Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons

References

• ATSDR . 1995 . Toxicological profile for polycyclic aromatic hydrocarbons . : 11 – 207 .
   Google Scholar
• Wojdani , A , Attarzadeh , M , Wolde-Tsadik , G and Alfred , LJ . 1984 . Immunocytotoxicity effects of polycyclic aromatic hydrocarbons on mouse lymphocytes . Toxicology , 31 : 181 – 189 .
   PubMed Web of Science ®Google Scholar
• Laupeze , B , Amiot , L , Sparfel , L , Le Ferrec , E , Fauchet , R and Fardel , O . 2002 . Polycyclic aromatic hydrocarbons affect functional differentiation and maturation of human monocyte-derived dendritic cells . J. Immunol. , 168 : 2652 – 2658 .
   PubMed Web of Science ®Google Scholar
• Upham , BL , Weis , LM and Trosko , JE . 1998 . Modulated gap junctional intercellular communication as a biomarker of PAH epigenetic toxicity: structure-function relationship . Environ. Health Perspect. , 106 : 975 – 981 .
   PubMed Web of Science ®Google Scholar
• Whitlock , JP . 1999 . Induction of cytochrome P4501A1 . Annu. Rev. Pharmacol. Toxicol. , 39 : 103 – 125 .
   PubMed Web of Science ®Google Scholar
• Wan , B , Sayler , GS and Schultz , TW . 2006 . Structure-activity relationships for flow cytometric data of smaller polycyclic aromatic hydrocarbons . SAR QSAR Environ. Res. , 17 ( 6 ) : 597 – 605 .
   PubMed Web of Science ®Google Scholar
• Severson , RF , Snook , ME , Higman , HC , Chortyk , OT and Akin , FJ . 1976 . “ Polynuclear aromatic hydrocarbons: chemistry, metabolism, and carcinogenesis ” . In Carcinogenesis , Edited by: Frudenthal , RI and Jones , PW . Vol. 1 , 269 New York : Raven Press .
   Google Scholar
• Rustemeier , K , Stabbert , R , Haussmann , HJ , Roemer , E and Carmines , EL . 2002 . Evaluation of the potential effects of ingredients added to cigarettes. Part 2: chemical composition of mainstream smoke . Food Chem. Toxicol. , 40 : 93 – 104 .
   PubMed Web of Science ®Google Scholar
• Mabilia , R , Cecinato , A , Tomasi Scianò , MC , Di Palo , V and Possanzino , M . 2004 . Characterization of polycyclic aromatic hydrocarbons and carbonyl compounds in diesel exhaust emissions . Ann. Chim. , 94 : 733 – 740 .
   PubMedGoogle Scholar
• Hamadeh , HK , Bushel , PB , Paules , R and Afshari , CA . 2001 . Discovery intoxicology: Mediation by gene expression array technology . J. Biochem. Mol. Toxicol. , 15 : 231 – 242 .
   PubMed Web of Science ®Google Scholar
• Burchiel , SK , Knall , CM , Davis , JW III , Paules , RS , Boggs , SE and Afshari , CA . 2001 . Analysis of genetic and epigenetic mechanisms of toxicity: Potential roles of toxicogenomics and proteomics in toxicology . Toxicol. Sci. , 59 : 193 – 195 .
   PubMed Web of Science ®Google Scholar
• Schultz , TW , Carlson , RE , Cronin , MTD , Hermens , JLM , Johnson , R , O'Brien , PJ , Roberts , DW , Siraki , A , Wallace , KD and Veith , GD . 2006 . A conceptual framework for predicting toxicity of reactive chemicals: Models for soft electrophilicity . SAR QSAR Environ. Res. , 17 : 413 – 428 .
   PubMed Web of Science ®Google Scholar
• Tsuchiya , S , Yamabe , M , Yamaguchi , Y , Kobayashi , Y , Konno , T and Tada , K . 1980 . Establishment and characterization of a human acute monocytic leukemia cell line (THP-1) . Int. J. Cancer , 26 : 171 – 176 .
   PubMed Web of Science ®Google Scholar
• Hayashi , S , Okabe-Kado , J , Honma , Y and Kawajiri , K . 1995 . Expression of Ah receptor (TCDD receptor) during human monocytic differentiation . Carcinogenesis. , 16 : 1403 – 1409 .
