EHP – 2013 – February

Monthly Archives: February 2013

test-from-s1

Mary Edbrooke February 14, 2013 Comments Off

Supplemental Material

Polymorphisms in Iron Homeostasis Genes and Urinary Cadmium Concentrations among Nonsmoking Women in Argentina and Bangladesh

Gerda Rentschler, Maria Kippler, Anna Axmon, Rubhana Raqib, Eva-Charlotte Ekström, Staffan Skerfving, Marie Vahter, Karin Broberg

Table of Contents: Page

Supplemental Material, Table S1 2

Genes and polymorphisms that were successfully genotyped.

Supplemental Material, Table S2

Polymorphisms that were genotyped but later excluded from the data evaluation. 4

Supplemental Material, Table S3 5

SNP-related modification of transcription factor binding sites

Supplemental Material, Table S4 7

Gene expression data for iron-related genes in the Andean women

Supplemental Material, Table S1. Genes and polymorphisms that were successfully genotyped (quality requirements: at least 90% of samples with clearly defined genotypes^a) ).

Gene Unigene Nr^b Protein name Location	rs nr^c	Polymorphism type^d	Allele frequencies Argentinean Andes	QC^a (%)	Allele frequencies Bangladesh	QC^a (%)
SLC11A2	rs149411	Intron C>T	75/25	96	37/63	99
Hs.505545	rs224572	Intron G>A	41/59	96	28/72	94
DMT1	rs224574	Intron C>T	1/99	98	10/90	99
NRAMP2	rs224575	Intron G>A	75/25	97	37/63	99
Chr 12q13	rs364627	Intron G>A	1/99	96	10/90	93
	rs407135	Intron C>A	8/92	97	34/66	100
	rs1005559	Intron T>A	7/93	97	24/76	96
	rs2269683	Intron C>T	34/66	96	9/91	99
	rs3809320	Upstream T>A	35/65	97	9/91	96
	rs6580779	5’ UTR G>T	1/99	96	10/90	95
	rs12366756	Intron G>A	7/93	98	24/76	99
	rs12830073	Intron T>C	6/94	96	24/76	90

SLC40A1	rs1123110	Intron C>T	12/88	95	34/66	97
Hs.643005	rs1439816	Intron C>G	12/88	97	22/78	100
FPN1	rs4145237	Intron C>G	15/85	97	33/67	99
Chr 2q32	rs4667287	Intron C>A	14/86	98	19/81	100
	rs11884632	Intron C>G	0/100	98	13/87	98

TF	rs12595	Intron G>A	58/43	98	41/59	99
Hs.518267	rs1049296	S589P T>C	4/96	98	21/79	99
Transferrin	rs1130459	5’ UTR A>G	6/94	98	25/75	97
Chr 3q22.1	rs1799852	L247L T>C	12/88	97	21/79	99
	rs2280673	Intron C>A	15/85	98	48/52	98
	rs2715627	Intron C>T	3/97	97	15/85	99
	rs3811647	Intron A>G	58/42	97	42/58	96
	rs4241357	Intron G>T	29/71	97	28/72	100
	rs4355280	Intron G>A	58/42	96	53/47	96
	rs4428180	Intron G>A	37/63	96	23/77	97
	rs4459901	Intron C>T	54/46	98	37/63	99
	rs4532136	Intron A>G	12/88	98	18/82	99
	rs6785596	Intron A>T	3/97	98	15/85	99
	rs6796795	Intron G>A	3/97	97	15/85	100
	rs8177184	Intron G>A	36/64	98	22/78	99
	rs8177186	5’ UTR T>G	12/88	96	18/82	97
	rs8177190	Intron T>C	25/75	97	9/91	97
	rs8177191	Intron A>G	2/98	98	7/93	99
	rs8177213	Intron C>A	27/73	97	14/86	96
	rs8177235	Intron A>G	14/86	97	16/84	97
	rs41298977	A76V T>C	0/100	98	0/100	99

Supplemental Material, Table S1 (cont.)

