Gene expression profiling and differentiation assessment in primary human hepatocyte cultures, established hepatoma cell lines, and human liver tissues

Toxicology and Applied Pharmacology

Volumn 222, Issue 1, 2007, Pages 42-56

  Olsavsky, Katy M ^a   Page, Jeanine L ^a   Johnson, Mary C ^a   Zarbl, Helmut ^b   Strom, Stephen C ^c   Omiecinski, Curtis J ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

DNA microarray; Human hepatocytes; In vitro hepatic model

Indexed keywords

BINDING PROTEIN; COLLAGEN TYPE 1; CONNEXIN 32; CYTOCHROME P450 2D6; DEXAMETHASONE; ENHANCER BINDING PROTEIN ALPHA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; MATRIGEL; MULTIDRUG RESISTANCE PROTEIN 1; PHENOBARBITAL; UNCLASSIFIED DRUG;

ARTICLE; BIOLOGY; CELL DIFFERENTIATION; CELL LINE; COMPARATIVE STUDY; CULTURE MEDIUM; DATA BASE; DONOR; EXTRACELLULAR MATRIX; FEMALE; GAP JUNCTION; GENE; GENE EXPRESSION PROFILING; GENE PROBE; HEPATOMA CELL; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOCHEMISTRY; IN VITRO STUDY; LIVER; LIVER CELL CULTURE; MALE;

ADOLESCENT; ADULT; AGED; ANTIGENS, DIFFERENTIATION; BIOLOGICAL MARKERS; BLOTTING, WESTERN; CARCINOMA, HEPATOCELLULAR; CELL DIFFERENTIATION; CELL LINE, TUMOR; CELLS, CULTURED; CHILD, PRESCHOOL; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; HEPATOCYTES; HUMANS; IMMUNOHISTOCHEMISTRY; INFANT; LIVER; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; PHENOBARBITAL; PHENOTYPE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA;

EID: 34250699025     PISSN: 0041008X     EISSN: 10960333     Source Type: Journal    
DOI: 10.1016/j.taap.2007.03.032     Document Type: Article

References (37)

