Abstract
Background
Currently, miRNAs are involved in the development of amyotrophic lateral sclerosis (ALS), and identifying circulating miRNAs that are causally associated with ALS risk as biomarkers is imperative.
Methods
We performed a two-sample Mendelian randomization study to evaluate the causal relationship between miRNAs and ALS. Our analysis was conducted using summary statistics from miRNA expression quantitative loci (eQTL) data of the Framingham Heart Study and ALS genome-wide association studies data. Another independent miRNA data was used to further validate.
Results
We identified eight unique miRNAs that were causally associated with ALS risk. Using expression data of miRNAs from an independent study, we validated three high-confidence miRNAs, namely hsa-miR-27b-3p, hsa-miR-139-5p, and hsa-miR-152-3p, which might have a potential causal effect on ALS risk.
Conclusion
We suggested that higher levels of hsa-miR-27b-3p and hsa-miR-139-5p had protective effects on ALS, whereas higher levels of hsa-miR-152-3p might act as a risk factor for ALS. The analytical framework presented in this study helps to understand the role of miRNAs in the development of ALS and to identify the biomarkers for ALS risk.
Similar content being viewed by others
Data availability
The data used to perform the analyses in this study were obtained from public genome-wide association studies summary statistics. Validation data were obtained from the study [26] through a request to the authors.
References
Bucchia M, Ramirez A, Parente V, Simone C, Nizzardo M, Magri F, Dametti S, Corti S (2015) Therapeutic development in amyotrophic lateral sclerosis. Clin Ther 37(3):668–680. https://doi.org/10.1016/j.clinthera.2014.12.020
Cloutier F, Marrero A, O'Connell C, Morin P Jr (2015) MicroRNAs as potential circulating biomarkers for amyotrophic lateral sclerosis. J Mol Neurosci 56(1):102–112. https://doi.org/10.1007/s12031-014-0471-8
Ajroud-Driss S, Siddique T (2015, 1852) Sporadic and hereditary amyotrophic lateral sclerosis (ALS). Biochim Biophys Acta (4):679–684. https://doi.org/10.1016/j.bbadis.2014.08.010
Rizzo F, Riboldi G, Salani S, Nizzardo M, Simone C, Corti S, Hedlund E (2014) Cellular therapy to target neuroinflammation in amyotrophic lateral sclerosis. Cell Mol Life Sci 71(6):999–1015. https://doi.org/10.1007/s00018-013-1480-4
Chiò A, Logroscino G, Traynor BJ, Collins J, Simeone JC, Goldstein LA, White LA (2013) Global epidemiology of amyotrophic lateral sclerosis: a systematic review of the published literature. Neuroepidemiology 41(2):118–130. https://doi.org/10.1159/000351153
Andersen PM, Al-Chalabi A (2011) Clinical genetics of amyotrophic lateral sclerosis: what do we really know? Nat Rev Neurol 7(11):603–615. https://doi.org/10.1038/nrneurol.2011.150
Bigio EH, Weintraub S, Rademakers R, Baker M, Ahmadian SS, Rademaker A, Weitner BB, Mao Q, Lee KH, Mishra M, Ganti RA, Mesulam MM (2013) Frontotemporal lobar degeneration with TDP-43 proteinopathy and chromosome 9p repeat expansion in C9ORF72: clinicopathologic correlation. Neuropathology 33(2):122–133. https://doi.org/10.1111/j.1440-1789.2012.01332.x
Kawahara Y, Mieda-Sato A (2012) TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes. Proc Natl Acad Sci USA 109(9):3347–3352. https://doi.org/10.1073/pnas.1112427109
Lagier-Tourenne C, Polymenidou M, Cleveland DW (2010) TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Hum Mol Genet 19(R1):R46–R64. https://doi.org/10.1093/hmg/ddq137
Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA 103(39):14385–14389. https://doi.org/10.1073/pnas.0603529103
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297. https://doi.org/10.1016/s0092-8674(04)00045-5
Cullen BR (2006) Viruses and microRNAs. Nat Gen 38:S25–S30. https://doi.org/10.1038/ng1793
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401–1414. https://doi.org/10.1016/j.cell.2007.04.040
Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Gen 38:S31–S36. https://doi.org/10.1038/ng1791
Sun K, Lai EC (2013) Adult-specific functions of animal microRNAs. Nat Rev Genet 14(8):535–548. https://doi.org/10.1038/nrg3471
Tan JY, Marques AC (2014) The miRNA-mediated cross-talk between transcripts provides a novel layer of posttranscriptional regulation. Adv Genet 85:149–199. https://doi.org/10.1016/b978-0-12-800271-1.00003-2
Al-Chalabi A, Hardiman O (2013) The epidemiology of ALS: a conspiracy of genes, environment and time. Nat Rev Neurol 9(11):617–628. https://doi.org/10.1038/nrneurol.2013.203
