Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough to reproduce VIA THE DEPOSITED PROCESSED DATA, not via the repo. The GitHub repo is illustrative R snippets (placeholders, unshipped intermediate .rds, unspecified per-sample params) so an end-to-end from-FASTQ rerun is out of 80/20 scope. But GEO GSE183842 deposits the authors' final processed snRNA counts.rds + per-nucleus metadata and snATAC metadata, which makes the headline numbers and central biology directly checkable. One «our HPC» job (2179401) reproduced 13/14 checkable claims essentially 1:1: snRNA 310,282 nuclei (paper 310,218; +0.02%), 22 samples, 5 groups, 16 cell types; snATAC 53,298 nuclei, 9 samples; and the key marker biology — Spp1/Il34/Pdgfb/Havcr1 maximal in injured-PT (iPT) cells and MR (Nr3c2) maximal in principal cells (PC), plus PCT=Cubn, PST=Slc7a13. One partial (Vcam1 max is Endo, though iPT is positive). NOTABLE: an apparent internal contradiction (Methods '53,298 nuclei' vs Fig 1A '310,218') was provisionally flagged as possible fabrication, then REFUTED by the data — 53,298 is the snATAC dataset and 310,218 the snRNA dataset (two assays); both reproduce, no fabrication indicated. NOT attempted (hard ~20%): from-FASTQ CellRanger/SoupX/DoubletFinder rerun, exact DEG counts (~2,700 vs ~200), tensor decomposition (scITD), hdWGCNA, CellChat, pseudotime/SCENIC, human iPT-signature clustering, snATAC peak/chromVAR motifs, and the raw 41/20 cluster counts (deposited metadata ships final cell-type labels only).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 95assessed: 2026-06-15 ⛓ 8f9820d18e94
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-15
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no human curator yet
- Last updated
- 2026-09-19
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnetMineralocorticoid excess drives hypertension-associated kidney disease through cell-type-specific gene regulation, and steroidal versus nonsteroidal mineralocorticoid receptor antagonists (and amiloride) differ in their kidney-protective mechanisms despite comparable blood-pressure lowering.
- ★ Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells mechanism
- ★ Finerenone, spironolactone, and amiloride all protect against cardiorenal damage in the DOCA-salt rat model finding
- ★ Finerenone is particularly effective at reducing albuminuria and improving gene expression changes in podocytes and proximal tubule cells, even with equivalent blood pressure reduction to other treatments finding
- ★ Accumulation of injured/profibrotic tubule cells expressing Spp1, Il34, and Pdgfb strongly correlates with the degree of fibrosis in rat kidneys finding
- ★ The Spp1/Il34/Pdgfb injured-tubule gene signature shows potential for classifying human kidney samples finding
- ★ Generated one of the first comprehensive single-cell expression and gene-regulatory (snRNA-Seq/snATAC-Seq) atlas of healthy and diseased rat kidney, made publicly available resource
- ★ Principal cells are the primary mineralocorticoid-sensitive cell type, with a minor contributory role for DCT2 and connecting tubule cells finding
- ★ Used an integrated multiomics approach (snRNA-Seq, snATAC-Seq, bulk RNA-Seq) to characterize DOCA-sensitive cells, genes, and drug responses method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| snRNA-Seq | whole rat kidney (22 samples; sham, DOCA-salt, DOCA+finerenone, DOCA+spironolactone, DOCA+amiloride) | uninephrectomy + DOCA + high-salt diet ± finerenone/spironolactone/amiloride | cell-type-specific gene expression and cluster identification | — |
| snATAC-Seq | whole rat kidney (9 samples) | uninephrectomy + DOCA + high-salt diet ± finerenone/spironolactone/amiloride | chromatin accessibility/open chromatin peaks, motif activity (chromVAR) | — |
| bulk RNA-Seq | rat kidney | DOCA-salt ± finerenone/spironolactone/amiloride | expression of MR target genes (e.g., Atp1a1, Pik3r3, Aqp2, Hsd11b2) | — |
| blood pressure measurement | live rat | uninephrectomy + DOCA + high-salt ± finerenone/spironolactone/amiloride | systolic and diastolic blood pressure | — |
| histology (H&E) | rat kidney and heart tissue | DOCA-salt ± finerenone/spironolactone/amiloride | glomerulosclerosis, proteinaceous casts, tubulointerstitial and cardiac fibrosis | — |
| Picrosirius red staining | rat kidney and heart tissue | DOCA-salt ± finerenone/spironolactone/amiloride | extent of fibrosis | — |
