Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning

Anna Roumpelaki KB. Package “MXM” Type Package Title Feature Selection (Including Multiple Solutions) and Bayesian Networks. 2022. https://cran.r-project.org/web/packages/MXM/MXM.pdf

Aronica E, Baas F, Iyer A, ten Asbroek ALMA, Morello G, Cavallaro S. Molecular classification of amyotrophic lateral sclerosis by unsupervised clustering of gene expression in motor cortex. Neurobiol Dis. 2015;74:359–76.

Article  CAS  Google Scholar 

Barredo Arrieta A, Díaz-Rodríguez N, Del Ser J, Bennetot A, Tabik S, Barbado A, et al. Explainable Artificial Intelligence (XAI): Concepts, taxonomies, opportunities and challenges toward responsible AI. Inf Fusion. 2020;1(58):82–115.

Article  Google Scholar 

Batra R, Hutt K, Vu A, Rabin SJ, Baughn MW, Libby RT, et al. Gene Expression Signatures of Sporadic ALS Motor Neuron Populations. Neuroscience. 2016. https://doi.org/10.1101/038448.

Article  Google Scholar 

Bean DM, Al-Chalabi A, Dobson RJB, Iacoangeli A. A knowledge-based machine learning approach to gene prioritisation in amyotrophic lateral sclerosis. Genes. 2020;11(6):668.

Article  CAS  Google Scholar 

Berge T, Eriksson A, Brorson IS, Høgestøl EA, Berg-Hansen P, Døskeland A, et al. Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls. Clin Proteomics. 2019;16(1):19.

Article  Google Scholar 

Bessodes N, Parain K, Bronchain O, Bellefroid EJ, Perron M. Prdm13 forms a feedback loop with Ptf1a and is required for glycinergic amacrine cell genesis in the Xenopus Retina. Neural Develop. 2017;12(1):16.

Article  Google Scholar 

Breiman L. Breiman and Cutler’s random forests for classification and regression. Mach Learn. 2001;45(1):5–32.

Article  Google Scholar 

Chen T, Guestrin C. XGBoost: A Scalable Tree Boosting System. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. San Francisco: ACM; 2016. p. 785–94.

Cicardi ME, Cristofani R, Rusmini P, Meroni M, Ferrari V, Vezzoli G, et al. Tdp-25 routing to autophagy and proteasome ameliorates its aggregation in amyotrophic lateral sclerosis target cells. Sci Rep. 2018;8(1):12390.

Article  Google Scholar 

DeglInnocenti D, Ramazzotti M, Sarchielli E, Monti D, Chevanne M, Vannelli GB, et al. Oxadiazon affects the expression and activity of aldehyde dehydrogenase and acylphosphatase in human striatal precursor cells: A possible role in neurotoxicity. Toxicology. 2019;411:110–21.

Article  CAS  Google Scholar 

Dinkova-Kostova AT, Kostov RV, Kazantsev AG. The role of Nrf2 signaling in counteracting neurodegenerative diseases. FEBS J. 2018;285(19):3576–90.

Article  CAS  Google Scholar 

Eisenstein M. Machine learning powers biobank-driven drug discovery. Nat Biotechnol. 2022;40:1303–5.

Article  CAS  Google Scholar 

Errico F, Cuomo M, Canu N, Caputo V, Usiello A. New insights on the influence of free d-aspartate metabolism in the mammalian brain during prenatal and postnatal life. Biochim Biophys Acta BBA - Proteins Proteomics. 2020;1868(10): 140471.

Article  CAS  Google Scholar 

Ghosh S, Chan CKK. Analysis of RNA-Seq data using tophat and cufflinks. Methods Mol Biol Clifton NJ. 2016;1374:339–61.

Article  CAS  Google Scholar 

Goldstein LH, Abrahams S. Changes in cognition and behaviour in amyotrophic lateral sclerosis: nature of impairment and implications for assessment. Lancet Neurol. 2013;12(4):368–80.

