Supporting data for “Developing a patient-derived stem cell platform to model inflammation in lupus nephritis”

<p dir="ltr">Lupus nephritis (LN) is a prevalent and life-threatening manifestation affecting 50-60% of systemic lupus erythematosus (SLE) patients. Complete remission is only achieved in <70% patients, and >25% LN patients experience repeated nephritic flares during the disease course. Unfortunately, ~15% patients progress to end-stage renal disease and require invasive treatment such as dialysis or transplantation. This raises a need for further understanding in LN immunopathogenesis to devise better therapeutic strategies for improving disease outcomes in patients. From mouse models and patient biopsy samples, macrophages have been identified as a key immune mediator and its interaction with resident kidney cells contribute to LN development. Currently, there is a lack of human disease model to study the dynamic interaction of macrophages and kidney tissues.</p><p dir="ltr">In this study, a patient-derived disease model comprising both macrophages and kidney organoids was generated for mechanistic study. Specifically, expanded potential pluripotent stem cell (EPSC) lines were generated from healthy individuals (HC), LN patients and SLE patients without nephritis (never-LN/ NLN), all with compatible potential in generating functional macrophages and kidney organoids with substantial proportion of glomerular cells for disease model construction. This allows characterisation of both compartments with pathogenic factors to identify changes that are relevant for LN development. </p><p dir="ltr">Characterisation of EPSC-macrophages indicated a substantial difference between LN patients and other individuals. LN macrophages were more sensitive to immune complex (IC) stimulation, as exemplified by upregulation in expression of co-stimulatory proteins CD40 and CD86 at low IC concentrations. Moreover, LN macrophages exerted potent inflammatory responses, as indicated by significant upregulation of cytokines such as IL6, TNFA when compared with other individuals after IC stimulation. Furthermore, transcriptome profiling identified further pathogenic changes in LN macrophages upon stimulation such as enrichment of pro-fibrotic genes THBS1 and TNC. Collectively, these changes in LN macrophages were potentially relevant to the prolonged inflammation in LN progression in this patient. Single-cell transcriptome profiling on the co-culture of macrophages and kidney organoids identified patient-specific differences that further support the susceptibility of LN development in the patient. In addition to hyper-inflammatory phenotypes in macrophages, podocyte integrity in LN patient were also compromised after IC stimulation. Moreover, both podocytes and tubule cells expressed genes related to extracellular matrix remodelling after stimulation, which might indicate their potential roles in substantiating tissue fibrosis during LN development. In contrast, macrophages and stromal cells from NLN patient presented changes that were important for resolving inflammation and preventing fibrotic development, such as upregulation of genes related to TGF- signalling and extracellular matrix degradation. This might be relevant for the absence of nephritic development in this patient. </p><p dir="ltr">This was the first study that has successfully generated a patient-derived model for mechanistic study on LN development. Interestingly, changes in macrophages and kidney cells were also identified in NLN patient that can potentially limit overt nephritic development and prevent irreversible damage on renal tissues. This highlights the importance of early regulation of nephritic responses and offers new opportunities for developing effective measures to promptly resolve inflammation during earlier stages of LN to preserve renal functions.</p><p><br></p>