concept for neurodegenerative disorders of ageing. Nat Rev Drug Discovery. 2020;19(9):609-633.

[56]

Tang D, Kang R, Berghe TV, Vandenabeele P, Kroemer G. The molecular machinery of regulated cell death. Cell Res. 2019;29(5):347-364.

[57]

Knopman DS, Amieva H, Petersen RC, et al. Alzheimer disease. Nat Rev Dis Primers. 2021;7(1):33.

[58]

Seeley WW, Crawford RK, Zhou J, Miller BL, Greicius MD. Neurodegenerative diseases target Large-Scale human brain networks. Neuron. 2009;62(1):42-52.

[59]

Ma C, Chang M, Lv H, et al. RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum. Genome Biol. 2018;19(1):68.

[60]

Li M, Zhao X, Wang W, et al. Ythdf2-mediated m(6)A mRNA clearance modulates neural development in mice. Genome Biol. 2018;19(1):69.

[61]

Yoon KJ, Ringeling FR, Vissers C, et al. Temporal control of mammalian cortical neurogenesis by m(6)A methylation. Cell. 2017;171(4):877-889.e17.

[62]

Chen J, Zhang YC, Huang C, et al. m(6)A regulates neurogenesis and neuronal development by modulating histone methyltransferase Ezh2. Genomics Insights. 2019;17(2):154-168.

[63]

Zhou J, Wan J, Gao X, Zhang X, Jaffrey SR, Qian SB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature. 2015;526(7574):591-594.

[64]

Engel M, Eggert C, Kaplick PM, et al. The role of m(6)A/m-RNA methylation in stress response regulation. Neuron. 2018;99(2):389-403.e9.

[65]

Livneh I, Moshitch-Moshkovitz S, Amariglio N, Rechavi G, Dominissini D. The m(6)A epitranscriptome: transcriptome plasticity in brain development and function. Nat Rev Neurosci. 2020;21(1):36-51.

[66]

Han M, Liu Z, Xu Y, et al. Abnormality of m6A mRNA methylation is involved in alzheimer’s disease. Front Neurosci. 2020;14:98.

[67]

Cannon JR, Greenamyre JT. The role of environmental exposures in neurodegeneration and neurodegenerative diseases. Toxicol Sci. 2011;124(2):225-250.

[68]

Uddin MB, Wang Z, Yang C. Dysregulations of functional RNA modifications in cancer, cancer stemness and cancer therapeutics. Theranostics. 2020;10(7):3164-3189.

[69]

Seo KW, Kleiner RE. Mechanisms of epitranscriptomic gene regulation. Biopolymers. 2021;112(1):e23403.

[70]

Frye M, Harada BT, Behm M, He C. RNA modifications modulate gene expression during development. Science. 2018;361(6409):1346-1349.

[71]

Wanowska E, McFeely A, Sztuba-Solinska J. The role of epitranscriptomic modifications in the regulation of RNA–Protein interactions. BioChem. 2022;2(4):241-259.

[72]

Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nature Cell Biol. 2019;21(5):552-559.

[73]

Nachtergaele S, He C. Chemical modifications in the life of an mRNA transcript. Annu Rev Genet. 2018;52:349-372.

[74]

Boo SH, Kim YK. The emerging role of RNA modifications in the regulation of mRNA stability. Exp Mol Med. 2020;52(3):400-408.

[75]

Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet. 2014;15:2014:127-150.

[76]

Choi S, Cho N, Kim KK. The implications of alternative pre-mRNA splicing in cell signal transduction. Exp Mol Med. 2023;55(4):755-766.

[77]

Wang C, Schmich F, Srivatsa S, Weidner J, Beerenwinkel N, Spang A. Context-dependent deposition and regulation of mRNAs in p-bodies. eLife. 2018;7:159376.

[78]

Franks TM, Lykke-Andersen J. The control of mRNA decapping and P-Body formation. Mol Cell. 2008;32(5):605-615.

[79]

Helm M, Motorin Y. Detecting RNA modifications in the epitranscriptome: predict and validate. Nat Rev Genet. 2017;18(5):275-291.

[80]

Tang Q, Li L, Wang Y, et al. RNA modifications in cancer. Br J Cancer. 2023;129(2):204-221.

[81]

Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet. 2023;24(6):363-381.

[82]

Satterlee JS, Basanta-Sanchez M, Blanco S, et al. Novel RNA modifications in the nervous system: form and function. J Neurosci. 2014;34(46):15170-15177.

[83]

Xu X, Johnson Z, Xie H. Neuronal depolarization induced RNA m(5)C methylation changes in mouse cortical neurons. Biology. 2022;11(7):988.

[84]

Zhang Y, Lu L, Li X. Detection technologies for RNA modifications. Exp Mol Med. 2022;54(10):1601-1616.

[85]

Jora M, Lobue PA, Ross RL, Williams B, Addepalli B. Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. Biochim et Biophys Acta -Gene Regulatory Mech. 2019;1862(3):280-290.

[86]

Krusnauskas R, Stakaitis R, Steponaitis G, Almstrup K, Vaitkiene P. Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and nanopore dRNA-seq. Epigenetics. 2023;18(1):2163365.

[87]

Wu F, Zhang S, Fan C, Huang S, Jiang H, Zhang J. High-Throughput sequencing reveals N(6)-Methyladenosine-modified LncRNAs as potential biomarkers in mice with liver fibrosis. Curr Gene Ther. 2023;23(5):371-390.

[88]

Ge R, Ye C, Peng Y, et al. m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nat Protoc. 2023;18(2):626-657.

[89]

Makhamreh A, Tavakoli S, Gamper H, et al. Messenger-RNA Modification Standards and Machine Learning Models Facilitate Absolute Site-Specific Pseudouridine Quantification. bioRxiv. 2022:2022.05.06.490948.

[90]

He PC, He C. m(6) A RNA methylation: from mechanisms to therapeutic potential. EMBO J. 2021;40(3):e105977.

[91]

Deng LJ, Deng WQ, Fan SR, et al. m6A modification: recent advances, anticancer targeted drug discovery and beyond. Mol Cancer. 2022;21(1):52.

[92]

Hill RA, Liu YY. N(6) -methyladenosine-RNA methylation promotes expression of solute carrier family 7 member 11, an uptake transporter of cystine for lipid reactive oxygen species scavenger glutathione synthesis, leading to hepatoblastoma ferroptosis resistance. Clin Transl Med. 2022;12(5):e889.

