Streamlining single-cell spatial transcriptomics for human kidney tissue

Single-cell spatial technologies have emerged in recent years, enabling characterization of tissue architecture and organization at unprecedented resolution. However, computational analysis of spatial transcriptomics data remains a bottleneck for scientific discoveries in the absence of dedicated bioinformatics expertise. Here, we describe a novel cell area normalization method and workflow to annotate 15 kidney cell types from a dataset generated using NanoString’s CosMx single-cell-resolution spatial transcriptomic platform. This approach enabled a comparison between two healthy kidney biopsies and two diseased samples. We validated our pipeline’s accuracy using gene expression analysis, demonstrating increased sensitivity compared with other normalization methods and consistency with pathological changes observed in biopsy-proven diabetic kidney disease (DKD). Using precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with regional enrichment of immune cells and differential gene expression. Injured proximal tubules showed the expected upregulation of <i>HAVCR1</i> and <i>VCAM1,</i> as well as other genes associated with diabetes, including <i>IL18</i>, <i>ITGA3</i>, and <i>ITGB1</i>. The workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training, providing accessible web-based tools for spatial data analysis. Kidney biopsy samples from two healthy patients and two diabetic kidney disease patients were analyzed using CosMx single-cell spatial transcriptomics. We developed a cell annotation and analysis pipeline using a novel cell area based normalization technique. Our workflow is fully integrated into the BioTuring SpatialX (Lens V2.0) platform, offering web-based analysis tools that provide a low barrier to entry for spatial data analysis. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform.Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches.Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes.Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform. Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches. Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes. Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution.