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Co-exposure of arsenic and uranium differentially alters gene expression in CD3/CD28 activated CD4+ T-cells.

General Information
Data Package:
Local Identifier:edi.10.3
Title:Co-exposure of arsenic and uranium differentially alters gene expression in CD3/CD28 activated CD4+ T-cells.
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Communities in the western region of the United States experience environmental exposure to metal mixtures from living in proximity to numerous unremediated abandoned uranium mines. Metals including arsenic and uranium co-occur in and around these sites at levels higher than the USEPA maximum contaminant levels (MCL). To address the potential effect of these metals on the activation of naïve CD4+ T-cells, we used RNA sequencing methods to determine the effect of exposure to arsenic, uranium or a mixture of arsenic and uranium. Arsenic induced a dose dependent effect on activation associated gene expression; targeting immune response genes at the lower dose. Increases in oxidative stress gene expression were observed at the with both arsenic doses. While uranium alone did not significantly alter activation associated gene expression, the mixture of uranium with arsenic demonstrated a combined effect relative to arsenic alone. The results demonstrate the need to investigate metal and metalloid mixtures at environmentally relevant concentrations to better understand the effect of these mixtures on T-cell activation, function and immune dysregulation.

Publication Date:2020-04-24

Time Period
Begin:
2020-04-23
End:
2020-04-23

People and Organizations
Contact:Schliz, Jodi R (University of New Mexico Health Sciences Center Division of Physical Therapy) [  email ]
Creator:Schliz, Jodi R (University of New Mexico Health Sciences Center Division of Physical Therapy)
Creator:Dashner-Titus, Erica J (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences)
Creator:Luo, Li (University of New Mexico Health Sciences Center Devision of Epidemiology)
Creator:Simmons, Karen (University of New Mexico Health Sciences Center)
Creator:MacKenzie, Debra A (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences)
Creator:Hudson, Laurie G (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences)
Associate:Schliz, Jodi R (University of New Mexico Health Sciences Center Division of Physical Therapy, Investigator)
Associate:Dashner-Titus, Erica J (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences, Investigator)
Associate:Luo, Li (University of New Mexico Health Sciences Center Devision of Epidemiology, Investigator)
Associate:Simmons, Karen (University of New Mexico Health Sciences Center, Investigator)
Associate:MacKenzie, Debra A (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences, Investigator)
Associate:Hudson, Laurie G (University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences, Investigator)

Data Entities
Data Table Name:
Supplemental Table 1
Description:
Supplemental Table 1. Significantly altered genes in the presence of 10 µM As
Data Table Name:
Supplemental Table 2
Description:
Supplemental Table 2. Significantly altered genes in response to 1 µM As treatment
Data Table Name:
Supplemental Table 3
Description:
Supplemental Table 3. Genes significantly altered with 1 µM As + 3 µM U treatment
Other Name:
Supplemental Table 4
Description:
Supplemental Table 4. Biological process genes enriched with 10 µM As
Other Name:
Supplemental Table 5
Description:
Supplemental Table 5. Reactome pathway genes enriched with 10 µM As
Other Name:
Supplemental Table 6
Description:
Supplemental Table 6. Biological process genes enriched with 1 µM As exposure
Other Name:
Supplemental Table 7
Description:
Supplemental Table 7. Reactome pathway genes enriched with 1 µM As exposure
Other Name:
Supplemental Table 8
Description:
Supplemental Table 8. Biological process genes enriched with 1 µM As + 3 µM U exposure
Other Name:
Supplemental Table 9
Description:
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Detailed Metadata

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Externally Defined Format:
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Data:https://pasta-s.lternet.edu/package/data/eml/edi/10/3/143ab86b61a85ebe871bc8d89970ecb9

Data Package Usage Rights

This data package is released to the "public domain" under Creative Commons CC0 1.0 "No Rights Reserved" (see: https://creativecommons.org/publicdomain/zero/1.0/). It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you.

