Submission
| Title: | Identification of scattered proximal tubule cells using Co-registered spatial transcriptomics and CO-Detection by indexing immunofluorescence |
| Co-Authors: |
Asghari, Mahla, Indiana University School of Medicine; Michael T. Eadon, Indiana University School of Medicine; Ricardo Melo Ferriera, Indiana University School of Medicine; Seth Winfree, University of Nebraska System; Yinghua Cheng, Indiana University School of Medicine; Carrie L. Phillips, Indiana University School of Medicine; Daria Barwinska, Indiana University School of Medicine; Michael J. Ferkowicz, Indiana University School of Medicine; Angela R. Sobo, Indiana University School of Medicine; Debora L. Gisch, Indiana University School of Medicine; Timothy A. Sutton, Indiana University School of Medicine; Ken Dunn, Indiana University School of Medicine; Katherine J. Kelly, Indiana University School of Medicine; Pierre C. Dagher, Indiana University School of Medicine; Tarek M. El-Achkar, Indiana University School of Medicine |
Abstract
Background/Significance/Rationale: CD90 is mainly expressed in mesenchymal stem cells as well as proximal tubules (PT) in kidney and hypothesized that it is upregulated in regenerative scattered tubular cells (STCs) of PTs. Using co-registered spatial transcriptomics (ST) and CO-Detection by indEXing (CODEX) immunofluorescence, we aimed to define a novel STC subcluster in the KPMP/HubMAP snRNAseq atlas.
Methods: On three human kidney tissue sections (10 µm thick), CODEX (44 antibodies including CD90 and megalin/LRP2) and ST (>20,000 genes detected) were used to align the protein and transcriptomes. Protein expression of THY1 and LRP2 defined regions for ST comparison. THY1+ LRP2+ and THY1- LRP2+ regions were compared together. Differentially expressed genes (DEGs) were used to define a novel subcluster in the snRNAseq atlas of >170,000 cells from 29 kidney biopsy samples. Then, enriched pathway analysis was done for the new STC subcluster. Aggregate THY1+ PT cluster representation was assessed in human kidney samples including 9 References, 6 Acute Kidney Injury (AKI) and 11 Chronic Kidney Disease (CKD) tissues, queried with ST.
Results/Findings: A novel STC subcluster was defined within the snRNAseq atlas. DEGs of STCs included THY1, SLC16A9, and PDZK1IP1. STC enriched pathways included Rho GTPase cycle, RAC1, growth factor signal transduction, and cell adhesion related pathways, consistent with the expected functions of this regenerative cell. Using Seurat anchor methodology, the THY1+ sub-cluster, defined by snRNAseq, mapped back to regions of THY1 protein expression. Aggerate THY1 PT cluster proportion decreased significantly (Reference= 18.9, AKI= 18.6, CKD= 13.1, t-test p-value=0.003) in CKD, not in AKI as compared to reference controls.
Conclusions/Discussion: The integration of CODEX, ST, and snRNAseq datasets facilitated the identification of an important regenerative PT cell type which was under-represented in the KPMP snRNAseq atlas.
Translational/Human Health Impact: Since THY1+ cells are involved in regeneration, CD90 could potentially be a biomarker for kidney disease and monitoring its progression.
