A Comprehensive Immune Cell Atlas of Cystic Kidney Disease Reveals the Involvement of Adaptive Immune Cells in Injury-Mediated Cyst Progression in Mice

Abstract

BackgroundInducible disruption of cilia-related genes in adult mice results in slowly progressive cystic disease, which can be greatly accelerated by renal injury.MethodsTo identify in an unbiased manner modifier cells that may be influencing the differential rate of cyst growth in injured versus non-injured cilia mutant kidneys at a time of similar cyst severity, we generated a single-cell atlas of cystic kidney disease. We conducted RNA-seq on 79,355 cells from control mice and adult-induced conditional Ift88 mice (hereafter referred to as cilia mutant mice) that were harvested approximately 7 months post-induction or 8 weeks post 30-minute unilateral ischemia reperfusion injury.ResultsAnalyses of single-cell RNA-seq data of CD45+ immune cells revealed that adaptive immune cells differed more in cluster composition, cell proportion, and gene expression than cells of myeloid origin when comparing cystic models with one another and with non-cystic controls. Surprisingly, genetic deletion of adaptive immune cells significantly reduced injury-accelerated cystic disease but had no effect on cyst growth in non-injured cilia mutant mice, independent of the rate of cyst growth or underlying genetic mutation. Using NicheNet, we identified a list of candidate cell types and ligands that were enriched in injured cilia mutant mice compared with aged cilia mutant mice and non-cystic controls that may be responsible for the observed dependence on adaptive immune cells during injury-accelerated cystic disease.ConclusionsCollectively, these data highlight the diversity of immune cell involvement in cystic kidney disease.

Immune Checkpoint Activity Regulates Polycystic Kidney Disease Progression

“…This suggests that CD8 + T cells may be actively inhibited by this pathway within the CME and likely fail to execute their proposed anti-cystogenic function. This finding is in line with our recently published findings using scRNAseq which showed an enrichment of CD8 + T cells that express the PD-1 transcript in slowly progressive, inducible PKD mice lacking kidney Ift88 compared to controls(53). Following the cancer paradigm, upregulation of PD-L1 on kidney macrophages and epithelial cells implies an active commitment to drive immunosuppression, which would allow for the cystic epithelium to escape immune-mediated killing.…”

“…In line with these findings, depletion of macrophages as well as inhibition of CCR2 or CSF1R have been shown to slow cyst growth in inducible, earlyonset or inducible, late-onset PKD models (10,14,15,18). Beyond macrophages, our previous publication using inducible kidney-specific Ift88 knockout mice, as well as our data here (Figure 4E) highlight an enrichment of TRegs in PKD kidneys (53). TRegs, just like TAMs, are known drivers of immunosuppression in cancer (63).…”

“…Using scRNAseq, we recently published that both Ctla4 and Pdcd1 , encoding PD-1, are expressed in CD8 + T cells of mice lacking Ift88 in the kidney and presenting with slowly progressive PKD(53). Based on these data, and the supportive rationale to combine anti-PD-1 and anti-CTLA-4 from the cancer field, we decided to test this approach in PKD.…”

“…Correlatively, recent cancer studies have shown that treatment with anti-CTLA-4 results in a reduction of intra-tumoral T Regs , representing a noncanonical mechanism that may contribute to therapeutic efficacy(55–57). The relevance of T Regs to PKD progression has not been studied, but we recently found an enrichment of this population in PKD kidneys of an adult-onset PKD model caused by inducible kidney-specific Ift88 loss versus controls(53). We confirmed that kidney T Reg numbers are significantly increased in BALB/cJ Pkd1 RC/RC mice at 3 months of age compared to age, strain, gender matched wildtypes; the 3-month time point representing the endpoint of our combination therapy study ( Figure 4E ).…”

“…Indeed, utilizing a combination therapy approach of anti-PD-1 and anti-CTLA-4 in BALB/cJ Pkd1 RC/RC mice slowed PKD progression compared to either monotherapy arm or control (Figure 3). We focused on CTLA-4 because we knew the gene is expressed in CD8 + T cells of inducible, kidney specific Ift88 knockout mice presenting with adult-onset PKD, and because the monoclonal antibody targeting this receptor has proven efficacious in multiple cancers leading to FDA approval of the drug as monotherapy and combination therapy with anti-PD-1 (39,40,(51)(52)(53).…”