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Cancer Epidemiology, Biomarkers & Prevention
Cancer Epidemiology, Biomarkers & Prevention
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Research Articles

Gene Expression Profiles in Peripheral Lymphocytes by Arsenic Exposure and Skin Lesion Status in a Bangladeshi Population

Maria Argos, Muhammad G. Kibriya, Faruque Parvez, Farzana Jasmine, Muhammad Rakibuz-Zaman and Habibul Ahsan
Maria Argos
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Muhammad G. Kibriya
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Faruque Parvez
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Farzana Jasmine
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Muhammad Rakibuz-Zaman
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Habibul Ahsan
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DOI: 10.1158/1055-9965.EPI-06-0106 Published July 2006
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    Figure 1.

    Electrograms of RNA. A. Electropherogram shows two distinct peaks corresponding to 18S and 28S. The two peaks represent 16.69% and 28.25%, respectively, of the total area for RNA (collectively 44.94%) with a 28S/18S ratio of 1.69. B. In this electropherogram, the dark line represents purified 1:10 diluted unfragmented labeled cRNA superimposed with the ladder. After the initial spike, the ladder peaks correspond to 200, 500, 1,000, 2,000, and 4,000 bp, respectively. The unfragmented labeled cRNA ranges from 500 to 3,000 bp with the median lying between 1K and 2K. C. In this electropherogram, the dark line displays 1:10 diluted fragmented labeled cRNA superimposed with the ladder. The electropherogram shows effective fragmentation with the median ∼60 to 70 bp.

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  • Table 1.

    Characteristics of study participants

    Skin lesions (n = 11)No arsenical skin lesions* (n = 5)No arsenical skin lesions* (n = 20)
    Well water arsenic (μg/L), mean (SD)342.7 (258.1)39.6 (49.5)94.5 (90.6)
    Urinary total arsenic (μg/g), mean (SD)467.8 (325.4)109.8 (66.1)279.7 (233.3)
    Age (y), mean (SD)35.0 (7.8)38.0 (6.7)26.4 (4.4)
    Females, n (%)9 (81.8)5 (100.0)14 (70.0)
    Smokers, n (%)2 (18.2)0 (0.0)3 (15.0)
    • ↵* Two groups of nonlesion arrays were analyzed separately because they differed on microarray quality-control metrics.

  • Table 2.

    Genes differentially down-regulated in the skin lesion versus nonlesion comparison

    Genbank accession no.Gene symbolGene descriptionRatio of geometric mean (lesion/nonlesion)
    NM_002089CXCL2Chemokine (C-X-C motif) ligand 20.037
    NM_004591CCL20Chemokine (C-C motif) ligand 200.059
    NM_000576IL1BIL-1β0.077
    NM_019006ZA20D3Zinc finger, A20 domain containing 30.122
    NM_000636SOD2Superoxide dismutase 2, mitochondrial0.112
    NM_000610CD44CD44 antigen (homing function and Indian blood group system)0.112
    NM_001001437CCL3Chemokine (C-C motif) ligand 30.091
    NM_002852PTX3Pentraxin-related gene, rapidly induced by IL-1β0.083
    NM_000594TNFTNF (superfamily, member 2)0.077
    NM_000891KCNJ2Potassium inwardly rectifying channel, subfamily J, member 20.101
    NM_003940USP13Ubiquitin-specific peptidase 130.158
    NM_003965CCRL2Chemokine (C-C motif) receptor like 20.128
    NM_003897IER3Immediate-early response 30.140
    M10098SRP68Signal recognition particle 68 kDa0.118
    NM_004566PFKFB36-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 30.147
    NM_014887PFAAP5Phosphonoformate immuno-associated protein 50.170
    M27830SOX18Sex-determining region Y-box 180.152
    NM_005346HSPA1BHeat shock protein 1B, 70-kDa0.086
    NM_007115TNFAIP6TNF-α-induced protein 60.115
    NM_005066SFPQSplicing factor proline/glutamine rich (polypyrimidine tract–binding protein associated)0.189
    NM_005751AKAP9A kinase (PRKA) anchor protein (yotiao) 90.198
    NM_003414ZNF267Zinc finger protein 2670.181
    AL049987MGC22265Hypothetical protein MGC222650.210
    NM_006186NR4A2Nuclear receptor subfamily 4, group A, member 20.170
    NM_002919RFX3Regulatory factor X, 3 (influences HLA class II expression)0.204
    NM_001001723TMEM1Transmembrane protein 10.216
    NM_004897MINPP1Multiple inositol polyphosphate histidine phosphatase, 10.228
    NM_003143SSBP1ssDNA-binding protein 10.210
    NM_018555ZNF331Zinc finger protein 3310.199
    NM_002922RGS1Regulator of G-protein signaling 10.179
    NM_002090CXCL3Chemokine (C-X-C motif) ligand 30.153
    NM_002078GOLGA4Golgi autoantigen, golgin subfamily A, 40.234
    NM_016166PIAS1Protein inhibitor of activated STAT 10.205
    NM_014961RIPXRap2-interacting protein X0.238
    NM_013293TRA2ATransformer 2α0.221
    NM_002984CCL4Chemokine (C-C motif) ligand 40.184
    NM_000577IL1RNIL-1 receptor antagonist0.174
    NM_004233CD83CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)0.198
    NM_020651PELI1Pellino homologue 1 (Drosophila)0.245
    NM_024116MGC5306Hypothetical protein MGC53060.242
    NM_005414SKILSKI-like0.244
    NM_002600PDE4BPhosphodiesterase 4B, cyclic AMP–specific (phosphodiesterase E4 dunce homologue, Drosophila)0.242
    NM_015675GADD45BGrowth arrest and DNA damage–inducible, β0.245
    AU146791UBE2E1Ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homologue, yeast)0.268
    NM_005004NDUFB8NADH dehydrogenase (ubiquinone) 1β subcomplex 8, 19 kDa0.275
    NM_002166ID2Inhibitor of DNA binding 2, dominant-negative helix-loop-helix protein0.267
    NM_015028TNIKTRAF2 and NCK-interacting kinase0.264
    NM_000575IL1AIL-1α0.187
    NM_000333ATXN7Ataxin 70.275
    NM_003715VDPVesicle docking protein p1150.294
    • NOTE: Duplicate genes removed from the list.

