From castaways to discoveries: unveiling treasures in skin RNAseq using a novel multidimensional data processing workflow including infection-host dynamics

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作   者：

Disha Bhargava;  Alec Labadie;  Rebecca L.Hanson-Rios-Stutz;  Austin Goodyke;  Ella M.Moses;  Akansha S.Das;  Sophie Vanderweele;  Janelle V.Lemon;  Taylor W.Cook;  David Pearson;  Joseph M.Redinger;  Adam J.Caulfield;  Rosemary Olivero;  Kate Foster;  Kurt Ashack;  Surender Rajasekaran;  Caleb P.Bupp;  Timothy J.Triche Jr.;  Connie M.Krawczyk;  Dave Chesla;  Matthew D.Sims;  Nicholas L.Hartog;  Jeremy W.Prokop; 

作者机构：

College of Veterinary Medicine;  Michigan State University;  Pediatric Intensive Care Unit;  University of Michigan;  United States;  Grand Rapids;  Washington;  Medical Genetics;  East Lansing;  Corewell Health;  Helen DeVos Children's Hospital;  Department of Large Animal Clinical Sciences;  Michigan;  Department of Pharmacology and Toxicology;  Dermatology Associates of West Michigan;  Department of Metabolism and Nutritional Programming;  Infectious Disease;  College of Human Medicine;  Regional Laboratory;  Washington and Jefferson College;  Van Andel Institute;  Dermatology;  Allergy and Immunology;  Pennsylvania;  Department of Biology;  Section of Infectious Diseases;  Office of Research;  Ann Arbor;  Van Andel Research Institute;  Center for Epigenetics;  School for Environment and Sustainability;  Royal Oak; 

期刊名称：

Physiological genomics

i s s n：

1094-8341

年卷期：

2025 年 57 卷 5 期

页   码：

343-356

页   码：

摘   要：

Defining physiology and methods to measure biological mechanisms is essential.Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies.Within this work,we have processed publicly available NCBI RNAseq datasets using a combination of bioinformatics tools for the largest physiological organ,the skin.In many datasets,we identify the quality of the sample,human transcript mapping,the sex of each sample,foreign RNA from bacteria/viruses/protists,and the presence of B/T-cell immune repertoire.Processing 8,274 samples from 132 different experiments for skin samples identifies common flora of skin with elevation of protists (such as Leishmania),bacteria (Staphylococcus,Cutibacterium acnes),and viruses [Human alphaherpesvirus (HSV),Human papillomavirus (HPV)] that may be involved in physiological differences.We observed samples with the Heilongjiang tick virus,human T-cell leukemia virus type I,and equine infectious anemia virus that likely play pathological roles in physiology.Integrating the various biomarkers identified five ideal datasets for skin pathologies that elucidated a novel correlation between the normal skin flora bacterium Bacillus megaterium with major histocompatibility complex (MHC) regulation and the immune repertoire clonal expansion,particularly in patients with hidradenitis suppurativa.Finally,we show that in multiple independent experiments,biological sex is associated with multiple sex chromosome gene differences,highlighting the importance of future work in studying sex differences in skin.Data integrations and multidimensional data mapping are critical for physiological omics advancements,and this work highlights the exciting ability to apply these tools to skin physiology.