Using whole genome scores to compare three clinical phenotyping methods in complex diseases

Song W, Huang H, Zhang CZ, Bates DW, Wright A. Using whole genome scores to compare three clinical phenotyping methods in complex diseases. Sci Rep. 2018 Jul 27;8(1):11360.

Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease

Parisa Shooshtari, Hailiang Huang, and Chris Cotsapas. 2017. “Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease.” Am J Hum Genet, 101, 1, Pp. 75-86. Abstract

Genome-wide association studies in autoimmune and inflammatory diseases (AID) have uncovered hundreds of loci mediating risk. These associations are preferentially located in non-coding DNA regions and in particular in tissue-specific DNase I hypersensitivity sites (DHSs). While these analyses clearly demonstrate the overall enrichment of disease risk alleles on gene regulatory regions, they are not designed to identify individual regulatory regions mediating risk or the genes under their control, and thus uncover the specific molecular events driving disease risk. To do so we have departed from standard practice by identifying regulatory regions which replicate across samples and connect them to the genes they control through robust re-analysis of public data. We find significant evidence of regulatory potential in 78/301 (26%) risk loci across nine autoimmune and inflammatory diseases, and we find that individual genes are targeted by these effects in 53/78 (68%) of these. Thus, we are able to generate testable mechanistic hypotheses of the molecular changes that drive disease risk.

Discovery of stimulation-responsive immune enhancers with CRISPR activation

Dimitre R Simeonov, Benjamin G Gowen, Mandy Boontanrart, Theodore L Roth, John D Gagnon, Maxwell R Mumbach, Ansuman T Satpathy, Youjin Lee, Nicolas L Bray, Alice Y Chan, Dmytro S Lituiev, Michelle L Nguyen, Rachel E Gate, Meena Subramaniam, Zhongmei Li, Jonathan M Woo, Therese Mitros, Graham J Ray, Gemma L Curie, Nicki Naddaf, Julia S Chu, Hong Ma, Eric Boyer, Frederic Van Gool, Hailiang Huang, Ruize Liu, Victoria R Tobin, Kathrin Schumann, Mark J Daly, Kyle K Farh, Mark K Ansel, Chun J Ye, William J Greenleaf, Mark S Anderson, Jeffrey A Bluestone, Howard Y Chang, Jacob E Corn, and Alexander Marson. 2017. “Discovery of stimulation-responsive immune enhancers with CRISPR activation.” Nature, 549, 7670, Pp. 111-115. Abstract

The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell-type-specific transcriptional programs and responses to extracellular cues. Systematic mapping of functional enhancers and their biological contexts is required to understand the mechanisms by which variation in non-coding genetic sequences contributes to disease. Functional enhancers can be mapped by genomic sequence disruption, but this approach is limited to the subset of enhancers that are necessary in the particular cellular context being studied. We hypothesized that recruitment of a strong transcriptional activator to an enhancer would be sufficient to drive target gene expression, even if that enhancer was not currently active in the assayed cells. Here we describe a discovery platform that can identify stimulus-responsive enhancers for a target gene independent of stimulus exposure. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. Using engineered mouse models, we found that sequence perturbation of the disease-associated Il2ra enhancer did not entirely block Il2ra expression, but rather delayed the timing of gene activation in response to specific extracellular signals. Enhancer deletion skewed polarization of naive T cells towards a pro-inflammatory T helper (TH17) cell state and away from a regulatory T cell state. This integrated approach identifies functional enhancers and reveals how non-coding variation associated with human immune dysfunction alters context-specific gene programs.

Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection

Huang H, Duggal P, Thio CL, Latanich R, Goedert JJ, Mangia A, Cox AL, Kirk GD, Mehta S, Aneja J, Alric L, Donfield SM, Cramp ME, Khakoo SI, Tobler LH, Busch M, Alexander GJ, Rosen HR, Edlin BR, Segal FP, Lauer GM, Thomas DL, Daly MJ, Chung RT, Kim AY. Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection. Sci Rep. 2017 Nov 20;7(1):15843.