| serum/urine biochemistry | rat blood and urine | DOCA-salt ± finerenone/spironolactone/amiloride | BUN, urinary albumin-creatinine ratio (proteinuria), plasma renin, electrolytes | — |
| chromVAR motif activity analysis | rat kidney snATAC-Seq clusters | none (computational analysis) | predicted cell-type-specific transcription factor motif activity | — |
- ▲ DOCA-salt rats developed severe hypertension compared with sham controls 181 vs 115 mmHg SBP
- ▼ Finerenone, spironolactone, and amiloride produced similar reductions in systolic and diastolic blood pressure
- ▼ Proteinuria was reduced by all treatments but reached statistical significance only in the finerenone group P=0.04
- ▼ Kidney-to-body-weight ratio was markedly increased by DOCA-salt treatment and reduced by finerenone, spironolactone, or amiloride
- – snRNA-Seq captured all known kidney cell types across 41 clusters after QC and batch correction 310,218 cells; 41 clusters
- – snATAC-Seq identified cell-type-specific accessible chromatin across 20 clusters 53,298 nuclei; 20 clusters
- – Label transfer between snRNA-Seq and snATAC-Seq datasets showed strong consistency 0.78 mean of maximum prediction score
- ▲ MR (Nr3c2) expression and open chromatin were highest in principal cells, with lower levels in DCT2 and connecting tubule cells
- pvalue P = 0.04 (finerenone significantly reduced proteinuria vs. DOCA-salt group)
- mean 181 mmHg (DOCA-salt) vs 115 mmHg (sham) (systolic blood pressure at end of study)
- count 310,218 cells (total cells retained after QC filtering in snRNA-Seq across 22 samples)
- count 41 clusters (cell clusters identified in snRNA-Seq after Harmony batch correction)
- count 53,298 nuclei (nuclei retained after QC filtering in snATAC-Seq across 9 samples)
- count 20 clusters (clusters identified in snATAC-Seq after Harmony batch correction)
- correlation 0.78 (mean of maximum prediction score) (consistency of label transfer between snRNA-Seq and snATAC-Seq cluster assignments)
- fold_change approximately 3-fold (cited prior-trial risk of hyperkalemia with spironolactone vs. ACEI/ARB alone (background))
Statistical methods review
Model: opusA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This study combined a rat DOCA-salt hypertension model with single-nucleus RNA-Seq, single-nucleus ATAC-Seq, and bulk RNA-Seq to map mineralocorticoid target cells and the effects of MRAs and amiloride. Phenotypic outcomes across treatment groups were summarized and explored with unbiased principal component analysis and hierarchical clustering, with at least one group comparison reported by a single p-value (proteinuria reduction with finerenone, P = 0.04). Single-cell analyses relied on clustering after Harmony batch correction, cell-type–specific differential expression, label transfer, Pearson correlation between gene expression and chromatin gene activity, and motif-activity analysis (chromVAR).
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Pearson's correlation test | consistency between gene expression (snRNA-Seq) and gene activity (snATAC-Seq) for top 3,000 highly variable genes | — | not stated |
| comparison reported as a p-value (specific test not stated) | proteinuria/UACR reduction in finerenone-treated vs DOCA-salt rats (P = 0.04) | — | not stated |
| group comparison of mean RNA counts per cell (specific test not stated) | DOCA-treated vs control animals (reported as not reaching statistical significance) | — | not stated |
| cell-type–specific differential expression analysis (method not specified in text shown) | marker-gene identification and MRA-sensitive gene calls across snRNA-Seq clusters | — | na |
| principal component analysis and hierarchical clustering | overall phenotypic similarity among rat samples (Supplemental Figure 2) | — | na |
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A single group difference (finerenone proteinuria reduction) was reported with one p-value (P = 0.04), with other groups noted as underpowered due to high UACR variance.↳ Could also: An overall test across all treatment arms (e.g., one-way ANOVA or Kruskal-Wallis) with a post-hoc procedure, or a pre-specified power/sample-size description, could also have been reported. — An omnibus test with planned contrasts would account for all groups simultaneously and control family-wise error across the multiple drug comparisons; reporting a power calculation would contextualize the high-variance outcomes.
