Differential expression of genes in amyotrophic lateral sclerosis revealed by profiling the post mortem cortex

References

• Julien J. P. Amyotrophic lateral sclerosis: unfolding the toxicity of the misfolded. Cell 2001; 104: 581–91
   PubMed Web of Science ®Google Scholar
• Rowland L. P., Shneider N. A. Amyotrophic lateral sclerosis. N Engl J Med 2001; 344: 1688–1700
   PubMed Web of Science ®Google Scholar
• Brooks B. R., Miller R. G., Swash M., Munsat T. L. El Escorial revisited: revised criteria for the diagnosis of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Other Motor Neuron Disord 2000; 1: 293–9
   PubMed Web of Science ®Google Scholar
• Vonsattel J. P., Aizawa H., Ge P., DiFiglia M., McKee A. C., MacDonald M., et al. An improved approach to prepare human brains for research. J Neuropathol Exp Neurol 1995; 54: 42–56
   PubMed Web of Science ®Google Scholar
• Lowe J., Leigh N. Disorders of movement and system degeneration. Greenfield's Neuropathology, D Graham, P Lantos. Arnold, London 2002; Vol. II: 372–87, 7th edn
   Google Scholar
• Cudkowicz M. E., McKenna‐Yasek D., Chen C., Hedley‐Whyte E. T., Brown R. H., Jr. Limited corticospinal tract involvement in amyotrophic lateral sclerosis subjects with the A4V mutation in the copper/zinc superoxide dismutase gene. Ann Neurol 1998; 43: 703–10
   PubMed Web of Science ®Google Scholar
• Irizarry R. A., Gautier L., Cope L. M. The analysis of Gene Expression Data: Methods and Software. Springer Verlag. 2003, Chapter 4 vol
   Google Scholar
• Irizarry R. A., Hobbs B., Collin F., Beazer‐Barclay Y. D., Antonellis K. J., Scherf U., et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003; 4: 249–64
   PubMed Web of Science ®Google Scholar
• Bolstad B. M., Irizarry R. A., Astrand M., Speed T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003; 19: 185–93
   PubMed Web of Science ®Google Scholar
• Tusher V. G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci. USA 2001; 98: 5116–21
   PubMed Web of Science ®Google Scholar
• Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc B 1995; 57: 289–300
   Web of Science ®Google Scholar
• Dangond F., Hwang D., Camelo S., Pasinelli P., Frosch M. P., Stephanopoulos G., et al. Molecular signature of late‐stage human ALS revealed by expression profiling of post mortem spinal cord gray matter. Physiol Genomics 2004; 16: 229–39
   PubMed Web of Science ®Google Scholar
• Malaspina A., Kaushik N., de Belleroche J. Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays. J Neurochem 2001; 77: 132–45
   PubMed Web of Science ®Google Scholar
• Ishigaki S., Niwa J., Ando Y., Yoshihara T., Sawada K., Doyu M., et al. Differentially expressed genes in sporadic amyotrophic lateral sclerosis spinal cords: screening by molecular indexing and subsequent cDNA microarray analysis. FEBS Lett 2002; 531: 354–8
   PubMed Web of Science ®Google Scholar
• Heath P. R., Shaw P. J. Update on the glutamatergic neurotransmitter system and the role of excitotoxicity in amyotrophic lateral sclerosis. Muscle Nerve 2002; 26: 438–58
   PubMed Web of Science ®Google Scholar
• Fray A. E., Ince P. G., Banner S. J., Milton I. D., Usher P. A., Cookson M. R., et al. The expression of the glial glutamate transporter protein EAAT2 in motor neuron disease: an immunohistochemical study. Eur J Neurosci 1998; 10: 2481–9
   PubMed Web of Science ®Google Scholar
• Roy J., Minotti S., Dong L., Figlewicz D. A., Durham H. D. Glutamate potentiates the toxicity of mutant Cu/Zn‐superoxide dismutase in motor neurons by postsynaptic calcium‐dependent mechanisms. J Neurosci 1998; 18: 9673–84
   PubMed Web of Science ®Google Scholar
• Rothstein J. D., van Kammen M., Levey A. I., Martin L. J., Kuncl R. W. Selective loss of glial glutamate transporter GLT‐1 in amyotrophic lateral sclerosis. Ann Neurol 1995; 38: 73–84
   PubMed Web of Science ®Google Scholar