[93]

Zhang C, Jian H, Shang S, et al. Crosstalk between m6A mRNAs and m6A circRNAs and the time-specific biogenesis of m6A circRNAs after OGD/R in primary neurons. Epigenetics. 2023;18(1):2181575.

[94]

Jiang X, Liu B, Nie Z, et al. The role of m6A modification in the biological functions and diseases. Signal Transduct Target Ther. 2021;6(1):74.

[95]

Zhang Y, Geng X, Li Q, et al. m6A modification in RNA: biogenesis, functions and roles in gliomas. J Exp Clin Cancer Res. 2020;39(1):192.

[96]

Wang S, Lv W, Li T, et al. Dynamic regulation and functions of mRNA m6A modification. Cancer Cell Int. 2022;22(1):48.

[97]

Wang Y, Li L, Li J, et al. The emerging role of m6A modification in regulating the immune system and autoimmune diseases. review. Front Cell Dev Biol. 2021;9:755691.

[98]

Song T, Lv S, Li N, et al. Versatile functions of RNA m6A machinery on chromatin. J Mol Cell Biol. 2022;14(3):mjac011.

[99]

Shu L, Huang X, Cheng X, Li X. Emerging roles of N6-Methyladenosine modification in neurodevelopment and neurodegeneration. Cells. 2021;10(10):2694.

[100]

Deng J, Chen X, Chen A, Zheng X. m6A RNA methylation in brain injury and neurodegenerative disease. Front Neurol. 2022;13:995747.

[101]

Nie F, Feng P, Song X, Wu M, Tang Q, Chen W. RNAWRE: a resource of writers, readers and erasers of RNA modifications database. 2020.2:baaa049.

[102]

Wang Y, Wang Y, Gu J, Su T, Gu X, Feng Y. The role of RNA m6A methylation in lipid metabolism. Front Endocrinol. 2022;13:866116.

[103]

Deng J, Chen X, Chen A, Zheng X. m(6)A RNA methylation in brain injury and neurodegenerative disease. Front Neurol. 2022;13:995747.

[104]

Chatterjee B, Shen CKJ, Majumder P. RNA modifications and RNA metabolism in neurological disease pathogenesis. Int J Mol Sci. 2021;22(21):11870.

[105]

Yu Z, Huang L, Xia Y, et al. Analysis of m6A modification regulators in the substantia nigra and striatum of MPTP-induced Parkinson’s disease mice. Neurosci Lett. 2022;791:136907.

[106]

Martinez De La Cruz B, Gell C, Markus R, Macdonald I, Fray R, Knight HM. m(6) A mRNA methylation in human brain is disrupted in lewy body disorders. Neuropathol Appl Neurobiol. 2023;49(1):e12885.

[107]

Pupak A, Singh A, Sancho-Balsells A, et al. Altered m6A RNA methylation contributes to hippocampal memory deficits in huntington’s disease mice. Cell Mol Life Sci. 2022;79(8):416.

[108]

Huang H, Song R, Wong JJL, Anggono V, Widagdo J. The N6-methyladenosine RNA landscape in the aged mouse hippocampus. Aging cell. 2023;22(1):e13755.

[109]

Sokpor G, Xie Y, Nguyen HP, Tuoc T. Emerging role of m(6) A methylome in brain development: implications for neurological disorders and potential treatment. Front Cell Dev Biol. 2021;9:656849.

[110]

Jiang L, Li X, Wang S, Yuan Z, Cheng J. The role and regulatory mechanism of m(6)A methylation in the nervous system. Front Genet. 2022;13:962774.

[111]

Yu J, She Y, Ji SJ. m(6)A modification in mammalian nervous system development, functions, disorders, and injuries. Front Cell Dev Biol. 2021;9:679662.

[112]

Du B, Zhang Y, Liang M, et al. N6-methyladenosine (m6A) modification and its clinical relevance in cognitive dysfunctions. Aging. 2021;13(16):20716-20737.

[113]

Lei C, Wang Q. The progression of N6-methyladenosine study and its role in neuropsychiatric disorders. Int J Mol Sci. 2022;23(11):5922.

[114]

Kisan A, Chhabra R. Modulation of gene expression by YTH domain family (YTHDF) proteins in human physiology and pathology. J Cell Physiol. 2023;238(1):5-31.

[115]

Castro-Hernández R, Berulava T, Metelova M, et al. Conserved reduction of m(6)A RNA modifications during aging and neurodegeneration is linked to changes in synaptic transcripts. Proceedings of the National Academy of Sciences. 2023;120(9):e2204933120.

[116]

Yon JH, Daniel-Johnson J, Carter LB, Jevtovic-Todorovic V. Anesthesia induces neuronal cell death in the developing rat brain via the intrinsic and extrinsic apoptotic pathways. Neuroscience. 2005;135(3):815-827.

[117]

Olney JW, Wozniak DF, Jevtovic-Todorovic V, Farber NB, Bittigau P, Ikonomidou C. Drug-induced apoptotic neurodegeneration in the developing brain. Brain Pathol. 2002;12(4):488-498.

[118]

Chen X, Wang J, Tahir M, et al. Current insights into the implications of m6A RNA methylation and autophagy interaction in human diseases. Cell Biosci. 2021;11(1):147.

[119]

Xu S, Li Y, Chen J, et al. Oxygen glucose deprivation/re-oxygenation-induced neuronal cell death is associated with Lnc-D63785 m6A methylation and miR-422a accumulation. Cell Death Dis. 2020;11(9):816.

[120]

Wilson DM, Cookson MR, Van Den Bosch L, Zetterberg H, Holtzman DM, Dewachter I. Hallmarks of neurodegenerative diseases. Cell. 2023;186(4):693-714.

[121]

Jiang L, Roberts R, Wong M, et al. Accumulation of m(6)A exhibits stronger correlation with MAPT than beta-amyloid pathology in an APP(NL-G-F)/MAPT(P301S) mouse model of Alzheimer’s disease. bioRxiv. 2023;2:534515.

[122]

Zhao F, Xu Y, Gao S, et al. METTL3-dependent RNA m6A dysregulation contributes to neurodegeneration in Alzheimer’s disease through aberrant cell cycle events. Mol Neurodegener. 2021;16(1):70.

[123]

Shafik AM, Zhang F, Guo Z, et al. N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease. Genome Biol. 2021;22(1):17.

