Comprehensive analysis of autoimmune-related genes in amyotrophic lateral sclerosis from the perspective of 3P medicine

Taylor JP, Brown RH Jr, Cleveland DW. Decoding ALS: from genes to mechanism. Nature. 2016;539:197–206.

PubMed  PubMed Central  Article  Google Scholar 

Golubnitschaja O, Costigliola V. General report & recommendations in predictive, preventive and personalised medicine 2012: white paper of the European Association for Predictive, Preventive and Personalised Medicine. EPMA J. 2012;3:14.

PubMed  PubMed Central  Article  Google Scholar 

Turner MR, Goldacre R, Ramagopalan S, Talbot K, Goldacre MJ. Autoimmune disease preceding amyotrophic lateral sclerosis: an epidemiologic study. Neurology. 2013;81:1222–5.

PubMed  PubMed Central  Article  Google Scholar 

Cui C, Longinetti E, Larsson H, Andersson J, Pawitan Y, Piehl F, Fang F. Associations between autoimmune diseases and amyotrophic lateral sclerosis: a register-based study. Amyotroph Lateral Scler Frontotemporal Degeneration. 2021;22:211–9.

Article  Google Scholar 

Li JY, Sun XH, Shen DC, Yang XZ, Liu MS, Cui LY. Clinical characteristics and prognosis of amyotrophic lateral sclerosis with autoimmune diseases. PLoS One. 2022;17:e0266529.

PubMed  PubMed Central  Article  Google Scholar 

Zeng P, Wang T, Zheng J, Zhou X. Causal association of type 2 diabetes with amyotrophic lateral sclerosis: new evidence from Mendelian randomization using GWAS summary statistics. BMC Med. 2019;17:225.

PubMed  PubMed Central  Article  Google Scholar 

Li CY, Yang TM, Ou RW, Wei QQ, Shang HF. Genome-wide genetic links between amyotrophic lateral sclerosis and autoimmune diseases. BMC Med. 2021;19:27.

PubMed  PubMed Central  Article  Google Scholar 

Balendra R, Isaacs AM. C9orf72-mediated ALS and FTD: multiple pathways to disease. Nat Rev Neurol. 2018;14:544–58.

PubMed  PubMed Central  Article  Google Scholar 

DeJesus-Hernandez M, Mackenzie IR, Boeve BF, Boxer AL, Baker M, Rutherford NJ, Nicholson AM, Finch NA, Flynn H, Adamson J, Kouri N, Wojtas A, Sengdy P, Hsiung GY, Karydas A, Seeley WW, Josephs KA, Coppola G, Geschwind DH, Wszolek ZK, Feldman H, Knopman DS, Petersen RC, Miller BL, Dickson DW, Boylan KB, Graff-Radford NR, Rademakers R. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 2011;72:245–56.

PubMed  PubMed Central  Article  Google Scholar 

Miller ZA, Sturm VE, Camsari GB, Karydas A, Yokoyama JS, Grinberg LT, Boxer AL, Rosen HJ, Rankin KP, Gorno-Tempini ML, Coppola G, Geschwind DH, Rademakers R, Seeley WW, Graff-Radford NR, Miller BL. Increased prevalence of autoimmune disease within C9 and FTD/MND cohorts: completing the picture. Neurol(R) Neuroimmunol Neuroinflammation. 2016;3:e301.

Article  Google Scholar 

Burberry A, Suzuki N, Wang JY, Moccia R, Mordes DA, Stewart MH, Suzuki-Uematsu S, Ghosh S, Singh A, Merkle FT, Koszka K, Li QZ, Zon L, Rossi DJ, Trowbridge JJ, Notarangelo LD, Eggan K. Loss-of-function mutations in the C9ORF72 mouse ortholog cause fatal autoimmune disease. Science Transl Med. 2016;8:347ra93.

Article  Google Scholar 

McCauley ME, O’Rourke JG, Yáñez A, Markman JL, Ho R, Wang X, Chen S, Lall D, Jin M, Muhammad A, Bell S, Landeros J, Valencia V, Harms M, Arditi M, Jefferies C, Baloh RH. C9orf72 in myeloid cells suppresses STING-induced inflammation. Nature. 2020;585:96–101.

PubMed  PubMed Central  Article  Google Scholar 

Fredi M, Cavazzana I, Biasiotto G, Filosto M, Padovani A, Monti E, Tincani A, Franceschini F, Zanella I. C9orf72 intermediate alleles in patients with amyotrophic lateral sclerosis, systemic lupus erythematosus, and rheumatoid arthritis. NeuroMol Med. 2019;21:150–9.

Article  Google Scholar 

Golubnitschaja O, Baban B, Boniolo G, Wang W, Bubnov R, Kapalla M, Krapfenbauer K, Mozaffari MS, Costigliola V. Medicine in the early twenty-first century: paradigm and anticipation - EPMA position paper 2016. EPMA J. 2016;7:23.

PubMed  PubMed Central  Article  Google Scholar 

Lu G, Hao X, Chen WH, Mu S. GAAD: a gene and autoimmiune disease association database. Genomics Proteomics Bioinformatics. 2018;16:252–61.

PubMed  PubMed Central  Article  Google Scholar 

Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, Furlong LI. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48:D845-d855.

