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Transcriptome Profiling of Neuronal Model Cell PC12 from Rat Pheochromocytoma

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Abstract

GeneChip® microarray is a cutting-edge technology being used to study the expression patterns of genes with in a particular cell type. In this study, the Affymetrix® RAE230A platform was used to profile stably expressed mRNA transcripts from PC12 cells at passage 5 and 15. The whole-cell PC12 transcriptome revealed that a total of 7,531 stable transcripts (P < 0.05), corresponding to 6,785 genes, were found to be consistently expressed between passage 5 and 15. The data analysis revealed 3,080 functional proteins, belonging to 13 families, which indicate that about 65% of the proteins expressed in PC12 cells are uncharacterized. By using our custom-built rat neuronal reference genome database, we mapped endogenously expressed stable neuronal transcripts from PC12 cells comprising about 765 genes responsible for neuronal function and disease. These neuronal transcripts were further analyzed to provide a genetic blueprint that can be used by neurobiologist to unravel the complex cellular and molecular mechanisms underlying biological functions and their associated signalling networks for diseases affecting the nervous system.

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Abbreviations

ERK:

Extracelular signal-regulated kinase

EST:

Expressed sequence tag

GABA:

γ-Aminobutyric acid

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

GCOS:

GeneChip® operating software

GenMAPP:

Gene map annotator and pathway profiler

GEO:

Gene expression omnibus

IPA:

Ingenuity® pathway analysis

JNK:

c-Jun N-terminal kinase

KEGG:

Kyoto encyclopaedia of genes and genomes

MAPK:

Mitogen-activated protein kinase

NGF:

Nerve growth factor

PACAP:

Pituitary adenylate cyclase-activating polypeptide

PKA:

Protein kinase A

qRT-PCR:

Quantitative reverse transcription-polymerase chain reaction

RAE230A:

Rat expression 230A

References

  • Anderson JP, Esch FS, Keim PS, Sambamurti K, Lieberburg I (1991) Exact cleavage site of Alzheimer amyloid precursor in neuronal PC-12 cells. Neurosci Lett 128:126–128. doi:10.1016/0304-3940(91)90775-O

    Article  PubMed  CAS  Google Scholar 

  • Ardizzone TD, Lu XH, Dwyer DS (2002) Calcium-independent inhibition of glucose transport in PC12 and L6 cells by calcium channel antagonists. Am J Physiol Cell Physiol 283:C579–C586

    PubMed  CAS  Google Scholar 

  • Arslan G, Fredholm BB (1999) Adenosine and P2 receptors in PC12 cells. Genotypic, phenotypic and individual differences. In: Illes P, Zimmermann H (eds) Progress in brain research, vol 120. Elsevier Science, Amsterdam, pp 301–310

    Google Scholar 

  • Bal-Price A, Brown GC (2000) Nitric-oxide-induced necrosis and apoptosis in PC12 cells mediated by mitochondria. J Neurochem 75:1455–1464. doi:10.1046/j.1471-4159.2000.0751455.x

    Article  PubMed  CAS  Google Scholar 

  • Burgoyne RD (1991) Control of exocytosis in adrenal chromaffin cells. Biochim Biophys Acta 1071:174–202

    PubMed  CAS  Google Scholar 

  • Chu XP, Miesch J, Johnson M, Root L, Zhu XM, Chen D, Simon RP, Xiong ZG (2002) Proton-gated channels in PC12 cells. J Neurophysiol 87:2555–2561

    PubMed  CAS  Google Scholar 

  • Clementi E, Scheer H, Raichman M, Meldolesi J (1992) ATP-induced Ca2+ influx is regulated via a pertussis toxin-sensitive mechanism in a PC12 cell clones. Biochem Biophys Res Commun 188:1184–1190. doi:10.1016/0006-291X(92)91356-U

    Article  PubMed  CAS  Google Scholar 

  • Fukuda M, Yamamoto A (2004) Effect of forskolin on synaptotagmin IV protein trafficking in PC12 cells. J Biochem 136:245–253. doi:10.1093/jb/mvh116

