Annelie Mollbrink

Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.

To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.

Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify pathway dynamics, distinguish regional differences between microglia and astrocyte populations at early time points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.

(Cell 182, 497–514.e1–e22; July 23, 2020) As a result of human error, the spatial feature plot labeled ITGB1 in Figure 6G was instead a duplicate of the ITGA3 data just below it. Additionally, in Figure S4C, the order of some of the bar labels on the plot were swapped, in particular, the order of Treg, CD4+ Naïve, NK, and CD8+ Naive. Both figures have been corrected online. We are confident that these inadvertent panel duplication and labeling errors did not have any effect on our analyses or on any conclusions drawn from the paper, and we apologize for the errors.Figure 6GCellular Crosstalk Landscape Associated with Leading Edge Niches (original)View Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure S4CT Cell Subset Characterization and Spatial Positioning (corrected)View Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure S4CT Cell Subset Characterization and Spatial Positioning (original)View Large Image Figure ViewerDownload Hi-res image Download (PPT) Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell CarcinomaJi et al.CellJune 23, 2020In BriefIntegration of high-dimensional multi-omics approaches to characterize human cutaneous squamous cell carcinoma identifies a tumor-specific keratinocyte population as well as the immune infiltrates and heterogeneity at tumor leading edges. Full-Text PDF Open Access