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RNA-seq analysis of human tonsil macrophage subsets

ABSTRACT: Numerous studies have shown in mouse that identity and function of macrophage populations are imprinted by their tissue of residence. By contrast, the properties of human tissue macrophages remain poorly understood. Here, we characterized human tonsil macrophages and identified 3 macrophage subsets with distinct phenotype, ontogeny and function. Using RNA-seq analysis, we found that CD36hi macrophages were transcriptionally related to monocytes, while CD36lo macrophages showed features of embryonic origin and CD36int macrophages had a mixed profile. Using scRNA-seq profiling of naïve and inflamed tonsils from non-human primates, we showed that monocyte engraftment did not pre-exist an immune challenge.

ORGANISM(S): Homo sapiens

PROVIDER: GSE207260 | GEO | 2023/03/24

REPOSITORIES: GEO

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Project description:To study characteristics of the orapharyngeal epithelia which may influence susceptibility or resistance to HIV, we performed microarray analysis of the tonsil and gingival epithelium.Tonsil epithelium has been implicated in HIV pathogenesis, but its role in oral transmission remains controversial. We performed microarray analysis of Laser Capture Microdissected tonsil and gingival epithelium. Our data revealed that genes related to immune functions such as antibody production and antigen processing were increasingly expressed in tonsil compared to the epithelium of another oro-pharyngeal site, gingival epithelium. Importantly, tonsil epithelium highly expressed genes associated with HIV entrapment and/or transmission, including the HIV co-receptor CXCR4 and the potential HIV binding molecules, FcRÎ³III, complement receptor 2, and various complement components. This increased expression of molecules involved in viral recognition, binding and entry may favor virus-epithelium interaction in an environment with reduced innate anti-viral mechanisms. Specifically, secretory leukocyte protease inhibitor, an innate molecule with anti-HIV activity, was minimal in the tonsil epithelium, in contrast to oral mucosa. Collectively, our data suggest that increased expression of molecules associated with HIV binding and entry coupled with decreased innate anti-viral factors may render the tonsil a potential site for oral transmission. Experiment Overall Design: To study characteristics of the orapharyngeal epithelia which may influence susceptibility or resistance to HIV, we performed microarray analysis of the tonsil and gingival epithelium. Experiment Overall Design: Human palatine tonsils were obtained from routine therapeutic tonsillectomies (sleep apnea and non-tonsillitis) performed on otherwise healthy adults at the George Washington University Hospital with informed consent (IRB #099920). Gingival tissues were collected from healthy sites with probing depths < 3mm, with no clinical evidence of inflammation during routine therapeutic periodontal surgery at the University of Maryland, Department of Periodontics, with informed consent (IRB#1201211). Tissues were immediately snap frozen for the microarray studies. CM performed immediately at 10x magnification, using a Leica AS LMD system (Leica Microsystems). Areas unequivocally identified as epithelium were outlined , laser-dissected and captured and RNA from the tissues isolated. Preparation of biotin-labeled cRNA, hybridization, and scanning were performed according to manufacturerâs two cycle protocol (Affymetrix, Santa Clara, CA). Fluorescence intensity was measured using the Affymetrix GeneChip scanner and GeneChip Operating Software (GCOS, Affymetrix). Experiment Overall Design: Samples GSM173679, GSM173680,GSM173681, GSM173682, GSM173683, GSM173684, GSM173685, GSM173686, GSM173688, GSM173690 were processed togehter as "batch 1", while samples GSM173687 and GSM173689 were processed as "batch 2" together with sample GSM173691 which is a repeat of GSM173690, which was processed for comparison between the two batches. Experiment Overall Design:

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RNA-seq analysis of human tonsil macrophage subsets

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