    Article  PubMed  CAS  Google Scholar 

  • Gerstin EH Jr, McMahon T, Dadgar J, Messing RO (1998) Protein kinase C delta mediates ethanol-induced up-regulation of L-type calcium channels. J Biol Chem 273:16409–16414. doi:10.1074/jbc.273.26.16409

    Article  PubMed  CAS  Google Scholar 

  • Greene LA, Rein G (1977) Synthesis, storage and release of acetylcholine by a noradrenergic pheochromocytoma cell line. Nature 268:349–351. doi:10.1038/268349a0

    Article  PubMed  CAS  Google Scholar 

  • Greene LA, Tischler AS (1976) Establishment of a noradrenergic clonal line of rat adrenal pheochromocytoma cells which respond to nerve growth factor. Proc Natl Acad Sci USA 73:2424–2428. doi:10.1073/pnas.73.7.2424

    Article  PubMed  CAS  Google Scholar 

  • Grumolato L, Elkahloun AG, Ghzili H, Alexandre D, Coulouarn C, Yon L, Salier JP, Eiden LE, Fournier A, Vaudry H, Anouar Y (2003) Microarray and suppression subtractive hybridization analyses of gene expression in pheochromocytoma cells reveal pleiotropic effects of pituitary adenylate cyclase-activating polypeptide on cell proliferation, survival, and adhesion. Endocrinology 144:2368–2379. doi:10.1210/en.2002-0106

    Article  PubMed  CAS  Google Scholar 

  • Grundschober C, Malosio ML, Astolfi L, Giordano T, Nef P, Meldolesi J (2002) Neurosecretion competence. A comprehensive gene expression program identified in PC12 cells. J Biol Chem 277:36715–36724. doi:10.1074/jbc.M203777200

    Article  PubMed  CAS  Google Scholar 

  • Igarashi S, Morita H, Bennett KM, Tanaka Y, Engelender S, Peters MF, Cooper JK, Wood JD, Sawa A, Ross CA (2003) Inducible PC12 cell model of Huntington’s disease shows toxicity and decreased histone acetylation. NeuroReport 14:565–568. doi:10.1097/00001756-200303240-00007

    Article  PubMed  CAS  Google Scholar 

  • Isom GE, Kanthasamy AG, Borowitz JL (1998) Mechanistic neurotoxicity studies using PC12 cells. In: Salem H, Katz SA (eds) Advances in animal alternatives for safety and efficacy testing. Taylor & Francis, Washington, pp 235–250

    Google Scholar 

  • Kane MD, Vanden Heuvel JP, Isom GE, Schwarz RD (1998) Differential expression of group I metabotropic glutamate receptors (mGluRs) in the rat pheochromocytoma cell line PC12: role of nerve growth factor and ras. Neurosci Lett 252:1–4. doi:10.1016/S0304-3940(98)00484-4

    Article  PubMed  CAS  Google Scholar 

  • Keilbaugh SA, Prusoff WH, Simpson MV (1991) The PC12 cell as a model for studies of the mechanism of induction of peripheral neuropathy by anti-HIV1 dideoxynucleoside analogs. Biochem Pharmacol 42:R5–R8. doi:10.1016/0006-2952(91)90672-R

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi S, Conforti L, Zhu WH, Beitner-Johnson D, Millhorn DE (1999) Role of the D2 dopamine receptor in molecular adaptation to chronic hypoxia in PC12 cells. Pflugers Arch 438:750–759. doi:10.1007/s004240051102

    Article  PubMed  CAS  Google Scholar 

  • Konu O, Xu X, Ma JZ, Kane J, Wang J, Shi SJ, Li MD (2004) Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells. Brain Res Mol Brain Res 121(1–2):102–113. doi:10.1016/j.molbrainres.2003.11.012

    Article  PubMed  CAS  Google Scholar 

  • Lattanzi W, Bernardini C, Gangitano C, Michetti F (2007) Hypoxia-like transcriptional activation in TMT-induced degeneration: microarray expression analysis on PC12 cells. J Neurochem 100:1688–1702

    PubMed  CAS  Google Scholar 

  • Lazarovici P, Jiang H, Fink D (1998) The 38-amino-acid form of pituitary adenylate cyclase-activating polypeptide induces neurite outgrowth in PC12 cells that is dependent on protein kinase C and extracellular signal-regulated kinase but not on protein kinase A, nerve growth factor receptor tyrosine kinase, p21 (ras) G protein, and pp60 (c-src) cytoplasmic tyrosine kinase. Mol Pharmacol 54:547–558

