Single nucleus RNA-sequencing data of aged mouse kidneys after sham surgery and ischemia-reperfusion injury
Tertiary lymphoid tissues (TLTs), which are ectopic lymphoid structures, develop in several kidney diseases and are associated with a worse renal prognosis. However, the mechanisms by which TLTs expand and exacerbate kidney injury remain unknown. Single nucleus RNA-sequencing (snRNA-seq) was performed on aged mouse kidneys with TLTs after ischemia-reperfusion injury. The results were validated using immunostaining and in situ hybridization in murine and human kidneys and in vitro experiments. snRNA-seq of injured kidneys with TLTs identified proinflammatory and profibrotic Vcam1+ injured proximal tubules (PTs) with activation of NF-kappaB and interferon (IFN)-inducible transcription factors. VCAM1+ PTs were preferentially localized around TLTs, driving inflammation and fibrosis through multiple chemokines and cytokines production. TNF-alpha and IFN-gamma were intensely expressed by lymphocytes inside TLTs, and these cytokines synergistically upregulated the expression of VCAM1 and chemokines in cultured PT cells. snRNA-seq also identified proinflammatory fibroblasts and profibrotic fibroblasts, which resided inside and outside TLTs, respectively. Proinflammatory fibroblasts with STAT1 activation inside TLTs produced various chemokines and cytokines, including CXCL9, CXCL10, and B cell-activating factor, contributing to lymphocyte recruitment and survival. IFN-gamma upregulated expression of these molecules in cultured fibroblasts in a STAT1-dependent manner, indicating the potential bidirectional interactions between IFN-gamma-producing CXCR3+ T cells and fibroblasts inside TLTs. The cellular and molecular components described here were also confirmed in human kidneys with TLTs. In conclusion, TLTs function as an inflammation amplifier by providing microenvironments that allow intense interactions between renal parenchymal cells and immune cells. These interactions might be new therapeutic targets for kidney diseases with TLT formation.