Data for "Diversity Outbred Mice Identify Population Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity"

Description



Background: Benzene inhalation by workers at levels below the current exposure threshold leads to hematotoxicity.


Objective: We sought to evaluate Diversity Outbred (DO) mice as a tool for exposure threshold assessment and to identify genetic factors that influence benzene induced genotoxicity.


Methods: We exposed male DO mice to benzene (0, 1, 10, or 100 ppm; 75 mice/exposure group) via inhalation for 28 days (6 h/day for 5 days/week). The study was repeated using two independent cohorts of 300 animals each. We measured micronuclei frequency in reticulocytes from peripheral blood and bone marrow and applied benchmark concentration modeling to estimate exposure thresholds. We genotyped the mice and performed linkage analysis.


Results: We observed a dose dependent increase in benzene induced chromosomal damage and estimated a benchmark concentration limit of 0.205 ppm benzene using DO mice. This estimate is an order of magnitude below the value estimated using B6C3F1 mice. We identified a locus on Chr 10 (31.87 Mb) that contained a pair of over-expressed sulfotransferases that were inversely correlated with genotoxicity.


Conclusions: The genetically diverse DO mice provided a reproducible response to benzene exposure. The DO mice display inter-individual variation in toxicity response and, as such, more accurately reflects the range of response that is observed in human populations. Studies using DO mice can localize genetic associations with high precision. The identification of sulfotransferases as candidate genes suggests that DO mice may provide additional insight into benzene induced genotoxicity.


Reference


Use of these data should cite the following references:

Diversity Outbred Mice Identify Population Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity
John E. French, Daniel M. Gatti, Daniel L. Morgan, Grace E. Kissling, Keith R. Shockley, Gabriel A. Knudsen, Kim Shepard, Herman C. Price, Deborah King, Kristine L. Witt, Lars C. Pedersen, Steven C. Munger, Karen L. Svenson, and Gary A. Churchill.
Env. Health Persp., 2014 (in press)


Data

 

Supplemental Materials

French_etal_Supplemental_Material.docx contains the supplemental table and figures referred to in the manuscript.

Benchmark Dose Modeling Software Files

The zip file contains the input and output files from the US Environmental Protection Agency's Benchmark Dose Modeling Software (BMDS), version 2.4. The BMDS software can be found at www.epa.gov .

The file French_etal_BMDS_files.zip contains the following files:

  •   1. French_et_at_benzene.ssn: BMDS modeling session file.
  •   2. B6C3F1_BMDS_output.xlsx: BMDS output for B6C3F1 mice.
  •   3. DO_BMDS_output.xlsx: BMDS output for DO mice.
  •   4. Benzene_0_100_both_cohorts.dax: MN-RET data for both cohorts; 0, 1, 10 & 100 ppm.
  •   5. benzene_0_100_cohort1.dax: MN-RET data for cohort 1; 0, 1, 10 & 100 ppm.
  •   6. benzene_0_100_cohort2.dax: MN-RET data for cohorts 2; 0, 1, 10 & 100 ppm.
  •   7. Benzene_0_10_both_cohorts.dax: MN-RET data for both cohorts; 0, 1 & 10 ppm.
  •   8. benzene_0_10_cohort1.dax: MN-RET data for cohort 1; 0, 1 & 10 ppm.
  •   9. benzene_0_10_cohort2.dax: MN-RET data for cohort 2; 0, 1 & 10 ppm.
  • 10. benzene_B6C3F1.dax: MN-RET data for B6C3F1; 0, 1, 10 & 100 ppm.
  • 11. benzene_B6C3F1_0_10ppm.dax: MN-RET data for B6C3F1; 0, 1 & 10ppm.
  • 12. benzene_EXP_1SD_LogNorm.opt: Modeling options file for DO: BMR1SD.
  • 13. benzene_EXP_10perc_LogNorm.opt: Modeling options file for DO: BMR10.
  • 14. B6C3F1_EXP_BMR1SD.opt: Modeling options file for B6C3F1: BMR1SD.
  • 15. B6C3F1_EXP_BMR10.opt: Modeling options file for B6C3F1: BMR10.

Phenotype Data

The phenotype data consists of cell counts of normochromatic erythrocytes (NCE) and reticulocytes (RET) as well as the counts of micronucleated (MN) cells in each population.

The columns in the Excel file French_etal_MNRET_Data.xlsx are:

Column NameDescription
SampleThe DO mouse ID.
CohortEither 1 or 2, indicating the experimental cohort.
DoseThe exposure concentration of benzene in ppm.
  
For blood measured pre-exposure:  
#NCENumber of normal NCEs.
#MN.NCENumber of micronucleated NCEs.
Total NCETotal NCEs.
#RETNumber of normal reticulocytes.
#MN.RETNumber of MN reticulocytes.
Total RETTotal number of reticulocytes.
%RET% reticulocytes in blood.
Expt.Experimental batch.
For blood measured post-exposure:  
#NCENumber of normal NCEs.
#MN.NCENumber of micronucleated NCEs.
Total NCETotal NCEs.
#RETNumber of normal reticulocytes.
#MN.RETNumber of MN reticulocytes.
Total RETTotal number of reticulocytes.
%RET% reticulocytes in blood.
Expt.Experimental batch.
For bone marrow measured post-exposure:  
#NCENumber of normal NCEs.
#MN.NCENumber of micronucleated NCEs.
Total NCETotal NCEs.
#RETNumber of normal reticulocytes.
#MN.RETNumber of MN reticulocytes.
Total RETTotal number of reticulocytes.
%RET% reticulocytes in blood.

Genotype Data

The mice were genotyped by Geneseek (Lincol.n NE) on the Mouse Universal Genotyping Array (MUGA). The data consist of both the raw output from the MUGA as well as reconstructed genomes for each DO mouse. Alion Mouse 31jan2012_FinalReport.txt contains the allele calls and array intensities. Sample_Map.txt contains the DO sample names. These sample IDs correspond to the "SampleŁ" column in the phenotype file.

The DO genomes were reconstructed in terms of founder haplotypes using the software package DOQTL. DOQTL reconstructs DO genomes and performs QTL mapping in DO mice and runs in the R programming language.

The file French_etal_genoprobs.zip contains the haplotype probabilities for 593 DO mice. Each *.csv file is a comma separated table for one DO mouse. MUGA markers are in rows and 36 founder diplotypes are in columns. Each cell contains the posterior probability that the mouse contains one of the 36 possible diplotypes at that marker. The zip file also contains a binary file (founder_probs.Rdata) with the founder haplotype allele dosages that can be used to perform mapping in DOQTL.

Quantitative Trait Locus Mapping Results

The Quantitative Trait Locus (QTL) was performed using DOQTL. These files can be opened and viewed in in R programming environment using DOQTL. The file French_etal_QTL_Results.zip contains two compressed R files (*.Rdata).

benzene.dose100.QTL.Rdata: QTL results for the phenotypes, including blood MN-RETand bone marrow MN-RET.
benzene.dose100.perms.Rdata: Permutations for the phenotypes.