Proteomic Analysis of Renal Biomarkers of Kidney Allograft Fibrosis—A Study in Renal Transplant Patients

Abstract

Renal transplantation is the preferred treatment of end stage renal disease, but allograft survival is limited by the development of interstitial fibrosis and tubular atrophy in response to various stimuli. Much effort has been put into identifying new protein markers of fibrosis to support the diagnosis. In the present work, we performed an in-depth quantitative proteomics analysis of allograft biopsies from 31 prevalent renal transplant patients and correlated the quantified proteins with the volume fraction of fibrosis as determined by a morphometric method. Linear regression analysis identified four proteins that were highly associated with the degree of interstitial fibrosis, namely Coagulation Factor XIII A chain (estimate 18.7, adjusted p < 0.03), Uridine Phosphorylase 1 (estimate 19.4, adjusted p < 0.001), Actin-related protein 2/3 subunit 2 (estimate 34.2, adjusted p < 0.05) and Cytochrome C Oxidase Assembly Factor 6 homolog (estimate −44.9, adjusted p < 0.002), even after multiple testing. Proteins that were negatively associated with fibrosis (p < 0.005) were primarily related to normal metabolic processes and respiration, whereas proteins that were positively associated with fibrosis (p < 0.005) were involved in catabolic processes, cytoskeleton organization and the immune response. The identified proteins may be candidates for further validation with regards to renal fibrosis. The results support the notion that cytoskeleton organization and immune responses are prevalent processes in renal allograft fibrosis.

Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant

“…24 Quantitative proteomic studies of allograft biopsies have shown factor XIII A chain to correlate with degree of fibrosis. 25 Further evidence that donor macrophages contribute to pathology in ABMR is their differential expression of C1QA, C1QB, and C1QC. C1q-binding DSAs have been shown to confer a poor prognosis after ABMR.…”

Altered Phosphorylation of Cytoskeleton Proteins in Peripheral Blood Mononuclear Cells Characterizes Chronic Antibody-Mediated Rejection in Kidney Transplantation

“…Among them, a comprehensive control network for the actin cytoskeleton including several subunits of the actin-related protein 2/3 complex was found uniquely expressed (upregulated) in patient samples with progressive injury and a high risk for graft loss [19]. A recent proteomic analysis of allograft biopsies from renal transplant patients supported these findings by demonstrating that increased expression of ARP2/3 subunit 2 correlated with kidney fibrosis [20]. We further confirm their observation adding a brand-new piece of information; however, we do not know how cytoskeleton modification in PBMC could be correlated with increased fibrosis in the graft.…”

“…We further confirm their observation adding a brand-new piece of information; however, we do not know how cytoskeleton modification in PBMC could be correlated with increased fibrosis in the graft. Indeed, these studies [19,20] employed a classical proteomic approach identifying the proteins up or downregulated at the graft tissue level, whereas we investigated circulating immune cells using what we may define a functional proteomic approach. More functional studies including the recruitment of these cells in the kidney and their role in inflammation and fibrosis in the graft should be performed to better clarify the role of PBMC's cytoskeleton modification in the pathogenesis of graft rejection.…”

Basement membrane proteins in various arterial beds from individuals with and without type 2 diabetes mellitus: a proteome study

“…ATA samples were prepared for proteomic analysis also as previously described [21]. In brief, sections were deparaffinized in chloroform, and proteins were extracted using 1 M DTT, 0.2 M TEAB and 10% sodium dodecyl sulphate, and incubated at 99 °C for 20 min, and then at 80 °C for 120 min.…”