Lupus nephritis affects approximately 40% of patients with systemic lupus erythematosus.1 Despite recent advances in immunosuppression therapy, many patients fail to achieve complete renal remission and go on to develop impaired renal function. The failure to control disease may reflect an incomplete understanding of immunologic mechanisms driving disease.
Prior work has shown that immune cell infiltration, especially of macrophages, is associated with pathologic tissue changes and decline in renal function in lupus nephritis.2 Thus, a deeper understanding of these cells could yield novel therapeutic targets, more accurate interpretation of histopathologic lesions, and better disease predictors.
Profiling Patient Samples Has Identified New Cell Types and Pathways in Active Lupus Nephritis
Because we do not fully understand the mechanisms leading to lupus nephritis, a major effort in the lupus field has been in “deconstructing” disease by deeply profiling individual cells collected from patient kidney biopsies and blood to discover cellular states and pathways that are active in disease.3
Using single-cell RNA sequencing, a powerful technology that simultaneously measures thousands of genes expressed in individual cells, we have discovered 21 immune cell-types dramatically enriched in lupus nephritis kidney biopsies compared with healthy kidneys as part of a National Institutes of Health (NIH) and pharmaceutical-sponsored consortium (Accelerating Medicines Partnership [AMP]).4 This has paved the way for a 200-patient study by AMP that will discover additional new cell types and pathways and tests for associations with clinical variables. These newly discovered immune cells represent the functional states that are relevant to human lupus nephritis, and include novel macrophage subsets whose role is not yet understood.
Mouse Models Recapitulate Aspects of Human Lupus Nephritis for Mechanistic Studies
As new cellular states and pathways are being discovered from patient samples, a critical follow-up includes validating targets to determine their role in disease. Since we cannot feasibly isolate macrophages (or other immune cells) from human kidney biopsies for mechanistic studies, we set out to understand whether and how mice recapitulate human lupus nephritis. We applied the same powerful technology, single-cell RNA sequencing, to macrophages collected from the kidneys and blood of 4 common lupus nephritis mouse strains during the development of kidney disease and compared our findings with those from human patient kidney biopsies.
We identified conserved macrophage subsets across species in lupus nephritis and made several discoveries. First, mouse and human macrophage subsets in active lupus nephritis shared gene programs that regulate kidney tissue repair, recruit additional immune cells to kidneys, modulate the local immune response, and expressed genes linked to human lupus genetic susceptibility. Second, while the kidney is complex and highly organized, conserved macrophage subsets localized to the same kidney compartments in mice and human biopsy sections, suggesting these cells carry out their effector functions in the same kidney microenvironment. Third, we observed that the locations of macrophages across kidney sections from the majority of patients mirrored locations in mouse kidney sections, suggesting that mice reflect patient-specific phenotypes.
Our findings support conserved roles of several macrophage subsets and identify for the first-time molecular targets shared in humans and mice that can be studied to determine their role in lupus nephritis.
With novel technologies like single-cell RNA sequencing and CRISPR-Cas9-based approaches to study gene functions, we hope that our findings (now in preparation for submission) open a new path using mouse models to more precisely study aspects of human disease.
Author’s Note: This project has been funded by the Rheumatology Research Foundation, Lupus Research Alliance, Lupus Foundation of America, and the US Department of Defense.
- Hoover PJ, Costenbader KH. Insights into the epidemiology and management of lupus nephritis from the US rheumatologist’s perspective. Kidney Int. 2016;90(3):487-492.
- Ryan MJ, Imig JD. Immune and inflammatory role in renal disease. Compr Physiol. 2013;3(2):957-976. doi:10.1002/cphy.c120028
- Hoover P, Der E, Berthier CC, et al. Accelerating medicines partnership: organizational structure and preliminary data from the phase 1 studies of lupus nephritis. Arthritis Care Res (Hoboken). 2020;72(2):233-242. doi:10.1002/acr.24066
- Arazi A, Rao DA, Berthier CC, et al. The immune cell landscape in kidneys of patients with lupus nephritis. Nat Immunol. 2019; 20(7):902-914. doi:10.1038/s41590-019-0398-x