Immune cell quantification of in situ inflammation partitions human lupus nephritis into mechanistic subtypes
Gabriel Casella, Madeleine S. Torcasso, Junting Ai, Thao P. Cao, Satoshi Hara, Michael S. Andrade, Deepjyoti Ghosh, Daming Shao, Anthony Chang, Kichul Ko, Anita S. Chong, Maryellen L. Giger, Marcus R. Clark
Gabriel Casella, Madeleine S. Torcasso, Junting Ai, Thao P. Cao, Satoshi Hara, Michael S. Andrade, Deepjyoti Ghosh, Daming Shao, Anthony Chang, Kichul Ko, Anita S. Chong, Maryellen L. Giger, Marcus R. Clark
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Clinical Research and Public Health Autoimmunity Immunology

Immune cell quantification of in situ inflammation partitions human lupus nephritis into mechanistic subtypes

Abstract

BACKGROUND In human lupus nephritis (LuN), tubulointerstitial inflammation (TII) is prognostically more important than glomerular inflammation. However, a comprehensive understanding of both TII complexity and heterogeneity is lacking.METHODS Herein, we used high-dimensional confocal microscopy, spatial transcriptomics, and specialized computer vision techniques to quantify immune cell populations and localize these within normal and diseased renal cortex structures. With these tools, we compared LuN to renal allograft rejection (RAR) and normal kidney tissues on 54 deidentified biopsies.RESULTS In both LuN and RAR, the 33 characterized immune cell populations formed discrete subgroups whose constituents covaried in prevalence across biopsies. In both diseases, these covariant immune cell subgroups organized into the same unique niches. Therefore, inflammation could be resolved into trajectories representing the relative prevalence and density of cardinal immune cell members of each covariant subgroup. Indeed, in any one biopsy, the inflammatory state could be characterized by quantifying constituent immune cell trajectories. Remarkably, LuN heterogeneity could be captured by quantifying a few myeloid immune cell trajectories, while RAR was more complex with additional T cell trajectories.CONCLUSIONS Our studies identify rules governing renal inflammation and thus provide an approach for resolving LuN into discrete mechanistic categories.FUNDING NIH (U19 AI 082724 [MRC], R01 AI148705 [MRC and ASC]), Chan Zuckerberg Biohub (MRC), and Lupus Research Alliance (MRC).

Authors

Gabriel Casella, Madeleine S. Torcasso, Junting Ai, Thao P. Cao, Satoshi Hara, Michael S. Andrade, Deepjyoti Ghosh, Daming Shao, Anthony Chang, Kichul Ko, Anita S. Chong, Maryellen L. Giger, Marcus R. Clark

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Figure 1

Cell detection in multiplex microscopy imaging of renal biopsy tissue.

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Cell detection in multiplex microscopy imaging of renal biopsy tissue. (...
(A) Histological scoring of patient-paired H&E and PAS biopsies. The mean autoimmune cohort and standard deviation of the histological features are shown. Mann-Whitney-U nonparametric difference in means P-values are shown. (B) CODEX antibody marker panel grouped by cell lineage or cellular activity most associated with that marker. (C) Workflow diagram of cell detection and segmentation. Cell nuclei are defined using Cellpose 2.0 on a 512×512 DAPI image after performing Human-in-the-loop model retraining. Cell body was subsequently approximated by performing nuclear dilation with Voronoi tessellation. 512×512 images of DAPI segmentations are then knitted and aligned with the 42 fluorescent channels. (D) UMAP dimensional reduction of cell body MFI from 30,000 cells randomly sampled. 10,000 cells are sampled from each of the 3 cohorts: Normal Kidney Control, Lupus Nephritis, and Renal Allograft Rejection. Cells are colored according to their cohort of origin: KC, LuN, and RAR. (E) UMAP dimensional reduction of cell body MFI from 30,000 cells randomly sampled. Cells are colored according to their cohort of origin.