    Google Scholar 

  • Lescallet J, Chicurel ME, Lipshutz R, Dalma-Weiszhasz DD (2004) Monitoring eukaryotic gene expression using oilgonucleotide microarrays. In: Shimkets RA (ed) Gene expression profiling: methods and protocols, methods in molecular biology, vol 258. Humana Press, Totowa, pp 71–94

    Chapter  Google Scholar 

  • Liu H, Felix R, Gurnett CA, De Waard M, Witcher DR, Campbell KP (1996) Expression and subunit interaction of voltage-dependent Ca2+ channels in PC12 cells. J Neurosci 16:7557–7565

    PubMed  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)). Methods 25:402–408

    Article  PubMed  CAS  Google Scholar 

  • Marek L, Levresse V, Amura C, Zentrich E, Putten VV, Nemenoff RA, Heasley LE (2004) Multiple signaling conduits regulate global differentiation-specific gene expression in PC12 cells. J Cell Physiol 201:459–469

    Google Scholar 

  • Margioris AN, Markogiannakis M, Makrigiannakis A, Gravanis A (1992) The PC12 rat pheochromocytoma cells synthesize dynorphin. Its secretion in modulated by nicotine and nerve growth factor. Endocrinology 131:703–709. doi:10.1210/en.131.2.703

    Article  PubMed  CAS  Google Scholar 

  • Margioris AN, Venihaki M, Stournaras C, Gravanis A (1995) PC12 cell as a model to study the effects of opiods on normal and tumoral adrenal chromaffin cells. Ann N Y Acad Sci 771:166–172. doi:10.1111/j.1749-6632.1995.tb44678.x

    Article  PubMed  CAS  Google Scholar 

  • Martin TFJ, Grishanin RN (2003) PC12 cells as a model for studies of regulated secretion in neuronal and endocrine cells. Methods Cell Biol 17:267–286. doi:10.1016/S0091-679X(03)01012-4

    Article  Google Scholar 

  • McCullough LA, Egan TM, Westfall TC (1998) Neuropeptide Y receptors involved in calcium channel regulation in PC12 cells. Regul Pept 75–76:101–107. doi:10.1016/S0167-0115(98)00058-5

    Article  PubMed  Google Scholar 

  • McMahon T, Andersen R, Metten P, Crabbe JC, Messing RO (2000) Protein kinase C epsilon mediates up-regulation of N-type calcium channels by ethanol. Mol Pharmacol 57:53–58

    PubMed  CAS  Google Scholar 

  • Park TJ, Chung S, Han MK, Kim UH, Kim KT (1998) Inhibition of voltage-sensitive calcium channels by the A2A adenosine receptor in PC12 cells. J Neurochem 71:1251–1260

    Article  PubMed  CAS  Google Scholar 

  • Peyrl A, Krapfenbauer K, Slavc I, Strobel T, Lubec G (2003) Proteomic characterization of the human cortical neuronal cell line HCN-2. J Chem Neuroanat 26:171–178. doi:10.1016/S0891-0618(03)00079-6

    Article  PubMed  CAS  Google Scholar 

  • Pittman RN, DiBenedetto AJ (1996) Apoptosis of undifferentiated and terminally differentiated PC12 cells. In: Holbrook NJ, Martin GR, Lockshin RA (eds) Cellular aging and cell death. Wiley-Liss, New York, pp 255–265

    Google Scholar 

  • Reber BFX, Reuter H (1991) Dependence of cytosolic calcium in differentiating rat pheochromocytoma cells on calcium channels and intracellular stores. J Physiol 435:145–162

    Google Scholar 

  • Roth JA, Horbinski C, Feng L, Dolan KG, Higgins D, Garrick MD (2000) Differential localization of divalent metal transporter 1 with and without iron response element in rat PC12 and sympathetic neuronal cells. J Neurosci 20:7595–7601