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Concordance between snRNA-Seq expression and snATAC-Seq gene activity was assessed with a Pearson correlation.↳ Could also: Spearman's rank correlation could also have been used. — A rank-based correlation is robust to non-linear monotonic relationships and outliers common in sparse single-cell count data, and would complement the Pearson estimate.
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Differential expression and MRA-sensitive gene calls were made across many genes and cell types without a stated multiplicity-correction method in the text shown.↳ Could also: An explicit false-discovery-rate procedure (e.g., Benjamini-Hochberg) with stated thresholds could also have been reported alongside the DE results. — Reporting the FDR method and cutoffs makes the genome-wide testing family explicit and conveys how the large number of simultaneous comparisons was handled.
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Phenotypic group separation was shown with unbiased PCA and hierarchical clustering.↳ Could also: A complementary supervised or distance-based test (e.g., PERMANOVA on the outcome matrix) could also have been applied. — A formal multivariate test would attach a significance statement to the visually apparent group separation, adding a quantitative complement to the descriptive ordination.
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Comparisons such as RNA counts and proteinuria were evaluated between treatment groups with small per-group animal numbers.↳ Could also: Reporting individual data points alongside an explicit dispersion measure (SD, IQR, or a 95% CI) and an effect size could also accompany each comparison. — For small-n in vivo groups, showing the full spread and effect magnitude conveys uncertainty more transparently than a p-value alone and is often preferred.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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Finerenone, spironolactone, and amiloride each similarly reduce systolic and diastolic blood pressure in DOCA-salt hypertensive ratsother doca-salt rat down 2024×1papers★ This paper is the founder (earliest)
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DOCA-salt uninephrectomized rats develop severe hypertension with systolic blood pressure of 181 mmHg versus 115 mmHg in sham controlsother doca-salt rat up 2024×1papers★ This paper is the founder (earliest)
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Finerenone significantly reduces DOCA-induced proteinuria in rats, the only MRA treatment reaching statistical significanceother doca-salt rat down 2024×1papers★ This paper is the founder (earliest)
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Atp1a1 and Pik3r3 expression is elevated by DOCA-salt injury and normalized by MRA treatment in rat kidneyRNA-seq rat kidney mixed 2024×1papers★ This paper is the founder (earliest)
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Nr3c2 (mineralocorticoid receptor) expression and chromatin accessibility are highest in principal cells of the rat kidney collecting ductsnRNA-seq rat kidney principal cell up 2024×1papers★ This paper is the founder (earliest)
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A profibrotic injured tubule cell population expressing Spp1, Il34, and Pdgfb expands in DOCA-salt injury and correlates with degree of kidney fibrosissnRNA-seq rat kidney up 2024×1papers★ This paper is the founder (earliest)
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Proximal tubule cells show substantially greater transcriptional dysregulation at 6 weeks versus 3 weeks of DOCA-salt hypertension, indicating progressive time-dependent tubular injurysnRNA-seq rat kidney up 2024×1papers★ This paper is the founder (earliest)
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — PMID 37906287 (DOCA Rat Kidney, MRA mechanism; Susztak lab, JCI 2023)
- Code: https://github.com/amin1990ab/DOCA_Rat_Kidney (custom R snippets, no license)
- Data: GEO GSE183842 (SuperSeries) → GSE183839 snRNA-seq, GSE183840 snATAC-seq, GSE183841 bulk RNA-seq
Nature of the shipped code
The repo is a set of illustrative R code snippets (one file per analysis: snRNAseq,
snATACseq, Integration, CellChat, bulk clustering, Tensor_Decomposition, WGCNA). They are
NOT a runnable pipeline: they contain placeholders ('path/to/your/cellranger/outs/folder',
#All 22 samples, pK = #depends on the previous step), reference unshipped intermediate
.rds objects (Rat.RNA.rds, Rat.ATAC.Idents.10.1.2022.rds), and omit per-sample
parameters (doublet pK, which clusters were manually removed). So a from-FASTQ end-to-end
rerun is not specified well enough and is out of 80/20 scope.
