The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the ‘missing heritability problem’. Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. The goal of our study was to explore a complimentary approach, which combines GWAS results with functional data in order to identify novel genetic associations with small effect sizes. To do so, we conducted a GWAS for lymphocyte count, a physiologic quantitative trait associated with asthma, in 462 Hutterites. In parallel, we performed a genome-wide gene expression study in lymphoblastoid cell lines from 96 Hutterites. We found significant support for genetic associations using the GWAS data when we considered variants near the 193 genes whose expression levels across individuals were most correlated with lymphocyte counts. Interestingly, these variants are also enriched with signatures of an association with asthma susceptibility, an observation we were able to replicate. The associated loci include genes previously implicated in asthma susceptibility as well as novel candidate genes enriched for functions related to T cell receptor signaling and adenosine triphosphate synthesis. Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility

Epstein-Barr virus associated post-transplant lymphoproliferative disorders: preventative measures and current treatments

Thesis (M.A.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.Lymphoproliferative disorders develop in 1-20% of solid organ and hematopoietic stem cell transplant surgeries and continue to be serious and potentially fatal post-surgery complications for patients. Epstein-Barr virus, which is estimated to have infected over 90% of the adult population, is a major risk factor for the development of a post-transplant lymphoproliferative disorder (PTLD) and is linked to the majority of cases. PTLD can be defined as an aberrant growth of lymphocytes typically attributed to the standard practice of immunosuppressive therapy post hematopoietic stem cell transplant or solid organ transplant procedures. Disorders range from a relatively harmless benign plasmacytic hyperplasia to an aggressive malignant lymphoma. The complexity of the patient population diagnosed with PTLD, as well as the broad spectrum of clinical and pathological manifestations of the disorder, make the use of a standardized therapeutic strategy impractical. This reason can also be attributed to the fact that large scale, randomized, controlled trials of therapeutic regimens are lacking. However, reduction of immunosuppression (RI) remains a frontline therapeutic strategy for PTLD and several studies have found success in combining RI and rituximab, an antibody that targets B-lymphocytes. As with other lymphomas, radiation and/or surgery to excise localized tumors are still widely used in the management of this disorder. Chemotherapy is mainly used as a salvage therapy when all else fails, since mortality rates from drug toxicity effects remain high. Novel approaches have shown much promise in initial studies. They include adoptive immunosuppression with EBV-specific cytotoxic T-lymphocytes and antiviral agents and alternative immunosuppressants with antineoplastic effects that slow down B-cell proliferation. Further research should be done to confirm safety and efficacy of these new modalities. Research attention has turned to the discovery of prophylactic strategies and the improvement of methods to attain earlier diagnoses ofPTLD. An EBV vaccine is being developed to prevent EBV infection, since EBV-serostatus is the major risk factor for PTLD. Innovations in EBV-DNA load monitoring have been proven helpful in the early diagnosis of PTLD, when therapies are most effective. There have been many developments in the prophylactic and therapeutic approaches to PTLD, but more research should be done in the future to confirm their efficacies. Additionally, an algorithm for PTLD treatment recommendations should be developed using information from previous studies. The algorithm would help clinicians decide on the best treatment method for their patients based on the success of patients with similar characteristics

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

<div><p>Recent gene expression QTL (eQTL) mapping studies have provided considerable insight into the genetic basis for inter-individual regulatory variation. However, a limitation of all eQTL studies to date, which have used measurements of steady-state gene expression levels, is the inability to directly distinguish between variation in transcription and decay rates. To address this gap, we performed a genome-wide study of variation in gene-specific mRNA decay rates across individuals. Using a time-course study design, we estimated mRNA decay rates for over 16,000 genes in 70 Yoruban HapMap lymphoblastoid cell lines (LCLs), for which extensive genotyping data are available. Considering mRNA decay rates across genes, we found that: (<em>i</em>) as expected, highly expressed genes are generally associated with lower mRNA decay rates, (<em>ii</em>) genes with rapid mRNA decay rates are enriched with putative binding sites for miRNA and RNA binding proteins, and (<em>iii</em>) genes with similar functional roles tend to exhibit correlated rates of mRNA decay. Focusing on variation in mRNA decay across individuals, we estimate that steady-state expression levels are significantly correlated with variation in decay rates in 10% of genes. Somewhat counter-intuitively, for about half of these genes, higher expression is associated with <em>faster</em> decay rates, possibly due to a coupling of mRNA decay with transcriptional processes in genes involved in rapid cellular responses. Finally, we used these data to map genetic variation that is specifically associated with variation in mRNA decay rates across individuals. We found 195 such loci, which we named RNA decay quantitative trait loci (“rdQTLs”). All the observed rdQTLs are located near the regulated genes and therefore are assumed to act in <em>cis</em>. By analyzing our data within the context of known steady-state eQTLs, we estimate that a substantial fraction of eQTLs are associated with inter-individual variation in mRNA decay rates.</p> </div

Relationship between gene expression levels and mRNA decay rates across individuals.

<p>A. QQ-plot of the t-statistics for association between steady-state expression levels and decay rates across individuals (y-axis) compared to the null distribution of t-statistics assessed by permutations (x-axis). The sign of the t-statistic indicates the direction of correlation. Genes with concordant relationships (orange) have negative t-statistics and genes with discordant relationships (purple) have positive t-statistics. B. Density distributions of the Pearson correlations (x-axis) between mRNA decay rates and PolII reads for genes with either concordant (orange) or discordant (purple) relationships between decay rates and steady-state expression levels across individuals.</p

Genes with discordant decay rates and steady-state gene expression levels.

<p>A list of the 9 genes that are in the top 5% of both the decay rate and steady-state gene expression distributions, thus showing evidence of both fast decay and high expression. The table lists the gene name (column 1), the Ensembl ID (column 2), the function of the gene (column 3), and evidence from the literature pointing towards negative feedback or autoregulatory functions for the gene (column 4).</p

Profiles of decay rates.

<p>A. Distribution of genome-wide decay profiles across the timecourse experiment (x-axis), where each decay curve shows the decrease in gene expression level (y-axis) relative to the untreated time point. Each line represents the gene-specific median decay profile, while the darkness of the lines indicates the number of genes sharing that decay profile (darker indicates more genes). B. Representative examples of individual-specific decay profiles (dotted lines) for two genes: <i>NFKBIE</i> (in red), which decays faster than average and <i>DCTN2</i> (in blue), which decays slower than average. Solid lines indicate the gene-specific median decay profile across all 70 individuals.</p