The molecular insights into the glomerulus injury and prognosis of patients with diabetic kidney disease by integrating proteomics and single-sell RNA sequencing

Background

As the leading cause of the end-stage renal disease (ESRD), the clinical and pathological trajectories as well as prognosis of diabetic kidney disease (DKD) patients vary between individuals and within a patient over time. Therefore, it is urgently needed to reveal the molecular insights into the glomerular injury and long-term kidney outcomes in DKD patients.

Methods

Glomeruli obtained from 50 biopsy-proven DKD patients underwent proteomics profiling and quantitative morphometric analysis. The clinical follow-up data for ten-years were collected. And the single-nucleus RNA sequencing (scRNA-seq) of diabetic nephropathy patients was used for integrative analysis.

Results

First, 1,047 glomeruli proteins were differential expression, among which 143, 39 and 18 ones were specifically expressed in podocyte, mesangial cell and endothelial cell. Six podocyte-specific ligands and ten mesangial cell-specific ligands were upregulated, those ligands could exert important function via interacting with corresponding receptors on receiver cells. Meanwhile, Mfuzz analysis showed that pathological progression of DKD glomerular was not gradual and monotonic, but passed through nonlinear and drastic transitions at the pathologic classification of class II and IV. The obviously upregulated proteins in class I-II mainly fall into the categories of metabolize, immunity, inflammation and apoptosis, and the proteins in class III-IV tend to executed functions of extracellular matrix deposition, collagen formation, complement and translation regulation. Furthermore, WGCNA analysis identified 191 proteins significantly associated with glomerular clinical or pathological phenotypes. Specially, seven phenotype-related proteins expressed in podocyte simultaneously associated with eGFR, proteinuria, serum creatinine, mesangial fraction and GBM thickness. Finally, by integrating the long-term kidney outcomes, we found that those glomerular cell-specific ligands and phenotype-related proteins were obviously related with kidney prognosis.

Conclusion

we have integrated clinical measurements, structural morphometry, long-term kidney outcomes and proteomics profiling of glomeruli from research kidney biopsies combined with scRNA-seq of diabetic nephropathy patients to explore the cell-specific molecular insights into glomerular injury as well as kidney prognosis. Thus, this study provides potential avenue for identification of urgently needed therapeutic targets and prognostic markers of diabetic kidney disease.