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Glucocorticoids and calcineurin inhibitors (CNI) are part of KDIGO guidelines for treatment of steroid resistant glomerular diseases. Despite widespread use, predicting whether a patient will respond to therapy remains elusive. Given toxicities associated with prolonged CNI use, identifying patients who are both likely and unlikely to respond to these therapies presents an opportunity to improve overall patient care.
We hypothesized that patients’ intrarenal molecular fingerprint could be predictive of eventual response to standard-of-care therapy and that this fingerprint could further be linked to non-invasive surrogate profiles in either the blood or urine. To address this, we first leveraged kidney biopsy transcriptomic profiles, medication data both pre-and post-biopsy, and clinical responses prospectively ascertained from study participants enrolled in the Nephrotic Syndrome Study Network (NEPTUNE).
Kidney biopsy cores obtained in RNAlater from NEPTUNE study participants were micro-dissected into glomerular (glom) and tubulointerstitial (tub) compartments. RNA was extracted and RNAeq libraries were generated in glom (n=325) and tub (n=360). Clinical phenotypes including, steroid and CNI exposure were recorded prior to biopsy and throughout study follow up. Weighted gene co-expression network analysis was performed to identify co-expressed gene modules associated with complete remission (CR) during CNI exposure. Functional enrichment analysis of co-expressed module genes was performed using Enrichr (Chen et al., BMC Bioinf., 2013).
In glom and tub, we identified 42 and 24 gene co-expression modules, respectively, as potential predictors of future response during CNI exposure. Owing to a significant pre-biopsy steroid exposure profile, our primary analyses assessed whether gene expression profiles in steroid naïve patients were predictive of any future complete remission during CNI exposure, followed by a secondary analysis of CNI response in a steroid exposed background. In tub, 3 modules (labeled dark red, turquoise, and dark green) were associated with CR during CNI exposure (p<0.05) in steroid naïve patients at time of biopsy, and 2 of the modules (turquoise and dark green) were also associated with CR during CNI exposure in steroid exposed patients (at time of biopsy, p<0.05). Functional enrichment analysis of module genes demonstrated enrichment immune, cytokine, and interferon signaling pathway genes (turquoise and dark green modules), and enrichment for genes expressed in endothelial cells (dark red module).
In steroid naïve patients, genes enriched in interferon, immune and cytokine signaling, and those related to endothelial cell biology were elevated in patients that did not respond to future CNI treatment. We are currently evaluating non-invasive surrogate profiles and assessing these profiles in orthogonal datasets with a goal of developing a biomarker assay that will be predictive of future CNI response.