Investigating cell death mechanisms in amyotrophic lateral sclerosis using transcriptomics

Frontiers in Cellular Neuroscience

Volumn 7, Issue DEC, 2013, Pages

  Heath, Paul R ^a   Kirby, Janine ^a   Shaw, Pamela J ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Amyotrophic lateral sclerosis; Cell death; Microarray; Transcriptomics

Indexed keywords

APOLIPOPROTEIN E; EPIDERMAL GROWTH FACTOR RECEPTOR; FERRITIN; NERVE GROWTH FACTOR;

AMYOTROPHIC LATERAL SCLEROSIS; CELL CYCLE REGULATION; CELL DEATH; CELL MIGRATION; CELL PROLIFERATION; DISEASE COURSE; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; PROTEIN EXPRESSION; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; UPREGULATION;

EID: 84890872365     PISSN: 16625102     EISSN: None     Source Type: Journal    
DOI: 10.3389/fncel.2013.00259     Document Type: Review

References (56)

1. Baciu, C., Thompson, K. J., Mougeot, J. L., Brooks, B. R., and Weller, J. W. (2012). The LO-BaFL method and ALS microarray expression analysis. BMC Bioinformatics 13:244. doi: 10.1186/1471-2105-13-244
2. Baumer, D., Ansorge, O., Almeida, M., and Talbot, K. (2010). The role of RNA processing in the pathogenesis of motor neuron degeneration. Expert Rev. Mol. Med. 12, e21. doi: 10.1017/S1462399410001523
3. Bernardini, C., Censi, F., Lattanzi, W., Barba, M., Calcagnini, G., Giuliani, A., et al. (2013). Mitochondrial network genes in the skeletal muscle of amyotrophic lateral sclerosis patients. PLoS One 8:e57739. doi: 10.1371/journal.pone. 0057739
4. Bolstad, B. M., Collin, F., Simpson, K. M., Irizarry, R. A., and Speed, T. P. (2004). Experimental design and low-level analysis of microarray data. Int. Rev. Neurobiol. 60, 25-58. doi: 10.1016/s0074-7742(04)60002-x
5. Boutahar, N., Wierinckx, A., Camdessanche, J. P., Antoine, J. C., Reynaud, E., and Lassabliere, F. (2011). Differential effect of oxidative or excitotoxic stress on the transcriptional profile of amyotrophic lateral sclerosis-linked mutant SOD1 cultured neurons. J. Neurosci. Res. 89, 1439-1450. doi: 10.1002/jnr.22672
6. Brockington, A., Ning, K., Heath, P. R., Wood, E., Kirby, J., Fusi, N., et al. (2013). Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity. Acta Neuropathol. 125, 95-109. doi: 10.1007/s00401-012-1058-5
7. Chen, H., Guo, Y., Hu, M., Duan, W., Chang, G., and Li, C. (2010). Differential expression and alternative splicing of genes in lumbar spinal cord of an amyotrophic lateral sclerosis mouse model. Brain Res. 1340, 52-69. doi: 10.1016/j. brainres.2010.03.075
8. Clark, T. A., Schweitzer, A. C., Chen, T. X., Staples, M. K., Lu, G., Wang, H., et al. (2007). Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol. 8, R64. doi: 10.1186/gb-2007-8-4-r64
9. Copois, V., Bibeau, F., Bascoul-Mollevi, C., Salvetat, N., Chalbos, P., Bareil, C., et al. (2007). Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J. Biotechnol. 127, 549-559. doi: 10.1016/j.jbiotec.2006.07.032
10. Cox, L. E., Ferraiuolo, L., Goodall, E. F., Heath, P. R., Higginbottom, A., Mortiboys, H., et al. (2010). Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). PLoS One 5:e9872. doi: 10.1371/journal. pone.0009872
11. Dangond, F., Hwang, D., Camelo, S., Pasinelli, P., Frosch, M. P., Stephanopoulos, G., et al. (2004). Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter. Physiol. Genomics 16, 229-239. doi: 10.1152/physiolgenomics.00087.2001
12. Dupuis, L., and Loeffler, J. P. (2009). Neuromuscular junction destruction during amyotrophic lateral sclerosis: insights from transgenic models. Curr. Opin. Pharmacol. 9, 341-346. doi: 10.1016/j.coph.2009.03.007