[124]

Nguyen TB, Miramontes R, Chillon-Marinas C, et al. Aberrant splicing in huntington’s disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. bioRxiv. 2023;2:565004.

[125]

He H, Zhang Q, Liao J, et al. METTL14is decreased and regulatesm6Amodification of α-synuclein in Parkinson’s disease. J Neurochem. 2023;166(3):609-622.

[126]

Song H, Zhang J, Liu B, et al. Biological roles of RNA m(5)C modification and its implications in cancer immunotherapy. Biomark Res. 2022;10(1):15.

[127]

Squires JE, Patel HR, Nousch M, et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 2012;40(11):5023-5033.

[128]

Wilkinson E, Cui YH, He YY. Roles of RNA modifications in diverse cellular functions. Front Cell Dev Biol. 2022;10:828683.

[129]

Zhang Q, Liu F, Chen W, et al. The role of RNA m(5)C modification in cancer metastasis. Int J Biol Sci. 2021;17(13):3369-3380.

[130]

Yang X, Yang Y, Sun BF, et al. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader. Cell Res. 2017;27(5):606-625.

[131]

Miao Z, Xin N, Wei B, et al. 5-hydroxymethylcytosine is detected in RNA from mouse brain tissues. Brain Res. 2016;1642:546-552.

[132]

Gao Y, Fang J. RNA 5-methylcytosine modification and its emerging role as an epitranscriptomic mark. RNA Biol. 2021;18(sup1):117-127.

[133]

Nombela P, Miguel-López B, Blanco S. The role of m6A, m5C and Ψ RNA modifications in cancer: novel therapeutic opportunities. Mol Cancer. 2021;20(1):18.

[134]

Yang X, Yang Y, Sun B-F. et al. 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 2017;27(5):606-625.

[135]

Jian H, Zhang C, Qi Z, et al. Alteration of mRNA 5-Methylcytosine modification in neurons after OGD/R and potential roles in cell stress response and apoptosis. Front Genet. 2021;12:633681.

[136]

Kavanagh T, Halder A, Drummond E. Tau interactome and RNA binding proteins in neurodegenerative diseases. Mol Neurodegener. 2022;17(1):66.

[137]

Sayad A, Najafi S, Hussen BM, et al. The emerging roles of the β-Secretase BACE1 and the long non-coding RNA BACE1-AS in human diseases: A focus on neurodegenerative diseases and cancer. Front Aging Neurosci. 2022;14:853180.

[138]

Cuevas-Diaz Duran R, González-Orozco JC, Velasco I, Wu JQ. Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. Front Cell Dev Biol. 2022;10:884748.

[139]

Karthiya R, Wasil SM, Khandelia P. Emerging role of N4-acetylcytidine modification of RNA in gene regulation and cellular functions. Mol Biol Rep. 2020;47(11):9189-9199.

[140]

Mathoux J, Henshall DC, Brennan GP. Regulatory mechanisms of the RNA modification m(6)A and significance in brain function in health and disease. Front Cell Neurosci. 2021;15:671932.

[141]

Saikia M, Fu Y, Pavon-Eternod M, He C, Pan T. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010;16(7):1317-1327.

[142]

Liu F, Clark W, Luo G, et al. ALKBH1-Mediated tRNA demethylation regulates translation. Cell. 2016;167(3):816-828.e16.

[143]

Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, et al. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016;530(7591):441-446.

[144]

Qi Z, Zhang C, Jian H, et al. N(1)-Methyladenosine modification of mRNA regulates neuronal gene expression and oxygen glucose deprivation/reoxygenation induction. Cell Death Discov. 2023;9(1):159.

[145]

Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci. 2022;59(3):203-218.

[146]

Qi Z, Zhang C, Jian H, et al. N1-Methyladenosine modification of mRNA regulates neuronal gene expression and oxygen glucose deprivation/reoxygenation induction. Cell Death Discov. 2023;9(1):159.

[147]

Xiong X, Li X, Yi C. N1-methyladenosine methylome in messenger RNA and non-coding RNA. Curr Opin Chem Biol. 2018;45:179-186.

[148]

Li J, Zhang H, Wang H. N1-methyladenosine modification in cancer biology: current status and future perspectives. Comput Struct Biotechnol J. 2022;20:6578-6585.

[149]

Shafik AM, Zhou H, Lim J, Dickinson B, Jin P. Dysregulated mitochondrial and cytosolic tRNA m1A methylation in alzheimer’s disease. Hum Mol Gen. 2022;31(10):1673-1680.

[150]

Jin H, Huo C, Zhou T, Xie S. m(1)A RNA modification in gene expression regulation. Genes. 2022;13(5):910.

[151]

Cerneckis J, Cui Q, He C, Yi C, Shi Y. Decoding pseudouridine: an emerging target for therapeutic development. Trends Pharmacol Sci. 2022;43(6):522-535.

[152]

Hamma T, Ferré-D’amaré AR. Pseudouridine synthases. Chem Biol. 2006;13(11):1125-1135.

[153]

Carlile TM, Martinez NM, Schaening C, et al. mRNA structure determines modification by pseudouridine synthase 1. Nat Chem Biol. 2019;15(10):966-974.

[154]

Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature. 2014;515(7525):143-146.

[155]

Schwartz S, Bernstein DA, Mumbach MR, et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell. 2014;159(1):148-162.

[156]

Song W, Ressl S, Tracey WD. Loss of pseudouridine synthases in the RluA family causes hypersensitive nociception in drosophila. G3. 2020;10(12):4425-4438.

[157]

Hee Lee S, Kim I, Chul Chung B. Increased urinary level of oxidized nucleosides in patients with mild-to-moderate Alzheimer’s disease. Clin Biochem. 2007;40(13-14):936-938.

[158]

deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA. Pseudouridine modification inhibits muscleblind-like 1 (MBNL1) binding to CCUG repeats and minimally structured RNA through reduced RNA flexibility. J Biol Chem. 2017;292(10):4350-4357.

[159]

Gatsiou A, Vlachogiannis N, Lunella FF, Sachse M, Stellos K. Adenosine-to-inosine RNA editing in health and disease. Antioxid Redox Signaling. 2018;29(9):846-863.

[160]

Flamand MN, Meyer KD. The epitranscriptome and synaptic plasticity. Curr Opin Neurobiol. 2019;59:41-48.

