3.1.2. Renal Tissue Transcriptomics

Sigdel T et al. analyzed tissue expression of selected 19 target genes, including those previously identified in tissue common rejection module (tCRM). Interestingly, they employed RNA extracted from archival fresh frozen paraffin-embedded renal biopsy tissue. Eight genes were related to specific cellular infiltrates, whereas the others reflected a "graft inflammation score" based on tCRM. This set of genes allowed to distinguish biopsies of stable grafts from those of recipients with AR and even borderline inflammation [56].

Molecular patterns such as upregulation of intrarenal complement regulatory genes discriminate accommodation from subclinical antibody-mediated rejection in AB0-incompatible KTx [92].

An intra-graft mRNA transcriptomic landscape of TCMR has been outlined through computational analysis and has shown an increased expression of innate immunity genes, such as genes for pattern recognition receptors, and a decreased expression of calcineurin, suggesting inadequate immunosuppression, as compared to stable graft [61].

Real time central molecular assessment of changes in mRNA expression in graft tissue through microarrays is the basis of "molecular microscope diagnostic system", which predicted risk of AR and graft failure with greater precision than conventional biopsy. Pathogenesis-based transcripts sets (PBTs) which segregate together and characterize different processes (e.g., IGF-gamma expression, T cell infiltrates), were employed to define "classifiers" which predict molecular phenotype, quantifying its likelihood with a score. Of importance, this approach has been validated in several independent cohorts [93,94].

Other studies have shown that endothelial associated transcripts (ENDATs) in biopsies of DSA-positive patients can reveal ABMR even in the absence of C4d positivity [58] and that ABMR-related endothelial genes RNA transcripts are expressed before histological onset of lesions, allowing excellent identification (AUC = 0.92) and potentially early, preemptive treatment of rejection [59].

Finally, single-cell transcriptomics can comprehensively describe cell types and states in a human kidney biopsy and was employed to analyze immune response in mixed rejection: 16 distinct cell types were identified, including different sub-clusters of activated endothelial cells [95]. This cell-based approach may provide a wealth of new biomarkers for ABMR in the future [96].
