Cellular and Molecular Neurobiology

, Volume 29, Issue 4, pp 533–548 | Cite as

Transcriptome Profiling of Neuronal Model Cell PC12 from Rat Pheochromocytoma

  • Ramasamy Saminathan
  • Arjunan Pachiappan
  • Luo Feng
  • Edward G. Rowan
  • Ponnampalam Gopalakrishnakone
Original Paper


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.


PC12 cells Microarray Gene expression Rat pheochromocytoma PC12 transcriptome 



Extracelular signal-regulated kinase


Expressed sequence tag


γ-Aminobutyric acid


Glyceraldehyde-3-phosphate dehydrogenase


GeneChip® operating software


Gene map annotator and pathway profiler


Gene expression omnibus


Ingenuity® pathway analysis


c-Jun N-terminal kinase


Kyoto encyclopaedia of genes and genomes


Mitogen-activated protein kinase


Nerve growth factor


Pituitary adenylate cyclase-activating polypeptide


Protein kinase A


Quantitative reverse transcription-polymerase chain reaction


Rat expression 230A



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.

Supplementary material

10571_2009_9345_MOESM1_ESM.pdf (53 kb)
Supplementary material 1 (PDF 52 kb)


  1. 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 PubMedCrossRefGoogle Scholar
  2. 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–C586PubMedGoogle Scholar
  3. 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 301–310Google Scholar
  4. 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 PubMedCrossRefGoogle Scholar
  5. Burgoyne RD (1991) Control of exocytosis in adrenal chromaffin cells. Biochim Biophys Acta 1071:174–202PubMedGoogle Scholar
  6. 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 87:2555–2561PubMedGoogle Scholar
  7. 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 PubMedCrossRefGoogle Scholar
  8. 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 PubMedCrossRefGoogle Scholar
  9. 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 PubMedCrossRefGoogle Scholar
  10. 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 PubMedCrossRefGoogle Scholar
  11. 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 PubMedCrossRefGoogle Scholar
  12. 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 PubMedCrossRefGoogle Scholar
  13. 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 PubMedCrossRefGoogle Scholar
  14. 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 PubMedCrossRefGoogle Scholar
  15. 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 235–250Google Scholar
  16. 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 PubMedCrossRefGoogle Scholar
  17. 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 PubMedCrossRefGoogle Scholar
  18. 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 PubMedCrossRefGoogle Scholar
  19. 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 PubMedCrossRefGoogle Scholar
  20. 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 100:1688–1702PubMedGoogle Scholar
  21. 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 54:547–558Google Scholar
  22. 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 71–94CrossRefGoogle Scholar
  23. 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 16:7557–7565PubMedGoogle Scholar
  24. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)). Methods 25:402–408PubMedCrossRefGoogle Scholar
  25. 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 201:459–469Google Scholar
  26. 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 PubMedCrossRefGoogle Scholar
  27. 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 PubMedCrossRefGoogle Scholar
  28. 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 CrossRefGoogle Scholar
  29. 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 PubMedCrossRefGoogle Scholar
  30. 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 57:53–58PubMedGoogle Scholar
  31. 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 71:1251–1260PubMedCrossRefGoogle Scholar
  32. 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 PubMedCrossRefGoogle Scholar
  33. 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 255–265Google Scholar
  34. Reber BFX, Reuter H (1991) Dependence of cytosolic calcium in differentiating rat pheochromocytoma cells on calcium channels and intracellular stores. J Physiol 435:145–162Google Scholar
  35. 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 20:7595–7601PubMedGoogle Scholar
  36. Shafer TJ, Atchison WD (1991) Transmitter, ion channel and receptor properties of pheochromocytoma (PC12) cells: a model for neurotoxicological studies. Neurotoxicology 12:473–492PubMedGoogle Scholar
  37. 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 282:1487–1495PubMedGoogle Scholar
  38. 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 279–327Google Scholar
  39. Spicer Z, Millhorn DE (2003) Oxygen sensing in neuroendocrine cells and other cell types: pheochromocytoma (PC12) cells as an experimental model. Endocr Pathol Winter 14:277–291CrossRefGoogle Scholar
  40. 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 PubMedCrossRefGoogle Scholar
  41. 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 426:95–116PubMedGoogle Scholar
  42. 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 PubMedCrossRefGoogle Scholar
  43. 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 PubMedCrossRefGoogle Scholar
  44. 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 305–320Google Scholar
  45. 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 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Ramasamy Saminathan
    • 1
    • 2
  • Arjunan Pachiappan
    • 1
  • Luo Feng
    • 1
  • Edward G. Rowan
    • 2
  • Ponnampalam Gopalakrishnakone
    • 1
  1. 1.Venom and Toxin Research Programme, Department of Anatomy, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
  2. 2.Division of Physiology and Pharmacology, Strathclyde Institute of Pharmacy and Biomedical SciencesUniversity of StrathclydeGlasgowUK

Personalised recommendations