Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach.
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 andp= 0.015 for protein expression). The most highly associated SNP, chr18:3417240 (p= 6.49 × 10-8), was nominally acis-expression quantitative trait locus (eQTL) of the geneTGIF1(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 ofTGIF1resulted in decreased protein expression of HOXD10 and increased resistance to colistin cytotoxicity. Furthermore, knockdown ofHOXD10in renal cells also resulted in increased resistance to colistin cytotoxicity, supporting the physiological relevance of the initial genomic associations.
Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. meadon@iupui.edu.|Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. meadon@iupui.edu.
Michael T
MT
Eadon
Juno Therapeutics, Seattle, WA 98109, USA. ronaldhause@junotherapeutics.com.
Ronald J
RJ
Hause
Department of Biological Sciences, University of Notre Dame, South Bend, IN 46556, USA. astark1@nd.edu.
Amy L
AL
Stark
Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. yicheng@iu.edu.
Ying-Hua
YH
Cheng
Department of Biology, Department of Computer Science, Loyola University Chicago, Chicago, IL 60660, USA. Hwheeler1@luc.edu.
Heather E
HE
Wheeler
Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. ksburges@iu.edu.
Kimberly S
KS
Burgess
Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. eabenson@iu.edu.
Eric A
EA
Benson
Department of Medicine, University of Chicago, Chicago, IL 60637, USA. pcunning@medicine.bsd.uchicago.edu.
Patrick N
PN
Cunningham
Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. rbacalla@iu.edu.
Robert L
RL
Bacallao
Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. pdaghe2@iu.edu.
Pierre C
PC
Dagher
Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. tskaar@iu.edu.
Todd C
TC
Skaar
Department of Medicine, University of Chicago, Chicago, IL 60637, USA. edolan@medicine.bsd.uchicago.edu.
M Eileen
ME
Dolan
D000900:Anti-Bacterial Agents / Q000009:adverse effects / Q000494:pharmacology* / Q000633:toxicity; D002460:Cell Line; D045744:Cell Line, Tumor; D003091:Colistin / Q000009:adverse effects / Q000494:pharmacology* / Q000633:toxicity; D004351:Drug Resistance / Q000235:genetics; D055106:Genome-Wide Association Study; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012097:Repressor Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
D000900:Anti-Bacterial Agents; D018398:Homeodomain Proteins; D012097:Repressor Proteins; C097504:TGIF1 protein, human; D014157:Transcription Factors; C072064:HOXD10 protein, human; D003091:Colistin
HOXD10; TGIF1; colistin; lymphoblastoid cell line; nephrotoxicity