What IS reproducible (deposited PROCESSED data → clear 1:1 checks)
GEO deposits the authors' final processed objects:
- GSE183839:
snRNAseq_counts.rds(count matrix),snRNAseq_metadata.txt(per-nucleus cell-type / sample / cluster annotations),snRNAseq_umap.txt - GSE183840:
snATACseq_peaks.rds,snATACseq_metadata.txt,snATACseq_umap.txt - GSE183841: bulk raw + TPM counts + metadata
From the per-nucleus metadata (small, auditable) we can directly check the paper's headline descriptive numbers; from counts.rds we can re-derive the key marker-gene claim.
In scope (attempted)
| # | Reported claim | Paper location | How reproduced |
|---|---|---|---|
| C1 | "clustering was performed on 53,298 nuclei" (vs Fig.1A legend "UMAP of 310,218") | Methods / Fig.1A | row count of snRNA metadata |
| C2 | "snRNA-Seq on 22 whole rat kidney samples from 5 different groups" | Results | distinct sample & group counts in metadata |
| C3 | "identified 41 clusters" (snRNA, post-Harmony) | Results / Suppl Fig 5 | distinct cluster count in metadata |
| C4 | named kidney cell types (Endo, Podo, PCT, PST, iPT, PC, DCT, IC_A/B, Mac, ... ~16) | Fig 2A / tensor script | distinct cell-type labels in metadata |
| C5 | "identified 20 clusters" (snATAC, post-Harmony) | Results / Suppl Fig 10 | distinct cluster count in ATAC metadata |
| C6 | iPT cells express Spp1, Il34, Pdgfb at highest levels; injury markers Havcr1, Vcam1 | Results, Fig 4C, Fig 7 | per-cell-type mean log-norm expression from counts.rds → iPT is argmax |
| C7 | MR (Nr3c2) expression highest in PC cells | Results, Fig 3B | per-cell-type mean expression of Nr3c2 → PC argmax |
Out of scope / not attempted (hard last ~20%, underspecified or heavy)
- From-FASTQ CellRanger + SoupX + DoubletFinder rerun (params per-sample unspecified).
- Exact DEG counts ("~2,700 DEGs in PT at 6 wk vs ~200 in others") — depends on exact subsetting/thresholds and group definitions not fully pinned.
- Tensor decomposition (scITD, "5 factors"), hdWGCNA modules, CellChat, pseudotime trajectory, SCENIC, human-sample hierarchical clustering — heavy and/or rely on unshipped intermediate objects; noted but not run.
- snATAC peak-level / chromVAR motif results beyond the cluster count.
Possible-fabrication / inconsistency flag
Methods state clustering on 53,298 nuclei, but the Figure 1A legend states a UMAP of 310,218 nuclei — a ~6× internal discrepancy. The deposited per-nucleus metadata row count adjudicates which (if either) is the real dataset size; recorded in claims.tsv (C1).
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Reproduction worked directly off the authors' deposited processed data (GEO GSE183839/GSE183840) and confirmed 13/14 checkable claims essentially 1:1: snRNA 310,282 vs 310,218 nuclei (+0.02%), 22 samples, 5 groups, 16 cell types, snATAC 53,298 nuclei/9 samples, plus all key marker biology (Spp1/Il34/Pdgfb/Havcr1→iPT, Nr3c2→PC, Cubn→PCT, Slc7a13→PST). The lone partial (Vcam1 argmax Endo, iPT positive at rank 9/16) is explained by Vcam1's dual endothelial role, and the provisional fabrication flag (53,298 vs 310,218) was correctly refuted as two distinct assays. Deviations are negligible and lie on no one's side; the deeper mechanistic analyses were left unattempted as scope, not refuted — so this is a clean, high-quality reproduction.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.