Article  Google Scholar 

Higa L, Zhang H. Stealing the spotlight: CUL4-DDB1 ubiquitin ligase docks WD40-repeat proteins to destroy. Cell Div. 2007;2(1):5.

Article  Google Scholar 

Joilin G, Leigh PN, Newbury SF, Hafezparast M. An overview of MicroRNAs as biomarkers of ALS. Front Neurol. 2019;7(10):186.

Article  Google Scholar 

Karim A, Su Z, West PK, Keon M, Shamsani J, et al. Molecular classification and interpretation of amyotrophic lateral sclerosis using deep convolution neural networks and shapley values. Genes. 2021;12(11):1754.

Article  CAS  Google Scholar 

Kotni MK, Zhao M, Wei DQ. Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. Orphanet J Rare Dis. 2016;11(1):148.

Article  Google Scholar 

Lagani V, Athineou G, Farcomeni A, Tsagris M, Tsamardinos I. Feature Selection with the R Package MXM : Discovering Statistically Equivalent Feature Subsets. J Stat Softw. 2017;80:7.

Article  Google Scholar 

Lederer CW, Torrisi A, Pantelidou M, Santama N, Cavallaro S. Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis. BMC Genomics. 2007;8(1):26.

Article  Google Scholar 

Leszczyński P, Śmiech M, Parvanov E, Watanabe C, Mizutani K, Taniguchi H. Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells. 2020;9(12):2603.

Article  Google Scholar 

Li Y, Shi F, Wang G, Lv J, Zhang H, Jin H, et al. Expression profile of immunoglobulin G glycosylation in children with epilepsy in Han nationality. Front Mol Neurosci. 2022;1(15): 843897.

Article  Google Scholar 

Liguori M, Nuzziello N, Introna A, Consiglio A, Licciulli F, D’Errico E, et al. Dysregulation of MicroRNAs and target genes networks in peripheral blood of patients with sporadic amyotrophic lateral sclerosis. Front Mol Neurosci. 2018;28(11):288.

Article  Google Scholar 

Liu W, Venugopal S, Majid S, Ahn IS, Diamante G, Hong J, et al. Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis. Neurobiol Dis. 2020;141: 104877.

Article  CAS  Google Scholar 

Loffreda A, Nizzardo M, Arosio A, Ruepp MD, Calogero RA, Volinia S, et al. miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis. Prog Neurobiol. 2020;190: 101803.

Article  CAS  Google Scholar 

Magen I, Yacovzada N, Warren JD, Heller C, Swift I, Bobeva Y, et al. microRNA-based predictor for diagnosis of frontotemporal dementia. Neurology. 2020. https://doi.org/10.1101/2020.01.22.20018408.

Article  Google Scholar 

Mathis S, Goizet C, Soulages A, Vallat JM, Masson GL. Genetics of amyotrophic lateral sclerosis: A review. J Neurol Sci. 2019;399:217–26.

Article  CAS  Google Scholar 

Mejzini R, Flynn LL, Pitout IL, Fletcher S, Wilton SD, Akkari PA. ALS Genetics, Mechanisms, and Therapeutics: Where Are We Now? Front Neurosci. 2019;6(13):1310.

Article  Google Scholar 

Miller SJ, Glatzer JC, Hsieh YC, Rothstein JD. Cortical astroglia undergo transcriptomic dysregulation in the G93A SOD1 ALS mouse model. J Neurogenet. 2018;32(4):322–35.

Article  CAS  Google Scholar 

Morello G, Guarnaccia M, Spampinato AG, La Cognata V, D’Agata V, Cavallaro S. Copy number variations in amyotrophic lateral sclerosis: piecing the mosaic tiles together through a systems biology approach. Mol Neurobiol. 2017;55(2):1299–322.

Article  Google Scholar 

Morello G, Guarnaccia M, Spampinato AG, La Cognata V, D’Agata V, Cavallaro S. Copy number variations in amyotrophic lateral sclerosis: piecing the mosaic tiles together through a systems biology approach. Mol Neurobiol. 2018;55(2):1299–322.