Hardiman O, van den Berg LH, Kiernan MC (2011) Clinical diagnosis and management of amyotrophic lateral sclerosis. Nat Rev Neurol 7(11):639–649. https://doi.org/10.1038/nrneurol.2011.153
Robberecht W, Philips T (2013) The changing scene of amyotrophic lateral sclerosis. Nat Rev Neurosci 14(4):248–264. https://doi.org/10.1038/nrn3430
Johnson R, Noble W, Tartaglia GG, Buckley NJ (2012) Neurodegeneration as an RNA disorder. Prog Neurobiol 99(3):293–315. https://doi.org/10.1016/j.pneurobio.2012.09.006
Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105(30):10513–10518. https://doi.org/10.1073/pnas.0804549105
Grasso M, Piscopo P, Confaloni A, Denti MA (2014) Circulating miRNAs as biomarkers for neurodegenerative disorders. Molecules (Basel, Switzerland) 19(5):6891–6910. https://doi.org/10.3390/molecules19056891
Schneider R, McKeever P, Kim T, Graff C, van Swieten JC, Karydas A, Boxer A, Rosen H, Miller BL, Laforce R Jr, Galimberti D, Masellis M, Borroni B, Zhang Z, Zinman L, Rohrer JD, Tartaglia MC, Robertson J (2018) Downregulation of exosomal miR-204-5p and miR-632 as a biomarker for FTD: a GENFI study. J Neurol Neurosurg Psychiatry 89(8):851–858. https://doi.org/10.1136/jnnp-2017-317492
Freischmidt A, Müller K, Zondler L, Weydt P, Volk AE, Božič AL, Walter M, Bonin M, Mayer B, von Arnim CA, Otto M, Dieterich C, Holzmann K, Andersen PM, Ludolph AC, Danzer KM, Weishaupt JH (2014) Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers. Brain 137(11):2938–2950. https://doi.org/10.1093/brain/awu249
Huan T, Rong J, Liu C, Zhang X, Tanriverdi K, Joehanes R, Chen BH, Murabito JM, Yao C, Courchesne P, Munson PJ, O'Donnell CJ, Cox N, Johnson AD, Larson MG, Levy D, Freedman JE (2015) Genome-wide identification of microRNA expression quantitative trait loci. Nat Commun 6:6601. https://doi.org/10.1038/ncomms7601
Nikpay M, Beehler K, Valsesia A, Hager J, Harper ME, Dent R, McPherson R (2019) Genome-wide identification of circulating-miRNA expression quantitative trait loci reveals the role of several miRNAs in the regulation of cardiometabolic phenotypes. Cardiovasc Res 115(11):1629–1645. https://doi.org/10.1093/cvr/cvz030
Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt J, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya SBN, Marangi G et al (2018) Genome-wide analyses identify KIF5A as a novel ALS gene. Neuron 97(6):1268–1283.e1266. https://doi.org/10.1016/j.neuron.2018.02.027
van Rheenen W, Shatunov A, Dekker AM, McLaughlin RL, Diekstra FP, Pulit SL, van der Spek RA, Võsa U, de Jong S, Robinson MR, Yang J, Fogh I, van Doormaal PT, Tazelaar GH, Koppers M, Blokhuis AM, Sproviero W, Jones AR, Kenna KP et al (2016) Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis. Nat Genet 48(9):1043–1048. https://doi.org/10.1038/ng.3622
Brooks BR (1994) El Escorial World Federation of Neurology criteria for the diagnosis of amyotrophic lateral sclerosis. Subcommittee on Motor Neuron Diseases/Amyotrophic Lateral Sclerosis of the World Federation of Neurology Research Group on Neuromuscular Diseases and the El Escorial "Clinical limits of amyotrophic lateral sclerosis" workshop contributors. J Neurol Sci 124:96–107. https://doi.org/10.1016/0022-510x(94)90191-0
Brooks BR, Miller RG, Swash M, Munsat TL, World Federation of Neurology Research Group on Motor Neuron Diseases (2000) El Escorial revisited: revised criteria for the diagnosis of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Other Motor Neuron Disord 1(5):293–299. https://doi.org/10.1080/146608200300079536
Davies NM, Holmes MV, Davey Smith G (2018) Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians. BMJ (Clinical research ed) 362:k601. https://doi.org/10.1136/bmj.k601
Walker VM, Davey Smith G, Davies NM, Martin RM (2017) Mendelian randomization: a novel approach for the prediction of adverse drug events and drug repurposing opportunities. Int J Epidemiol 46(6):2078–2089. https://doi.org/10.1093/ije/dyx207
Chang L, Zhou G, Soufan O, Xia J (2020) miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology. Nucleic Acids Res 48(W1):W244–w251. https://doi.org/10.1093/nar/gkaa467
Huang HY, Lin YC, Li J, Huang KY, Shrestha S, Hong HC, Tang Y, Chen YG, Jin CN, Yu Y, Xu JT, Li YM, Cai XX, Zhou ZY, Chen XH, Pei YY, Hu L, Su JJ, Cui SD et al (2020) miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res 48(D1):D148–d154. https://doi.org/10.1093/nar/gkz896
