Project description:This study presents a single cell and spatially resolved transcriptomics analysis of human breast cancers. We develop a single cell method of intrinsic subtype classification (scSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using CITE-Seq provides high-resolution immune profiles, including novel PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell surface protein expression through differentiation within 3 major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into anti-tumor immune regulation. Using single cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed ‘ecotypes’, with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.
Project description:Breast cancers are complex cellular ecosystems where heterotypic interactions play central roles in disease progression and response to therapy. However, our knowledge of their cellular composition and organization is limited. Here we present a single-cell and spatially resolved transcriptomics analysis of human breast cancers. We developed a single-cell method of intrinsic subtype classification (SCSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) provides high-resolution immune profiles, including new PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell-surface protein expression through differentiation within three major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into antitumor immune regulation. Using single-cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed 'ecotypes', with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.
Project description:Human skin provides both physical integrity and immunological protection from the external environment, using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combined advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantified 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe here the quantitative distribution of structural proteins, known and novel proteins specific to cellular subsets and those with specialized immunological funtions such as cytokines and chemokines. We anticipate this proteomic atlas of human skin will become an essential community resource for basic and translational research (www.skin.science).
Project description:Cis-regulatory elements (CREs) precisely control the spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) binding motifs controlling cell-type specification and maintenance. We identified non-cell autonomous activity of NIN-LIKE PROTEIN 7 (NLP7), the Nodule Inception (NIN) gene regulatory network and de novo enriched TF motifs in the nodule infected cells. With comprehensive developmental trajectories for endosperm and embryo, we found that 13 sucrose transporters, sharing the DOF11 binding motif, were co-up-regulated in late peripheral endosperm and identified the key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
Project description:Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.
Project description:Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.
Project description:Understanding the spatial distribution of T cells is pivotal to decrypting immune dysfunction in cancer. Current spatially resolved transcriptomics fall short in directly annotating T cell receptors (TCRs), limiting the comprehension of anti-cancer immunity. We introduce a novel technology, Spatially Resolved T Cell Receptor Sequencing (SPTCR-seq), integrating target enrichment and long-read sequencing for highly sensitive TCR sequencing. This approach yields an on-target rate of ~85%, and via a bespoke computational pipeline, it provides meticulous spatial mapping, error correction, and UMI refinement. SPTCR-seq outperforms PCR-based methods, offering superior reconstruction of the complete TCR architecture, inclusive of V, D, J regions and the vital complementarity-determining region 3 (CDR3). Applying SPTCR-seq, we reveal local T cell diversity, clonal expansion, and transcriptional evolution across spatially distinct niches in glioblastoma, identifying critical involvement of NK and B cells in spatial T cell adaptation. SPTCR-seq, by bridging spatially resolved omics and TCR sequencing, stands as a robust tool for exploring T cell dysfunction in cancers and beyond.