Pharmacology - Facilities

Genome Sciences Facility

Our Functional Genomics Core Facility offers:

Consultations on Experimental Design & Data Validation
RNA, DNA, Protein Quality Control
Gene expression Micro-array Analysis ( mRNA and miRNA )
SNP/CNV Micro-array Analysis
Data Analysis
Quantitative Real-time PCR Analysis ( RNA, DNA, SNP )

Located in the Hershey Center for Applied Research, Room 3200.

A calendar has been set up for scheduling time on instruments. Functional Genomics personnel will also list upcoming time off on this calendar so you can plan accordingly if you require assistance.

http://genomics.calendarhost.com/

Important Instrumentation Purchases and Services have been made possible through Tobacco Settlement Funds (TSF), Juvenile Diabetes Research Foundation funds (JDRF), and through the Penn State Cancer Institute (PSCI) contract with the Department of the Navy.
Genome Sciences Facilities & Equipment

The Genome Sciences Facility, contains the following equipment:

Agilent 2100 Bioanalyzer
Nanodrop Spectrophotometer
Molecular Devices M2 UV/Vis/Fluor spectrophotometer for nucleic acid and protein QA/QC
An ABI 7900HT system with robotic plate handler is available for qPCR workflows

For micro-array analyses, equipment includes:

Axon 4000B micro-array scanner
GE Healthcare Codelink Bioarray Parallel Processing System
Illumina BeadStation system
Illumina BeadExpress system
Agilent Genespring, Illumina GenomeStudio software licenses

Additionally the facility contains refrigerators, -20ºC and -80ºC freezers, and associated small equipment (e.g. multichannel, electronic, and accordion pipettes).
Recent Publications

1. Abcouwer SF, Lin C-M, Wolpert EB, Shanmugam S, Schaefer EW, Freeman WM, Barber AJ, Antonetti DA (2010). Vascular permeability and apoptosis are separable processes in retinal ischemia-reperfusion injury: Effects of ischemic preconditioning, bevacizumab and etanercept. IOVS. Jun 16. Epub ahead of print.

2. Balliet, RM, Chen, G, Gallagher, CJ, Dellinger, RW, Sun, D, and Lazarus, P (2009). Characterization of UGTs active against SAHA and association between SAHA glucuronidation activity phenotype with UGT genotype. Cancer Res 69, 2981-2989.

3. Barthéléry M, Salli U, Freeman WM, Vrana KE (2009). 2-DIGE identification of differentially expressed hNRNPs and transcription factors during neural differentiation of human ES cells Proteomics: Clinical Applications. 3:505-514.

4. Bayerl, MG, Bruggeman, RD, Conroy, EJ, Hengst, JA, King, TS, Jimenez, M, Claxton, DF, and Yun, JK (2008). Sphingosine kinase 1 protein and mRNA are over expressed in non-Hodgkin lymphomas and are attractive targets for novel pharmacological interventions. Leuk Lymphoma 49, 948-954

5. Blake, DC, Jr., Mikse, OR, Freeman, WM, and Herzog, CR (2010). FOXO3a elicits a pro-apoplectic transcription program and cellular response to human lung carcinogen nicotine-derived nitrosaminoketone (NNK). Lung Cancer 67, 37-47.

6. Blevins-Primeau, AS, Sun, D, Chen, G, Sharma, AK, Gallagher, CJ, Amin, S, and Lazarus, P (2009). Functional significance of UDP - glucuronosyl transference variants in the metabolism of active tamoxifen metabolites. Cancer Res 69, 1892-1900.

7. Bortner, JD, Jr, Das, A, Umstead, TM, Freeman, WM, Somiari, R, Aliaga, C, Phelps, DS, and El-Bayoumy, K (2009). Down-regulation of 14-3-3 isoforms and annexin A5 proteins in lung adenocarcinoma induced by the tobacco-specific nitrosamine NNK in the A/J mouse revealed by proteomic analysis. J Proteome Res 8, 4050-4061.

8. Bowyer JF, Pogge AR, Delongchamp RR, O'Callaghan JP, Patel KM, Vrana KE, Freeman WM (2007). A threshold neurotoxic amphetamine exposure inhibits synaptic plasticity gene expression in the parietal cortex. Neuroscience. 144:66-76.

9. Brucklacher RM, Patel KM, Bixler GV, VanGuilder HD, Antonetti DA, Lin C-M, LaNoue KM, Barber AJ, Gardner TW, Bronson SK, Freeman WM (2008). Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response. BMC Medical Genomics. 1:26.

10. Chen, G, Blevins-Primeau, AS, Dellinger, RW, Muscat, JE, and Lazarus, P (2007). Glucuronidation of nicotine and cotinine by UGT2B10: loss of function by the UGT2B10 Codon 67 (Asp>Tyr) polymorphism. Cancer Res 67, 9024-9029.

