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Team IDs Cell Type-Specific Expression Effects for Regulatory Variants

NEW YORK (GenomeWeb News) – Up to 80 percent of regulatory variants appear to operate in a cell type-specific way, according to a paper appearing in the advanced, online edition of Science today.

Researchers from the University of Geneva, the Wellcome Trust Sanger Institute, and Harvard University used SNP and expression arrays to investigate how the function of genetic variants influencing gene expression differs between three human cell lines. Their results suggest that between 69 and 80 percent of expression quantitative trait loci, or eQTL, identified influenced gene expression in just one of the three cell types tested.

"Overall, the degree of tissue specification, for me, was a surprise," co-corresponding author Emmanouil Dermitzakis told GenomeWeb Daily News. Dermitzakis, formerly a population and comparative genomics researcher at the Wellcome Trust Sanger Institute, is currently affiliated with the department of genetic medicine and development at the University of Geneva.

Genetic variation can lead to gene expression differences both within and between individuals and populations. But while past studies have looked at the effect of genetic variants in specific tissues, differences in regulatory variants between tissues from the same individual have received less attention.

"In general, people haven't been doing this analysis in different tissues in the same individual," Dermitzakis said. But, he explained, "If you look at every phenotype — including disease — every phenotype is a tissue-specific effect."

Dermitzakis has been investigating the genetics of gene expression for some time. For the latest study, he and his colleagues were interested in exploring whether they could detect eQTLs and tease apart how the actions of regulatory variants differed by cell type.

To simultaneously determine which variants have regulatory effects and compare the action of these variants between cell types, the researchers used Illumina 550K SNP arrays and Illumina WG-6 v3 expression arrays to genotype cells and look at gene expression in an unbiased way.

The team focused on three cell types — primary fibroblasts, LCLs, and primary T-cells — from 85 individuals. These samples came from the GenCord project, an effort to collect cell lines from umbilical cord samples taken from Western European individuals.

After tossing out data on ten individuals who appeared to represent outliers based on principal components analysis, the team was left with information representing 75 individuals.

When they narrowed in on cis-eQTLs, acting near transcription start sites, the researchers found that just 8.5 percent were shared between all of the cell types tested. Another 12 percent acted in two of the three cell types and 79.5 percent were cell type-specific.

In general, the team found fewer and fewer cis-eQTLs as they looked further away from transcription starts sites. But the patterns also varied depending on whether the eQTLs were shared or cell type-specific. Whereas eQTLs acting in several cell types tended to be closer to transcription start sites and exert strong influences over expression, the cell type-specific eQTLs were often farther away, exerting weaker effects.

That pattern is consistent with results from previous studies suggesting enhancers that are found farther from genes are more likely to be tissue specific than those close to the gene, Dermitzakis said.

In the future, the researchers plan to investigate how genetic variants affect other types of phenotypes in the cells. They also plan to do some RNA sequencing using second-generation technologies to get a more high resolution view of gene expression, alternative splicing, transcript structure, and so on, Dermitzakis said.

Together, the results suggest that truly understanding the repertoire and roles of regulatory variants will require investigating their activity in many different cell types.

For his part, Dermitzakis predicts that progress in induced pluripotent stem cell research will ultimately benefit such studies. In the future, as researchers continue finding ways to specifically guide the differentiation of stem cells, he explained, it should be possible to compare the biology of a many cell types generated from iPS cells from the same individual.

"iPS cells is going to be the future of this kind of analysis," Dermitzakis said, noting that such an approach would also provide an opportunity to study stages throughout differentiation rather than just a tissue end point.

Nevertheless, despite the high degree of tissue specificity identified in the current study, those involved say it's likely that groups of cell types with similar patterns will become apparent as more and more tissues are evaluated.

"[W]e expect diminishing returns in discovery of eQTLs, and it is possible that there is a minimum set of informative tissues for the majority of regulatory variants," the authors concluded. "Our study highlights the need for extensive interrogation of regulatory variation in multiple cell types and tissues to elucidate their differential functional properties."

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