• Lin C. L., Bristol L. A., Jin L., Dykes‐Hoberg M., Crawford T., Clawson L. Aberrant RNA processing in a neurodegenerative disease: the cause for absent EAAT2, a glutamate transporter, in amyotrophic lateral sclerosis. Neuron 1998; 20: 589–602
   PubMed Web of Science ®Google Scholar
• Arlotta P., Molyneaux B. J., Chen J., Inoue J., Kominami R., Macklis J. D. Neuronal subtype‐specific genes that control corticospinal motor neuron development in vivo. Neuron 2005; 45: 207–21
   PubMed Web of Science ®Google Scholar
• Baksh S., Spamer C., Heilmann C., Michalak M. Identification of the Zn2+ binding region in calreticulin. FEBS Lett 1995; 376: 53–7
   PubMed Web of Science ®Google Scholar
• Li Z., Stafford W. F., Bouvier M. The metal ion binding properties of calreticulin modulate its conformational flexibility and thermal stability. Biochemistry 2001; 40: 11193–201
   PubMed Web of Science ®Google Scholar
• Guo L., Groenendyk J., Papp S., Dabrowska M., Knoblach B., Kay C., et al. Identification of an N‐domain histidine essential for chaperone function in calreticulin. J Biol Chem 2003; 278: 50645–53
   PubMed Web of Science ®Google Scholar
• Rakhit R., Cunningham P., Furtos‐Matei A., Dahan S., Qi X. F., Crow J. P., et al. Oxidation‐induced misfolding and aggregation of superoxide dismutase and its implications for amyotrophic lateral sclerosis. J Biol Chem 2002; 277: 47551–6
   PubMed Web of Science ®Google Scholar
• Herold A., Bucurenci N., Mazilu E., Szegli G., Sidenco L., Baican I. Zinc aspartate in vivo and in vitro modulation of reactive oxygen species production by human neutrophils and monocytes. Roum Arch Microbiol Immunol 1993; 52: 101–8
   PubMedGoogle Scholar
• Chen S. M., Young T. K. Effects of zinc deficiency on endogenous antioxidant enzymes and lipid peroxidation in glomerular cells of normal and five‐sixths nephrectomized rats. J Formos Med Assoc 1998; 97: 750–6
   PubMed Web of Science ®Google Scholar
• Carter J. E., Truong‐Tran A. Q., Grosser D., Ho L., Ruffin R. E., Zalewski P. D. Involvement of redox events in caspase activation in zinc‐depleted airway epithelial cells. Biochem Biophys Res Commun 2002; 297: 1062–70
   PubMed Web of Science ®Google Scholar
• Cao G. H., Chen J. D. Effects of dietary zinc on free radical generation, lipid peroxidation, and superoxide dismutase in trained mice. Arch Biochem Biophys 1991; 291: 147–53
   PubMed Web of Science ®Google Scholar
• Martyshkin D. V., Mirov S. B., Zhuang Y. X., Crow J. P., Ermilov V., Beckman J. S. Fluorescence assay for monitoring Zn‐deficient superoxide dismutase in vitro. Spectrochim Acta A Mol Biomol Spectrosc 2003; 59: 3165–75
   PubMed Web of Science ®Google Scholar
• Blessing H., Kraus S., Heindl P., Bal W., Hartwig A. Interaction of selenium compounds with zinc finger proteins involved in DNA repair. Eur J Biochem 2004; 271: 3190–9
   PubMedGoogle Scholar
• Ermilova I. P., Ermilov V. B., Levy M., Ho E., Pereira C., Beckman J. S. Protection by dietary zinc in ALS mutant G93A SOD transgenic mice. Neurosci Lett 2005; 379: 42–6
   PubMed Web of Science ®Google Scholar
• Connor J. R., Wang X. S., Patton S. M., Menzies S. L., Troncoso J. C., Earley C. J., et al. Decreased transferrin receptor expression by neuromelanin cells in restless legs syndrome. Neurology 2004; 62: 1563–7
   PubMed Web of Science ®Google Scholar
• Mullner E. W., Neupert B., Kuhn L. C. A specific mRNA binding factor regulates the iron‐dependent stability of cytoplasmic transferrin receptor mRNA. Cell 1989; 58: 373–82
   PubMed Web of Science ®Google Scholar
• Yasui M., Ota K., Garruto R. M. Concentrations of zinc and iron in the brains of Guamanian patients with amyotrophic lateral sclerosis and Parkinsonism dementia. Neurotoxicology 1993; 14: 445–50
   PubMed Web of Science ®Google Scholar
• Kasarskis E. J., Tandon L., Lovell M. A., Ehmann W. D. Aluminum, calcium, and iron in the spinal cord of patients with sporadic amyotrophic lateral sclerosis using laser microprobe mass spectroscopy: a preliminary study. J Neurol Sci 1995; 130: 203–8