Gene Unigene Nr^b Protein name Location	rs nr^c	Polymorphism type^d	Allele frequencies Argentinean Andes	QC^a (%)	Allele frequencies Bangladesh	QC^a (%)

TFR2	rs7385804	Intron C>A	18/82	96 (*)	37/63	100
Hs.544932	rs10247962	Intron G>A	2/98	98	24/76	99
TFR2	rs34242818	I238M G>C	0/100	98	1/99	98
Chr 7q22

TFRC	rs2284889	Intron T>C	27/73	97	50/50	98
Hs.529618	rs3736651	Intron T>A	43/57	96	21/79	99
TFRC	rs3761717	Intron C>G	73/27	97	49/51	94
Chr 3q29	rs3804141	Intron A>G	26/74	97 (*)	14/86	100
	rs9859260	Intron G>A	73/27	97	50/50	95
	rs9859401	Intron T>G	27/73	97	49/51	95
	rs11185506	Intron C>G	27/73	97	49/51	98
	rs13072608	Intron G>A	73/27	97	49/51	96
	rs41301381	L212V G>C	0/100	98	0/100	100

^a QC percent represents the percentage of samples with clearly defined genotypes (based on Sequenom mass spectrometry analysis). None of the SNPs showed Hardy-Weinberg disequilibrium in both populations. SNPs that demonstrated disequilibrium in one of the populations are marked with (*).

^bUnigene accession number from NCBI (National Center for Biotechnology Information) Unigene Database (website: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene).

^C rs numbers from NCBI SNP Database (website: http://www.ncbi.nlm.nih.gov/SNP).

^d When applicable, amino acid position/gene region is denoted. The rare allele in Bangladesh is denoted first.

Supplemental Material, Table S2. Polymorphisms that were genotyped but later excluded from the data evaluation.

Gene	rs nr^a	Polymorphism type^b	QC^cArgentinean Andes (%)	QC^c Bangladesh (%)	Reason for exclusion
SLC11A2	rs224446	3′ UTR A>G	82	88	too low analytical quality
	rs17216051	T298I C>T	98	99	no variants detected
	rs17216086	W500R T>C	97	99	no variants detected
	rs17222449	Q290R A>G	97	99	no variants detected
	rs17222470	H62Y C>T	98	99	no variants detected
SLC40A1	rs11568350	H248Q T>G	97	99	no variants detected
	rs45606432	L443P T>C	97	100	no variants detected
TFRC	rs3817672	S142G A>G	78	89	too low analytical quality

^a rs numbers from NCBI SNP Database (website: http://www.ncbi.nlm.nih.gov/SNP).

^b When applicable, amino acid position/gene region is denoted.

^c QC percent represents the percentage of samples with clearly defined genotypes (based on Sequenom mass spectrometry analysis).

Supplemental Material, Table S3. SNP-related modification of transcription factor binding sites according to the ElDorado database^a. SNPs analyzed were associated with concentrations of Cd biomarkers or ferritin (see Result section of the main text).

Gene SNP	Allele	Effect	Site affected Family/Factor	Description
*TFRC*
rs3804141	G -> A	new	HOXC/HOX_PBX	HOX/PBX binding sites
	G -> A	new	SNAP/PSE02	Proximal sequence element (PSE) of RNA polymerase III-transcribed genes
TF
rs12595	A -> G	lost	FKHD/HNF3.01	Hepatocyte nuclear factor 3 (alpha, beta) (FOXA1, FOXA2)
	A -> G	new	HOMF/HMX2.02	Hmx2/Nkx5-2 homeodomain transcription factor
	A -> G	new	MYT1/MYT1.01	MyT1 zinc finger transcription factor involved in primary neurogenesis
rs3811647	G -> A	new	NR2F/TR2.01	Nuclear hormone receptor TR2, DR5 binding sites
rs4459901	T -> C	new	CREB/CREB.02	cAMP-responsive element binding protein
	T -> C	new	CREB/ATF1.01	Activating transcription factor 1
	T -> C	new	CREB/CREB1.01	cAMP-responsive element binding protein 1
	T -> C	new	E4FF/E4F.01	GLI-Krueppel-related transcription factor, regulator of adenovirus E4 promoter
	T -> C	new	HIFF/HIF1.01	Hypoxia induced factor-1 (HIF-1)
	T -> C	lost	LHXF/ISL1.01	Pancreatic and intestinal lim-homeodomain factor
	T -> C	lost	PDX1/PDX1.01	Pdx1 (IDX1/IPF1) pancreatic and intestinal homeodomain TF
	T -> C	lost	RXRF/RAR_RXR.03	Retinoic acid receptor / retinoid X receptor heterodimer, DR5 sites

Supplemental Material, Table S3 (cont.)

