Background In human lupus nephritis (LN), tubulointerstitial inflammation (TII) on biopsy predicts refractory disease and progression to end stage renal disease (ESRD). However, while approximately half of patients with moderate or severe TII develop ESRD, half do not. Therefore, we hypothesized that TII is heterogeneous with distinct inflammatory states each associated with different renal outcomes.

Methods We interrogated renal biopsies from LN longitudinal (55 patients) and cross-sectional cohorts using both conventional and highly-multiplex (24 analytes) confocal microscopy. To accurately segment cells across whole biopsies, and to understand their spatial relationships, we trained and implemented a suite of computer vision tools, including multiple parallel Mask-R convolutional neural networks. This evolution of our previous analytic pipeline, Cell Distance Mapping (CDM)(Nat Immunol, 2019, 20:503), we refer to as CDM version 4.

Results Across biopsies, B cell densities were strongly associated with protection from ESRD (p=2x10^-8, Mann-Whitney). In contrast, CD4- T cell population densities, which included CD8, gd and double negative (CD4-CD8-, DN) T cells, predicted progression to ESRD (p=5.7x10^-16). Breath first search and other analyses revealed inflammation was organized into different discrete niches each with unique characteristics including enrichment for specific cell populations. B cell were often organized into large clusters with CD4 T cells including T follicular helper-like cells. In contrast, the CD4- T cell populations formed small dispersed clusters which, on a per patient basis, predicted progression to ESRD (p=0.004).

Conclusions These data reveal that in LN, specific in situ inflammatory states are associated with the failure of conventional therapy and progression to ESRD.

Acknowledgments These studies were funded by the NIH Autoimmunity Centers of Excellence and Lupus Research Alliance.