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Defining Trends in Global Gene Expression in Arabian Horses with Cerebellar Abiotrophy

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Abstract

Equine cerebellar abiotrophy (CA) is a hereditary neurodegenerative disease that affects the Purkinje neurons of the cerebellum and causes ataxia in Arabian foals. Signs of CA are typically first recognized either at birth to any time up to 6 months of age. CA is inherited as an autosomal recessive trait and is associated with a single nucleotide polymorphism (SNP) on equine chromosome 2 (13074277G>A), located in the fourth exon of TOE1 and in proximity to MUTYH on the antisense strand. We hypothesize that unraveling the functional consequences of the CA SNP using RNA-seq will elucidate the molecular pathways underlying the CA phenotype. RNA-seq (100 bp PE strand-specific) was performed in cerebellar tissue from four CA-affected and five age-matched unaffected horses. Three pipelines for differential gene expression (DE) analysis were used (Tophat2/Cuffdiff2, Kallisto/EdgeR, and Kallisto/Sleuth) with 151 significant DE genes identified by all three pipelines in CA-affected horses. TOE1 (Log2(foldchange) = 0.92, p = 0.66) and MUTYH (Log2(foldchange) = 1.13, p = 0.66) were not differentially expressed. Among the major pathways that were differentially expressed, genes associated with calcium homeostasis and specifically expressed in Purkinje neurons, CALB1 (Log2(foldchange) = −1.7, p < 0.01) and CA8 (Log2(foldchange) = −0.97, p < 0.01), were significantly down-regulated, confirming loss of Purkinje neurons. There was also a significant up-regulation of markers for microglial phagocytosis, TYROBP (Log2(foldchange) = 1.99, p < 0.01) and TREM2 (Log2(foldchange) = 2.02, p < 0.01). These findings reaffirm a loss of Purkinje neurons in CA-affected horses along with a potential secondary loss of granular neurons and activation of microglial cells.

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References

  1. de Lahunta A. Abiotrophy in domestic animals: a review. Can J Vet Res. 1990;54(1):65–76.

    PubMed  PubMed Central  Google Scholar 

  2. Koehler JW, Newcomer BW, Holland M, Caldwell JM. A novel inherited cerebellar abiotrophy in a cohort of related goats. J Comp Pathol. 2015;153(2–3):135–9.

    Article  CAS  PubMed  Google Scholar 

  3. Sato J, Yamada N, Kobayashi R, Tsuchitani M, Kobayashi Y. Morphometric analysis of progressive changes in hereditary cerebellar cortical degenerative disease (abiotrophy) in rabbits caused by abnormal synaptogenesis. J Toxicol Pathol. 2015;28(2):73–8.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Shearman JR, Cook RW, McCowan C, Fletcher JL, Taylor RM, Wilton AN. Mapping cerebellar abiotrophy in Australian kelpies. Anim Genet. 2011;42(6):675–8.

    Article  CAS  PubMed  Google Scholar 

  5. DeBowes RM, Leipold HW, Turner-Beatty M. Cerebellar abiotrophy. Vet Clin North Am Equine Pract. 1987;3(2):345–52.

    CAS  PubMed  Google Scholar 

  6. Blanco A, Moyano R, Vivo J, Flores-Acuna R, Molina A, Blanco C, et al. Purkinje cell apoptosis in Arabian horses with cerebellar abiotrophy. J Vet Med A Physiol Pathol Clin Med. 2006;53(6):286–7.

    Article  CAS  PubMed  Google Scholar 

  7. Cavalleri JM, Metzger J, Hellige M, Lampe V, Stuckenschneider K, Tipold A, et al. Morphometric magnetic resonance imaging and genetic testing in cerebellar abiotrophy in Arabian horses. BMC Vet Res. 2013;9:105.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Palmer AC, Blakemore WF, Cook WR, Platt H, Whitwell KE. Cerebellar hypoplasia and degeneration in the young Arab horse: clinical and neuropathological features. Vet Rec. 1973;93(3):62–6.

    Article  CAS  PubMed  Google Scholar 

  9. Brault LS, Cooper CA, Famula TR, Murray JD, Penedo MC. Mapping of equine cerebellar abiotrophy to ECA2 and identification of a potential causative mutation affecting expression of MUTYH. Genomics. 2011;97(2):121–9.

    Article  CAS  PubMed  Google Scholar 

  10. Brault LS, Famula TR, Penedo MC. Inheritance of cerebellar abiotrophy in Arabians. Am J Vet Res. 2011;72(7):940–4.

    Article  PubMed  Google Scholar 

  11. Wagner E, Clement SL, Lykke-Andersen J. An unconventional human Ccr4-Caf1 deadenylase complex in nuclear cajal bodies. Mol Cell Biol. 2007;27(5):1686–95.

    Article  CAS  PubMed  Google Scholar 

  12. Zheng D, Ezzeddine N, Chen CY, Zhu W, He X, Shyu AB. Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. J Cell Biol. 2008;182(1):89–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Machyna M, Heyn P, Neugebauer KM. Cajal bodies: where form meets function. Wiley Interdiscip Rev RNA. 2013;4(1):17–34.

