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Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease

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Abstract

We previously found C9orf72-associated (c9ALS) and sporadic amyotrophic lateral sclerosis (sALS) brain transcriptomes comprise thousands of defects, among which, some are likely key contributors to ALS pathogenesis. We have now generated complementary methylome data and combine these two data sets to perform a comprehensive “multi-omic” analysis to clarify the molecular mechanisms initiating RNA misregulation in ALS. We found that c9ALS and sALS patients have generally distinct but overlapping methylome profiles, and that the c9ALS- and sALS-affected genes and pathways have similar biological functions, indicating conserved pathobiology in disease. Our results strongly implicate SERPINA1 in both C9orf72 repeat expansion carriers and non-carriers, where expression levels are greatly increased in both patient groups across the frontal cortex and cerebellum. SERPINA1 expression is particularly pronounced in C9orf72 repeat expansion carriers for both brain regions, where SERPINA1 levels are strictly down regulated across most human tissues, including the brain, except liver and blood, and are not measurable in E18 mouse brain. The altered biological networks we identified contain critical molecular players known to contribute to ALS pathology, which also interact with SERPINA1. Our comprehensive combined methylation and transcription study identifies new genes and highlights that direct genetic and epigenetic changes contribute to c9ALS and sALS pathogenesis.

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References

  1. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A et al (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13:R87. doi:10.1186/gb-2012-13-10-r87

    Article  PubMed  PubMed Central  Google Scholar 

  2. Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008) The eukaryotic genome as an RNA machine. Science 319:1787–1789. doi:10.1126/science.1155472

    Article  CAS  PubMed  Google Scholar 

  3. Belzil VV, Bauer PO, Gendron TF, Murray ME, Dickson D, Petrucelli L (2014) Characterization of DNA hypermethylation in the cerebellum of c9FTD/ALS patients. Brain Res 1584:15–21. doi:10.1016/j.brainres.2014.02.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Belzil VV, Bauer PO, Prudencio M, Gendron TF, Stetler CT, Yan IK et al (2013) Reduced C9orf72 gene expression in c9FTD/ALS is caused by histone trimethylation, an epigenetic event detectable in blood. Acta Neuropathol 126:895–905. doi:10.1007/s00401-013-1199-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Belzil VV, Gendron TF, Petrucelli L (2012) RNA-mediated toxicity in neurodegenerative disease. Mol Cell Neurosci 56C:406–419. doi:10.1016/j.mcn.2012.12.006

    Google Scholar 

  6. Belzil VV, Katzman RB, Petrucelli L (2016) ALS and FTD: an epigenetic perspective. Acta Neuropathol. doi:10.1007/s00401-016-1587-4

    PubMed  PubMed Central  Google Scholar 

  7. Byrne S, Heverin M, Elamin M, Bede P, Lynch C, Kenna K et al (2013) Aggregation of neurologic and neuropsychiatric disease in amyotrophic lateral sclerosis kindreds: a population-based case-control cohort study of familial and sporadic amyotrophic lateral sclerosis. Ann Neurol 74:699–708. doi:10.1002/ana.23969

    Article  PubMed  Google Scholar 

  8. Byrne S, Walsh C, Lynch C, Bede P, Elamin M, Kenna K et al (2011) Rate of familial amyotrophic lateral sclerosis: a systematic review and meta-analysis. J Neurol Neurosurg Psychiatry 82:623–627. doi:10.1136/jnnp.2010.224501

    Article  PubMed  Google Scholar 

  9. Cox DW (2001) Alpha-1-antitrypsin. In: Scriver CRB, Sly AL, Valle D (eds) The metabolic and molecular bases of inherited disease, vol IV, 8th edn. McGraw-Hill, New York, pp 5559–5584

    Google Scholar 

  10. Donnelly CJ, Zhang PW, Pham JT, Haeusler AR, Mistry NA, Vidensky S et al (2013) RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron 80:415–428. doi:10.1016/j.neuron.2013.10.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Fratta P, Mizielinska S, Nicoll AJ, Zloh M, Fisher EM, Parkinson G et al (2012) C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes. Sci Rep 2:1016. doi:10.1038/srep01016

    Article  PubMed  PubMed Central  Google Scholar 

  12. Gendron TF, van Blitterswijk M, Bieniek KF, Daughrity LM, Jiang J, Rush BK et al (2015) Cerebellar c9RAN proteins associate with clinical and neuropathological characteristics of C9ORF72 repeat expansion carriers. Acta Neuropathol 130:559–573. doi:10.1007/s00401-015-1474-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Gibson SB, Figueroa KP, Bromberg MB, Pulst SM, Cannon-Albright L (2014) Familial clustering of ALS in a population-based resource. Neurology 82:17–22. doi:10.1212/01.wnl.0000438219.39061.da