Gene SNP	Allele	Effect	Site affected Family/Factor	Description
rs8177186	G -> T	new	CART/PHOX2.01	Phox2a (ARIX) and Phox2b
	G -> T	new	CART/CART1.01	Cart-1 (cartilage homeoprotein 1)
	G -> T	new	PARF/DBP.01	Albumin D-box binding protein
	G -> T	lost	TEAF/TEAD.01	TEA domain-containing factors, transcriptional enhancer factors 1,3,4,5
*TFR2*
rs7385804	C -> A	new	BCDF/PCE1.01	Photoreceptor conserved element 1
	C -> A	new	DLXF/DLX3.01	Distal-less 3 homeodomain transcription factor
	C -> A	new	HBOX/GSH2.01	Homeodomain transcription factor Gsh-2
	C -> A	new	HOMF/MSX2.01	Muscle segment homeobox 2, homologue of Drosophila (HOX 8)
	C -> A	new	NKXH/NKX25.02	Homeodomain factor Nkx-2.5/Csx, tinman homolog low affinity sites
	C -> A	new	OCT1/OCT1.06	Octamer-binding factor 1
	C -> A	lost	SORY/HBP1.01	HMG box-containing protein 1
	C -> A	lost	TEAF/TEAD.01	TEA domain-containing factors, transcriptional enhancer factors 1,3,4,5

^a Version 08-2011 of the Genomatix software suite (http://www.genomatix.de/en/index.html)

Supplemental Material, Table S4. Gene expression data for iron-related genes measured in peripheral blood in the Andean women (N=72).

Gene	Probe	Probe	Expression^a		Spearman correlation coefficients (p-values)
		location	Median	(Range)	TF^b	TFR2^b	TFRC^b	SLC11A2^b	SLC40A1^b
TF	ILMN_1768425	exon 17	112	(86-147)
TFR2	ILMN_1724738	exon 18	111	(91-138)	0.18 (0.1)
TFRC	ILMN_1674243	exon 19	294	(168-773)	0.05 (0.7)	-0.12 (0.3)
SLC11A2	ILMN_1745034	exon 19b	132	(101-201)	-0.19 (0.1)	-0.21 (0.08)	0.32 (0.006)
SLC40A1	ILMN_1761833	exon 8	255	(117-570)	0.15 (0.2)	0.09 (0.4)	0.56 (3.8E-07)	0.17 (0.2)
SLC40A1	ILMN_2053103	exon 8	400	(184-1021)	0.22 (0.06)	0.11 (0.3)	0.55 (7.33E-07)	0.25 (0.03)	0.92 (1.5E-29)

^a Gene expression is presented in relative fluorescence units.

^bP-values are written in parentheses.

Association of Osteoarthritis with Perfluorooctanoate and Perfluorooctane Sulfonate in NHANES 2003–2008

Sam Duvall February 14, 2013 Comments Off

Sarah A. Uhl¹, Tamarra James-Todd², and Michelle L. Bell¹

Managing the Health Effects of Temperature in Response to Climate Change: Challenges Ahead

Sam Duvall February 12, 2013 Comments Off

Cunrui Huang,^1,2,3 Adrian G Barnett,¹ Zhiwei Xu,¹ Cordia Chu,^2,3 Xiaoming Wang,⁴ Lyle R Turner,¹ and Shilu Tong¹

ONE Nano: NIEHS’s Strategic Initiative on the Health and Safety Effects of Engineered Nanomaterials

Sam Duvall February 12, 2013 Comments Off

Thaddeus T. Schug¹, Anne F. Johnson², David M. Balshaw³, Stavros Garantziotis⁴, Nigel J. Walker⁵, Christopher Weis⁶, Srikanth S. Nadadur¹,and Linda S. Birnbaum⁶

An Unlikely Duo: Air Pollution’s Link to Low Birth Weight, with Tracey Woodruff

Podcast: Play in new window

Maternal Exposure to Particulate Air Pollution and Term Birth Weight: A Multi-Country Evaluation of Effect and Heterogeneity