[161]

Nishikura K. A-to-I editing of coding and non-coding RNAs by ADARs. Nat Rev Mol Cell Biol. 2016;17(2):83-96.

[162]

Stefl R, Xu M, Skrisovska L, Emeson RB, Allain FH-T. Structure and specific RNA binding of ADAR2 double-stranded RNA binding motifs. Structure. 2006;14(2):345-355.

[163]

Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G. RNA-editing-mediated exon evolution. Genome Biol. 2007;8:R29.

[164]

Rueter SM, Dawson TR, Emeson RB. Regulation of alternative splicing by RNA editing. Nature. 1999;399(6731):75-80.

[165]

Terajima H, Yoshitane H, Ozaki H, et al. ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm. Nature Genet. 2017;49(1):146-151.

[166]

Livingston JH, Lin J-P. Dale RC, et al. A type I interferon signature identifies bilateral striatal necrosis due to mutations in ADAR1. J Med Genet. 2014;51(2):76-82.

[167]

Karki A, Campbell KB, Mozumder S, Fisher AJ, Beal PA. Impact of disease-associated mutations on the deaminase activity of ADAR1. Biochemistry. 2024;63(3):282-293.

[168]

Heraud-Farlow JE, Walkley CR. What do editors do? understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs. Open Biol. 2020;10(7):200085.

[169]

Song B, Shiromoto Y, Minakuchi M, Nishikura K. The role of RNA editing enzyme ADAR1 in human disease. WIREs RNA. 2022;13(1):e1665.

[170]

Costa Cruz PH, Kawahara Y. RNA Editing in Neurological and Neurodegenerative Disorders. In: E Picardi,G Pesole, eds. RNA Editing: Methods and Protocols. Springer US;2021:309-330.

[171]

Zhai J, Koh JH, Soong TW. RNA editing of ion channels and receptors in physiology and neurological disorders. Oxford Open Neurosci. 2022;1:kvac010.

[172]

Mansi L, Tangaro MA, LoGiudice C, et al. REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. Nucleic Acids Res. 2021;49(D1):D1012-D1019.

[173]

Khermesh K, D’Erchia AM, Barak M, et al. Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer’s disease. RNA. 2016;22(2):290-302.

[174]

Akbarian S, Smith MA, Jones EG. Editing for an AMPA receptor subunit RNA in prefrontal cortex and striatum in Alzheimer’s disease, huntington’s disease and schizophrenia. Brain Res. 1995;699(2):297-304.

[175]

Shelton SB, Reinsborough C, Xhemalce B. Who watches the watchmen: roles of RNA modifications in the RNA interference pathway. PLoS Genet. 2016;12(7):e1006139.

[176]

Teng PC, Liang Y, Yarmishyn AA, et al. RNA modifications and epigenetics in modulation of lung cancer and pulmonary diseases. Int J Mol Sci. 2021;22(19):10592.

[177]

Decrécy-Lagard V, Boccaletto P, Mangleburg CG, et al. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res. 2019;47(5):2143-2159.

[178]

Ontiveros RJ, Stoute J, Liu KF. The chemical diversity of RNA modifications. Biochem J. 2019;476(8):1227-1245.

[179]

Nie F, Tang Q, Liu Y, et al. RNAME: A comprehensive database of RNA modification enzymes. Comput Struct Biotechnol J. 2022;20:6244-6249.

[180]

Lee SY, Kim JJ, Miller KM. Emerging roles of RNA modifications in genome integrity. Briefings Funct Genomics. 2021;20(2):106-112.

[181]

Chen Z, Tyler JK. The chromatin landscape channels DNA double-strand breaks to distinct repair pathways. Front Cell Dev Biol. 2022;10:909696.

[182]

Sessa G, Gómez-González B, Silva S, et al. BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair. EMBO J. 2021;40(7):e106018.

[183]

Mullally G, Aelst K, Naqvi MM, et al. 5’ modifications to CRISPR-Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage. Nucleic Acids Res. 2020;48(12):6811-6823.

[184]

Scheuren M, Möhner J, Zischler H. R-loop landscape in mature human sperm: regulatory and evolutionary implications. Front Genet. 2023;14:1069871.

[185]

Lu B, Zhang P, Chen S, et al. Genome-wide mapping of R-Loops in single cells reveals cell-type specific roles for R-Loops in hematopoietic cell identity. Blood. 2023;142:242.

[186]

Han NR, Kim YK, Ahn S, Hwang TY, Lee H, Park HJ. A comprehensive phenotype of non-motor impairments and distribution of alpha-synuclein deposition in Parkinsonism-Induced mice by a combination injection of MPTP and probenecid. Front Aging Neurosci. 2020;12:599045.

[187]

Rui WJ, Li S, Yang L, et al. Microglial AIM2 alleviates antiviral-related neuro-inflammation in mouse models of Parkinson’s disease. GLIA. 2022;70(12):2409-2425.

[188]

Chen X, Wang Z, Yang W, Fu Y. Levodopa improves behavioral deficits of mice with parkinson’s disease symptoms via curbing NLRP3 inflammasome activation and enhancing tyrosine hydroxylase levels in the striatum and substantia nigra. J Integr Neurosci. 2024;23(1):2.

[189]

Lu M, Su C, Qiao C, Bian Y, Ding J, Hu G. Metformin prevents dopaminergic neuron death in MPTP/P-Induced mouse model of Parkinson’s disease via autophagy and mitochondrial ROS clearance. Int J Neuropsychopharmacol. 2016;19(9):pyw047.

[190]

Seo MH, Kwon D, Kim SH, Yeo S. Association between decreased SGK1 and increased intestinal alpha-synuclein in an MPTP mouse model of Parkinson’s disease. Int J Mol Sci. 2023;24(22):16408.

[191]

Gao Y, Sheng D, Chen W. Regulatory mechanism of miR-20a-5p in neuronal damage and inflammation in lipopolysaccharide-induced BV2 cells and MPTP-HCl-induced Parkinson’s disease mice. Psychogeriatrics. 2024;24(4):752-764.

[192]

Clarke JP, Thibault PA, Salapa HE, Levin MC. A comprehensive analysis of the role of hnRNP A1 function and dysfunction in the pathogenesis of neurodegenerative disease. Front Mol Biosci. 2021;8:659610.

