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High Resolution Spatial Transcriptomics using seq-FISH+

使用 seq-FISH 进行高分辨率空间转录组学

基本信息

批准号：
10404444
负责人：
John E Harris
金额：
$ 38.09万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-09-12 至 2027-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10404444
关键词：
Address Affect Antibodies Atlases Autoimmunity Biological Process Biopsy Bulla Cell Communication Cells Clone Cells Communication Complement Complex Data Dendritic Cells Dermal Epidermis Equilibrium Fluorescent in Situ Hybridization Freezing Gene Targeting Genes Genetic Transcription Goals Image Immune In Situ Individual Inflammation Inflammatory Knowledge Label Lead Lesion Ligands Location Maps Messenger RNA Microscope Modification Normal tissue morphology Organ Pathogenesis Pigments Population Positioning Attribute Privatization Process Punch Biopsy RNA Receptor Cell Research Resolution Signal Transduction Skin Spatial Distribution Structure T cell clonality T cell receptor repertoire sequencing T-Cell Receptor T-Lymphocyte Techniques Technology Tissues Transcript Translational Research Tumor-infiltrating immune cells Vitiligo White Spots cell type cellular imaging design health disparity improved in silico innovation insight interest keratinocyte melanocyte multiple omics receptor receptor expression single cell analysis single-cell RNA sequencing skin disorder skin lesion transcriptome transcriptomics treatment strategy

项目摘要

Much has been learned about mechanisms that drive autoimmunity by studying vitiligo, a dis- ease of the skin that results from destruction of pigment-producing melanocytes. This results in disfiguring white spots that are particularly devastating for those with darker skin, which thus leads to health disparities for the most vulnerable of our population. We generated an extensive set of preliminary data using single cell RNA sequencing (scRNA-Seq) that revealed hun- dreds of conversations that are unique to vitiligo lesions involving every cell type of the epider- mis. These data indicate that cells and their signaling networks within affected and unaffected vitiligo skin are in fact more complex than previously appreciated. Yet because scRNA-Seq re- quires disruption of the tissue, the position of each cell and their communications within the skin remains unknown. We hypothesize that cells connected in silico by matching induced ligand-receptor expression are in close physical proximity in situ, and that T cell clones marked by identical T cell receptor (TCR) sequences associate in physical contact with melanocytes. The objective of the High- Resolution Spatial Transcriptomics Research Core using sequential fluorescence in situ hybridi- zation (seqFISH+) is to use our highly innovative platform to provide spatial context to T cell clonality, cellular positioning, and cell-cell communications revealed by the complementary, syn- ergistic Center Projects 1+2. Our seqFISH+ platform provides a cutting-edge, innovative ap- proach to map RNA expression in tissues with high accuracy and sub-diffraction-limit resolution, allowing for identification of cell classes, expressed genes, and spatial organization in tissues. This approach will be applied in the following specific aims: 1) Identify the position and distribu- tion of T cell clones marked by unique TCR sequences within tissue; and 2) Reveal the spatial organization of communicating cells by receptor-ligand mapping directly within vitiligo lesions. We will use punch biopsies taken from the same vitiligo lesions that have been analyzed by sin- gle cell techniques in each Project. We will design seqFISH+ probes that complement TCR se- quences and ligand-receptor pairs for hybridization, which will indicate the spatial distribution of T cell clonality and cell-cell communications through ligand-receptor pairing. This Research core combines a highly innovative conceptual approach with cutting-edge technology. The prelimi- nary data, investigative team, and innovative plan provides a robust and unique opportunity for discovery of the fundamental mechanisms by which immune cells target self-tissues, which may lead to improved treatment strategies.

通过研究白癜风（一种疾病），我们已经了解了许多驱动自身免疫的机制