  • Table 3.

    Gene Ontology categories from skin lesion and nonlesion comparison

    GO ClassificationNo. genesFisher statistic permutation PKolmogorov-Smirnov permutation P
    RNA splicing via transesterification reactions540.000010.00050
    RNA splicing via transesterification reactions with bulged adenosine as nucleophile540.000010.00050
    Nuclear mRNA splicing via spliceosome540.000010.00050
    RNA splicing750.000010.00009
    mRNA metabolism880.000090.00001
    Ubiquitin thiolesterase activity210.000100.00067
    Ubiquitin-specific protease activity210.000100.00067
    Thiolester hydrolase activity210.000100.00067
    mRNA processing780.000100.00013
    Ribonucleoprotein complex890.001720.00009
    tRNA modification110.001960.03898
    Translation470.003000.08347
    Ubiquitin-dependent protein catabolism380.003090.00065
    Modification-dependent protein catabolism380.003090.00065
    tRNA aminoacylation for protein translation100.003160.07688
    Amino acid activation100.003160.07688
    tRNA aminoacylation100.003160.07688
    RNA modification160.004390.04396
    Hexose transport90.006560.00010
    Monosaccharide transport90.006560.00010
    Glucose transport90.006560.00010
    P-P-bond hydrolysis-driven transporter activity60.008160.00279
    RNA localization90.009170.00485
    RNA-nucleus export90.009170.00485
    mRNA-nucleus export90.009170.00485
    Nucleic acid transport90.009170.00485
    RNA transport90.009170.00485
    mRNA transport90.009170.00485
    Establishment of RNA localization90.009170.00485
    Nucleolus260.023190.00363
    Protein amino acid glycosylation220.027780.00144
    Glycoprotein metabolism250.035260.00422
    Spliceosome complex230.050390.00039
    Protein folding660.056080.00283
    O-linked glycosylation60.071420.00371
    Carrier activity450.086730.00482
    Cyclic nucleotide phosphodiesterase activity110.092730.00320
    Glycerophosphoinositol inositolphosphodiesterase activity110.092730.00320
    Ubiquitin ligase complex830.098140.00134
    Phosphoric diester hydrolase activity130.140500.00118
    Unfolded protein binding310.156270.00389
  • Table 4.

    Pathway comparison from skin lesion and nonlesion comparison restricted to female never-smokers

    PathwayNo. genesFisher statistic permutation PKolmogorov-Smirnov permutation P
    Signal transduction through IL-1 receptor120.003960.02551
    Genbank accession no.Gene symbolGene description
    NM_002228JUNv-jun sarcoma virus 17 oncogene homologue (avian)
    NM_020529NFKBIANuclear factor of κ light polypeptide gene enhancer in B-cell inhibitor, α
    NM_001315MAPK14Mitogen-activated protein kinase 14
    NM_000576IL1BIL-1β
    NM_000600IL6IL-6 (IFN-β2)
    NM_004620TRAF6TNF receptor–associated factor 6
    NM_000594TNFTNF (superfamily, member 2)
    NM_000575IL1AIL-1α
    NM_003998NFKB1Nuclear factor of κ light polypeptide gene enhancer in B cells 1 (p105)
    NM_001278CHUKConserved helix-loop-helix ubiquitous kinase
    NM_003188MAP3K7Mitogen-activated protein kinase kinase kinase 7
    XM_042066MAP3K1Mitogen-activated protein kinase kinase kinase 1
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Cancer Epidemiology Biomarkers & Prevention: 15 (7)
July 2006
Volume 15, Issue 7
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Gene Expression Profiles in Peripheral Lymphocytes by Arsenic Exposure and Skin Lesion Status in a Bangladeshi Population
Maria Argos, Muhammad G. Kibriya, Faruque Parvez, Farzana Jasmine, Muhammad Rakibuz-Zaman and Habibul Ahsan
Cancer Epidemiol Biomarkers Prev July 1 2006 (15) (7) 1367-1375; DOI: 10.1158/1055-9965.EPI-06-0106

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Gene Expression Profiles in Peripheral Lymphocytes by Arsenic Exposure and Skin Lesion Status in a Bangladeshi Population
Maria Argos, Muhammad G. Kibriya, Faruque Parvez, Farzana Jasmine, Muhammad Rakibuz-Zaman and Habibul Ahsan
Cancer Epidemiol Biomarkers Prev July 1 2006 (15) (7) 1367-1375; DOI: 10.1158/1055-9965.EPI-06-0106
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