[193]

Feng J, Zhou J, Lin Y, Huang W. hnRNP A1 in RNA metabolism regulation and as a potential therapeutic target. Front Pharmacol. 2022;13:986409.

[194]

Zhao L, Fan T, Han Y, Wang Y, Jiang Y, Liu F. Demethylase FTO activity analysis based on methyl sensitive enzyme MazF and hybridization chain reaction. Sens Actuators, B. 2021;341:129983.

[195]

Lee M, Kim B, Kim VN. Emerging roles of RNA modification: m6A and U-Tail. Cell. 2014;158(5):980-987.

[196]

Annapoorna PK, Iyer H, Parnaik T, Narasimhan H, Bhattacharya A, Kumar A. FTO: an emerging molecular player in neuropsychiatric diseases. Neuroscience. 2019;418:15-24.

[197]

Tang J, Su Q, Guo Z, et al. N6-methyladenosine(m6A) demethylase FTO regulates cellular apoptosis following cobalt-induced oxidative stress. Environ Pollut. 2022;297:118749.

[198]

Chen X, Sun R-X. Wang J-N. Lactylation-driven FTO-mediated m6A modification of CDK2 aggravates diabetic microvascular anomalies. bioRxiv. 2023;1:541470.

[199]

Garofalo M, Pandini C, Bordoni M, et al. Alzheimer’s, Parkinson’s disease and amyotrophic lateral sclerosis gene expression patterns divergence reveals different grade of RNA metabolism involvement. Int J Mol Sci. 2020;21(24):9500.

[200]

Jiapaer Z, Su D, Hua L, et al. Regulation and roles of RNA modifications in aging-related diseases. Aging cell. 2022;21(7):e13657.

[201]

Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry. 2022;27(9):3633-3646.

[202]

Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: review of top 25 Most-Studied RNA modifications. Int J Mol Sci. 2022;23(22):13851.

[203]

Lee S-M, Koo B, Carré C, et al. Exploring the brain epitranscriptome: perspectives from the NSAS summit. Front Neurosci. 2023;17:1291446.

[204]

Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry. 2022;27(9):3633-3646.

[205]

Huang H, Weng H, Deng X, Chen J. RNA modifications in cancer: functions, mechanisms, and therapeutic implications. Ann Rev Cancer Biol. 2020;4:221-240.

[206]

Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener. 2021;10(1):16.

[207]

Qu W, Zhuang Y, Li X. The roles of epigenetic modifications in neurodegenerative diseases. J Zhejiang Univ. 2021;50(5):642-650.

[208]

Park SA, Ahn SI, Gallo JM. Tau mis-splicing in the pathogenesis of neurodegenerative disorders. BMB Rep. 2016;49(8):405-413.

[209]

Fujita K, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating divergent transcriptomes through mRNA splicing and its modulation using various small compounds. Int J Mol Sci. 2020;21(6):2026.

[210]

Lee Y, Rio DC. Mechanisms and regulation of alternative Pre-mRNA splicing. Annu Rev Biochem. 2015;84:291-323.

[211]

Adhikari S, Xiao W, Zhao YL, Yang YG. m(6)A: signaling for mRNA splicing. RNA Biol. 2016;13(9):756-759.

[212]

Liu Y, Zhang Y, Lu F, Wang J. Interactions between RNA m6A modification, alternative splicing, and poly(A) tail revealed by MePAIso-seq. 2. bioRxiv. 2021;

[213]

Liu X, Wang Y, Chang G, Wang F, Wang F, Geng X. Alternative splicing of hTERT Pre-mRNA: A potential strategy for the regulation of telomerase activity. Int J Mol Sci. 2017;18(3):567.

[214]

Voigt A, Herholz D, Fiesel FC, et al. TDP-43-mediated neuron loss in vivo requires RNA-binding activity. PLoS One. 2010;5(8):e12247.

[215]

Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet. 2023;14:1089053.

[216]

Perdivara I, Petrovich R, Allinquant B, Deterding LJ, Tomer KB, Przybylski M. Elucidation of O-Glycosylation structures of the β-Amyloid precursor protein by liquid chromatography? mass spectrometry using electron transfer dissociation and collision induced dissociation. J Proteome Res. 2009;8(2):631-642.

[217]

Bednářová A, Hanna M, Durham I, et al. Lost in translation: defects in transfer RNA modifications and neurological disorders. Front Mol Neurosci. 2017;10:135.

[218]

Hou Y-M, Gamper H, Yang W. Post-transcriptional modifications to tRNA—a response to the genetic code degeneracy. RNA. 2015;21(4):642-644.

[219]

Manickam N, Joshi K, Bhatt MJ, Farabaugh PJ. Effects of tRNA modification on translational accuracy depend on intrinsic codon–anticodon strength. Nucleic Acids Res. 2016;44(4):1871-1881.

[220]

Lorenz C, Lünse C, Mörl M. tRNA modifications: impact on structure and thermal adaptation. Biomolecules. 2017;7(2):35.

[221]

Yu Z, Huang L, Xia Y, et al. Analysis of m6A modification regulators in the substantia nigra and striatum of MPTP-induced Parkinson’s disease mice. Neurosci Lett. 2022;791:136907.

[222]

Ivanov A, Memczak S, Wyler E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 2015;10(2):170-177.

[223]

Guo C, Ma Y-Y. Calcium permeable-AMPA receptors and excitotoxicity in neurological disorders. Front Neural Circuits. 2021;15:711564.

[224]

Hao X, Shiromoto Y, Sakurai M, et al. ADAR1 downregulation by autophagy drives senescence independently of RNA editing by enhancing p16INK4a levels. Nature Cell Biol. 2022;24(8):1202-1210.

[225]

Hosaka T, Tsuji H, Kwak S. Roles of aging, circular RNAs, and RNA editing in the pathogenesis of amyotrophic lateral sclerosis: potential biomarkers and therapeutic targets. Cells. 2023;12(10):1443.

[226]

Gonçalves PB, Sodero ACR, Cordeiro Y. Green tea epigallocatechin-3-gallate (EGCG) targeting protein misfolding in drug discovery for neurodegenerative diseases. Biomolecules. 2021;11(5):767.

[227]

Tang Z, Cao J, Yao J, et al. KDM1A-mediated upregulation of METTL3 ameliorates Alzheimer’s disease via enhancing autophagic clearance of p-tau through m6A-dependent regulation of STUB1. Free Radic Biol Med. 2023;195:343-358.