13. Durrenberger, P. F., Filiou, M. D., Moran, L. B., Michael, G. J., Novoselov, S., Cheetham, M. E., et al. (2009). DnaJB6 is present in the core of Lewy bodies and is highly up-regulated in parkinsonian astrocytes. J. Neurosci. Res. 87, 238-245. doi: 10.1002/jnr.21819
14. Egawa, N., Kitaoka, S., Tsukita, K., Naitoh, M., Takahashi, K., Yamamoto, T., et al. (2012). Drug screening for ALS using patient-specific induced pluripotent stem cells. Sci. Transl. Med. 4, 145ra104. doi: 10.1126/scitranslmed.3004052
15. Ferraiuolo, L., De Bono, J. P., Heath, P. R., Holden, H., Kasher, P., Channon, K. M., et al. (2009). Transcriptional response of the neuromuscular system to exercise training and potential implications for ALS. J. Neurochem. 109, 1714-1724. doi: 10.1111/j.1471-4159.2009.06080.x
16. Ferraiuolo, L., Heath, P. R., Holden, H., Kasher, P., Kirby, J., and Shaw, P. J. (2007). Microarray analysis of the cellular pathways involved in the adaptation to and progression of motor neuron injury in the SOD1 G93A mouse model of familial ALS. J. Neurosci. 27, 9201-9219. doi: 10.1523/jneurosci.1470-07.2007
17. Ferraiuolo, L., Higginbottom, A., Heath, P. R., Barber, S., Greenald, D., Kirby, J., et al. (2011). Dysregulation of astrocyte-motoneuron cross-talk in mutant superoxide dismutase 1-related amyotrophic lateral sclerosis. Brain 134, 2627-2641. doi: 10.1093/brain/awr193
18. Figueroa-Romero, C., Hur, J., Bender, D. E., Delaney, C. E., Cataldo, M. D., Smith, A. L., et al. (2012). Identification of epigenetically altered genes in sporadic amyotrophic lateral sclerosis. PLoS One 7:e52672. doi: 10.1371/journal.pone. 0052672
19. Fukada, Y., Yasui, K., Kitayama, M., Doi, K., Nakano, T., Watanabe, Y., et al. (2007). Gene expression analysis of the murine model of amyotrophic lateral sclerosis: studies of the Leu126delTT mutation in SOD1. Brain Res. 1160, 1-10. doi: 10.1016/j.brainres.2007.05.044
20. Harrison, P. J., Heath, P. R., Eastwood, S. L., Burnet, P. W., Mcdonald, B., and Pearson, R. C. (1995). The relative importance of premortem acidosis and postmortem interval for human brain gene expression studies: selective mRNA vulnerability and comparison with their encoded proteins. Neurosci. Lett. 200, 151-154. doi: 10.1016/0304-3940(95)12102-a
21. Hashimoto, K., Honda, A., Hayashi, Y., Inuzuka, T., Satoh, M., and Hozumi, I. (2009). DNA microarray analysis of transcriptional responses of mouse spinal cords to physical exercise. J. Toxicol. Sci. 34, 445-448. doi: 10.2131/jts.34.445
22. Hedlund, E., Karlsson, M., Osborn, T., Ludwig, W., and Isacson, O. (2010). Global gene expression profiling of somatic motor neuron populations with different vulnerability identify molecules and pathways of degeneration and protection. Brain 133, 2313-2330. doi: 10.1093/brain/awq167
23. Henriques, A., and Gonzalez De Aguilar, J. L. (2011). Can transcriptomics cut the gordian knot of amyotrophic lateral sclerosis? Curr. Genomics 12, 506-515. doi: 10.2174/138920211797904043
24. Hu, M., Guo, Y., Chen, H., Duan, W., and Li, C. (2013). Exon array analysis of alternative splicing of genes in SOD1G93A transgenic mice. Appl. Biochem. Biotechnol. 170, 301-319. doi: 10.1007/s12010-013-0155-9
25. Huang da, W., Sherman, B. T., and Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57. doi: 10.1038/nprot.2008.211