    Article  CAS  PubMed  Google Scholar 

  14. Parker R, Sheth UP. Bodies and the control of mRNA translation and degradation. Mol Cell. 2007;25(5):635–46.

    Article  CAS  PubMed  Google Scholar 

  15. Cougot N, Bhattacharyya SN, Tapia-Arancibia L, Bordonne R, Filipowicz W, Bertrand E, et al. Dendrites of mammalian neurons contain specialized P-body-like structures that respond to neuronal activation. J Neurosci. 2008;28(51):13793–804.

    Article  CAS  PubMed  Google Scholar 

  16. Baltanas FC, Casafont I, Weruaga E, Alonso JR, Berciano MT, Lafarga M. Nucleolar disruption and cajal body disassembly are nuclear hallmarks of DNA damage-induced neurodegeneration in purkinje cells. Brain Pathol. 2011;21(4):374–88.

    Article  CAS  PubMed  Google Scholar 

  17. Oka S, Ohno M, Tsuchimoto D, Sakumi K, Furuichi M, Nakabeppu Y. Two distinct pathways of cell death triggered by oxidative damage to nuclear and mitochondrial DNAs. EMBO J. 2008;27(2):421–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lee HM, Hu Z, Ma H, Greeley Jr GH, Wang C, Englander EW. Developmental changes in expression and subcellular localization of the DNA repair glycosylase, MYH, in the rat brain. J Neurochem. 2004;88(2):394–400.

  19. Sheng Z, Oka S, Tsuchimoto D, Abolhassani N, Nomaru H, Sakumi K, et al. 8-Oxoguanine causes neurodegeneration during MUTYH-mediated DNA base excision repair. J Clin Invest. 2012;122(12):4344–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Plotz G, Casper M, Raedle J, Hinrichsen I, Heckel V, Brieger A, et al. MUTYH gene expression and alternative splicing in controls and polyposis patients. Hum Mutat. 2012;33(7):1067–74.

    Article  CAS  PubMed  Google Scholar 

  21. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Wu D, Lim E, Vaillant F, Asselin-Labat ML, Visvader JE, Smyth GK. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics. 2010;26(17):2176–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420(6915):563–73.

    Article  PubMed  Google Scholar 

  24. Joshi NAJNF. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files 2011 [cited (Version 1.33)]. Software]. Available from: https://github.com/najoshi/sickle.

  25. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Bray N, Pimentel, H., Melsted, P. & Lior, Pachter. Near-optimal RNA-Seq quantification. 2015;arXiv:1505.02710.

  27. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31(1):46–53.

    Article  CAS  PubMed  Google Scholar 

  28. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.

    Article  CAS  PubMed  Google Scholar 

  29. Team RDC. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistcal Computing; 2010.

  30. Kuhn A, Kumar A, Beilina A, Dillman A, Cookson MR, Singleton AB. Cell population-specific expression analysis of human cerebellum. BMC Genomics. 2012:13:610.

  31. Kirsch L, Liscovitch N, Chechik G. Localizing genes to cerebellar layers by classifying ISH images. PLoS Comput Biol. 2012;8(12):e1002790.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Bettencourt C, Ryten M, Forabosco P, Schorge S, Hersheson J, Hardy J, et al. Insights from cerebellar transcriptomic analysis into the pathogenesis of ataxia. JAMA Neurol. 2014;71(7):831–9.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016;44(D1):D336–42.

    Article  PubMed  Google Scholar 

  34. Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013;8(8):1551–66.

    Article  PubMed  Google Scholar 

  35. D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, et al. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008;9:66.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Shen EH, Overly CC, Jones AR. The Allen human brain atlas: comprehensive gene expression mapping of the human brain. Trends Neurosci. 2012;35(12):711–4.

    Article  CAS  PubMed  Google Scholar 

  37. Biolatti C, Gianella P, Capucchio MT, Borrelli A, D'Angelo A. Late onset and rapid progression of cerebellar abiotrophy in a domestic shorthair cat. J Small Anim Pract. 2010;51(2):123–6.

    Article  CAS  PubMed  Google Scholar 

  38. Forman OP, De Risio L, Matiasek K, Platt S, Mellersh C. Spinocerebellar ataxia in the Italian Spinone dog is associated with an intronic GAA repeat expansion in ITPR1. Mamm Genome. 2015;26(1–2):108–17.

    Article  CAS  PubMed  Google Scholar 

  39. Sato J, Sasaki S, Yamada N, Tsuchitani M. Hereditary cerebellar degenerative disease (cerebellar cortical abiotrophy) in rabbits. Vet Pathol. 2012;49(4):621–8.

    Article  CAS  PubMed  Google Scholar 

  40. Whittington RJ, Morton AG, Kennedy DJ. Cerebellar abiotrophy in crossbred cattle. Aust Vet J. 1989;66(1):12–5.

    Article  CAS  PubMed  Google Scholar 

  41. Forabosco P, Ramasamy A, Trabzuni D, Walker R, Smith C, Bras J, et al. Insights into TREM2 biology by network analysis of human brain gene expression data. Neurobiol Aging. 2013;34(12):2699–714.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Block ML, Hong JS. Microglia and inflammation-mediated neurodegeneration: multiple triggers with a common mechanism. Prog Neurobiol. 2005;76(2):77–98.

