Molecular characterization of kidney compartments from serial biopsies to differentiate treatment responders from non-responders in lupus nephritis

The immune pathways that define treatment response and non-response in lupus nephritis (LN) are unknown. To characterize these intra-renal pathways, transcriptomic analysis of protocol kidney biopsies was done. Kidney biopsies were done at flare (Bx1) and after treatment (Bx2) in 58 LN patients and healthy controls (HC). Glomeruli and tubulointerstitium (TI) were isolated using laser microdissection. RNA was extracted and analyzed by nanostring. Transcript expression from clinical complete (CR), partial (PR) and non-responders (NR) were compared at Bx1 and Bx2 and to HC. Top transcripts that differentiate CR from NR were identified. Confocal microscopy and urine ELISA was done to evaluate the protein expression of top transcripts. At Bx1 cluster analysis determined that glomerular integrin, neutrophil, and chemokine/cytokine, and TI chemokine, T cell and leukocyte adhesion genes differentiated NR from CR. At Bx2, glomerular monocyte, extracellular matrix, and interferon, and TI interferon, complement, and T cell transcripts differentiated NR from CR. Protein analysis recapitulated top transcript findings. Urine C5a and FN1 differentiated NR from CR after treatment. Transcript analysis of serial kidney biopsies taken during the treatment of LN demonstrated how gene expression in the kidney changes with clinically successful and unsuccessful therapy. These insights into the molecular landscape of response and non-response may help better align LN management with the pathogenesis of kidney injury. 58 paired kidney biopsies from patients with proliferative lupus nephritis (class III, class IV or class III/IV+V) were initially evaluated. This is a well defined, well curated dataset with clinical and histologic data available for all patients. Glomeruli and tubulointerstitium (TI) was isolated separately and samples with adequate RNA were submitted for nanostring analysis. Overall, 70 glomerular samples and 92 TI samples were submitted for nanostring analysis (35 glomerular and 46 TI pairs). Pre-implantation donor kidney biopsies (n=10) served as healthy controls. All kidney biopsy tissue used for this study were from FFPE blocks. 574 immune transcripts were analyzed by nanostring. Technical replicates with control samples are included Please note that the 'Nanostring_RAW_1-21.xlsx' contains raw data in 21 spreadsheets for all samples as indicated in the corresponding sample description field.