Landscape of innate immune system transcriptome and acute T-cell mediated rejection of human kidney allografts

Acute rejection of human allografts has been viewed mostly through the lens of adaptive immunity, and the intragraft landscape of innate immunity genes has not been characterized in an unbiased fashion. We did RNA sequencing of 34 kidney allograft biopsy specimens from 34 adult recipients; 16 were categorized as Banff acute T-cell mediated rejection (TCMR) and 18 as normal. Computational analysis of intragraft mRNA transcriptome identified significantly higher abundance of mRNA for pattern recognition receptors in TCMR compared to normal biopsies, as well as increased expression of mRNAs for cytokines, chemokines, interferons, and caspases. Intragraft levels of calcineurin mRNA were higher in TCMR biopsies suggesting under immunosuppression compared to normal biopsies. Cell-type enrichment analysis revealed higher abundance of dendritic cells and macrophages in TCMR biopsies. Damage associated molecular patterns, the endogenous ligands for pattern recognition receptors, as well markers of DNA damage were higher in TCMR. mRNA expression patterns supported increased calcium flux and indices of endoplasmic, cellular oxidative, and mitochondrial stress were higher in TCMR. Expression of mRNAs in major metabolic pathways were decreased in TCMR. Our global and unbiased transcriptome profiling identified heightened expression of innate immune system genes during an episode of TCMR in human kidney allografts. We studied 34 adult kidney transplant recipients, a subset of kidney allograft recipients transplanted and followed at our center. Biopsies were done under ultrasound guidance and were read and reported independently by two renal pathologists at our center (S.S and S.V.S), based on the Banff 2017 update of the Banff ‘97 classification of allograft pathology (64, 65). Biopsy tissue sections were stained with hematoxylin and eosin, periodic acid–Schiff, and Masson trichrome, as well as for polyomavirus, and for complement factor 4 degradation product d (C4d). Each patient provided a single biopsy sample for this study.