Susan Booker February 6, 2013 Comments Off

Payam Dadvand,^1,2,3 Jennifer Parker,⁴ Michelle L. Bell,⁵ Matteo Bonzini,⁶ Michael Brauer,⁷ Lyndsey Darrow,⁸ Ulrike Gehring,⁹ Svetlana V. Glinianaia,¹⁰ Nelson Gouveia,¹¹Eun-hee Ha,¹² Jong Han Leem,¹³ Edith H. van den Hooven,^14,15 Bin Jalaludin,^16,17,18 Bill M. Jesdale,¹⁹ Johanna Lepeule,^20,21,22 Rachel Morello-Frosch,^19,23 Geoffrey G. Morgan,^24,25 Angela Cecilia Pesatori,²⁶ Frank H. Pierik,¹⁵ Tanja Pless-Mulloli,¹⁰ David Q. Rich,²⁷ Sheela Sathyanarayana,²⁸ Juhee Seo,¹² Rémy Slama,^21,22 Matthew Strickland,⁸ Lillian Tamburic,²⁹ Daniel Wartenberg,³⁰ Mark J Nieuwenhuijsen,^1,2,3 Tracey J. Woodruff³¹

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Sam Duvall February 5, 2013 Comments Off

Dennie G.A.J. Hebels¹, Panagiotis Georgiadis², Hector C. Keun^3,4, Toby J. Athersuch^3,4, Paolo Vineis³, Roel Vermeulen⁵, Lützen Portengen⁵, Ingvar A. Bergdahl⁶, Göran Hallmans⁷, Domenico Palli⁸, Benedetta Bendinelli⁸, Vittorio Krogh⁹, Rosario Tumino¹⁰, Carlotta Sacerdote^11,12, Salvatore Panico¹³, Jos C.S. Kleinjans¹, Theo M.C.M. de Kok¹, Martyn T. Smith¹⁴, and Soterios A. Kyrtopoulos²

Arsenic Exposure from Drinking Water and QT-Interval Prolongation: Results from the Health Effects of Arsenic Longitudinal Study

Sam Duvall February 5, 2013 Comments Off

Yu Chen¹, Fen Wu¹, Faruque Parvez², Alauddin Ahmed³, Mahbub Eunus³, Tyler R. McClintock⁴, Tazul Islam Patwary³, Tariqul Islam³, Anajan Kumar Ghosal³, Shahidul Islam³, Rabiul Hasan³, Diane Levy², Golam Sarwar³, Vesna Slavkovich², Alexander van Geen⁵, Joseph H. Graziano², and Habibul Ahsan⁶

Endocrine-Disrupting Chemicals (EDCs): In Vitro Mechanism of Estrogenic Activation and Differential Effects on ER Target Genes

Sam Duvall February 5, 2013 Comments Off

Yin Li¹, Colin J. Luh¹, Katherine A. Burns¹, Yukitomo Arao¹, Zhongliang Jiang¹, Christina T. Teng², Raymond R. Tice², and Kenneth S. Korach¹

Environmental and Occupational Interventions for Primary Prevention of Cancer: A Cross-Sectorial Policy Framework

Sam Duvall February 5, 2013 Comments Off

Carolina Espina¹, Miquel Porta², Joachim Schüz³, Ildefonso Hernández Aguado⁴, Robert V. Percival⁵, Carlos Dora¹, Terry Slevin⁶, Julietta Rodriguez Guzman⁷, Tim Meredith¹, Philip J. Landrigan⁸, Maria Neira¹

1 2 3 4 5

Monthly Archives: February 2013

test-from-s1

Association of Osteoarthritis with Perfluorooctanoate and Perfluorooctane Sulfonate in NHANES 2003–2008

Managing the Health Effects of Temperature in Response to Climate Change: Challenges Ahead

ONE Nano: NIEHS’s Strategic Initiative on the Health and Safety Effects of Engineered Nanomaterials

An Unlikely Duo: Air Pollution’s Link to Low Birth Weight, with Tracey Woodruff

Maternal Exposure to Particulate Air Pollution and Term Birth Weight: A Multi-Country Evaluation of Effect and Heterogeneity

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Arsenic Exposure from Drinking Water and QT-Interval Prolongation: Results from the Health Effects of Arsenic Longitudinal Study

Endocrine-Disrupting Chemicals (EDCs): In Vitro Mechanism of Estrogenic Activation and Differential Effects on ER Target Genes

Environmental and Occupational Interventions for Primary Prevention of Cancer: A Cross-Sectorial Policy Framework

Recent Advance Publications

Recent Tweets