First Gene Expression Profiling of the Chronic Transplant Arteriopathy On FFPE Renal Biopsies.

Abstract

Background: Chronic rejection shows varying combination of lesions such as transplant glomerulopathy, interstitial fibrosis/tubular atrophy and chronic transplant arteriopathy (CTA) which is characterized by larger arteries with intimal fibrosis, thickening of intima, invasion of proliferated smooth muscle cells and infiltrates of mononuclear cells. Several independent coexisting factors contribute to the characteristic morphological features of CTA which are the final event of different non-immunological and immunological pathways. Since smooth muscle cells respond to growth factors and vasoactive peptides we applied transcriptomics on archival formalin-fixed, paraffin-embedded (FFPE) renal tissue of patient with CTA for searching genes responsible for the production of humoral factors. Materials and Methods: Total RNA from 21 CTA biopsies was processed using cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) Assay (Illumina). Fifty-two renal tissue samples obtained from cadaveric donors were used as controls. Results: Using fold change ≥2 and a false discovery rate<0.05, we identify 191 differentially modulated genes in CTA respect to cadaveric donors. Principal Component Analysis 3-D analysis showed that the two groups had significant differences in gene expression distribution indicating two transcriptionally distant populations. A Gene Set Enrichment Analysis approach showed functional gene set differentially expressed such as allograft rejection, and graft versus host disease. In particular, we focus on 9 modulated genes belonging to the leukocyte endothelial transmigration pathway, 16 up-regulated genes belonging to cell adhesion molecules pathway and 16 modulated genes belonging to natural killer mediated cytotoxicity, that were modulated more than 1.5 fold. Discussion and Conclusions: This study shows, for the first time, that a characteristic gene expression profile occurs in CTA. The in vivo and in vitro validation studies of some identified genes may help in evolving strategies for diagnosis and treatment targeted to specific mechanisms.