Article  CAS  Google Scholar 

Nakamura T, Ohnuma T, Hanzawa R, Takebayashi Y, Takeda M, Nishimon S, et al. Associations of common copy number variants in glutathione S-transferase mu 1 and D-dopachrome tautomerase-like protein genes with risk of schizophrenia in a Japanese population. Am J Med Genet B Neuropsychiatr Genet. 2015;168(7):630–6.

Article  CAS  Google Scholar 

Nakamura R, Misawa K, Tohnai G, Nakatochi M, Furuhashi S, Atsuta N, et al. A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis. Commun Biol. 2020;3(1):526.

Article  CAS  Google Scholar 

Norsk Regnesentral NS. Package ‘shapr’ Title Prediction Explanation with Dependence-Aware Shapley Values. 2021. https://cran.r-project.org/web/packages/shapr/shapr.pdf

Pantelidou M, Zographos SE, Lederer CW, Kyriakides T, Pfaffl MW, Santama N. Differential expression of molecular motors in the motor cortex of sporadic ALS. Neurobiol Dis. 2007;26(3):577–89.

Article  CAS  Google Scholar 

Phukan J, Pender NP, Hardiman O. Cognitive impairment in amyotrophic lateral sclerosis. Lancet Neurol. 2007;6(11):994–1003.

Article  CAS  Google Scholar 

Prudencio M, Belzil VV, Batra R, Ross CA, Gendron TF, Pregent LJ, et al. Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat Neurosci. 2015;18(8):1175–82.

Article  CAS  Google Scholar 

Pun FW, Liu BHM, Long X, Leung HW, Leung GHD, Mewborne QT, et al. Identification of therapeutic targets for amyotrophic lateral sclerosis using PandaOmics – An AI-Enabled Biological Target Discovery Platform. Front Aging Neurosci. 2022;28(14): 914017.

Article  Google Scholar 

Ragagnin AMG, Shadfar S, Vidal M, Jamali MS, Atkin JD. Motor Neuron Susceptibility in ALS/FTD. Front Neurosci. 2019;27(13):532.

Article  Google Scholar 

Rubino E, Di Stefano M, Galimberti D, Serpente M, Scarpini E, Fenoglio C, et al. C9ORF72 hexanucleotide repeat expansion frequency in patients with Paget’s disease of bone. Neurobiol Aging. 2020;85:154.e1-154.e3.

Article  CAS  Google Scholar 

Saris CG, Horvath S, van Vught PW, van Es MA, Blauw HM, Fuller TF, et al. Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics. 2009;10(1):405.

Article  Google Scholar 

Sha Q, Zhang Z, Schymick JC, Traynor BJ, Zhang S. Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis. BMC Med Genet. 2009;10(1):86.

Article  Google Scholar 

Sharma A, Chunduri A, Gopu A, Shatrowsky C, Crusio WE, Delprato A, et al. Common genetic signatures of Alzheimer’s disease in Down Syndrome. F1000 Res. 2021;9:1299.

Article  Google Scholar 

Shibata N, Yamamoto T, Hiroi A, Omi Y, Kato Y, Kobayashi M. Activation of STAT3 and inhibitory effects of pioglitazone on STAT3 activity in a mouse model of SOD1-mutated amyotrophic lateral sclerosis. Neuropathology. 2010;30(4):353–60.

Article  Google Scholar 

Shtilbans A, Choi SG, Fowkes ME, Khitrov G, Shahbazi M, Ting J, et al. Differential gene expression in patients with amyotrophic lateral sclerosis. Amyotroph Lateral Scler. 2011;12(4):250–6.

Article  CAS  Google Scholar 

Silroy U, Bhowal A. Identifying causal genes for Amyotrophic Lateral Sclerosis (ALS) by Meta Analysis of Gene Expression Data. Int J Eng Sci Math. 2018;7(3):89.

Google Scholar 

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