Genetic variants contributing to colistin cytotoxicity: Identification of TGIF1 and HOXD10 using a population genomics approach

Michael Eadon, Ronald J. Hause, Amy L. Stark, Ying Hua Cheng, Heather E. Wheeler, Kimberly S. Burgess, Eric Benson, Patrick N. Cunningham, Robert Bacallao, Pierre Dagher, Todd Skaar, M. Eileen Dolan

Research output: Contribution to journalArticle

Abstract

Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines. To this end, we employed International HapMap lymphoblastoid cell lines (LCLs) of Yoruban ancestry with known genetic information to perform a genome-wide association study (GWAS) with cellular sensitivity to colistin. Further association studies revealed that single nucleotide polymorphisms (SNPs) associated with gene expression and protein expression were significantly enriched in SNPs associated with cytotoxicity (p ≤ 0.001 for gene and p = 0.015 for protein expression). The most highly associated SNP, chr18:3417240 (p = 6.49 × 10-8), was nominally a cis-expression quantitative trait locus (eQTL) of the gene TGIF1 (transforming growth factor β (TGFβ)-induced factor-1; p = 0.021) and was associated with expression of the protein HOXD10 (homeobox protein D10; p = 7.17 × 10-5). To demonstrate functional relevance in a murine colistin nephrotoxicity model, HOXD10 immunohistochemistry revealed upregulated protein expression independent of mRNA expression in response to colistin administration. Knockdown of TGIF1 resulted in decreased protein expression of HOXD10 and increased resistance to colistin cytotoxicity. Furthermore, knockdown of HOXD10 in renal cells also resulted in increased resistance to colistin cytotoxicity, supporting the physiological relevance of the initial genomic associations.

Original languageEnglish (US)
Article number661
JournalInternational Journal of Molecular Sciences
Volume18
Issue number3
DOIs
StatePublished - Mar 18 2017

Fingerprint

Colistin
Metagenomics
Cytotoxicity
Proteins
proteins
Nucleotides
Genes
Polymorphism
polymorphism
nucleotides
Single Nucleotide Polymorphism
genome
cultured cells
markers
Gram-Negative Bacterial Infections
Cells
HapMap Project
Kidney
Homeodomain Proteins
Cell Line

Keywords

  • Colistin
  • HOXD10
  • Lymphoblastoid cell line
  • Nephrotoxicity
  • TGIF1

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Computer Science Applications
  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

Genetic variants contributing to colistin cytotoxicity : Identification of TGIF1 and HOXD10 using a population genomics approach. / Eadon, Michael; Hause, Ronald J.; Stark, Amy L.; Cheng, Ying Hua; Wheeler, Heather E.; Burgess, Kimberly S.; Benson, Eric; Cunningham, Patrick N.; Bacallao, Robert; Dagher, Pierre; Skaar, Todd; Dolan, M. Eileen.

In: International Journal of Molecular Sciences, Vol. 18, No. 3, 661, 18.03.2017.

Research output: Contribution to journalArticle

Eadon, Michael ; Hause, Ronald J. ; Stark, Amy L. ; Cheng, Ying Hua ; Wheeler, Heather E. ; Burgess, Kimberly S. ; Benson, Eric ; Cunningham, Patrick N. ; Bacallao, Robert ; Dagher, Pierre ; Skaar, Todd ; Dolan, M. Eileen. / Genetic variants contributing to colistin cytotoxicity : Identification of TGIF1 and HOXD10 using a population genomics approach. In: International Journal of Molecular Sciences. 2017 ; Vol. 18, No. 3.
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abstract = "Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines. To this end, we employed International HapMap lymphoblastoid cell lines (LCLs) of Yoruban ancestry with known genetic information to perform a genome-wide association study (GWAS) with cellular sensitivity to colistin. Further association studies revealed that single nucleotide polymorphisms (SNPs) associated with gene expression and protein expression were significantly enriched in SNPs associated with cytotoxicity (p ≤ 0.001 for gene and p = 0.015 for protein expression). The most highly associated SNP, chr18:3417240 (p = 6.49 × 10-8), was nominally a cis-expression quantitative trait locus (eQTL) of the gene TGIF1 (transforming growth factor β (TGFβ)-induced factor-1; p = 0.021) and was associated with expression of the protein HOXD10 (homeobox protein D10; p = 7.17 × 10-5). To demonstrate functional relevance in a murine colistin nephrotoxicity model, HOXD10 immunohistochemistry revealed upregulated protein expression independent of mRNA expression in response to colistin administration. Knockdown of TGIF1 resulted in decreased protein expression of HOXD10 and increased resistance to colistin cytotoxicity. Furthermore, knockdown of HOXD10 in renal cells also resulted in increased resistance to colistin cytotoxicity, supporting the physiological relevance of the initial genomic associations.",
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AU - Cheng, Ying Hua

AU - Wheeler, Heather E.

AU - Burgess, Kimberly S.

AU - Benson, Eric

AU - Cunningham, Patrick N.

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