1. Annaert P.P., and Brouwer K.L. Assessment of drug interactions in hepatobiliary transport using rhodamine 123 in sandwich-cultured rat hepatocytes. Drug Metab. Dispos. 33 (2005) 388-394
2. Assem M., Schuetz E.G., Leggas M., Sun D., Yasuda K., Reid G., Zelcer N., Adachi M., Strom S., Evans R.M., Moore D.D., Borst P., and Schuetz J.D. Interactions between hepatic Mrp4 and Sult2a as revealed by the constitutive androstane receptor and Mrp4 knockout mice. J. Biol. Chem. 279 (2004) 22250-22257
3. Baldi P., and Long A.D. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17 (2001) 509-519
4. Ben Ze'ev A., Robinson G.S., Bucher N.L., and Farmer S.R. Cell-cell and cell-matrix interactions differentially regulate the expression of hepatic and cytoskeletal genes in primary cultures of rat hepatocytes. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 2161-2165
5. Boess F., Kamber M., Romer S., Gasser R., Muller D., Albertini S., and Suter L. Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver slices compared to the in vivo liver gene expression in rats: possible implications for toxicogenomics use of in vitro systems. Toxicol. Sci. 73 (2003) 386-402
6. Currie R.A., Orphanides G., and Moggs J.G. Mapping molecular responses to xenoestrogens through Gene Ontology and pathway analysis of toxicogenomic data. Reprod. Toxicol. 20 (2005) 433-440
7. Dallas P.B., Gottardo N.G., Firth M.J., Beesley A.H., Hoffmann K., Terry P.A., Freitas J.R., Boag J.M., Cummings A.J., and Kees U.R. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR-how well do they correlate?. BMC Genomics 6 (2005) 59
8. De Smet K., Loyer P., Gilot D., Vercruysse A., Rogiers V., and Guguen-Guillouzo C. Effects of epidermal growth factor on CYP inducibility by xenobiotics, DNA replication, and caspase activations in collagen I gel sandwich cultures of rat hepatocytes. Biochem. Pharmacol. 61 (2001) 1293-1303
9. Farkas D., and Tannenbaum S.R. Characterization of chemically induced hepatotoxicity in collagen sandwiches of rat hepatocytes. Toxicol. Sci. 85 (2005) 927-934
10. Hamadeh H.K., Bushel P.R., Jayadev S., Martin K., DiSorbo O., Sieber S., Bennett L., Tennant R., Stoll R., Barrett J.C., Blanchard K., Paules R.S., and Afshari C.A. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 67 (2002) 219-231
11. Hassett C., Lin J., Carty C.L., Laurenzana E.M., and Omiecinski C.J. Human hepatic microsomal epoxide hydrolase: comparative analysis of polymorphic expression. Arch. Biochem. Biophys. 337 (1997) 275-283
12. Hoffmaster K.A., Turncliff R.Z., LeCluyse E.L., Kim R.B., Meier P.J., and Brouwer K.L. P-glycoprotein expression, localization, and function in sandwich-cultured primary rat and human hepatocytes: relevance to the hepatobiliary disposition of a model opioid peptide. Pharm. Res. 21 (2004) 1294-1302
13. Jeffery I.B., Higgins D.G., and Culhane A.C. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7 (2006) 359
14. Jessen B.A., Mullins J.S., De Peyster A., and Stevens G.J. Assessment of hepatocytes and liver slices as in vitro test systems to predict in vivo gene expression. Toxicol. Sci. 75 (2003) 208-222
15. Kern A., Bader A., Pichlmayr R., and Sewing K.F. Drug metabolism in hepatocyte sandwich cultures of rats and humans. Biochem. Pharmacol. 54 (1997) 761-772
16. Kostrubsky V.E., Ramachandran V., Venkataramanan R., Dorko K., Esplen J.E., Zhang S., Sinclair J.F., Wrighton S.A., and Strom S.C. The use of human hepatocyte cultures to study the induction of cytochrome P-450. Drug Metab. Dispos. 27 (1999) 887-894
17. LeCluyse E., Bullock P., Madan A., Carroll K., and Parkinson A. Influence of extracellular matrix overlay and medium formulation on the induction of cytochrome P-450 2B enzymes in primary cultures of rat hepatocytes. Drug Metab. Dispos. 27 (1999) 909-915
18. Liu X., Chism J.P., LeCluyse E.L., Brouwer K.R., and Brouwer K.L. Correlation of biliary excretion in sandwich-cultured rat hepatocytes and in vivo in rats. Drug Metab. Dispos. 27 (1999) 637-644
19. McClintick J.N., and Edenberg H.J. Effects of filtering by present call on analysis of microarray experiments. BMC Bioinformatics 7 (2006) 49
20. McCune J.S., Hawke R.L., LeCluyse E.L., Gillenwater H.H., Hamilton G., Ritchie J., and Lindley C. In vivo and in vitro induction of human cytochrome P4503A4 by dexamethasone. Clin. Pharmacol. Ther. 68 (2000) 356-366
21. Moghe P.V., Berthiaume F., Ezzell R.M., Toner M., Tompkins R.G., and Yarmush M.L. Culture matrix configuration and composition in the maintenance of hepatocyte polarity and function. Biomaterials 17 (1996) 373-385
22. Parkinson A. An overview of current cytochrome P450 technology for assessing the safety and efficacy of new materials. Toxicol. Pathol. 24 (1996) 48-57
23. Richert L., Binda D., Hamilton G., Viollon-Abadie C., Alexandre E., Bigot-Lasserre D., Bars R., Coassolo P., and LeCluyse E. Evaluation of the effect of culture configuration on morphology, survival time, antioxidant status and metabolic capacities of cultured rat hepatocytes. Toxicol. In Vitro 16 (2002) 89-99
24. Rockett J.C., and Hellmann G.M. Confirming microarray data-is it really necessary?. Genomics 83 (2004) 541-549
25. Rodriguez-Antona C., Donato M.T., Boobis A., Edwards R.J., Watts P.S., Castell J.V., and Gomez-Lechon M.J. Cytochrome P450 expression in human hepatocytes and hepatoma cell lines: molecular mechanisms that determine lower expression in cultured cells. Xenobiotica 32 (2002) 505-520
26. Rosenfeld J.M., Vargas Jr. R., Xie W., and Evans R.M. Genetic profiling defines the xenobiotic gene network controlled by the nuclear receptor pregnane X receptor. Mol. Endocrinol. 17 (2003) 1268-1282
27. Sidhu J.S., Farin F.M., and Omiecinski C.J. Influence of extracellular matrix overlay on phenobarbital-mediated induction of CYP2B1, 2B2, and 3A1 genes in primary adult rat hepatocyte culture. Arch. Biochem. Biophys. 301 (1993) 103-113
28. Sidhu J.S., Liu F., and Omiecinski C.J. Phenobarbital responsiveness as a uniquely sensitive indicator of hepatocyte differentiation status: requirement of dexamethasone and extracellular matrix in establishing the functional integrity of cultured primary rat hepatocytes. Exp. Cell Res. 292 (2004) 252-264
29. Strom S.C., Pisarov L.A., Dorko K., Thompson M.T., Schuetz J.D., and Schuetz E.G. Use of human hepatocytes to study P450 gene induction. Methods Enzymol. 272 (1996) 388-401
30. Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., Diemer K., Muruganujan A., and Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13 (2003) 2129-2141
31. Thomas P.D., Kejariwal A., Guo N., Mi H., Campbell M.J., Muruganujan A., and Lazareva-Ulitsky B. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 34 (2006) W645-W650
32. Tuschl G., and Mueller S.O. Effects of cell culture conditions on primary rat hepatocytes-cell morphology and differential gene expression. Toxicology 218 (2006) 205-215
33. Ueda A., Hamadeh H.K., Webb H.K., Yamamoto Y., Sueyoshi T., Afshari C.A., Lehmann J.M., and Negishi M. Diverse roles of the nuclear orphan receptor CAR in regulating hepatic genes in response to phenobarbital. Mol. Pharmacol. 61 (2002) 1-6
34. Wilkening S., Stahl F., and Bader A. Comparison of primary human hepatocytes and hepatoma cell line Hepg2 with regard to their biotransformation properties. Drug Metab. Dispos. 31 (2003) 1035-1042
35. Wu Y., Zhang X., Bardag-Gorce F., Robel R.C., Aguilo J., Chen L., Zeng Y., Hwang K., French S.W., Lu S.C., and Wan Y.J. Retinoid X receptor alpha regulates glutathione homeostasis and xenobiotic detoxification processes in mouse liver. Mol. Pharmacol. 65 (2004) 550-557
36. Zhang J., Huang W., Chua S.S., Wei P., and Moore D.D. Modulation of acetaminophen-induced hepatotoxicity by the xenobiotic receptor CAR. Science 298 (2002) 422-424
37. Zhang J., Huang W., Qatanani M., Evans R.M., and Moore D.D. The constitutive androstane receptor and pregnane X receptor function coordinately to prevent bile acid-induced hepatotoxicity. J. Biol. Chem. 279 (2004) 49517-49522