    Article  PubMed  PubMed Central  Google Scholar 

  14. Guerreiro R, Bras J, Hardy J (2015) SnapShot: genetics of ALS and FTD. Cell 160(798):e791. doi:10.1016/j.cell.2015.01.052

    Google Scholar 

  15. Haeusler AR, Donnelly CJ, Periz G, Simko EA, Shaw PG, Kim MS et al (2014) C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature 507:195–200. doi:10.1038/nature13124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84. doi:10.1038/nrg3863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Jung J, Bonini N (2007) CREB-binding protein modulates repeat instability in a Drosophila model for polyQ disease. Science 315:1857–1859. doi:10.1126/science.1139517

    Article  CAS  PubMed  Google Scholar 

  18. Kalsheker NA (1996) Alpha 1-antichymotrypsin. Int J Biochem Cell Biol 28:961–964

    Article  CAS  PubMed  Google Scholar 

  19. Kamboh MI, Minster RL, Kenney M, Ozturk A, Desai PP, Kammerer CM et al (2006) Alpha-1-antichymotrypsin (ACT or SERPINA3) polymorphism may affect age-at-onset and disease duration of Alzheimer’s disease. Neurobiol Aging 27:1435–1439. doi:10.1016/j.neurobiolaging.2005.07.015

    Article  CAS  PubMed  Google Scholar 

  20. Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572. doi:10.1093/bioinformatics/btr167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lam L, Chin L, Halder RC, Sagong B, Famenini S, Sayre J et al (2016) Epigenetic changes in T-cell and monocyte signatures and production of neurotoxic cytokines in ALS patients. FASEB J. doi:10.1096/fj.201600259RR

    PubMed  PubMed Central  Google Scholar 

  22. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Liu EY, Russ J, Wu K, Neal D, Suh E, McNally AG et al (2014) C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD. Acta Neuropathol 128:525–541. doi:10.1007/s00401-014-1286-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009) RNA regulation of epigenetic processes. BioEssays 31:51–59. doi:10.1002/bies.080099

    Article  CAS  PubMed  Google Scholar 

  25. Morahan JM, Yu B, Trent RJ, Pamphlett R (2009) A genome-wide analysis of brain DNA methylation identifies new candidate genes for sporadic amyotrophic lateral sclerosis. Amyotroph Lateral Scler 10:418–429. doi:10.3109/17482960802635397

    Article  CAS  PubMed  Google Scholar 

  26. Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15:423–437. doi:10.1038/nrg3722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Nagase T, Nakayama M, Nakajima D, Kikuno R, Ohara O (2001) Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res 8:85–95

    Article  CAS  PubMed  Google Scholar 

  28. Neumann M, Sampathu DM, Kwong LK, Truax AC, Micsenyi MC, Chou TT et al (2006) Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314:130–133

    Article  CAS  PubMed  Google Scholar 

  29. Pace JM, Corrado M, Missero C, Byers PH (2003) Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1. Matrix Biol 22:3–14

    Article  CAS  PubMed  Google Scholar 

  30. Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G (2013) Enhancers: five essential questions. Nat Rev Genet 14:288–295. doi:10.1038/nrg3458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Polymenidou M, Lagier-Tourenne C, Hutt KR, Bennett CF, Cleveland DW, Yeo GW (2012) Misregulated RNA processing in amyotrophic lateral sclerosis. Brain Res 1462:3–15. doi:10.1016/j.brainres.2012.02.059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Prell T, Grosskreutz J (2013) The involvement of the cerebellum in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 14:507–515. doi:10.3109/21678421.2013.812661

    Article  CAS  PubMed  Google Scholar 

  33. Prudencio M, Belzil VV, Batra R, Ross CA, Gendron TF, Pregent LJ et al (2015) Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat Neurosci 18:1175–1182. doi:10.1038/nn.4065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Rademakers R, van Blitterswijk M (2013) Motor neuron disease in 2012: novel causal genes and disease modifiers. Nat Rev Neurol 9:63–64. doi:10.1038/nrneurol.2012.276

    Article  CAS  PubMed  Google Scholar 

  35. Renoux AJ, Todd PK (2012) Neurodegeneration the RNA way. Prog Neurobiol 97:173–189. doi:10.1016/j.pneurobio.2011.10.006

    Article  CAS  PubMed  Google Scholar 

  36. Renton AE, Chio A, Traynor BJ (2014) State of play in amyotrophic lateral sclerosis genetics. Nat Neurosci 17:17–23. doi:10.1038/nn.3584

    Article  CAS  PubMed  Google Scholar 

  37. Spitz F (2016) Gene regulation at a distance: from remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol. doi:10.1016/j.semcdb.2016.06.017

    PubMed  Google Scholar 

  38. Su Z, Zhang Y, Gendron TF, Bauer PO, Chew J, Yang WY et al (2014) Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS. Neuron 83:1043–1050. doi:10.1016/j.neuron.2014.07.041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Tan RH, Kril JJ, McGinley C, Hassani M, Masuda-Suzukake M, Hasegawa M et al (2016) Cerebellar neuronal loss in amyotrophic lateral sclerosis cases with ATXN2 intermediate repeat expansions. Ann Neurol 79:295–305. doi:10.1002/ana.24565

    Article  CAS  PubMed  Google Scholar 

  40. Therrien M, Dion PA, Rouleau GA (2016) ALS: recent Developments from Genetics Studies. Curr Neurol Neurosci Rep 16:59. doi:10.1007/s11910-016-0658-1

    Article  PubMed  Google Scholar 

  41. Wang YC, Liu HC, Liu TY, Hong CJ, Tsai SJ (2001) Genetic association analysis of alpha-1-antichymotrypsin polymorphism in Parkinson’s disease. Eur Neurol 45:254–256. doi:10.1159/000052138

  42. Xi Z, Rainero I, Rubino E, Pinessi L, Bruni AC, Maletta RG et al (2014) Hypermethylation of the CpG-island near the C9orf72 G4C2-repeat expansion in FTLD patients. Hum Mol Genet. doi:10.1093/hmg/ddu279

    PubMed  Google Scholar 

  43. Xi Z, Yunusova Y, van Blitterswijk M, Dib S, Ghani M, Moreno D et al (2014) Identical twins with the C9orf72 repeat expansion are discordant for ALS. Neurology 83:1476–1478. doi:10.1212/WNL.0000000000000886

    Article  PubMed  PubMed Central  Google Scholar 

  44. Xi Z, Zhang M, Bruni AC, Maletta RG, Colao R, Fratta P et al (2015) The C9orf72 repeat expansion itself is methylated in ALS and FTLD patients. Acta Neuropathol 129:715–727. doi:10.1007/s00401-015-1401-8

    Article  CAS  PubMed  Google Scholar 

  45. Xi Z, Zinman L, Moreno D, Schymick J, Liang Y, Sato C et al (2013) Hypermethylation of the CpG island near the G4C2 repeat in ALS with a C9orf72 expansion. Am J Hum Genet 92:981–989. doi:10.1016/j.ajhg.2013.04.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Zeng Q, Subramaniam VN, Wong SH, Tang BL, Parton RG, Rea S et al (1998) A novel synaptobrevin/VAMP homologous protein (VAMP5) is increased during in vitro myogenesis and present in the plasma membrane. Mol Biol Cell 9:2423–2437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Zhang K, Donnelly CJ, Haeusler AR, Grima JC, Machamer JB, Steinwald P et al (2015) The C9orf72 repeat expansion disrupts nucleocytoplasmic transport. Nature 525:56–61. doi:10.1038/nature14973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We are extremely grateful to all individuals who agreed to donate their brains to research. This study was supported by the National Institutes of Health/National Institute on Aging [AG16574-17 J PILOT (V.V.B.)]; National Institutes of Health/National Institute of Neurological Disorders and Stroke [R21NS074121 (K.B.B.), P01NS084974 (D.W.D., K.B.B., and R.R.]; Mayo Clinic Center for Individualized Medicine (V.V.B., K.B.B., and H.L.); ALS Association (K.B.B.), Donors Cure Foundation (H.L.), and the Robert Packard Center for ALS Research at Johns Hopkins. V.V.B. is recipient of the Career Transition Award from ALS Canada and Brain Canada, the Milton Safenowitz Post-Doctoral Fellowship from the Amyotrophic Lateral Sclerosis Association, the Post-Doctoral Fellowship from the Canadian Institutes of Health Research, the Career Development Award for Young Investigators in Neurosciences from the Siragusa Foundation, and the Research Fellowship from the Robert and Clarice Smith & Abigail Van Buren Alzheimer’s Disease Research Foundation. M.T.W.E received the PhRMA Foundation Research Starter grant.

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Authors and Affiliations

  1. Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA

    Mark T. W. Ebbert, Luc J. Pregent, Rebecca J. Lank, Rebecca B. Katzman, Karen Jansen-West, Yuping Song, Dennis W. Dickson, Rosa Rademakers & Veronique V. Belzil

  2. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA

    Christian A. Ross, Cheng Zhang, Edroaldo Lummertz da Rocha & Hu Li

  3. Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA

    Carla Palmucci, Pamela Desaro, Amelia E. Robertson, Ana M. Caputo & Kevin B. Boylan

  4. Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA

    Tamas Ordog

  5. Department of Physiology and Medical Engineering, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA

    Tamas Ordog

  6. Stem Cell Transplantation Program, Department of Pediatric Hematology and Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA, USA

    Edroaldo Lummertz da Rocha

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  1. Mark T. W. Ebbert
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  19. Veronique V. Belzil
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Correspondence to Hu Li or Veronique V. Belzil.

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Ebbert, M.T.W., Ross, C.A., Pregent, L.J. et al. Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease. Acta Neuropathol 134, 715–728 (2017). https://doi.org/10.1007/s00401-017-1760-4

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