Biology subjects

Knowles, D. A.

Publications and source records attributed to Knowles, D. A..

3 recordsLinked to original sources

bioRxiv2018

Landscape of stimulation-responsive chromatin across diverse human immune cells

The immune system is controlled by a balanced interplay among specialized cell types transitioning between resting and stimulated states. Despite its importance, the regulatory landscape of this system has not yet been fully characterized. To address this gap, we collected ATAC-seq and RNA-seq data under resting and stimulated conditions for 25 immune cell types from peripheral blood of four healthy individuals, and seven cell types from three fetal thymus samples. We found that stimulation caused widespread chromatin remodeling, including a large class of response elements shared between stimulated B and T cells. Furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the critical importance of these cell states in autoimmunity. Use of allele-specific read-mapping identified thousands of variants that alter chromatin accessibility in particular conditions. Notably, variants associated with changes in stimulation-specific chromatin accessibility were not enriched for associations with gene expression regulation in whole blood - a tissue commonly used in eQTL studies. Thus, large-scale maps of variants associated with gene regulation lack a condition important for understanding autoimmunity. As a proof-of-principle we identified variant rs6927172, which links stimulated T cell-specific chromatin dysregulation in the TNFAIP3 locus to ulcerative colitis and rheumatoid arthritis. Overall, our results provide a broad resource of chromatin landscape dynamics and highlight the need for large-scale characterization of effects of genetic variation in stimulated cells.

genomics↗

bioRxiv2017

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes

Anthracycline-induced cardiotoxicity (ACT) is a key limiting factor in setting optimal chemotherapy regimes for cancer patients, with almost half of patients expected to ultimately develop congestive heart failure given high drug doses. However, the genetic basis of sensitivity to anthracyclines such as doxorubicin remains unclear. To begin addressing this, we created a panel of iPSC-derived cardiomyocytes from 45 individuals and performed RNA-seq after 24h exposure to varying levels of doxorubicin. The transcriptomic response to doxorubicin is substantial, with the majority of genes being differentially expressed across treatments of different concentrations and over 6000 genes showing evidence of differential splicing. Overall, our observations indicate that splicing fidelity decreases in the presence of doxorubicin. We detect 376 response-expression QTLs and 42 response-splicing QTLs, i.e. genetic variants that modulate the individual transcriptomic response to doxorubicin in terms of expression and splicing changes respectively. We show that inter-individual variation in transcriptional response is predictive of cell damage measured in vitro using a cardiac troponin assay, which in turn is shown to be associated with in vivo ACT risk. Finally, the molecular QTLs we detected are enriched in lower ACT GWAS p-values, further supporting the in vivo relevance of our map of genetic regulation of cellular response to anthracyclines.

genomics↗

bioRxiv2017

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis acting genotype-environment interactions (GxE) - genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate interaction quantitative trait loci (iQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.

genetics↗