Integrative Systems Analysis of Calcineurin Inhibitor Action on Podocytes and Proximal Tubular Epithelial Cells
Bibliographic record
Abstract
Background: Calcineurin inhibitors (CNI), including Cyclosporin A (CSA), Tacrolimus (TAC) and Voclosporin (VCS) are used to treat proteinuric kidney disease. The mechanisms driving differential podocyte and tubular cell responses upon clinical exposure are poorly understood. Here, we tested the in vitro cellular response of these three most commonly used CNIs using a combination of integrated systems biology methods. Methods: We used high content image analysis to assess the changes in cytoskeletal and focal adhesion architecture; isobaric-tagged LC-MS/MS to assess altered proteomic response; image-based and colorimetric assays to assess viability and metabolic response. For all above assays, immortalized human podocytes and proximal tubular epithelial cells were treated with increasing doses of CSA, TAC and VCS. Respective drug dose responses were mapped back to the translational plasma concentrations as measured in the associated clinical trial. Results: All CNIs were well tolerated by immortalized human podocytes with minimal change in viability. Immortalized human tubular epithelial cells also showed little change in cell viability with high levels of cell death only in the highest doses of TAC. Morphometric changes were similar in CNIs, with increased focal adhesion area and aspect ratio. Levels of remodeling for all CNIs mirrored their respective calcineurin IC50 values with VCS showing a more robust dose response for both altered focal complex signaling and cell spreading. Quantitative proteomics at the physiologically relevant drug doses recapitulated the altered focal adhesion complex signatures for all CNIs. While network analyses of the differentially abundant podocyte adhesome showed a core CNI proteomic signature, this was supplemented by differing peripheral drug-specific networks that showed different neighborhoods for each CNI. Conclusions: While integrated viability, proteomic and high-content morphometric analyses show a common CNI-induced signature within human proximal tubular epithelial cells and podocytes, differences were observed among CSA, TAC and VCS for both differentially abundant proteins and drug dose responses. Consistent adhesome and cytoskeletal changes may point to a conserved biophysical role of calcineurin in podocytes with differences in off-target effects. Funding: Commercial Support - Aurinia
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".