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Role of HRTPT in kidney proximal epithelial cell regeneration: Integrative differential expression and pathway analyses using microarray and scRNA-seq |
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| Authors: | Swojani Shrestha Sonalika Singhal Matthew Kalonick Rachel Guyer Alexis Volkert Seema Somji Scott H Garrett Donald A Sens Sandeep K Singhal |
| Institution: | 1. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA
Contribution: Conceptualization (equal), Data curation (equal), Formal analysis (equal), Validation (equal), Writing - original draft (equal), Writing - review & editing (equal);2. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA Contribution: Conceptualization (equal), Data curation (equal), Formal analysis (equal), Methodology (equal), Writing - review & editing (equal);3. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA Contribution: Data curation (equal), Resources (equal), Writing - original draft (equal);4. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA Contribution: Data curation (equal), Writing - original draft (equal);5. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA Contribution: Data curation (equal), Writing - original draft (equal), Writing - review & editing (equal);6. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA Contribution: Data curation (equal), Formal analysis (equal), Funding acquisition (lead), Investigation (equal), Methodology (equal), Project administration (equal), Supervision (equal), Validation (equal), Writing - original draft (equal), Writing - review & editing (equal);7. Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, USA |
| Abstract: | Damage to proximal tubules due to exposure to toxicants can lead to conditions such as acute kidney injury (AKI), chronic kidney disease (CKD) and ultimately end-stage renal failure (ESRF). Studies have shown that kidney proximal epithelial cells can regenerate particularly after acute injury. In the previous study, we utilized an immortalized in vitro model of human renal proximal tubule epithelial cells, RPTEC/TERT1, to isolate HRTPT cell line that co-expresses stem cell markers CD133 and CD24, and HREC24T cell line that expresses only CD24. HRTPT cells showed most of the key characteristics of stem/progenitor cells; however, HREC24T cells did not show any of these characteristics. The goal of this study was to further characterize and understand the global gene expression differences, upregulated pathways and gene interaction using scRNA-seq in HRTPT cells. Affymetrix microarray analysis identified common gene sets and pathways specific to HRTPT and HREC24T cells analysed using DAVID, Reactome and Ingenuity software. Gene sets of HRTPT cells, in comparison with publicly available data set for CD133+ infant kidney, urine-derived renal progenitor cells and human kidney-derived epithelial proximal tubule cells showed substantial similarity in organization and interactions of the apical membrane. Single-cell analysis of HRTPT cells identified unique gene clusters associated with CD133 and the 92 common gene sets from three data sets. In conclusion, the gene expression analysis identified a unique gene set for HRTPT cells and narrowed the co-expressed gene set compared with other human renal–derived cell lines expressing CD133, which may provide deeper understanding in their role as progenitor/stem cells that participate in renal repair. |
| Keywords: | CD133 CD24 Cell regeneration Human renal epithelial cell 24 TERT (HREC24T) cells Human renal tubular precursor tert (HRTPT) cells Microarray renal progenitor cells |