26. Ince, P. G., Highley, J. R., Kirby, J., Wharton, S. B., Takahashi, H., Strong, M. J., et al. (2011). Molecular pathology and genetic advances in amyotrophic lateral sclerosis: an emerging molecular pathway and the significance of glial pathology. Acta Neuropathol. 122, 657-671. doi: 10.1007/s00401-011-0913-0
27. Ishigaki, S., Niwa, J., Ando, Y., Yoshihara, T., Sawada, K., Doyu, M., et al. (2002). Differentially expressed genes in sporadic amyotrophic lateral sclerosis spinal cords-screening by molecular indexing and subsequent cDNA microarray analysis. FEBS Lett. 531, 354-358. doi: 10.1016/s0014-5793(02)03546-9
28. Jiang, Y. M., Yamamoto, M., Kobayashi, Y., Yoshihara, T., Liang, Y., Terao, S., et al. (2005). Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis. Ann. Neurol. 57, 236-251. doi: 10.1002/ana.20379
29. Kannanayakal, T. J., and Eberwine, J. (2005). mRNA methods used in dissecting gene expression of the brain. Ageing Res. Rev. 4, 513-528. doi: 10.1016/j.arr.2005. 09.001
30. Kirby, J., Halligan, E., Baptista, M. J., Allen, S., Heath, P. R., Holden, H., et al. (2005). Mutant SOD1 alters the motor neuronal transcriptome: implications for familial ALS. Brain 128, 1686-1706. doi: 10.1093/brain/awh503
31. Kirby, J., Heath, P. R., Shaw, P. J., and Hamdy, F. C. (2007). Gene expression assays. Adv. Clin. Chem. 44, 247-292. doi: 10.1016/s0065-2423(07)44008-2
32. Kirby, J., Menzies, F. M., Cookson, M. R., Bushby, K., and Shaw, P. J. (2002). Differential gene expression in a cell culture model of SOD1-related familial motor neurone disease. Hum. Mol. Genet. 11, 2061-2075. doi: 10.1093/hmg/11.17.2061
33. Kirby, J., Ning, K., Ferraiuolo, L., Heath, P. R., Ismail, A., Kuo, S. W., et al. (2011). Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis. Brain 134, 506-517. doi: 10.1093/brain/awq345
34. Kogenaru, S., Qing, Y., Guo, Y., and Wang, N. (2012). RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics 13:629. doi: 10.1186/1471-2164-13-629
35. Kudo, L. C., Parfenova, L., Vi, N., Lau, K., Pomakian, J., Valdmanis, P., et al. (2010). Integrative gene-tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis. Hum. Mol. Genet. 19, 3233-3253. doi: 10.1093/hmg/ddq232
36. Kumimoto, E. L., Fore, T. R., and Zhang, B. (2013). Transcriptome profiling following neuronal and glial expression of ALS-linked SOD1 in Drosophila. G3 (Bethesda). doi: 10.1534/g3.113.005850. [Epub ahead of print].
37. Lederer, C. W., Torrisi, A., Pantelidou, M., Santama, N., and Cavallaro, S. (2007). Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis. BMC Genomics 8:26. doi: 10.1186/1471-2164-8-26
38. Malaspina, A., Kaushik, N., and De Belleroche, J. (2001). Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays. J. Neurochem. 77, 132-145. doi: 10.1046/j.1471-4159.2001. 00231.x
39. Mead, R. J., Higginbottom, A., Allen, S. P., Kirby, J., Bennett, E., Barber, S. C., et al. (2013). S[+] Apomorphine is a CNS penetrating activator of the Nrf2-ARE pathway with activity in mouse and patient fibroblast models of amyotrophic lateral sclerosis. Free Radic. Biol. Med. doi: 10.1016/j.freeradbiomed.2013.04. 018. [Epub ahead of print].
40. Mougeot, J. L., Li, Z., Price, A. E., Wright, F. A., and Brooks, B. R. (2011). Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway. BMC Med. Genomics 4:74. doi: 10.1186/1755-8794-4-74
41. Offen, D., Barhum, Y., Melamed, E., Embacher, N., Schindler, C., and Ransmayr, G. (2009). Spinal cord mRNA profile in patients with ALS: comparison with transgenic mice expressing the human SOD-1 mutant. J. Mol. Neurosci. 38, 85-93. doi: 10.1007/s12031-007-9004-z