Re DB, Le Verche V, Yu C, Amoroso MW, Politi KA, Phani S, Ikiz B, Hoffmann L, Koolen M, Nagata T, Papadimitriou D, Nagy P, Mitsumoto H, Kariya S, Wichterle H, Henderson CE, Przedborski S (2014) Necroptosis drives motor neuron death in models of both sporadic and familial ALS. Neuron 81(5):1001–1008. https://doi.org/10.1016/j.neuron.2014.01.011
Ito Y, Ofengeim D, Najafov A, Das S, Saberi S, Li Y, Hitomi J, Zhu H, Chen H, Mayo L, Geng J, Amin P, DeWitt JP, Mookhtiar AK, Florez M, Ouchida AT, Fan JB, Pasparakis M, Kelliher MA et al (2016) RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS. Science (New York, NY) 353(6299):603–608. https://doi.org/10.1126/science.aaf6803
Morrice JR, Gregory-Evans CY, Shaw CA (2017) Necroptosis in amyotrophic lateral sclerosis and other neurological disorders. Biochim Biophys Acta Mol Basis Dis 1863(2):347–353. https://doi.org/10.1016/j.bbadis.2016.11.025
Liguori M, Nuzziello N, Introna A, Consiglio A, Licciulli F, D'Errico E, Scarafino A, Distaso E, Simone IL (2018) Dysregulation of MicroRNAs and target genes networks in peripheral blood of patients with sporadic amyotrophic lateral sclerosis. Front Mol Neurosci 11:288. https://doi.org/10.3389/fnmol.2018.00288
Campos-Melo D, Droppelmann CA, He Z, Volkening K, Strong MJ (2013) Altered microRNA expression profile in Amyotrophic Lateral Sclerosis: a role in the regulation of NFL mRNA levels. Mol Brain 6:26. https://doi.org/10.1186/1756-6606-6-26
Hawley ZCE, Campos-Melo D, Strong MJ (2020) Evidence of a negative feedback network between TDP-43 and miRNAs dependent on TDP-43 nuclear localization. J Mol Biol 432(24):166695. https://doi.org/10.1016/j.jmb.2020.10.029
Raheja R, Regev K, Healy BC, Mazzola MA, Beynon V, Von Glehn F, Paul A, Diaz-Cruz C, Gholipour T, Glanz BI, Kivisakk P, Chitnis T, Weiner HL, Berry JD, Gandhi R (2018) Correlating serum microRNAs and clinical parameters in amyotrophic lateral sclerosis. Muscle Nerve 58(2):261–269. https://doi.org/10.1002/mus.26106
Kurita H, Yabe S, Ueda T, Inden M, Kakita A, Hozumi I (2020) MicroRNA-5572 is a novel microRNA-regulating SLC30A3 in sporadic amyotrophic lateral sclerosis. Int J Mol Sci 21(12):4482. https://doi.org/10.3390/ijms21124482
Zhai K, Liu B, Gao L (2020) Long-noncoding RNA TUG1 promotes Parkinson’s disease via modulating MiR-152-3p/PTEN pathway. Hum Gene Ther 31(23-24):1274–1287. https://doi.org/10.1089/hum.2020.106
Zhang A, Qian Y, Qian J (2019) MicroRNA-152-3p protects neurons from oxygen-glucose-deprivation/reoxygenation-induced injury through upregulation of Nrf2/ARE antioxidant signaling by targeting PSD-93. Biochem Biophys Res Commun 517(1):69–76. https://doi.org/10.1016/j.bbrc.2019.07.012
Acknowledgements
We thank all the GWAS consortiums for making the summary data publicly available, and we are grateful to all the investigators and participants who contributed to those studies. We thank Majid Nikpay for providing the miRNA eQTL data used in this study for validation.
Author information
Authors and Affiliations
Contributions
Conceptualization: Xusheng Huang; methodology: Yahui Zhu, Mao Li, Zhengqing He, Xinyuan Pang, Rongrong Du; formal analysis and investigation: Yahui Zhu, Mao Li, Zhengqing He, Xinyuan Pang, Rongrong Du, Wenxiu Yu, Jinghong Zhang, Jiongming Bai, Jiao Wang; writing – original draft preparation: Yahui Zhu; writing – review and editing: Xusheng Huang; resources: Yahui Zhu; supervision: Xusheng Huang. All authors approved the version to be published.
Corresponding author
Ethics declarations
Ethical approval
Ethical review and approval were waived for this study due to this study used summary data from GWAS and did not involve individual data. All studies that contributed data to this analysis were approved by the relevant institutional review board.
Informed consent
Patient informed consent was waived due to this study used summary data from GWAS and did not involve individual data.
Consent for publication
Patient consent was waived due to this study used summary data from GWAS and did not involve individual data.
Conflict of interest
The authors declare no competing interests.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Zhu, Y., Li, M., He, Z. et al. Evaluating the causal association between microRNAs and amyotrophic lateral sclerosis. Neurol Sci 44, 3567–3575 (2023). https://doi.org/10.1007/s10072-023-06860-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10072-023-06860-3