Human - murine concordance of molecular signatures in nerve-sparing murine partial bladder outlet obstruction (NeMO)
Bibliographic record
Abstract
ABSTRACT Recently we demonstrated the utility of a nerve-sparing mid-urethra model of partial outlet obstruction (NeMO) that has high consistency and minimal mortalities, unlike the traditional model proximal to the bladder neck. Our goal was to uncover potential therapeutic targets by investigating the genome wide transcriptional changes and pathways altered in NeMO to compare with published human bladder obstruction data. We performed RNAseq and analysed the differentially upregulated and downregulated genes for associated pathways, transcription factor binding site analysis (TFBS), upstream regulators and Gene Set Enrichment Analysis (GSEA). NeMO increased bladder mass, relative bladder mass and hyperactivity, and decreased voiding efficiency. In NeMO vs. sham, 831 genes were differentially expressed (adjusted p<0.05) and correlated significantly with at least one physiologic parameter. Gene ontology revealed an enrichment for matrix pathways in the up regulated genes, and for cardiac contraction, oxidative phosphorylation and pyruvate metabolism in down regulated genes. TFBS analysis revealed a differential regulation of up vs downregulated genes, with KLF4 strongly associated with the downregulated genes. Downregulated genes of Human bladder obstruction were also associated with the TFBS of KLF4. GSEA of the NeMO gene set confirmed the DAVID results, but also showed a cluster of cytokine activation genes. In human bladder underactive obstruction, cytokines were also highly upregulated. The common cytokine pathway upregulation provided an example of the use of RNAseq for uncovering potential new therapeutic targets. As TNF and the innate immune pathways were strongly implicated in both human and mouse, and TNF is produced by macrophages, we depletion macrophages with clodronate (CL) during NeMO. Although CL did not block hypertrophy, it significantly decreased NeMO-induced hyperactive voiding (p<0.01) and increased voiding efficiency (p<0.05). The expression of several cytokines/chemokines correlated significantly with bladder functional parameters such as residual volumes, and hyperactivity. Conclusions: Gene expression signatures of NeMO were consistent with human bladder obstruction, supporting the use of the nerve-sparing mouse obstruction model for therapeutic exploration.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".