Article Figures & Data
Figures
- 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.
Tables
- 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 symbol Gene description Ratio of geometric mean (lesion/nonlesion) NM_002089 CXCL2 Chemokine (C-X-C motif) ligand 2 0.037 NM_004591 CCL20 Chemokine (C-C motif) ligand 20 0.059 NM_000576 IL1B IL-1β 0.077 NM_019006 ZA20D3 Zinc finger, A20 domain containing 3 0.122 NM_000636 SOD2 Superoxide dismutase 2, mitochondrial 0.112 NM_000610 CD44 CD44 antigen (homing function and Indian blood group system) 0.112 NM_001001437 CCL3 Chemokine (C-C motif) ligand 3 0.091 NM_002852 PTX3 Pentraxin-related gene, rapidly induced by IL-1β 0.083 NM_000594 TNF TNF (superfamily, member 2) 0.077 NM_000891 KCNJ2 Potassium inwardly rectifying channel, subfamily J, member 2 0.101 NM_003940 USP13 Ubiquitin-specific peptidase 13 0.158 NM_003965 CCRL2 Chemokine (C-C motif) receptor like 2 0.128 NM_003897 IER3 Immediate-early response 3 0.140 M10098 SRP68 Signal recognition particle 68 kDa 0.118 NM_004566 PFKFB3 6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 0.147 NM_014887 PFAAP5 Phosphonoformate immuno-associated protein 5 0.170 M27830 SOX18 Sex-determining region Y-box 18 0.152 NM_005346 HSPA1B Heat shock protein 1B, 70-kDa 0.086 NM_007115 TNFAIP6 TNF-α-induced protein 6 0.115 NM_005066 SFPQ Splicing factor proline/glutamine rich (polypyrimidine tract–binding protein associated) 0.189 NM_005751 AKAP9 A kinase (PRKA) anchor protein (yotiao) 9 0.198 NM_003414 ZNF267 Zinc finger protein 267 0.181 AL049987 MGC22265 Hypothetical protein MGC22265 0.210 NM_006186 NR4A2 Nuclear receptor subfamily 4, group A, member 2 0.170 NM_002919 RFX3 Regulatory factor X, 3 (influences HLA class II expression) 0.204 NM_001001723 TMEM1 Transmembrane protein 1 0.216 NM_004897 MINPP1 Multiple inositol polyphosphate histidine phosphatase, 1 0.228 NM_003143 SSBP1 ssDNA-binding protein 1 0.210 NM_018555 ZNF331 Zinc finger protein 331 0.199 NM_002922 RGS1 Regulator of G-protein signaling 1 0.179 NM_002090 CXCL3 Chemokine (C-X-C motif) ligand 3 0.153 NM_002078 GOLGA4 Golgi autoantigen, golgin subfamily A, 4 0.234 NM_016166 PIAS1 Protein inhibitor of activated STAT 1 0.205 NM_014961 RIPX Rap2-interacting protein X 0.238 NM_013293 TRA2A Transformer 2α 0.221 NM_002984 CCL4 Chemokine (C-C motif) ligand 4 0.184 NM_000577 IL1RN IL-1 receptor antagonist 0.174 NM_004233 CD83 CD83 antigen (activated B lymphocytes, immunoglobulin superfamily) 0.198 NM_020651 PELI1 Pellino homologue 1 (Drosophila) 0.245 NM_024116 MGC5306 Hypothetical protein MGC5306 0.242 NM_005414 SKIL SKI-like 0.244 NM_002600 PDE4B Phosphodiesterase 4B, cyclic AMP–specific (phosphodiesterase E4 dunce homologue, Drosophila) 0.242 NM_015675 GADD45B Growth arrest and DNA damage–inducible, β 0.245 AU146791 UBE2E1 Ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homologue, yeast) 0.268 NM_005004 NDUFB8 NADH dehydrogenase (ubiquinone) 1β subcomplex 8, 19 kDa 0.275 NM_002166 ID2 Inhibitor of DNA binding 2, dominant-negative helix-loop-helix protein 0.267 NM_015028 TNIK TRAF2 and NCK-interacting kinase 0.264 NM_000575 IL1A IL-1α 0.187 NM_000333 ATXN7 Ataxin 7 0.275 NM_003715 VDP Vesicle docking protein p115 0.294 NOTE: Duplicate genes removed from the list.