   PubMedGoogle Scholar
• Ng , D , Kokot , N , Hiura , T , Faris , M , Saxon , A and Nel , A . 1998 . Macrophage activation by polycyclic aromatic hydrocarbons: Evidence for the involvement of stress-actiavted protein kinases, activor protein-1, and antioxidant response elements . J. Immunol. , 161 : 942 – 951 .
   PubMed Web of Science ®Google Scholar
• Hiura , TS , Kaszubowski , MP , Li , N and Nel , AE . 1999 . Chemicals in diesel exhaust particles generate reactive oxygen radicals and induce apoptosis in macrophages . J. Immunol. , 163 : 5582 – 5591 .
   PubMed Web of Science ®Google Scholar
• Wu , Z , Irizarry , R , Gentleman , R , Martinez-Murillo , F and Spencer , F . 2004 . A model based background adjustment for oligonucleotide expression arrays . J. Amer. Stat. Assoc. , 99 : 909 – 917 .
   Web of Science ®Google Scholar
• Tusher , VG , Tibsgiran , R and Chu , G . 2001 . Significant analysis of microarrays applied to the ionizing radiation response . PNAS , 98 : 5116 – 5121 .
   PubMed Web of Science ®Google Scholar
• McShane , LM , Radmacher , MD , Freidlin , B , Yu , R , Li , MC and Simon , R . 2002 . Methods of assessing reproducibility of clustering patterns observed in analyses of microarray data . Bioinformatics , 18 : 1462 – 1469 .
   PubMed Web of Science ®Google Scholar
• Simon , R , Radmacher , MD , Dobbin , K and McShane , LM . 2003 . Pitfalls in the analysis of DNA microarray data: Class prediction methods . J. Nat. Cancer Inst. , 95 : 14 – 18 .
   PubMed Web of Science ®Google Scholar
• Pfaffl , MW . 2001 . A new mathematical model for relative quantification in real-time RT-PCR . Nucleic Acids Res. , 29 : 2002 – 2007 .
   Web of Science ®Google Scholar
• Pfaffl , MW , Horgan , GW and Dempfle , L . 2002 . Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR . Nucleic Acids Res. , 20 : 1 – 10 .
   Google Scholar
• Tibshirani , R , Hastie , T , Narasimhan , B and Chu , G . 2002 . Diagnosis of multiple cancer types by shrunken centroids of gene expression . PNAS , 99 : 6567 – 6572 .
   PubMed Web of Science ®Google Scholar
• Roos , PH and Bolt , HM . 2005 . Cytochrome P450 interactions in human cancers: new aspects considering CYP1B1 . Expert Opin. Drug Metab. Toxicol. , 1 : 187 – 202 .
   PubMedGoogle Scholar
• Larsen , MC , Brake , PB , Pollenz , RS and Jefcoate , CR . 2004 . Linked expression of Ah receptor, ARNT, CYP1A1, and CYP1B1 in rat mammary epithelia, in vitro, is each substantially elevated by specific extracellular matrix interactions that precede branching morphogenesis . Toxicol. Sci. , 82 : 46 – 61 .
   Google Scholar
• Shimada , T and Fujii-Kuriyama , Y . 2004 . Metabolic activation of polycyclic aromatic hydrocarbons to carcinogens by cytochromes P450 1A1 and 1B1 . Cancer Sci. , 95 : 1 – 6 .
   PubMed Web of Science ®Google Scholar
• McFadyen , MC and Murray , GI . 2005 . Cytochrome P450 1B1: a novel anticancer therapeutic target . Future Oncol. , 1 : 259 – 263 .
   PubMedGoogle Scholar
• Toutenhoofd , SL and Strehler , EE . 2002 . Regulation of calmodulin mRNAs in differentiating human IMR-32 neuroblastoma cells . Biochim. Biophys. Acta , 1600 : 95 – 104 .
   PubMed Web of Science ®Google Scholar
• Yui , S , Nakatani , Y and Mikami , M . 2003 . Calprotectin (S100A8/S100A9), an inflammatory protein complex from neutrophils with a broad apoptosis-inducing activity . Biol. Pharm. Bull. , 26 : 753 – 760 .
