High-resolution spatial transcriptomics through light patterning

通过光图案化的高分辨率空间转录组学

• 批准号: 10341212
• 负责人: Georg Seelig
• 金额: $ 17.81万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10341212
• 关键词: Adoption; Antibodies; Architecture; B-Cell Lymphomas; Back; Bar Codes; Biological Process; Cell Nucleus; Cell-Matrix Junction; Cells; Censuses; Characteristics; Chemistry; Clinical; Complementary DNA; Computing Methodologies; Cultured Cells; DNA; Disease; Dissociation; Drug resistance; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Heart; Heterogeneity; Hodgkin Disease; Immune Evasion; Immunohistochemistry; Immunomodulators; In Situ Hybridization; Individual; Knowledge; Label; Length; Ligation; Light; Lighting; Liquid substance; Location; Maps; Mature B-Lymphocyte; Measures; Methods; Molecular; Nuclear; Optics; Pattern; Pharmaceutical Preparations; Phenotype; Positioning Attribute; Procedures; Proteins; Protocols documentation; RNA; Reaction; Reproducibility; Research Personnel; Research Project Grants; Resistance; Resolution; Sampling; Series; Shapes; Split-Pool Ligation Transcriptome sequencing; Techniques; Technology; Time; Tissues; Transcript; Tumor Tissue; Work; anticancer research; base; cancer diagnosis; cell type; combinatorial; cost; detection sensitivity; experimental study; flexibility; genome-wide; immunomodulatory therapies; improved; indexing; innovation; instrument; interest; new therapeutic target; patient stratification; predicting response; preservation; prototype; response; single-cell RNA sequencing; spatial relationship; success; tool; transcriptome; transcriptomics; treatment response; tumor; tumor heterogeneity; tumor microenvironment

PROJECT SUMMARY The cellular composition of a tumor as well as the spatial arrangement of cells within the tumor are major determinants of the response to therapy and the emergence of resistance. To improve our understanding of tumor heterogeneity, accelerate the discovery of new drug targets or enable better patient stratification it is thus necessary to develop tools that can resolve molecularly defined cell types within a tumor and capture their spatial relationships. Driven by progress in single-cell RNA sequencing (scRNA-seq) technologies, a complete census of molecularly defined cell types within a tumor is now within reach. However, because scRNA-seq requires dissociated cells and cannot preserve information about the spatial arrangement of cells in their original context, it gives an incomplete picture of the relationship between gene expression, cell type identity and tumor architecture. The need for technologies that measure gene expression in single cells while retaining position information has long been recognized, but existing solutions have insufficient cellular throughput, spatial resolution, or gene detection sensitivity. We propose to develop Combinatorial Light-Activated Spatial Sequencing (CLASSeq), a transformative approach to spatial transcriptomics that overcomes these limitations. CLASSeq uses patterned light illumination to attach DNA barcodes encoding location information to all cells of interest within a tissue section, with spatial resolution limited only by the wavelength of light. Spatial barcodes are sequenced together with cellular transcriptomes after dissociating the tissue into individual cells or nuclei, and tissue-wide gene expression patterns are computationally recreated. Because sequencing is performed after dissociation, any established scRNA-seq workflow can be used, enabling high sensitivity and cell throughput. To achieve high throughput and reproducibility, and facilitate wide adoption, we will work toward automating the labeling workflow by constructing a prototype instrument that integrates fluidics for barcode delivery with patterned illumination. To validate our approach and demonstrate its utility to cancer research, CLASSeq will be used to characterize cellular diversity and organization in Hodgkin lymphoma, a mature B-cell lymphoma in which the tumor microenvironment niche is critical to the tumor's success for host immune evasion and thus governs the response or lack thereof to clinical immune modulatory therapies.

项目总结

项目成果

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.

• DOI: 10.1038/s41598-021-94732-1
• 发表时间: 2021-08-04
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Grancharova T;Gerbin KA;Rosenberg AB;Roco CM;Arakaki JE;DeLizo CM;Dinh SQ;Donovan-Maiye RM;Hirano M;Nelson AM;Tang J;Theriot JA;Yan C;Menon V;Palecek SP;Seelig G;Gunawardane RN
• 通讯作者: Gunawardane RN