- Table 3.
Gene Ontology categories from skin lesion and nonlesion comparison
GO Classification No. genes Fisher statistic permutation P Kolmogorov-Smirnov permutation P RNA splicing via transesterification reactions 54 0.00001 0.00050 RNA splicing via transesterification reactions with bulged adenosine as nucleophile 54 0.00001 0.00050 Nuclear mRNA splicing via spliceosome 54 0.00001 0.00050 RNA splicing 75 0.00001 0.00009 mRNA metabolism 88 0.00009 0.00001 Ubiquitin thiolesterase activity 21 0.00010 0.00067 Ubiquitin-specific protease activity 21 0.00010 0.00067 Thiolester hydrolase activity 21 0.00010 0.00067 mRNA processing 78 0.00010 0.00013 Ribonucleoprotein complex 89 0.00172 0.00009 tRNA modification 11 0.00196 0.03898 Translation 47 0.00300 0.08347 Ubiquitin-dependent protein catabolism 38 0.00309 0.00065 Modification-dependent protein catabolism 38 0.00309 0.00065 tRNA aminoacylation for protein translation 10 0.00316 0.07688 Amino acid activation 10 0.00316 0.07688 tRNA aminoacylation 10 0.00316 0.07688 RNA modification 16 0.00439 0.04396 Hexose transport 9 0.00656 0.00010 Monosaccharide transport 9 0.00656 0.00010 Glucose transport 9 0.00656 0.00010 P-P-bond hydrolysis-driven transporter activity 6 0.00816 0.00279 RNA localization 9 0.00917 0.00485 RNA-nucleus export 9 0.00917 0.00485 mRNA-nucleus export 9 0.00917 0.00485 Nucleic acid transport 9 0.00917 0.00485 RNA transport 9 0.00917 0.00485 mRNA transport 9 0.00917 0.00485 Establishment of RNA localization 9 0.00917 0.00485 Nucleolus 26 0.02319 0.00363 Protein amino acid glycosylation 22 0.02778 0.00144 Glycoprotein metabolism 25 0.03526 0.00422 Spliceosome complex 23 0.05039 0.00039 Protein folding 66 0.05608 0.00283 O-linked glycosylation 6 0.07142 0.00371 Carrier activity 45 0.08673 0.00482 Cyclic nucleotide phosphodiesterase activity 11 0.09273 0.00320 Glycerophosphoinositol inositolphosphodiesterase activity 11 0.09273 0.00320 Ubiquitin ligase complex 83 0.09814 0.00134 Phosphoric diester hydrolase activity 13 0.14050 0.00118 Unfolded protein binding 31 0.15627 0.00389 - Table 4.
Pathway comparison from skin lesion and nonlesion comparison restricted to female never-smokers
Pathway No. genes Fisher statistic permutation P Kolmogorov-Smirnov permutation P Signal transduction through IL-1 receptor 12 0.00396 0.02551 Genbank accession no. Gene symbol Gene description NM_002228 JUN v-jun sarcoma virus 17 oncogene homologue (avian) NM_020529 NFKBIA Nuclear factor of κ light polypeptide gene enhancer in B-cell inhibitor, α NM_001315 MAPK14 Mitogen-activated protein kinase 14 NM_000576 IL1B IL-1β NM_000600 IL6 IL-6 (IFN-β2) NM_004620 TRAF6 TNF receptor–associated factor 6 NM_000594 TNF TNF (superfamily, member 2) NM_000575 IL1A IL-1α NM_003998 NFKB1 Nuclear factor of κ light polypeptide gene enhancer in B cells 1 (p105) NM_001278 CHUK Conserved helix-loop-helix ubiquitous kinase NM_003188 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 XM_042066 MAP3K1 Mitogen-activated protein kinase kinase kinase 1
July 2006
Volume 15, Issue 7
Volume 15, Issue 7
Gene Expression Profiles in Peripheral Lymphocytes by Arsenic Exposure and Skin Lesion Status in a Bangladeshi Population
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