   PubMed Web of Science ®Google Scholar
• Smith M. A., Nunomura A., Zhu X., Takeda A., Perry G. Metabolic, metallic, and mitotic sources of oxidative stress in Alzheimer's disease. Antioxid Redox Signal 2000; 2: 413–20
   PubMed Web of Science ®Google Scholar
• Wang X. S., Lee S., Simmons Z., Boyer P., Scott K., Liu W., et al. Increased incidence of the Hfe mutation in amyotrophic lateral sclerosis and related cellular consequences. J Neurol Sci 2004; 227: 27–33
   PubMed Web of Science ®Google Scholar
• Urushitani M., Kurisu J., Tsukita K., Takahashi R. Proteasomal inhibition by misfolded mutant superoxide dismutase 1 induces selective motor neuron death in familial amyotrophic lateral sclerosis. J Neurochem 2002; 83: 1030–42
   Google Scholar
• Hyun D. H., Lee M., Halliwell B., Jenner P. Proteasomal inhibition causes the formation of protein aggregates containing a wide range of proteins, including nitrated proteins. J Neurochem 2003; 86: 363–73
   PubMed Web of Science ®Google Scholar
• Kabashi E., Agar J. N., Taylor D. M., Minotti S., Durham H. D. Focal dysfunction of the proteasome: a pathogenic factor in a mouse model of amyotrophic lateral sclerosis. J Neurochem 2004; 89: 1325–35
   PubMed Web of Science ®Google Scholar
• Bardag‐Gorce F., French B. A., Lue Y. H., Nguyen V., Wan Y. J., French S. W. Mallory bodies formed in proteasome‐depleted hepatocytes: an immunohistochemical study. Exp Mol Pathol 2001; 70: 7–18
   PubMed Web of Science ®Google Scholar
• Leigh P. N., Anderton B. H., Dodson A., Gallo J. M., Swash M., Power D. M. Ubiquitin deposits in anterior horn cells in motor neuron disease. Neurosci Lett 1988; 93: 197–203
   PubMed Web of Science ®Google Scholar
• Jiang Y. M., Yamamoto M., Kobayashi Y., Yoshihara T., Liang Y., Terao S., et al. Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis. Ann Neurol 2005; 57: 236–51
   PubMed Web of Science ®Google Scholar
• Arendt T., Rodel L., Gartner U., Holzer M. Expression of the cyclin‐dependent kinase inhibitor p16 in Alzheimer's disease. Neuroreport 1996; 7: 3047–9
   PubMed Web of Science ®Google Scholar
• Vincent I., Rosado M., Davies P. Mitotic mechanisms in Alzheimer's disease?. J Cell Biol 1996; 132: 413–25
   PubMed Web of Science ®Google Scholar
• Vincent I., Jicha G., Rosado M., Dickson D. W. Aberrant expression of mitotic cdc2/cyclin B1 kinase in degenerating neurons of Alzheimer's disease brain. J Neurosci 1997; 17: 3588–98
   PubMed Web of Science ®Google Scholar
• McShea A., Harris P. L., Webster K. R., Wahl A. F., Smith M. A. Abnormal expression of the cell cycle regulators P16 and CDK4 in Alzheimer's disease. Am J Pathol 1997; 150: 1933–9
   PubMed Web of Science ®Google Scholar
• Busser J., Geldmacher D. S., Herrup K. Ectopic cell cycle proteins predict the sites of neuronal cell death in Alzheimer's disease brain. J Neurosci 1998; 18: 2801–7
   PubMed Web of Science ®Google Scholar
• Husseman J. W., Nochlin D., Vincent I. Mitotic activation: a convergent mechanism for a cohort of neurodegenerative diseases. Neurobiol Aging 2000; 21: 815–28
   PubMed Web of Science ®Google Scholar
• Ranganathan S., Scudiere S., Bowser R. Hyperphosphorylation of the retinoblastoma gene product and altered subcellular distribution of E2F‐1 during Alzheimer's disease and amyotrophic lateral sclerosis. J Alzheimers Dis 2001; 3: 377–85
   PubMed Web of Science ®Google Scholar
• Yang Y., Geldmacher D. S., Herrup K. DNA replication precedes neuronal cell death in Alzheimer's disease. J Neurosci 2001; 21: 2661–8
   PubMed Web of Science ®Google Scholar
• Cleveland D. W., Bruijn L. I., Wong P. C., Marszalek J. R., Vechio J. D., Lee M. K., et al. Mechanisms of selective motor neuron death in transgenic mouse models of motor neuron disease. Neurology 1996; 47: S54–61, discussion S52–61
