Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology
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 in...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | JID Innovations |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667026724000651 |
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| author | Christina Cho Nazgol-Sadat Haddadi Michal Kidacki Gavitt A. Woodard Saeed Shakiba Ümmügülsüm Yıldız-Altay Jillian M. Richmond Matthew D. Vesely |
| author_facet | Christina Cho Nazgol-Sadat Haddadi Michal Kidacki Gavitt A. Woodard Saeed Shakiba Ümmügülsüm Yıldız-Altay Jillian M. Richmond Matthew D. Vesely |
| author_sort | Christina Cho |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-276c70eb015546d98c8b60972919b5c6 |
| institution | Kabale University |
| issn | 2667-0267 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | JID Innovations |
| spelling | doaj-art-276c70eb015546d98c8b60972919b5c62025-01-11T06:42:10ZengElsevierJID Innovations2667-02672025-01-0151100317Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in DermatologyChristina Cho0Nazgol-Sadat Haddadi1Michal Kidacki2Gavitt A. Woodard3Saeed Shakiba4Ümmügülsüm Yıldız-Altay5Jillian M. Richmond6Matthew D. Vesely7Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USADepartment of Dermatology, University of Massachusetts Medical School, Worcester, Massachusetts, USADepartment of Dermatology, Yale School of Medicine, New Haven, Connecticut, USADepartment of Surgery, Yale School of Medicine, New Haven, Connecticut, USADepartment of Dermatology, University of Massachusetts Medical School, Worcester, Massachusetts, USADepartment of Dermatology, University of Massachusetts Medical School, Worcester, Massachusetts, USADepartment of Dermatology, University of Massachusetts Medical School, Worcester, Massachusetts, USADepartment of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Correspondence: Matthew D. Vesely, Department of Dermatology, Yale School of Medicine, 333 Cedar Street, PO Box 208059, New Haven, Connecticut 06520, USA.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.http://www.sciencedirect.com/science/article/pii/S2667026724000651Cutaneous lupusDigital spatial profilingLichen planusPsoriasisSpatial transcriptomics |
| spellingShingle | Christina Cho Nazgol-Sadat Haddadi Michal Kidacki Gavitt A. Woodard Saeed Shakiba Ümmügülsüm Yıldız-Altay Jillian M. Richmond Matthew D. Vesely Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology JID Innovations Cutaneous lupus Digital spatial profiling Lichen planus Psoriasis Spatial transcriptomics |
| title | Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology |
| title_full | Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology |
| title_fullStr | Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology |
| title_full_unstemmed | Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology |
| title_short | Spatial Transcriptomics in Inflammatory Skin Diseases Using GeoMx Digital Spatial Profiling: A Practical Guide for Applications in Dermatology |
| title_sort | spatial transcriptomics in inflammatory skin diseases using geomx digital spatial profiling a practical guide for applications in dermatology |
| topic | Cutaneous lupus Digital spatial profiling Lichen planus Psoriasis Spatial transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2667026724000651 |
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