Human clinical genome-wide association studies (GWAS) have helped identify disease trait and pharmacogenomic loci without the need for biological under- standing. Molecular GWAS - associating genetic variation with traits such as gene expression - have been slow to fill the mechanistic gaps. While tissue specificity, lack of DNA resolution, and the need for better data integration are no dou bt important bottlenecks in molecular GWAS, there is also a very poor general understanding of which molecular phenotypes are important and how best to model them. Added to this is the clear need for a greater understanding of the strengths and weaknesses facing in vitro (and ex vivo) models as hypoth- esis generating and GWAS validation tools. The studies in this work focus on RNA expression in a popular human model: lymphoblastoid cell lines (LCLs). Chapters 2 and 3 examine microRNA (miRNA) and messenger RNA (mRNA) expression in a total of 300 genotyped human LCLs. The expression of only one miRNA could be associated with a nearby genetic variant. This result was observed in both the African and European samples studied, in a separate val- idation data set, and was technically validated with quantitative PCR. While limited genotype resolution and small sample sizes are likely to be important contributors to this low hit rate, the results strongly suggest experimental con- founders. Highly expressed miRNAs reflected the transformed nature of the cells, highly correlated miRNAs enriched for EBV and malaria associated tar- get mRNA genes, and several miRNAs that were differentially expressed be- tween the European and African samples suggested differential EBV transfer- mation. Chapter 4 presents a study on single cells from some of the same samples, to test the hypothesis that the lack of tissue spatial resolution is an important limiting factor in human genetic epidemiology. Experimental con- founders were also considered: sample growth was found to associate with the expression of several genes. Cell-to-cell gene correlations and distributions made it possible to propose how genes change their expression, functionally differ from each other, and are able to alter their behaviours without altered whole-tissue expression. The results suggest which type of genes are more likely to be susceptible to genetic effects, and propose promoter behaviours altered by genetic variants located near to 13 genes. From these whole-tissue and single cell results the broad conclusion is that, while LCLs are likely to be inappropriate for the study of miRNA genetics, their functional genomics at higher spatial resolution shows promise as a more mechanistic approach for the study of germline genetics.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:572601 |
| Date | January 2012 |
| Creators | Wills, Quintin Frank |
| Contributors | Holmes, Chris |
| Publisher | University of Oxford |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
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