[228]

Tedesco B, Ferrari V, Cozzi M, et al. The role of small heat shock proteins in protein misfolding associated motoneuron diseases. Int J Mol Sci. 2022;23(19):11759.

[229]

Tamagno E, Guglielmotto M, Vasciaveo V, Tabaton M. Oxidative stress and beta amyloid in Alzheimer’s disease which comes first: the chicken or the egg? Antioxidants. 2021;10(9):1479.

[230]

Franzmeier N, Ren J, Damm A, et al. The BDNF Val66Met SNP modulates the association between beta-amyloid and hippocampal disconnection in Alzheimer’s disease. Mol Psychiatry. 2021;26(2):614-628.

[231]

Srinivasan E, Chandrasekhar G, Chandrasekar P, et al. Alpha-synuclein aggregation in Parkinson’s disease. Front Med. 2021;8:736978.

[232]

Hallacli E, Kayatekin C, Nazeen S, et al. The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell. 2022;185(12):2035-2056.e33.

[233]

Franich NR, Hickey MA, Zhu C, et al. Phenotype onset in Huntington’s disease knock-in mice is correlated with the incomplete splicing of the mutant huntingtin gene. J Neurosci Res. 2019;97(12):1590-1605.

[234]

Trist BG, Fifita JA, Hogan A, et al. Co-deposition of SOD1, TDP-43 and p62 proteinopathies in ALS: evidence for multifaceted pathways underlying neurodegeneration. Acta Neuropathol Commun. 2022;10(1):122.

[235]

Chen Y, Wang H, Ying Z, Gao Q. Ibudilast enhances the clearance of SOD1 and TDP-43 aggregates through TFEB-mediated autophagy and lysosomal biogenesis: the new molecular mechanism of ibudilast and its implication for neuroprotective therapy. Biochem Biophys Res Commun. 2020;526(1):231-238.

[236]

Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell. 2014;56(1):55-66.

[237]

Hanan M, Simchovitz A, Yayon N, et al. A Parkinson’s disease circ RNA s resource reveals a link between circ SLC 8A1 and oxidative stress. EMBO Mol Med. 2020;12(9):e11942.

[238]

Pupak A, Singh A, Sancho-Balsells A, et al. Altered m6A RNA methylation contributes to hippocampal memory deficits in huntington’s disease mice. Cell Mol Life Sci. 2022;79(8):416.

[239]

Bhat VD, Jayaraj J, Babu K. RNA and neuronal function: the importance of post-transcriptional regulation. Oxf Open Neurosci. 2022;7:kvac011.

[240]

Barutcu AR, Long Y, Motamedi M. Editorial: RNA-mediated epigenetic and transcriptional regulation. Front Genet. 2022;13:928335.

[241]

Zuo S, Li L, Wen X, et al. NSUN2-mediated m5C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression. Clin Transl Med. 2023;13(5):e1273.

[242]

Boo SH, Kim YK. The emerging role of RNA modi fications in the regulation of mRNA stability. Exp Mol Med. 2020;52:400-408.

[243]

Anantharaman A, Tripathi V, Khan A, et al. ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins. Nucleic Acids Res. 2017;45(7):4189-4201.

[244]

Huang H, Weng H, Sun W, et al. Recognition of RNA N(6)-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nature Cell Biol. 2018;20(3):285-295.

[245]

Shi H, Wei J, He C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol Cell. 2019;74(4):640-650.

[246]

Chen X-Y, Zhang J, Zhu J-S. The role of m 6 A RNA methylation in human cancer. Mol Cancer. 2019;18:1-9.

[247]

Huang H, Weng H, Chen J. The biogenesis and precise control of RNA m6A methylation. TIG. 2020;36(1):44-52.

[248]

Lee Y, Choe J, Park OH, Kim YK. Molecular mechanisms driving mRNA degradation by m6A modification. TIG. 2020;36(3):177-188.

[249]

Mugridge JS, Coller J, Gross JD. Structural and molecular mechanisms for the control of eukaryotic 5′–3′ mRNA decay. Nat Struct Mol Biol. 2018;25(12):1077-1085.

[250]

Mauer J, Luo X, Blanjoie A, et al. Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature. 2017;541(7637):371-375.

[251]

Wu Y-Y, Kuo H-C. Functional roles and networks of non-coding RNAs in the pathogenesis of neurodegenerative diseases. J Biomed Sci. 2020;27:49.

[252]

Zhou S, Yu X, Wang M, et al. Long non-coding RNAs in pathogenesis of neurodegenerative disorders. Front Cell Dev Biol. 2021;9:719247.

[253]

Pozdyshev DV, Zharikova AA, Medvedeva MV, Muronetz VI. Differential analysis of A-to-I mRNA edited sites in parkinson’s disease. Genes. 2021;13(1):14.

[254]

Chen X, Yu C, Guo M, et al. Down-regulation of m6A mRNA methylation is involved in dopaminergic neuronal death. ACS Chem Neurosci. 2019;10(5):2355-2363.

[255]

Leonetti AM, Chu MY, Ramnaraign FO, Holm S, Walters BJ. An emerging role of m6A in memory: A case for translational priming. Int J Mol Sci. 2020;21(20):7447.

[256]

Shine JM, Bell PT, Matar E, et al. Dopamine depletion alters macroscopic network dynamics in Parkinson’s disease. Brain. 2019;142(4):1024-1034.

[257]

Karikari AA, McFleder RL, Ribechini E, et al. Neurodegeneration by α-synuclein-specific T cells in AAV-A53T-α-synuclein Parkinson’s disease mice. Brain Behav Immun. 2022;101:194-210.

[258]

Zhu R, Luo Y, Li S, Wang Z. The role of microglial autophagy in Parkinson’s disease. Front Aging Neurosci. 2022;14:1039780.

[259]

Selberg S, Yu L-Y. Bondarenko O, et al. Small-molecule inhibitors of the RNA M6A demethylases FTO potently support the survival of dopamine neurons. Int J Mol Sci. 2021;22(9):432419.

[260]

Song H, Chen J, Huang J, et al. Epigenetic modification in parkinson’s disease. Front Cell Dev Biol. 2023;11:1123621.

[261]

Mead RJ, Shan N, Reiser HJ, Marshall F, Shaw PJ. Amyotrophic lateral sclerosis: A neurodegenerative disorder poised for successful therapeutic translation. Nat Rev Drug Discovery. 2023;22(3):185-212.

