The new pathology: dissecting cellular responses in lupus nephritis

SLE is a prototypic chronic autoimmune disease characterised by the production of wide spectrum of autoantibodies to ubiquitous antigens such as anti-dsDNA, targeting multiple organs. Lupus Nephritis (LN) is serious complication of SLE impacting ~50% of people with SLE and characterised by renal immune-complex (IC) deposition. Current methods of classifying LN are reliant on histological and clinical evidence, and do not reliably predict disease progression, while understanding of the cellular mechanisms of pathology is incomplete.
Mouse lupus models share clinical features of human disease including renal involvement and represent a way to manipulate and study early active disease on a homogenous background. Using two murine models of LN this thesis aims to understand identify disease drivers and potential therapeutic targets, and to establish an approach applicable to human kidney in the future.
To establish a platform to characterise LN in vivo, I phenotypically characterised two murine models of early LN, an inducible model using the TLR7 agonist imiquimod, and MRL/lpr, deficient in apoptotic mediator Fas. Immune phenotyping of both models shows systemic disease consistent with SLE. IMQ kidneys showed IC deposition, mesangial expansion, and endothelial proliferation consistent with class-II LN and MRL/lpr mice additionally developed crescents, and disease consistent with class-III LN.
Single cell transcriptomic data from the kidneys of imiquimod treated mice identified alterations in mesangial cells suggestive of de-differentiation and adoption of a fibroblast- like phenotype, associated with downregulation of Itga8. In the kidneys of MRL/lpr mice, early S1/S2 proximal tubule segments were identified as interferon (IFN) susceptible targets. Integrated analysis across the models identified enriched intrarenal, T, B, and myeloid populations in LN. MRL/lpr mice had the largest immune infiltrate, including NK and CD8 T cells expressing markers of cytotoxicity, exhaustion, and degranulation. Shared innate immune renal phenotypes across models included increased CD11bhi resident macrophage populations, expressing genes implicated in phagocytosis and efferocytosis, with trajectory analysis suggesting these macrophages may arise from increased patrolling non-classical monocytes. Altered pan immune signatures included differentially enhanced expression of homing receptor Itga4, which was validated at the protein level in the kidneys of MRL/lpr mice, identifying it as a potential target for in vivo assessment.
Taking forward transcriptomically identified targets, blockade of Itga4 in MRL/lpr mice did not have any impact on disease progression but did reduce proportions of non-classical monocyte infiltration in the kidney. To test the role of ITGA8 in mesangial cells, ITGA8 was knocked down in vitro, resulting in a more fibroblast like phenotype, akin to that seen in the kidneys of imiquimod treated mice. Restoration of expression in knockdown cell lines rescued the phenotype, confirming a gene specific effect and suggesting a functional role for this ITGA8 in mesangial fibrosis, suggesting both a potential therapeutic target and an in vitro model for future screens.
Integrated kidney snRNA-seq in two LN models delineates individual renal cell signatures and a shared immune signature, which may be important in early active disease. Our comprehensive kidney single nuclei approach is generalisable and highlights candidate genes for functional validation. A similar integrated approach will be directly applicable to human pathology.

Keywords: immune complex deposition
snrna-seq
SLE
lupus nephritis
autoimmunity
renal disease
Advisor: Bull, K
Cornall, R