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Background N-glycosylation is one of the most common post-translational modifications in humans, and these alterations are associated with kidney diseases. Methods A novel technological approach, single-cell N-acetyllactosamine sequencing (scLacNAc-seq), was applied to simultaneously detect N-glycosylation expression and the transcriptome at single-cell resolution in three human kidney tissues from zero-time biopsy. Cell clusters, glycation abundance in each cell cluster, functional enrichment analysis, cell-cell crosstalk, and Pseudotime analysis were applied. Results Using scLacNAc-seq, 24,247 cells and 22 cell clusters were identified, and N-glycan abundance in each cell was obtained. Transcriptome analysis revealed a close connection between capillary endothelial cells (CapECs) and parietal epithelial cells (PECs). PECs and CapECs communicate with each other through several pairs of ligand receptors (e.g., TGFB1-EGFR, GRN-EGFR, TIMP1-FGFR2, VEGFB-FLT1, ANGPT2-TEK, and GRN-TNFRSF1A). Finally, a regulatory network of cell–cell crosstalk between PECs and CapECs was constructed, which is involved in cell development. Conclusions We here, for the first time, constructed the glycosylation profile of 22 cell clusters in the human kidney from time-zero biopsy. Moreover, cell–cell communication between PECs and CapECs through the ligand–receptor system may play a crucial regulatory role in cell proliferation.

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