Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology

Christina Cho; Nazgol-Sadat Haddadi; Michal Kidacki; Gavitt A. Woodard; Saeed Shakiba; Ümmügülsüm Yıldız-Altay; Jillian M. Richmond; Matthew D. Vesely

doi:10.1016/j.xjidi.2024.100317

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Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology

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Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology

Christina Cho, Nazgol-Sadat Haddadi, Michal Kidacki, Gavitt A. Woodard, Saeed Shakiba, Ümmügülsüm Yıldız-Altay, Jillian M. Richmond and Matthew D. Vesely

JID innovations, Vol.5(1), 100317

01/01/2025

DOI: 10.1016/j.xjidi.2024.100317

PMCID: PMC11570843

PMID: 39559817

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https://doi.org/10.1016/j.xjidi.2024.100317View

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Abstract

The spatial organization of the skin is critical for its function. In particular, the skin immune microenvironment is arranged spatially and temporally, such that imbalances in the immune milieu are indicative of disease. Spatial transcriptomic platforms are helping to provide additional insights into aberrant inflammation in tissues that are not captured by tissue processing required for single-cell RNA sequencing. In this paper, we discuss a technical and user experience overview of NanoString's GeoMx Digital Spatial Profiler to perform in-depth spatial analysis of the transcriptome in inflammatory skin diseases. Our objective is to provide potential pitfalls and methods to optimize RNA capture that are not readily available in the manufacturer’s guidelines. We use concrete examples from our experiments to demonstrate these strategies in inflammatory skin diseases, including psoriasis, lichen planus, and discoid lupus erythematosus. Overall, we hope to illustrate the potential of digital spatial profiling to dissect skin disease pathogenesis in a spatially resolved manner and provide a framework for other skin biology investigators using digital spatial profiling.

Cutaneous lupus

Digital spatial profiling

Lichen planus

Psoriasis

Spatial transcriptomics

Details

Title: Subtitle: Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology
Creators: Christina Cho - Yale University
Nazgol-Sadat Haddadi - University of Massachusetts Chan Medical School
Michal Kidacki - Yale University
Gavitt A. Woodard - Yale University
Saeed Shakiba - University of Massachusetts Chan Medical School
Ümmügülsüm Yıldız-Altay - University of Massachusetts Chan Medical School
Jillian M. Richmond - University of Massachusetts Chan Medical School
Matthew D. Vesely - Yale University
Resource Type: Journal article
Publication Details: JID innovations, Vol.5(1), 100317
DOI: 10.1016/j.xjidi.2024.100317
PMID: 39559817
PMCID: PMC11570843
NLM abbreviation: JID Innov
ISSN: 2667-0267
eISSN: 2667-0267
Publisher: Elsevier Inc
Language: English
Date published: 01/01/2025
Academic Unit: Dermatology; Internal Medicine
Record Identifier: 9984949218402771

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