Keywords

By Thesaurus:
(No thesaurus)Uranium, arsenic, T-lymphocytes, mixed metals

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Human naïve CD4+ T cells (Cat # 70026) were purchased from Stemcell Technologies (MA, USA).

Single‐end sequencing, 75 base pairs read length was performed.

Each FASTQ file contains a sequence identifier, raw sequence letters and quality values for the sequence.

Instrument(s):Illumina Next-Seq 500 platform performed by the National Center for Genome Resources (Santa Fe, NM)
Quality Control
Quality Control Step 1: 
Description:
Low count gene filtering was performed to ensure sequencing data quality. We retained genes that have at least 5 read counts in at least one of the samples for further analysis. Differential expression analysis was conducted for the pre-filtered genes using R/Bioconductor package DESEQ2

People and Organizations

Creators:
Individual: Jodi R Schliz
Organization:University of New Mexico Health Sciences Center Division of Physical Therapy
Email Address:
jschliz@salud.unm.edu
Individual: Erica J Dashner-Titus
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
edashner@salud.unm.edu
Individual: Li Luo
Organization:University of New Mexico Health Sciences Center Devision of Epidemiology
Email Address:
lluo@salud.unm.edu
Individual: Karen Simmons
Organization:University of New Mexico Health Sciences Center
Email Address:
karsimmons@salud.unm.edu
Individual: Debra A MacKenzie
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
dmackenzie@salud.unm.edu
Individual: Laurie G Hudson
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
lhudson@salud.unm.edu
Contacts:
Individual: Jodi R Schliz
Organization:University of New Mexico Health Sciences Center Division of Physical Therapy
Email Address:
jschliz@salud.unm.edu
Associated Parties:
Individual: Jodi R Schliz
Organization:University of New Mexico Health Sciences Center Division of Physical Therapy
Email Address:
jschliz@salud.unm.edu
Role:Investigator
Individual: Erica J Dashner-Titus
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
edashner@salud.unm.edu
Role:Investigator
Individual: Li Luo
Organization:University of New Mexico Health Sciences Center Devision of Epidemiology
Email Address:
lluo@salud.unm.edu
Role:Investigator
Individual: Karen Simmons
Organization:University of New Mexico Health Sciences Center
Email Address:
karsimmons@salud.unm.edu
Role:Investigator
Individual: Debra A MacKenzie
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
dmackenzie@salud.unm.edu
Role:Investigator
Individual: Laurie G Hudson
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
lhudson@salud.unm.edu
Role:Investigator

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2020-04-23
End:
2020-04-23

Project

Parent Project Information:

Title:UNM METAL EXPOSURE TOXICITY ASSESSMENT ON TRIBAL LANDS IN THE SOUTHWEST (METALS) SUPERFUND RESEARCH PROGRAM
Personnel:
Individual: Johnnye L Lewis
Organization:University of New Mexico Community Environmental Health Program
Email Address:
jlewis@cybermesa.com
Role:Principal Investigator
Funding: NIH NIEHS: 1P42ES025589-01A1
Related Project:
Title:Center for Native American Health Equity Research
Personnel:
Individual: Johnnye L Lewis
Organization:University of New Mexico Community Environmental Health Program
Email Address:
jlewis@cybermesa.com
Role:Principal Investigator
Funding: NIH NIEHS: P50ES026102
Related Project:
Title:Native Environmental Health Equity Center
Personnel:
Individual: Johnnye L Lewis
Organization:University of New Mexico Community Environmental Health Program
Email Address:
jlewis@cybermesa.com
Role:Principal Investigator
Funding: USEPA: 83615701
Related Project:
Title:UNM Comprehensive Cancer Center
Personnel:
Individual: Erica J Dashner-Titus
Organization:University of New Mexico Health Sciences Center Department of Pharmaceutical Sciences
Email Address:
edashner@salud.unm.edu
Role:Investigator
Funding: NCI: 2P30CA118100

Maintenance

Maintenance:
Description:completed
Frequency:
Other Metadata

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