Rochman, M; Travers, J; Miracle, CE; Bedard, MC; Wen, T; Azouz, NP; Caldwell, JM; Kiran, K; Sherrill, JD; Davis, BP; Rymer, JK; Kaufman, KM; Aronow, BJ; Rothenberg, ME. Profound loss of esophageal tissue differentiation in patients with eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2017; 140(3):738-749.e3.
This translational research study uncovered that loss of esophageal tissue identity and epithelial differentiation are a key part of the pathogenesis of eosinophilic esophagitis (EoE), the most common of several allergic conditions of the gastrointestinal tract that are collectively called eosinophilic gastrointestinal disorders (EGIDs).
Sampson, HA; Shreffler, WG; Yang, WH; Sussman, GL; Brown-Whitehorn, TF; Nadeau, KC; Cheema, AS; Leonard, SA; Pongracic, JA; Sauvage-Delebarre, C; Assa'ad, AH; de Blay, F; Bird, JA; Tilles, SA; Boralevi, F; Bourrier, T; Hebert, J; Green, TD; van Wijk, R; Knulst, AC; Kanny, G; Schneider, LC; Kowalski, ML; Dupont, C. Effect of Varying Doses of Epicutaneous Immunotherapy vs Placebo on Reaction to Peanut Protein Exposure Among Patients With Peanut Sensitivity A Randomized Clinical Trial. Journal of the American Medical Association. 2017; 318(18):1798-1809.
Epicutaneous immunotherapy represents a new paradigm for how to treat peanut and other food allergies in a safe and effective way. This publication reports a large clinical trial of epicutaneous immunotherapy for peanut allergy. The positive results of this VIPES (Viaskin Peanut’s Efficacy and Safety), double-blind, placebo-controlled, randomized, multicenter phase IIb clinical trial, and subsequent open-label extension support the now ongoing comprehensive Phase III program in children with peanut allergy, continues to expand the understanding of the long-term benefits of food allergy desensitization.
Vallabh, S; Kartashov, AV; Barski, A. Analysis of ChIP-seq and RNA-seq data with biowardrobe. Methods in molecular biology (Clifton, N.J.). 2018; 1783:343-360.
The massive amount of information produced by chromatin immunoprecipitation (ChIP) sequencing, RNA sequencing, and other next-generation sequencing (NGS)-based methods requires computational data analysis, yet biologists performing these experiments often lack training in bioinformatics and expertise in programming. The creation of the BioWardrobe Experiment Management Platform allow users to store, visualize, and analyze NGS data using a biologist-friendly, web-based interface without the need for programming expertise. This report details its use for ChIP and RNA sequencing, increasing accessibility of NGS approaches to biologists in diverse scientific fields.
Sherrill, JD; Kc, K; Wang, X; Wen, T; Chamberlin, A; Stucke, EM; Collins, MH; Abonia, JP; Peng, Y; Wu, Q; Putnam, PE; Dexheimer, PJ; Aronow, BJ; Kottyan, LC; Kaufman, KM; Harley, JB; Huang, T; Rothenberg, ME. Whole-exome sequencing uncovers oxidoreductases DHTKD1 and OGDHL as linkers between mitochondrial dysfunction and eosinophilic esophagitis. JCI insight. 2018; 3(8):e99922.
Using whole-exome sequencing (WES) and family-based trio analysis, this study identified a series of rare genetic variants implicating the oxidoreductases DHTKD1 and OGDHL in the genetic etiology of eosinophilic esophagitis (EoE), an allergic inflammatory esophageal disorder, and underscore a potential pathogenic role for mitochondrial dysfunction in EoE.
Martin, LJ; He, H; Collins, MH; Abonia, JP; Biaggini Myers, JM; Eby, M; Johansson, H; Kottyan, LC; Khurana Hershey, GK; Rothenberg, ME. Eosinophilic esophagitis (EoE) genetic susceptibility is mediated by synergistic interactions between EoE-specific and general atopic disease loci. Journal of Allergy and Clinical Immunology. 2018; 141(5):1690-1698.
This research study found enrichment of atopic disease in patients with eosinophilic esophagitis (EoE), an esophageal inflammatory disease. In addition, the study discovered the mediation of EoE genetic susceptibility by synergistic interactions between EoE-specific (TSLP, CAPN14) and general atopic disease (IL4/KIF3A) loci. The findings help to explain the high degree of atopic disease comorbidity in children with EoE. Identification of these effects may help to better predict disease susceptibility and bring EoE closer to benefiting from precision medicine.