[262]

Jiapaer Z, Su D, Hua L, et al. Regulation and roles of RNA modifications in aging-related diseases. Aging cell. 2022;21(7):e13657.

[263]

Hideyama T, Yamashita T, Suzuki T, et al. Induced loss of ADAR2 engenders slow death of motor neurons from Q/R Site-Unedited GluR2. J Neurosci. 2010;30(36):11917-11925.

[264]

Hideyama T, Yamashita T, Aizawa H, et al. Profound downregulation of the RNA editing enzyme ADAR2 in ALS spinal motor neurons. Neurobiol Dis. 2012;45(3):1121-1128.

[265]

Kwak S, Nishimoto Y, Yamashita T. Newly identified ADAR-mediated A-to-I editing positions as a tool for ALS research. RNA Biol. 2008;5(4):193-197.

[266]

McMillan M, Gomez N, Hsieh C, et al. RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia. Mol Cell. 2023;83(2):219-236.e7.

[267]

Kamal M, Pratap AR, Naved M, et al. Machine learning and image processing enabled evolutionary framework for brain MRI analysis for alzheimer’s disease detection. Comput Intell Neurosci. 2022;2022:5261942.

[268]

Karran E, Mercken M, Strooper BD. The amyloid cascade hypothesis for alzheimer’s disease: an appraisal for the development of therapeutics. Nat Rev Drug Discovery. 2011;10(9):698-712.

[269]

Mehta RI, Schneider JA. What is ‘alzheimer’s disease’? the neuropathological heterogeneity of clinically defined Alzheimer’s dementia. Curr Opin Neurol. 2021;34(2):237-245.

[270]

Zhang R, Zhang Y, Guo F, Li S, Cui H. RNA N6-Methyladenosine modifications and its roles in alzheimer’s disease. Front Cell Neurosci. 2022;16:820378.

[271]

Calzoni E, Argentati C, Cesaretti A, et al. RNA modifications in neurodegenerations. Epitranscriptomics, 2021.

[272]

Saha A, Bello D, Fernández-Tejada A. Advances in chemical probing of protein O-GlcNAc glycosylation: structural role and molecular mechanisms. Chem Soc Rev. 2021;50(18):10451-10485.

[273]

Wu W, Lee I, Spratt H, Fang X, Bao X. tRNA-Derived fragments in alzheimer’s disease: implications for new disease biomarkers and neuropathological mechanisms. J Alzheimer’s Dis. 2021;79(2):793-806.

[274]

Gámez-Valero A, Guisado-Corcoll A, Herrero-Lorenzo M, Solaguren-Beascoa M, Martí E. Non-Coding RNAs as sensors of oxidative stress in neurodegenerative diseases. Antioxidants. 2020;9(11):1095.

[275]

Fu Y, Lee I, Lee YS, Bao X. Small non-coding transfer RNA-Derived RNA fragments (tRFs):their biogenesis, function and implication in human diseases. Genomics Inform. 2015;13(4):94-101.

[276]

Nikolac Perkovic M, Videtic Paska A, Konjevod M, et al. Epigenetics of alzheimer’s disease. Biomolecules. 2021;11(2):195.

[277]

Chen Y-S, Yang W-L. Zhao Y-L, Yang Y-G. Dynamic transcriptomic m5C and its regulatory role in RNA processing. WIREs RNA. 2021;12(4):e1639.

[278]

PerezGrovas-Saltijeral A, Rajkumar AP, Knight HM. Differential expression of m(5)C RNA methyltransferase genes NSUN6 and NSUN7 in alzheimer’s disease and traumatic brain injury. Mol Neurobiol. 2023;60(4):2223-2235.

[279]

Kim YA, Siddiqui T, Blaze J, et al. RNA methyltransferase NSun2 deficiency promotes neurodegeneration through epitranscriptomic regulation of tau phosphorylation. Acta Neuropathol. 2023;145(1):29-48.

[280]

Wang X, Xie J, Tan L, et al. N6-methyladenosine-modified circRIMS2 mediates synaptic and memory impairments by activating GluN2B ubiquitination in alzheimer’s disease. Transl Neurodegener. 2023;12(1):53.

[281]

Zhou LL, Yang CG. Targeting epitranscriptomic proteins for therapeutic intervention. Biochemistry. 2020;59(2):125-127.

[282]

Berdasco M, Esteller M. Towards a druggable epitranscriptome: compounds that target RNA modifications in cancer. Br J Pharmacol. 2022;179(12):2868-2889.

[283]

Walgrave H, Zhou L, De Strooper B, Salta E. The promise of microRNA-based therapies in Alzheimer’s disease: challenges and perspectives. Mol Neurodegener. 2021;16(1):76.

[284]

Panda S, Chatterjee O, Chatterjee S. Nucleic Acid-Based Strategies to Treat Neurodegenerative disorders. In: S Chatterjee, S Chattopadhyay, eds. Nucleic Acid Biology and its Application in Human Diseases. Springer Nature Singapore;2023:105-133.

[285]

Silva AC, Lobo DD, Martins IM, et al. Antisense oligonucleotide therapeutics in neurodegenerative diseases: the case of polyglutamine disorders. Brain. 2019;143(2):407-429.

[286]

Wood MJA, Trulzsch B, Abdelgany A, Beeson D. Therapeutic gene silencing in the nervous system. Hum Mol Gen. 2003;12(suppl 2):R279-R284.

[287]

Atoi PA Mass spectrometric studies of RNA modification patterns in mammals.2023.

[288]

Sundaram P, Kurniawan H, Byrne ME, Wower J. Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci. 2013;48(1-2):259-271.

[289]

Kong AHY, Wu AJ, Ho OKY, et al. Exploring the potential of aptamers in targeting neuroinflammation and neurodegenerative disorders: opportunities and challenges. Int J Mol Sci. 2023;24(14):11780.

[290]

Akamatsu M, Yamashita T, Teramoto S, et al. Testing of the therapeutic efficacy and safety of AMPA receptor RNA aptamers in an ALS mouse model. Life Science Alliance. 2022;5(4):e202101193.

[291]

Singh RN, Seo J, Singh NN. RNA in spinal muscular atrophy: therapeutic implications of targeting. Expert Opin Ther Targets. 2020;24(8):731-743.

