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.

对移植物活检转录谱的分析是研究 T 细胞介导的排斥反应 (TCMR)（也称为急性细胞排斥反应）的一种很有前途的策略。然而，移植活检的大量 RNA 测序可能无法捕捉到急性排斥反应的焦点性质。在此，我们使用整个外显子组 GeoMX 数字空间分析平台研究了慢性活动性 TCMR 发作患者的肾移植活检中的五个感兴趣的肾小管和三个肾小球区域，以及两个不同的正常肾脏对照活检的类似区域。所有肾切片均来自石蜡块。总体而言，炎症基因在 TCMR 活检的管状区域显着上调，并显示与 T 细胞活化、分化和增殖相关的基因本体术语丰富。对 TCMR 管状感兴趣区域变异系数最高的 100 个基因的富集分析表明，这些高度可变的基因与肾脏发育和损伤有关，有趣的是，与各个感兴趣区域的 2019 年班夫分类病理评分无关. 空间转录组学使我们能够揭示 TCMR 活检不同区域以前未被重视的变异性，该变异性与移植物对同种免疫攻击的反应有关，而不是对免疫细胞的反应。因此，我们的方法有可能破译急性细胞排斥反应和其他具有局灶性的肾脏疾病的临床相关新致病机制和治疗靶点。