42. Okaty, B. W., Sugino, K., and Nelson, S. B. (2011). Cell type-specific transcrip-tomics in the brain. J. Neurosci. 31, 6939-6943. doi: 10.1523/jneurosci.0626-11. 2011
43. Perrin, F. E., Boisset, G., Docquier, M., Schaad, O., Descombes, P., and Kato, A. C. (2005). No widespread induction of cell death genes occurs in pure motoneurons in an amyotrophic lateral sclerosis mouse model. Hum. Mol. Genet. 14, 3309-3320. doi: 10.1093/hmg/ddi357
44. Popova, T., Mennerich, D., Weith, A., and Quast, K. (2008). Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. BMC Genomics 9:91. doi: 10.1186/1471-2164-9-91
45. Preece, P., Virley, D. J., Costandi, M., Coombes, R., Moss, S. J., Mudge, A. W., et al. (2003). An optimistic view for quantifying mRNA in post-mortem human brain. Brain Res. Mol. Brain Res. 116, 7-16. doi: 10.1016/s0169-328x(03)00208-0
46. Rosenfeld, S. (2010). Do DNA microarrays tell the story of gene expression? Gene Regul. Syst. Bio. 4, 61-73. doi: 10.4137/grsb.s4657
47. Saris, C. G., Groen, E. J., Koekkoek, J. A., Veldink, J. H., and Van Den Berg, L. H. (2013). Meta-analysis of gene expression profiling in amyotrophic lateral sclerosis: a comparison between transgenic mouse models and human patients. Amyotroph. Lateral Scler. Frontotemporal Degener. 14, 177-189. doi: 10.3109/21678421.2012.729842
48. Saris, C. G., Horvath, S., Van Vught, P. W., Van Es, M. A., Blauw, H. M., Fuller, T. F., et al. (2009). Weighted gene co-expression network analysis of the peripheral blood from amyotrophic lateral sclerosis patients. BMC Genomics 10:405. doi: 10.1186/1471-2164-10-405
49. Saxena, S., Cabuy, E., and Caroni, P. (2009). A role for motoneuron subtype-selective ER stress in disease manifestations of FALS mice. Nat. Neurosci. 12, 627-636. doi: 10.1038/nn.2297
50. Shtilbans, A., Choi, S. G., Fowkes, M. E., Khitrov, G., Shahbazi, M., Ting, J., et al. (2011). Differential gene expression in patients with amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. 12, 250-256. doi: 10.3109/17482968.2011. 560946
51. Tomita, H., Vawter, M. P., Walsh, D. M., Evans, S. J., Choudary, P. V., Li, J., et al. (2004). Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol. Psychiatry 55, 346-352. doi: 10.1016/j.biopsych.2003.10.013
52. Trabzuni, D., Ryten, M., Walker, R., Smith, C., Imran, S., Ramasamy, A., et al. (2011). Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies. J. Neurochem. 119, 275-282. doi: 10.1111/j.1471-4159.2011.07432.x
53. Vargas, M. R., Pehar, M., Diaz-Amarilla, P. J., Beckman, J. S., and Barbeito, L. (2008). Transcriptional profile of primary astrocytes expressing ALS-Transcriptomics in ALS research linked mutant SOD1. J. Neurosci. Res. 86, 3515-3525. doi: 10.1002/jnr. 21797
54. Wang, X. S., Simmons, Z., Liu, W., Boyer, P. J., and Connor, J. R. (2006). Differential expression of genes in amyotrophic lateral sclerosis revealed by profiling the post mortem cortex. Amyotroph. Lateral Scler. 7, 201-210. doi: 10.1080/17482960600947689
55. Wilkes, T. M., Devonshire, A. S., Ellison, S. L., and Foy, C. A. (2010). Evaluation of a novel approach for the measurement of RNA quality. BMC Res. Notes 3:89. doi: 10.1186/1756-0500-3-89
56. Yoshihara, T., Ishigaki, S., Yamamoto, M., Liang, Y., Niwa, J., Takeuchi, H., et al. (2002). Differential expression of inflammation-and apoptosis-related genes in spinal cords of a mutant SOD1 transgenic mouse model of familial amyotrophic lateral sclerosis. J. Neurochem. 80, 158-167. doi: 10.1046/j.0022-3042.2001. 00683.x