   PubMed Web of Science ®Google Scholar
• Julien J. P., Beaulieu J. M. Cytoskeletal abnormalities in amyotrophic lateral sclerosis: beneficial or detrimental effects?. J Neurol Sci 2000; 180: 7–14
   PubMed Web of Science ®Google Scholar
• Hadano S., Hand C. K., Osuga H., Yanagisawa A., Otomo A., Devon R. S., et al. A gene encoding a putative GTPase regulator is mutated in familial amyotrophic lateral sclerosis 2. Nat Genet 2001; 29: 166–73
   PubMed Web of Science ®Google Scholar
• Yang Y., Hentati A., Deng H. X., Dabbagh O., Sasaki T., Hirano M., et al. The gene encoding alsin, a protein with three guanine‐nucleotide exchange factor domains, is mutated in a form of recessive amyotrophic lateral sclerosis. Nat Genet 2001; 29: 160–5
   PubMed Web of Science ®Google Scholar
• Bar‐Sagi D., Hall A. Ras and Rho GTPases: a family reunion. Cell 2000; 103: 227–38
   PubMed Web of Science ®Google Scholar
• Mhatre M., Floyd R. A., Hensley K. Oxidative stress and neuroinflammation in Alzheimer's disease and amyotrophic lateral sclerosis: common links and potential therapeutic targets. J Alzheimers Dis 2004; 6: 147–57
   PubMed Web of Science ®Google Scholar
• Li M., Ona V. O., Guegan C., Chen M., Jackson‐Lewis V., Andrews L. J., et al. Functional role of caspase‐1 and caspase‐3 in an ALS transgenic mouse model. Science 2000; 288: 335–9
   PubMed Web of Science ®Google Scholar
• Shang X. Z., Zhu H., Lin K., Tu Z., Chen J., Nelson D. R., et al. Stabilized beta‐catenin promotes hepatocyte proliferation and inhibits TNFalpha‐induced apoptosis. Lab Invest 2004; 84: 332–41
   PubMed Web of Science ®Google Scholar
• Guegan C., Vila M., Rosoklija G., Hays A. P., Przedborski S., et al. Recruitment of the mitochondrial‐dependent apoptotic pathway in amyotrophic lateral sclerosis. J Neurosci 2001; 21: 6569–76
   PubMed Web of Science ®Google Scholar
• Albers D. S., Beal M. F. Mitochondrial dysfunction and oxidative stress in aging and neurodegenerative disease. J Neural Transm Suppl 2000; 59: 133–54
   PubMedGoogle Scholar
• Ro L. S., Lai S. L., Chen C. M., Chen S. T. Deleted 4977‐bp mitochondrial DNA mutation is associated with sporadic amyotrophic lateral sclerosis: a hospital‐based case‐control study. Muscle Nerve 2003; 28: 737–43
   PubMed Web of Science ®Google Scholar
• Menzies F. M., Cookson M. R., Taylor R. W., Turnbull D. M., Chrzanowska‐Lightowlers Z. M., Dong L., et al. Mitochondrial dysfunction in a cell culture model of familial amyotrophic lateral sclerosis. Brain 2002; 125: 1522–33
   PubMed Web of Science ®Google Scholar
• Lukiw W. J. Gene expression profiling in fetal, aged, and Alzheimer hippocampus: a continuum of stress‐related signaling. Neurochem Res 2004; 29: 1287–97
   PubMed Web of Science ®Google Scholar
• Carmeliet P. Blood vessels and nerves: common signals, pathways and diseases. Nat Rev Genet 2003; 4: 710–20
   PubMed Web of Science ®Google Scholar
• Lambrechts D., Storkebaum E., Morimoto M., Del‐Favero J., Desmet F., Marklund S. L., et al. VEGF is a modifier of amyotrophic lateral sclerosis in mice and humans and protects motor neurons against ischemic death. Nat Genet 2003; 34: 383–94
   PubMed Web of Science ®Google Scholar
• Schratzberger P., Schratzberger G., Silver M., Curry C., Kearney M., Magner M., et al. Favorable effect of VEGF gene transfer on ischemic peripheral neuropathy. Nat Med 2000; 6: 405–13
   PubMed Web of Science ®Google Scholar
• Jin K. L., Mao X. O., Greenberg D. A. Vascular endothelial growth factor: direct neuroprotective effect in in vitro ischemia. Proc Natl Acad Sci. USA 2000; 97: 10242–7
   PubMed Web of Science ®Google Scholar
• Oosthuyse B., Moons L., Storkebaum E., Beck H., Nuyens D., Brusselmans K., et al. Deletion of the hypoxia‐response element in the vascular endothelial growth factor promoter causes motor neuron degeneration. Nat Genet 2001; 28: 131–8
   PubMed Web of Science ®Google Scholar