11. Chen, G, Dellinger, RW, Gallagher, CJ, Sun, D, and Lazarus, P (2008). Identification of a prevalent functional missense polymorphism in the UGT2B10 gene and its association with UGT2B10 inactivation against tobacco-specific nitrosamines. Pharmacogenet Genomics 18, 181-191.

12. Chen, G, Dellinger, RW, Sun, D, Spratt, TE, and Lazarus, P (2008). Glucuronidation of tobacco-specific nitrosamines by UGT2B10. Drug Metab Dispos 36, 824-830.

13. Ding, W, Mouzaki, M, You, H, Laird, JC, Mato, J, Lu, SC, and Rountree, CB (2009). CD133+ liver cancer stem cells from methionine adenosyl transferase 1A-deficient mice demonstrate resistance to transforming growth factor (TGF)-beta-induced apoptosis. Hepatology 49, 1277-1286.

14. Elftman, MD, Norbury, CC, Bonneau, RH, and Truckenmiller, ME (2007). Corticosterone impairs dendritic cell maturation and function. Immunology 122, 279-290.

15. Feith, DJ, Bol, DK, Carboni, JM, Lynch, MJ, Sass-Kuhn, S, Shoop, PL, and Shantz, LM (2005). Induction of ornithine decarboxylase activity is a necessary step for mitogen-activated protein kinase kinase-induced skin tumorigenesis. Cancer Res 65, 572-578.

16. Feith, DJ, Shantz, LM, Shoop, PL, Keefer, KA, Prakashagowda, C, and Pegg, AE (2007). Mouse skin chemical carcinogenesis is inhibited by antizyme in promotion- sensitive and promotion-resistant genetic backgrounds. Mol Carcinog 46, 453-465.

17. Fort PE, Freeman WM, Kimball SR, Singh RSJ, Gardner TW. The retinal proteome in experimental diabetic retinopathy: Upregulation of Beta and Gamma-crystalline and reversal by insulin (2009). Mol. Cell. Proteomics. 8:767-779.

18. Freeman WM, Lull ME, Patel KM, Brucklacher RM, Morgan D, Roberts DCS, Vrana KE (2010). Gene expression changes in the mesolimbic pathway following abstinence from cocaine self-administration. BMC Neuroscience 2010; 11:29.

19. Freeman WM, Bixler GV, Brucklacher RM, Lin C-M, Patel KM, VanGuilder HD, LaNoue KM, Barber AJ, Antonetti DA, Gardner TW, Bronson SK (2009). A novel multi-step evaluation process of preclinical drug development biomarkers. The Pharmacogenomics Journal. Dec 8. Epub ahead of print.

20. Freeman WM, Bixler GV, Brucklacher RM, Kimball SR, Jefferson LS, Bronson SK. Transcriptomic comparison of the retina in two mouse models of diabetes (2009). Journal of Ocular Biology, Diseases, and Informatics. 2:202-213.

21. Freeman WM, Patel KM, Lull ME, Erwin MS, Bruchlacker RM, Morgan D, Roberts DCS, Vrana KE (2008). Persistent alterations in mesolimbic gene expression with abstinence from cocaine self-administration. Neuropsychopharmacology. 33:1807-1817.

22. Gallagher, CJ, Ahn, K, Knipe, AL, Dyer, AM, Richie, JP, Jr, Lazarus, P, and Muscat, JE (2009). Association between haplotypes of manganese superoxide dismutase (SOD2), smoking, and lung cancer risk. Free Radic Biol Med 46, 20-24.

23. Gallagher, CJ, Kadlubar, FF, Muscat, JE, Ambrosone, CB, Lang, NP, and Lazarus, P (2007). The UGT2B17 gene deletion polymorphism and risk of prostate cancer. A case-control study in Caucasians. Cancer Detect Prev 31, 310-315.

24. Gallagher, CJ, Muscat, JE, Hicks, AN, Zheng, Y, Dyer, AM, Chase, GA, Richie, J, and Lazarus, P (2007). The UDP-glucuronosyltransferase 2B17 gene deletion polymorphism: sex-specific association with urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol glucuronidation phenotype and risk for lung cancer. Cancer Epidemiol Biomarkers Prev 16, 823-828.

25. Hodge DL, Yang J, Buschman MD, Schaughency PM, Dang H, Bere W, Yang Y, Savan R, Subleski JJ, Yin XM, Loughran TP Jr, Young HA. Interleukin-15 enhances proteasomal degradation of bid in normal lymphocytes: implications for large granular lymphocyte leukemia. Cancer Res. 2009 May 1;69(9):3986-94.

26. Iwona Hirschler-Laszkiewicz, Qin Tong, Kathleen Conrad, Wenyi Zhang, Wesley W. Flint, Alistair J. Barber, Dwayne L. Barber, Joseph Y. Cheung, and Barbara A. Miller TRPC3 Activation by Erythropoietin Is Modulated by TRPC6. J. Biol. Chem. 2009 284: 4567-4581.

