Characterization of single-nucleotide polymorphisms relevant to inflammatory bowel disease in commonly used gastrointestinal cell lines.
BACKGROUND
The era of genome-wide association studies (GWAS) has led to the identification of many inflammatory bowel disease (IBD)-associated single-nucleotide polymorphisms (SNPs) with unknown function. The next step would be to identify the functional consequences of these polymorphisms in order to target them efficiently for therapeutic purposes. One way to study this type of genetic variation is the use of cell line models. However, to characterize the functional effect of a SNP, it is important to know if the selected cell line model itself carries the studied genetic variation. Here, we genotyped 50 IBD markers across 32 susceptibility genes in 9 commonly used gastrointestinal cell lines.


METHODS
We used Sequenom, TaqMan, and DNA sequencing for the genotyping. To determine the expression profile of the selected genes, we conducted real-time RT-PCR.


RESULTS
We found variant SNPs in all analyzed cell lines. Almost every minor allele was carried by at least one of the tested cell lines. We analyzed the effect of 4 SNPs in more detail using quantitative real-time RT-PCR (qRT-PCR) comprising genes ATG16L1, CD14, MDR1, and OCTN2. According to our data, only 2 of the commonly studied SNPs in MDR1 and CD14 have an impact on gene expression.


CONCLUSIONS
We have identified genotype variants in all analyzed cell lines. Some of them are functional and alter the response to drugs (MDR1) or affect bacterial recognition (TLR4, NOD2). Our results highlight that the genotype should not be neglected in experimental design when using model cell lines.
Huebner
Claudia
C
Discipline of Nutrition, FM&HS, The University of Auckland, Auckland, New Zealand. c.huebner@auckland.ac.nz
Petermann
Ivonne
I
Lam
Wen Jiun
WJ
Shelling
Andrew N
AN
Ferguson
Lynnette R
LR
D000483:Alleles; D018938:Caco-2 Cells; D002460:Cell Line; D002869:Chromosome Aberrations; D020869:Gene Expression Profiling; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease; D005838:Genotype; D045325:HCT116 Cells; D019073:HT29 Cells; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D005819:Genetic Markers