   PubMed Web of Science ®Google Scholar
• Arumugam , T , Simeone , DM , Van Golen , K and Logsdon , CD . 2005 . S100P promotes pancreatic cancer growth, survival, and invasion . Clin. Cancer Res. , 11 : 5356 – 5364 .
   PubMed Web of Science ®Google Scholar
• Salama , I , Malone , PS , Mihaimeed , F and Jones , JL . 2008 . A review of the S100 proteins in cancer . Eur. J. Surg. Oncol. , 34 : 357 – 484 .
   PubMed Web of Science ®Google Scholar
• Matsuzaki , Y , Takaoka , Y , Hitomi , T , Nishino , H and Sakai , T . 2004 . Activation of protein kinase C promotes human cancer cell growth through downregulation of p18(INK4c) . Oncogene , 23 : 5409 – 5414 .
   PubMed Web of Science ®Google Scholar
• Arcellana-Panlilio , MY , Egeler , RM , Ujack , E , Magliocco , A , Stuart , GC , Robbins , SM and Coppes , MJ . 2002 . Evidence of a role for the INK4 family of cyclin-dependent kinase inhibitors in ovarian granulosa cell tumors . Genes Chromosomes Cancer. , 35 : 176 – 181 .
   Google Scholar
• Rivera , A , Mavila , A , Bayless , KJ , Davis , GE and Maxwell , SA . 2006 . Cyclin A1 is a p53-induced gene that mediates apoptosis, G2/M arrest, and mitotic catastrophe in renal, ovarian, and lung carcinoma cells . Cell. Mol. Life Sci. , 63 : 1425 – 1439 .
   PubMed Web of Science ®Google Scholar
• Zandbergen , F , Mandard , S , Escher , P , Tan , NS , Patsouris , D , Jatkoe , T , Rojas-Caro , S , Madore , S , Wahli , W , Tafuri , S , Müller , M and Kersten , S . 2005 . The G0/G1 switch gene 2 is a novel PPAR target gene.The G0/G1 switch gene 2 is a novel PPAR target gene . Biochem. J. , 392(Pt 2) : 313 – 324 .
   Google Scholar
• Mibayashi , M , Nakad , K and Nagata. , K . 2002 . Promoted cell death of cells expressing human MxA by influenza virus infection . Microbiol. Immunol. , 46 : 29 – 36 .
   Google Scholar
• Kang , DC , Gopalkrishnan , RV , Lin , L , Randolph , A , Valerie , K , Pestka , S and Fisher , PB . 2004 . Expression analysis and genomic characterization of human melanoma differentiation associated gene-5, mda-5: a novel type I interferon-responsive apoptosis-inducing gene . Oncogene , 23 : 1789 – 1800 .
   PubMed Web of Science ®Google Scholar
• Sasaki , T , Knyazev , PG , Cheburkin , Y , Göhring , W , Tisi , D , Ullrich , A , Timpl , R and Hohenester , E . 2002 . Crystal structure of a C-terminal fragment of growth arrest-specific protein Gas6. Receptor tyrosine kinase activation by laminin G-like domains . J. Biol. Chem. , 277 : 44164 – 44170 .
   Google Scholar
• Hasanbasic , I , Cuerquis , J , Varnum , B and Blostein , MD . 2004 . Intracellular signaling pathways involved in Gas6-Axl-mediated survival of endothelial cells . Am. J. Physiol. Heart Circ. Physiol. , 287 : H1207 – H1213 .
   PubMed Web of Science ®Google Scholar
• Nilsson , C , Johansson , U , Johansson , AC , Kagedal , K and Ollinger , K . 2006 . Cytosolic acidification and lysosomal alkalinization during TNF-alpha induced apoptosis in U937 cells . Apoptosis , 11 : 1149 – 1159 .
   PubMedGoogle Scholar
• Yuan , J , Murrell , GA , Trickett , A and Wang , MX . 2003 . Involvement of cytochrome c release and caspase-3 activation in the oxidative stress-induced apoptosis in human tendon fibroblasts . Biochim. Biophys. Acta. , 1641 : 35 – 41 .
