Streamlining Spatial Transcriptomics for Human Kidney Tissue
Vo, S.; Meadows, K.; Do, H.; Chapman, K.; Andonegui, G.; Muruve, D. A.; Pham, T.; Chun, J.
Show abstract
Single-cell spatial technologies have emerged in recent years, enabling tissue architecture and organization characterization at unprecedented resolution. However, computational analysis of spatial transcriptomics data is often a bottleneck for scientific discoveries in the absence of a dedicated bioinformatician. Here, we describes a workflow to annotate cell types from a dataset generated using NanoStrings CosMx single-cell resolution spatial transcriptomic technology, enabling a comparison between healthy kidney biopsies and diseased tissue. We validated our pipelines accuracy with both gene expression analysis and pathological changes associated with biopsy-proven diabetic kidney disease (DKD). Through precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with DKD tissue showing regional enrichment of immune cells and differential gene expression. Notably, injured proximal tubules had the expected increased expression of HAVCR1 and VCAM1 and genes associated with diabetes, including IL18, ITGA3 and ITGB1. The entire workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport 96%
- Therapeutic splice modulation of COL4A5 reinstates collagen IV assembly in an organoid model of X-linked Alport syndrome 95%
- NAD+ activates renal metabolism and protects from chronic kidney disease in a model of Alport syndrome 94%
Similar papers in this journal
- Measuring renal cortical cell-specific mitochondrial metabolism 94%
- Tcf21 as a Founder Transcription Factor in Specifying Foxd1 Cells to the Juxtaglomerular Cell Lineage 94%
- The transcription factor TCF21 is necessary for adoption of cell fates by Foxd1+ stromal progenitors during kidney development 94%
Similar papers in this journal
- Multi-omic Characterization of Human Tubular Epithelial Cell Response to Serum 96%
- Proximal tubule cells contribute to the thin descending limb of the loop of Henle during mouse kidney development 95%
- Integrin alpha1 beta1 promotes interstitial fibrosis in a mouse model of polycystic kidney disease 95%
Similar papers in this journal
- Mice with renal-specific alterations of stem cell-associated signaling develop symptoms of chronic kidney disease but surprisingly no tumors 96%
- Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts 95%
- Blockade of mTOR ameliorates IgA Nephropathy by correcting CD89 and CD71 dysfunctions in humanized mice 93%
Similar papers in this journal
- Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis 96%
- Gucy1α1 specifically marks kidney, heart, lung and liver fibroblasts 95%
- Multiple instance learning with pathology foundation models effectively predicts kidney disease diagnosis and clinical classification 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.