    Article  CAS  PubMed  Google Scholar 

  43. Cvetanovic M, Ingram M, Orr H, Opal P. Early activation of microglia and astrocytes in mouse models of spinocerebellar ataxia type 1. Neuroscience. 2015;289:289–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Guillot-Sestier MV, Doty KR, Gate D, Rodriguez Jr J, Leung BP, Rezai-Zadeh K, et al. Il10 deficiency rebalances innate immunity to mitigate Alzheimer-like pathology. Neuron. 2015;85(3):534–48.

  45. LE F, Tirolo C, Testa N, Caniglia S, Morale MC, Marchetti B. Glia as a turning point in the therapeutic strategy of Parkinson's disease. CNS Neurol Disord Drug Targets. 2010;9(3):349–72.

    Article  Google Scholar 

  46. Sultan M, Amstislavskiy V, Risch T, Schuette M, Dokel S, Ralser M, et al. Influence of RNA extraction methods and library selection schemes on RNA-seq data. BMC Genomics. 2014;15:675.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Papadimitriou D, Le Verche V, Jacquier A, Ikiz B, Przedborski S, Re DB. Inflammation in ALS and SMA: sorting out the good from the evil. Neurobiol Dis. 2010;37(3):493–502.

    Article  CAS  PubMed  Google Scholar 

  48. Kaya N, Aldhalaan H, Al-Younes B, Colak D, Shuaib T, Al-Mohaileb F, et al. Phenotypical spectrum of cerebellar ataxia associated with a novel mutation in the CA8 gene, encoding carbonic anhydrase (CA) VIII. Am J Med Genet B Neuropsychiatr Genet. 2011;156B(7):826–34.

    Article  PubMed  Google Scholar 

  49. Hirota J, Ando H, Hamada K, Mikoshiba K. Carbonic anhydrase-related protein is a novel binding protein for inositol 1,4,5-trisphosphate receptor type 1. Biochem J. 2003;372(Pt 2):435–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Okubo Y, Suzuki J, Kanemaru K, Nakamura N, Shibata T, Iino M. Visualization of Ca2+ filling mechanisms upon synaptic inputs in the endoplasmic reticulum of cerebellar Purkinje cells. J Neurosci. 2015;35(48):15837–46.

    Article  CAS  PubMed  Google Scholar 

  51. Paxinos G. Cerebellum and Cerebellar Connections. In: Science E, editor. The Rat Nervous System. 4th ed. Burlington: Elsevier Science; 2014. p. 1053.

  52. Anderson WA, Flumerfelt BA. Long-term effects of parallel fiber loss in the cerebellar cortex of the adult and weanling rat. Brain Res. 1986;383(1–2):245–61.

    Article  CAS  PubMed  Google Scholar 

  53. Neuman T, Keen A, Zuber MX, Kristjansson GI, Gruss P, Nornes HO. Neuronal expression of regulatory helix-loop-helix factor Id2 gene in mouse. Dev Biol. 1993;160(1):186–95.

    Article  CAS  PubMed  Google Scholar 

  54. Sullivan JM, Havrda MC, Kettenbach AN, Paolella BR, Zhang Z, Gerber SA, et al. Phosphorylation regulates Id2 degradation and mediates the proliferation of neural precursor cells. Stem Cells. 2016;34(5):1321–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Cho DH, Hong YM, Lee HJ, Woo HN, Pyo JO, Mak TW, et al. Induced inhibition of ischemic/hypoxic injury by APIP, a novel Apaf-1-interacting protein. J Biol Chem. 2004;279(38):39942–50.

    Article  CAS  PubMed  Google Scholar 

  56. Ko DC, Gamazon ER, Shukla KP, Pfuetzner RA, Whittington D, Holden TD, et al. Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. Proc Natl Acad Sci U S A. 2012;109(35):E2343–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This project was funded in part by the Arabian Horse Foundation as well as the Animal Science Department and Veterinary Genetics Laboratory, University of California, Davis. Samples were provided by private donors and University of Pennsylavania, Colorado State University, and University of Kentucky. Additional acknowledgements to Dr. Tamer Mansour for his valuable advice concerning bioinformatics and Dr. Rebecca Bellone for overall critique of the project.

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Authors and Affiliations

  1. Department of Animal Science, University of California, Davis, USA

    E. Y. Scott & J. D. Murray

  2. Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, USA

    M. C. T. Penedo

  3. Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, USA

    M. C. T. Penedo, J. D. Murray & C. J. Finno

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  1. E. Y. Scott
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Scott, E.Y., Penedo, M.C.T., Murray, J.D. et al. Defining Trends in Global Gene Expression in Arabian Horses with Cerebellar Abiotrophy. Cerebellum 16, 462–472 (2017). https://doi.org/10.1007/s12311-016-0823-8

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