   PubMed Web of Science ®Google Scholar
• An , J , Chen , Y and Huang , Z . 2004 . Critical upstream signals of cytochrome C release induced by a novel Bcl-2 inhibitor . J. Biol. Chem. , 279 : 19133 – 19140 .
   PubMedGoogle Scholar
• Petry , A , Djordjevic , T , Weitnauer , M , Kietzmann , T , Hess , J and Görlach , A . 2006 . NOX2 and NOX4 mediate proliferative response in endothelial cells . Antioxid. Redox. Signal , 8 : 1473 – 1484 .
   PubMed Web of Science ®Google Scholar
• Savina , A , Jancic , C , Hugues , S , Guermonprez , P , Vargas , P , Moura , IC , Lennon-Duménil , AM , Seabra , MC , Raposo , G and Amigorena , S . 2006 . NOX2 controls phagosomal pH to regulate antigen processing during crosspresentation by dendritic cells . Cell , 126 : 205 – 218 .
   PubMed Web of Science ®Google Scholar
• Haque , MA , Li , P , Jackson , SK , Zarour , HM , Hawes , JW , Phan , UT , Maric , M , Cresswell , P and Blum , JS . 2002 . Absence of gamma-interferon-inducible lysosomal thiol reductase in melanomas disrupts T cell recognition of select immunodominant epitopes . J. Exp. Med. , 195 : 1267 – 1277 .
   Google Scholar
• O'Donnell , PW , Haque , A , Klemsz , MJ , Kaplan , MH and Blum , JS . 2004 . Cutting edge: induction of the antigen-processing enzyme IFN-gamma-inducible lysosomal thiol reductase in melanoma cells Is STAT1-dependent but CIITA-independent . J. Immunol. , 173 : 731 – 735 .
   Google Scholar
• Fajas , L , Debril , MB and Auwerx , J . 2001 . Peroxisome proliferator-activated receptor-gamma: from adipogenesis to carcinogenesis . J. Mol. Endocrinol. , 27 : 1 – 9 .
   PubMed Web of Science ®Google Scholar
• Mahadevan , B , Keshava , C , Musafia-Jeknic , T , Pecaj , A , Weston , A and Baird , WM . 2005 . Altered gene expression patterns in MCF-7 cells induced by the urban dust particulate complex mixture standard reference material 1649a . Cancer Res. , 65 : 1251 – 1258 .
   PubMed Web of Science ®Google Scholar
• Shimada , T , Hayes , CL , Yamazaki , H , Amin , S , Hecht , SS , Guengerich , FP and Sutter , TR . 1996 . Activation of chemically diverse procarcinogens by human cytochrome P-450 1B1 . Cancer Res. , 56 : 2979 – 2984 .
   PubMed Web of Science ®Google Scholar
• Spink , DC , Katz , BH , Hussain , MM , Spink , BC , Wu , SJ , Liu , N , Pause , R and Kaminsky , LS . 2002 . Induction of CYP1A1 and CYP1B1 in T-47D human breast cancer cells by benzo[a]pyrene is diminished by arsenite . Drug Metab. Dispos. , 30 : 262 – 269 .
   PubMed Web of Science ®Google Scholar
• IARC . 1987 . “ Overall evaluations of carcinogenicity: An updating of IARC monographs, volumes 1 to 42. Monographs on the Evaluation of the Carcinogenic Risk of Chemicals to Humans, Supplement 7 ” . In International Agency for Research on Cancer 56 Lyon
   Google Scholar
• Chaloupka , K , Steinberg , M , Santostefano , M , Rodriguez , LV , Goldstein , L and Safe , S . 1995 . Induction of Cypla-1 and Cypla-2 gene expression by a reconstituted mixture of polynuclear aromatic hydrocarbons in B6C3F1 mice . Chem. Biol. Interact. , 96 : 207 – 221 .
   PubMed Web of Science ®Google Scholar
• Tithof , PK , Elgayyar , M , Cho , Y , Guan , W , Fisher , AB and Peters-Golden , M . 2002 . FASEB J DOI: 10.1096/fj.01-0909fje
   Google Scholar
• Eisen , M , Spellman , P , Brown , P and Botstein , D . 1998 . Cluster analysis and display of genome-wide expression patterns . PNAS , 95 : 14863 – 14868 .
   PubMed Web of Science ®Google Scholar