PubMed  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.

PubMed  PubMed Central  Article  Google Scholar 

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics (Oxford England). 2012;28:882–3.

Article  Google Scholar 

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1:417–25.

PubMed  PubMed Central  Article  Google Scholar 

Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7.

PubMed  PubMed Central  Article  Google Scholar 

Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49:D605-d612.

PubMed  Article  Google Scholar 

Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics (Oxford England). 2010;26:1572–3.

Article  Google Scholar 

Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017;18:220.

PubMed  PubMed Central  Article  Google Scholar 

Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006;98:262–72.

PubMed  Article  Google Scholar 

Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D. The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Res. 2014;42:e133.

PubMed  PubMed Central  Article  Google Scholar 

Camu W, Mickunas M, Veyrune JL, Payan C, Garlanda C, Locati M, Juntas-Morales R, Pageot N, Malaspina A, Andreasson U, Kirby J, Suehs C, Saker S, Masseguin C, De Vos J, Zetterberg H, Shaw PJ, Al-Chalabi A, Leigh PN, Tree T, Bensimon G. Repeated 5-day cycles of low dose aldesleukin in amyotrophic lateral sclerosis (IMODALS): a phase 2a randomised, double-blind, placebo-controlled trial. EBioMedicine. 2020;59:102844.

PubMed  PubMed Central  Article  Google Scholar 

Rosen DR, Siddique T, Patterson D, Figlewicz DA, Sapp P, Hentati A, Donaldson D, Goto J, O’Regan JP, Deng HX, et al. Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis. Nature. 1993;362:59–62.

PubMed  Article  Google Scholar 

Gurney ME, Pu H, Chiu AY, Dal Canto MC, Polchow CY, Alexander DD, Caliendo J, Hentati A, Kwon YW, Deng HX, et al. Motor neuron degeneration in mice that express a human Cu, Zn superoxide dismutase mutation. Science (New York NY). 1994;264:1772–5.

Article  Google Scholar 

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411–20.

PubMed  PubMed Central  Article  Google Scholar 

Tian Y, Morris TJ, Webster AP, Yang Z, Beck S, Feber A, Teschendorff AE. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics (Oxford England). 2017;33:3982–4.

Article  Google Scholar 

Drachman DB, Kuncl RW. Amyotrophic lateral sclerosis: an unconventional autoimmune disease? Ann Neurol. 1989;26:269–74.

PubMed  Article  Google Scholar 

Appel SH, Smith RG, Engelhardt JI, Stefani E. Evidence for autoimmunity in amyotrophic lateral sclerosis. J Neurol Sci. 1994;124(Suppl):14–9.

PubMed  Article  Google Scholar 

Lu CH, Allen K, Oei F, Leoni E, Kuhle J, Tree T, Fratta P, Sharma N, Sidle K, Howard R, Orrell R, Fish M, Greensmith L, Pearce N, Gallo V, Malaspina A. Systemic inflammatory response and neuromuscular involvement in amyotrophic lateral sclerosis. Neurol(R) Neuroimmunol Neuroinflammation. 2016;3:e244.

Article  Google Scholar 

Rafiq MK, Lee E, Bradburn M, McDermott CJ, Shaw PJ. Creatine kinase enzyme level correlates positively with serum creatinine and lean body mass, and is a prognostic factor for survival in amyotrophic lateral sclerosis. Eur J Neurol. 2016;23:1071–8.

PubMed  Article  Google Scholar 

Moreno-Martínez L, de la Torre M, Toivonen JM, Zaragoza P, García-Redondo A, Calvo AC, Osta R. Circulating cytokines could not be good prognostic biomarkers in a mouse model of amyotrophic lateral sclerosis. Front Immunol. 2019;10:801.

PubMed  PubMed Central  Article  Google Scholar 

Murdock BJ, Zhou T, Kashlan SR, Little RJ, Goutman SA, Feldman EL. Correlation of peripheral immunity with rapid amyotrophic lateral sclerosis progression. JAMA Neurol. 2017;74:1446–54.

PubMed  PubMed Central  Article  Google Scholar 

Murdock BJ, Goutman SA, Boss J, Kim S, Feldman EL. Amyotrophic lateral sclerosis survival associates with neutrophils in a sex-specific manner. Neurol(R) Neuroimmunol Neuroinflammation. 2021;8

Murdock BJ, Famie JP, Piecuch CE, Raue KD, Mendelson FE, Pieroni CH, Iniguez SD, Zhao L, Goutman SA, Feldman EL. NK cells associate with ALS in a sex- and age-dependent manner. JCI insight. 2021;6.

Cui C, Ingre C, Yin L, Li X, Andersson J, Seitz C, Ruffin N, Pawitan Y, Piehl F and Fang F. Correlation between leukocyte phenotypes and prognosis of amyotrophic lateral sclerosis. ELife. 2022;11

Gadoth A, Nefussy B, Bleiberg M, Klein T, Artman I, Drory VE. Transglutaminase 6 antibodies in the serum of patients with amyotrophic lateral sclerosis. JAMA Neurol. 2015;72:676–81.

PubMed  Article  Google Scholar 

留言 (0)

沒有登入
gif