[292]

Razlansari M, Jafarinejad S, Rahdar A, et al. Development and classification of RNA aptamers for therapeutic purposes: an updated review with emphasis on cancer. Mol Cell Biochem. 2023;478(7):1573-1598.

[293]

Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The role of lncRNAs in gene expression regulation through mRNA stabilization. Non-coding RNA. 2021;7(1):3.

[294]

Zhou S, Yu X, Wang M, et al. Long non-coding RNAs in pathogenesis of neurodegenerative disorders review. Front Cell Dev Biol. 2021;9:719247.

[295]

Zhang M, He P, Bian Z. Long noncoding RNAs in neurodegenerative diseases: pathogenesis and potential implications as clinical biomarkers. Front Mol Neurosci. 2021;14:685143.

[296]

Policarpo R, Sierksma A, De Strooper B, d’Ydewalle C. From junk to function: LncRNAs in CNS health and disease. Front Mol Neurosci. 2021;14:714768.

[297]

Jiang H, Zhang Y, Yue J, et al. Non-coding RNAs: the neuroinflammatory regulators in neurodegenerative diseases. Front Neurol. 2022;13:929290.

[298]

Calzoni E, Argentati C, Cesaretti A, et al. RNA Modifications in Neurodegenerations. In: S Jurga, J Barciszewski, eds. Epitranscriptomics. Springer International Publishing, 2021:23-77.

[299]

Chatterjee B, Shen C-KJ. Majumder P. RNA modifications and RNA metabolism in neurological disease pathogenesis. Int J Mol Sci. 2021;22(21):11870.

[300]

Wiener D, Schwartz S. The epitranscriptome beyond m6A. Nat Rev Genet. 2021;22(2):119-131.

[301]

Wu P. Inhibition of RNA-binding proteins with small molecules. Nat Rev Chem. 2020;4(9):441-458.

[302]

Tzelepis K, De Braekeleer E, Yankova E, et al. Pharmacological inhibition of the RNA m6A writer METTL3 as a novel therapeutic strategy for acute myeloid leukemia. Blood. 2019;134:403.

[303]

Fiorentino F, Menna M, Rotili D, Valente S, Mai A. METTL3 from target validation to the first Small-Molecule inhibitors: A medicinal chemistry journey. J Med Chem. 2023;66(3):1654-1677.

[304]

Du Y, Yuan Y, Xu L, et al. Discovery of METTL3 small molecule inhibitors by virtual screening of natural products. Front Pharmacol. 2022;13:878135.

[305]

Liao L, He Y, Li S-J. et al. Anti-HIV drug elvitegravir suppresses cancer metastasis via increased proteasomal degradation of m6A methyltransferase METTL3. Cancer Res. 2022;82(13):2444-2457.

[306]

Cummings J, Lee G, Ritter A, Sabbagh M, Zhong K. Alzheimer’s disease drug development pipeline:2019. Alzheimer’s Dementia: Transl Res Clin Interventions. 2019;5:272-293.

[307]

Li Y, Cheng X, Chen Y, Zhou T, Li D, Zheng WV. METTL3 facilitates the progression of hepatocellular carcinoma by modulating the m6A level of USP7. Am J Transl Res. 2021;13(12):13423-13437.

[308]

Zhang XW, Feng N, Liu YC, et al. Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy. Sci Adv. 2022;8(32):eabo0789.

[309]

Jia G, Fu Y, Zhao X, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011;7(12):885-887.

[310]

Zhou H, Wang B, Sun H, Xu X, Wang Y. Epigenetic regulations in neural stem cells and neurological diseases. Stem Cells Int. 2018;2018:1-10.

[311]

Karagianni K, Pettas S, Christoforidou G, et al. A systematic review of common and Brain-Disease-Specific RNA editing alterations providing novel insights into neurological and neurodegenerative disease manifestations. Biomolecules. 2022;12(3):465.

[312]

Grozhik AV, Olarerin-George AO, Sindelar M, Li X, Gross SS, Jaffrey SR. Antibody cross-reactivity accounts for widespread appearance of m1A in 5′UTRs. Nat Commun. 2019;10(1):5126.

[313]

Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nature Methods. 2015;12(8):767-772.

[314]

Chokkalla AK, Mehta SL, Vemuganti R. Epitranscriptomic modifications modulate normal and pathological functions in CNS. Transl Stroke Res. 2022;13(1):1-11.

[315]

Spencer AP, Torrado M, Custódio B, et al. Breaking barriers: bioinspired strategies for targeted neuronal delivery to the central nervous system. Pharmaceutics. 2020;12(2):192.

[316]

Hawkins BT, Davis TP. The blood-brain barrier/neurovascular unit in health and disease. Pharmacol Rev. 2005;57(2):173-185.

[317]

Yang Y, Rosenberg GA. Blood–brain barrier breakdown in acute and chronic cerebrovascular disease. Stroke. 2011;42(11):3323-3328.

[318]

Sochocka M, Diniz BS, Leszek J. Inflammatory response in the CNS: friend or foe? Mol Neurobiol. 2017;54:8071-8089.

[319]

Nance E, Pun SH, Saigal R, Sellers DL. Drug delivery to the central nervous system. Rev Infect Dis. 2022;7(4):314-331.

[320]

Gosselet F, Loiola RA, Roig A, Rosell A, Culot M. Central nervous system delivery of molecules across the blood-brain barrier. Neurochem Int. 2021;144:104952.

[321]

Koch JC, Tatenhorst L, Roser A-E. Saal K-A, Tönges L, Lingor P. ROCK inhibition in models of neurodegeneration and its potential for clinical translation. Pharmacol Ther. 2018;189:1-21.

[322]

Koch JC, Tatenhorst L, Roser AE, Saal KA, Tönges L, Lingor P. ROCK inhibition in models of neurodegeneration and its potential for clinical translation. Pharmacol Ther. 2018;189:1-21.

[323]

Moutinho M, Codocedo JF, Puntambekar SS, Landreth GE. Nuclear receptors as therapeutic targets for neurodegenerative diseases: lost in translation. Annu Rev Pharmacol Toxicol. 2019;59:237-261.

RIGHTS & PERMISSIONS

2024 The Author(s). Ibrain published by Affiliated Hospital of Zunyi Medical University (AHZMU) and Wiley-VCH GmbH.

AI Summary AI Mindmap
PDF

440

Accesses

0

Citation

Detail

Sections
Recommended

AI思维导图

/