The spatially resolved transcriptional profile of acute T cell–mediated rejection in a kidney allograft

Fadi Salem, Laura Perin, Sargis Sedrakyan, Andrea Angeletti, Gian Marco Ghiggeri, Maria Cristina Coccia, Marty Ross, Miguel Fribourg, Paolo Cravedi

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Analysis of the transcriptional profile of graft biopsies represents a promising strategy to study T cell–mediated-rejection (TCMR), also known as acute cellular rejection. However, bulk RNA sequencing of graft biopsies may not capture the focal nature of acute rejection. Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. All kidney sections were from paraffin blocks. Overall, inflammatory genes were significantly upregulated in the tubular areas of the TCMR biopsy and showed an enrichment for gene-ontology terms associated with T-cell activation, differentiation, and proliferation. Enrichment analysis of the 100 genes with the highest coefficient of variation across the TCMR tubular regions of interest revealed that these highly variable genes are involved in kidney development and injury and interestingly do not associate with the 2019 Banff classification pathology scores within the individual regions of interest. Spatial transcriptomics allowed us to unravel a previously unappreciated variability across different areas of the TCMR biopsy related to the graft response to the alloimmune attack, rather than to the immune cells. Thus, our approach has the potential to decipher clinically relevant, new pathogenic mechanisms, and therapeutic targets in acute cellular rejection and other kidney diseases with a focal nature.

Original languageEnglish
Pages (from-to)131-136
Number of pages6
JournalKidney International
Issue number1
StatePublished - Jan 2022


  • biopsy
  • kidney transplant
  • spatial transcriptomic


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