    PubMed  CAS  Google Scholar 

  • Shafer TJ, Atchison WD (1991) Transmitter, ion channel and receptor properties of pheochromocytoma (PC12) cells: a model for neurotoxicological studies. Neurotoxicology 12:473–492

    PubMed  CAS  Google Scholar 

  • Solem M, McMahon T, Messing RO (1997) Protein kinase A regulates inhibition of N- and P/Q-type calcium channels by ethanol in PC12 cells. J Pharmacol Exp Ther 282:1487–1495

    PubMed  CAS  Google Scholar 

  • Sombers LA, Ewing AG (2002) Electrochemical Monitoring of Exocytosis from Individual PC12 Cells in Culture. In: Brajter-Toth A, Chambers JQ (eds) Electroanalytical methods for biological materials. Marcel Dekker, New York, pp 279–327

    Google Scholar 

  • Spicer Z, Millhorn DE (2003) Oxygen sensing in neuroendocrine cells and other cell types: pheochromocytoma (PC12) cells as an experimental model. Endocr Pathol Winter 14:277–291

    Article  CAS  Google Scholar 

  • Traina G, Bagnoli P (1999) Mechanisms mediating somatostatin-induced reduction of cytosolic free calcium in PC12 cells. Neurosci Lett 265:123–126. doi:10.1016/S0304-3940(99)00222-0

    Article  PubMed  CAS  Google Scholar 

  • Usowicz MM, Porzig H, Becker C, Reuter H (1990) Differential expression by nerve growth factor of two types of Ca2+ channels in rat phaeochromocytoma cell lines. J Physiol 426:95–116

    PubMed  CAS  Google Scholar 

  • Vaudry D, Chen Y, Ravni A, Hamelink C, Elkahloun AG, Eiden LE (2002a) Analysis of the PC12 cell transcriptome after differentiation with pituitary adenylate cyclase-activating polypeptide (PACAP). J Neurochem 83:1272–1284. doi:10.1046/j.1471-4159.2002.01242.x

    Article  PubMed  CAS  Google Scholar 

  • Vaudry D, Stork PJ, Lazarovici P, Eiden LE (2002b) Signaling pathways for PC12 cell differentiation: making the right connections. Science 296:1648–1649. doi:10.1126/science.1071552

    Article  PubMed  CAS  Google Scholar 

  • Yanagawa B, Taylor L, Deisher TA, Ng R, Schreiner GF, Triche TJ, Yang D, McManus BM (2005) Affymetrix oligonucleotide analysis of gene expression in the injured heart. In: Sun Z (ed) Molecular cardiology: methods and protocols, methods in molecular medicine, vol 112. Humana Press, Totowa, pp 305–320

    Google Scholar 

  • Yang W, Liu P, Liu Y, Wang Q, Tong Y, Ji J (2006) Proteomic analysis of rat pheochromocytoma PC12 cells. Proteomics 6:2982–2990. doi:10.1002/pmic.200500036

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We are thankful to National University of Singapore for funding [R-181-000-089-112] and facilities to carry out this work. And, we are also grateful to Mr. Akira Niwayama, Director, Commercial Operations (Asia Pacific), Redwood City, CA, USA, for his extended support in providing IPA software (Ingenuity® Systems) and Mr. Len Sheng Wong, Genomax Technologies Pte Ltd, Singapore, for his technical support in analyzing Affymetrix® Genechip® expression data using GeneSpring GX 7.3.1 software.

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Authors and Affiliations

  1. Venom and Toxin Research Programme, Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore

    Ramasamy Saminathan, Arjunan Pachiappan, Luo Feng & Ponnampalam Gopalakrishnakone

  2. Division of Physiology and Pharmacology, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0NR, UK

    Ramasamy Saminathan & Edward G. Rowan

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  1. Ramasamy Saminathan
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  2. Arjunan Pachiappan
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  3. Luo Feng
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  5. Ponnampalam Gopalakrishnakone
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Correspondence to Ponnampalam Gopalakrishnakone.

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Saminathan, R., Pachiappan, A., Feng, L. et al. Transcriptome Profiling of Neuronal Model Cell PC12 from Rat Pheochromocytoma. Cell Mol Neurobiol 29, 533–548 (2009). https://doi.org/10.1007/s10571-009-9345-y

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