Spatial transcriptomics reveals distinct role of monocytes/macrophages with high FCGR3A expression in kidney transplant rejections

Kidney transplant rejections are classified as active antibody mediated rejection (AMR) and cell mediated rejection (TCMR), with AMR primarily driven by antibodies produced by B cells, whereas TCMR is mediated by T lymphocytes that orchestrate cellular immune responses against the graft. Emerging evidence highlights the essential roles of innate immune cells in rejections, especially monocytes/macrophages and natural killer (NK) cells. However, the roles of specific innate immune cell subpopulations in kidney allograft rejection remain incompletely understood. Exploiting the spatial transcriptomics and formalin-fixed paraffin-embedded (FFPE) core needle biopsies from human kidney allografts, we demonstrated that non-rejection, AMR, acute TCMR and chronic active AMR have distinct transcriptomic features. Subclusters of monocytes/macrophages with high Fc gamma receptor IIIA (FCGR3A) expression were identified in C4d-positive active AMR and acute TCMR, and the spatial distribution of these cells corresponded to the characteristic histopathological features. Key markers related to monocyte/macrophage activation and innate alloantigen recognition were upregulated, along with metabolic pathways associated with trained immunity in AMR and TCMR. Taking together, these findings revealed that intragraft monocytes/macrophages with high FCGR3A expression play a critical role in kidney transplant rejections. Overall design: We selected 8 cases based on histopathological and clinical features (Table 1), representing 4 diagnostic groups: 1) non-rejection conditions; 2) Active AMR; 3) Acute TCMR; 4) Chronic active AMR. The clinical diagnosis is interpreted by our renal pathologists based on the 2018 Banff Criteria. We performed 10x Genomic Visium spatial transcriptomics analysis on H&E - stained sections from archived FFPE core needle biopsies of human kidney allografts following Visium Spatial Gene Expression for FFPE workflow.

肾移植排斥反应可分为抗体介导性排斥反应（active antibody mediated rejection, AMR）与细胞介导性排斥反应（cell mediated rejection, TCMR），其中AMR主要由B细胞产生的抗体驱动，而TCMR则由介导移植物抗细胞免疫应答的T淋巴细胞所介导。日益增多的研究证据表明，先天免疫细胞在移植排斥反应中发挥关键作用，尤其是单核细胞/巨噬细胞与自然杀伤（natural killer, NK）细胞。然而，特定先天免疫细胞亚群在肾同种异体移植排斥反应中的作用仍未完全阐明。
本研究借助人类肾同种异体移植物的空间转录组学数据与福尔马林固定石蜡包埋（formalin-fixed paraffin-embedded, FFPE）核心针穿刺活检标本，证实无排斥反应、AMR、急性TCMR以及慢性活动性AMR具有各自独特的转录组特征。在C4d阳性的活动性AMR与急性TCMR样本中，我们鉴定出高表达Fcγ受体ⅢA（Fc gamma receptor IIIA, FCGR3A）的单核细胞/巨噬细胞亚簇，且这类细胞的空间分布与特征性组织病理学表现高度契合。与单核细胞/巨噬细胞活化、先天同种抗原识别相关的关键标志物均表达上调，同时AMR与TCMR样本中与训练免疫（trained immunity）相关的代谢通路亦出现上调。综上，本研究结果揭示：移植物内高表达FCGR3A的单核细胞/巨噬细胞在肾移植排斥反应中发挥关键作用。
总体实验设计：我们根据组织病理学与临床特征筛选了8例样本（见表1），涵盖4个诊断组别：1）无排斥反应状态；2）活动性AMR；3）急性TCMR；4）慢性活动性AMR。本研究的临床诊断由本中心肾脏病理学家依据2018年版班夫标准（Banff Criteria）进行判定。我们遵循Visium FFPE空间基因表达实验流程，对人类肾同种异体移植物的存档FFPE核心针穿刺活检标本的苏木精-伊红（hematoxylin-eosin, H&E）染色切片开展10x Genomics Visium空间转录组学分析。