27. Jaishankar A, Barthéléry M, Freeman WM, Salli U, Vrana KE (2009). Human Embryonic and Mesenchymal Stem Cells Express Different Nuclear Proteomes. Stem Cells Develop. 18:793-802.

28. Kline, CL, Jackson, R, Engelman, R, Pledger, WJ, Yeatman, TJ, and Irby, RB (2008). Src kinase induces tumor formation in the c-SRC C57BL/6 mouse. Int J Cancer 122, 2665-2673.

29. Kuntz-Melcavage, KL, Brucklacher RM, Grigson PS, Freeman WM, Vrana KE (2009). Gene expression changes in a heroin behavioral incubation model. BMC Neuroscience. 10:95.

30. Olson, KC, Dellinger, RW, Zhong, Q, Sun, D, Amin, S, Spratt, TE, and Lazarus, P (2009). Functional characterization of low-prevalence missense polymorphisms in the UDP-glucuronosyltransferase 1A9 gene. Drug Metab Dispos 37, 1999-2007.

31. Origanti, S, and Shantz, LM (2007). Ras transformation of RIE-1 cells activates cap-independent translation of ornithine decarboxylase: regulation by the Raf/MEK/ERK and phosphatidylinositol 3-kinase pathways. Cancer Res 67, 4834-4842.

32. Pastor, DM, Irby, RB, Poritz, LS (2010). Tumor necrosis factor alpha Induces p53 up-regulated modulator of apoptosis expression in colorectal cancer cell lines. Dis Colon Rectum 53, 257-63.

33. Prokopczyk, B, Sinha, I, Trushin, N, Freeman, WM, and El-Bayoumy, K (2009). Gene expression profiles in HPV-immortalized human cervical cells treated with the nicotine-derived carcinogen 4- (methylnitrosamino)-1-(3-pyridyl)-1-butanone. Chem Biol Interact 177, 173-180.

34. Roff, A, and Wilson, RT (2008). A novel SNP in a vitamin D response element of the CYP24A1 promoter reduces protein binding, transactivation, and gene expression. J Steroid Biochem Mol Biol 112, 47- 54.

35. Salli, U, Fox, TE, Carkaci-Salli, N, Sharma, A, Robertson, GP, Kester, M, and Vrana, K (2008). Propagation of undifferentiated human embryonic stem cells with nano-liposomal ceramide. Stem Cells Dev 18, 55-65.

36. Shah, MV, Zhang, R, Irby, R, Kothapalli, R, Liu, X, Arrington, T, Frank, B, Lee, NH, and Loughran, TP, Jr (2008). Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes. Blood 112, 770-781.

37. Spidel, JL, Wilson, CB, Craven, RC, and Wills, JW (2007). Genetic studies of the beta-hairpin loop of Rous sarcoma virus capsid protein. J Virol 81, 1288-1296.

38. Sudol, M, Tran, M, Nowak, MG, Flanagan, JM, Robertson, GP, and Katzman, M (2009). A nonradioactive plate-based assay for stimulators of nonspecific DNA nicking by HIV-1 integrase and other nucleases. Anal Biochem 396, 223-230.

39. VanGuilder HD, Brucklacher RM, Patel K, Ellis RW, Freeman WM, Barber AJ. (2008) Diabetes downregulates presynaptic proteins and reduces basal synapsin I phosphorylation in rat retina. Eur J Neurosci. 28:1-11.

40. Van Guilder HD, Vrana KE, Freeman WM (2008). 25 years of quantitative PCR for gene expression analysis. BioTechniques. 44: 619-626.

41. Vunta, H, Belda, BJ, Arner, RJ, Channa Reddy, C, Vanden Heuvel, JP, and Sandeep Prabhu, K (2008). Selenium attenuates pro-inflammatory gene expression in acrophages. Mol Nutr Food Res 52, 1316-1323.

42. Yang, J, Liu, X, Nyland, SB, Zhang, R, Ryland, LK, Broeg, K, Baab, KT, Jarbadan, NR, Irby, R, and Loughran, TP, Jr (2009). Platelet-derived growth factor mediates survival of leukemic large granular lymphocytes via an autocrine regulatory pathway. Blood 115, 51-60.

43. You, H, Ding, W, Rountree, CB (2010). Epigenetic regulation of cancer stem cell marker CD133 by transforming growth factor-beta. Hepatology. 52:945-5329.

44. Zhang B, Ramesh G, Uematsu S, Akira S, Reeves WB. TLR4 signaling mediates inflammation and tissue injury in nephrotoxicity (2008). J Am Soc Nephrol. 19:923-32.

45. Zheng, Y, Sun, D, Sharma, AK, Chen, G, Amin, S, and Lazarus, P (2007). Elimination of antiestrogenic effects of active tamoxifen metabolites by glucuronidation. Drug Metab Dispos 35, 1942-1948.