Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
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.
- ✓Reported values are derivable from the shared data
- ✓The central claim held under reproduction
- 🟡Could not use the authors’ exact input data
- 🟡Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🟡A deviation was attributed to the published material
- 🟡The deviation was non-trivial in magnitude
- 🟡Overall, the reproduction showed a material discrepancy
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 for the ONE publicly reproducible result; rest of paper not reproducible. Triage: the paper's OWN sequencing data is on-request ('Materials available upon request from the lead author') and the paper ships NO analysis code -- the harvested github.com/mjoppich/poreSTAT link is a FALSE POSITIVE (co-author M. Joppich's unrelated Oxford-Nanopore fast5 tool, never cited by the paper). So all of the paper's own computational results (mouse macrophage scRNA-seq, low-input RNA-seq, bulk RNA-seq) are OUT OF SCOPE = data_restricted; NOT attempted. The single public, reproducible surface is the paper's reanalysis of the EXTERNAL dataset GSE131778 (Wirka et al. human coronary scRNA-seq) behind Fig 1D-E. We reproduced it 1:1 by running the named pipeline (Seurat + SCTransform) on the public processed matrix: of 23 chemokines, CCL2 is the #1 most-expressed in mural-cell clusters (5.58, 3.6x the next gene) -- matching 'CCL2 most prominently expressed chemokine'; CXCL9 is 20/23, near-zero -- matching 'CXCL9 comparably low'. MIF is expressed but mid-pack (8/23), so the 'CCL2 AND MIF robust' co-claim reproduces only partially. Deviations: Seurat 5.5.0 used (paper: Seurat 4.0.4) after older Seurat4/SeuratObject4/Matrix combos failed an ABI/Graph-class check on «our HPC»; comparison is qualitative/rank-based since the paper reports no numeric values; cluster annotation is data-driven, not matched to the paper's exact labels/UMAP. NOT attempted: exact UMAP/cluster reproduction, the paper's own-data pipelines (no public data + no code). Grades are provisional; a human reviewer decides.
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 83assessed: 2026-06-15 ⛓ a091dd66fb52
✎ 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
- 2026-08-05
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: opusThe authors hypothesized that mural cells (pericytes and smooth muscle cells) actively communicate with vascular macrophages via secreted chemokines to sustain the vascular macrophage niche and maintain a pro-resolving, homeostatic macrophage phenotype, thereby counteracting chronic inflammation such as atherosclerosis.
- ★ Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche. mechanism
- ★ Vascular macrophages reside in a dedicated niche along mural cells across micro- and macro-vascular beds and form tight, frequent MC-MΦ contacts. finding
- ★ MC-specific deletion of CCL2 (Ccl2MCΔ/Δ) reduces perivascular macrophage coverage and shifts the macrophage transcriptome toward a less homeostatic, more inflammatory phenotype. finding
- ★ A distinct chemotactic SMC (cSMC) subset expresses high levels of macrophage chemoattractants (CCL2 most prominent) mediating SMC-MΦ interactions, and SMC-derived CCL2 ameliorates atheroprogression. finding
- CCL2 stimulation enhances macrophage survival in vitro independent of macrophage origin (embryonic vs bone marrow-derived). finding
- Reanalysis of human coronary and murine atherosclerosis scRNA-seq identifies CCL2 and MIF as robustly expressed MC chemokines. method
- Intravital multi-photon Ca2+/morphology imaging (Cx3cr1-MΦCa-rep) allows simultaneous tracking of macrophage positioning, morphology, and calcium activity in vivo. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| In vivo multi-photon intravital imaging of Ca2+ and morphology | Cx3cr1-MΦCa-rep (Cx3cr1Cre-ERT2; PC-G5-tdT) mice, skin/ear microvasculature | laser-induced sterile microinjury | macrophage Ca2+ activity, morphology, time to reach injury | — |
| Confocal/airy-scan in vivo and ex vivo whole-mount imaging | MCRFP-rep; Cx3cr1-MΦGFP-rep (Ng2-DsRed; Cx3cr1GFP; ApoE−/−) mice; mesentery, heart, aorta, kidney, lung, stomach | none / 3-month western diet for atherosclerosis | MC-MΦ cell-cell contacts; MΦ marker co-expression (F4/80, CD11c) | — |
| In vivo imaging with CCL2 neutralization | Cx3cr1-MΦGFP-rep mice | isotype vs CCL2-neutralizing antibody (local + systemic) | time to form first dendrites; time to reach laser microinjury | — |
| In vitro macrophage survival assay | peritoneal macrophages; embryonic vs bone marrow-derived MΦs | CCL2, MIF, or M-CSF stimulation under starvation stress | % macrophage survival over time | — |
| Single-cell RNA-seq (reanalysis) | human coronary arteries (Wirka et al.); murine aortic roots from SMClin atherosclerotic mice | atherosclerosis | cytokine/chemokine expression in SMC/MC clusters; SMC-MΦ chemokine-receptor interactome | GEO GSE131780 |
| Single-cell RNA-seq of FACS-enriched macrophages | kidney and lung CD45+CD11bhiCD64hiF4/80hi cells from Ccl2MCΔ/Δ and Ccl2MC+/+ mice | MC-specific Ccl2 knockout (Ng2cre; Ccl2fl/fl; ApoE−/−) | MΦ subcluster frequencies and differential gene expression | — |
| Immunofluorescence staining / morphometry | kidney sections; brachiocephalic artery (BCA) and aortic valve plaques from Ccl2SMC+/+ and Ccl2SMCΔ/Δ mice | MC/SMC-specific Ccl2 deletion; 14-week western diet | CD68+/ACTA2+/LGALS3+ areas, plaque size, vascular remodeling, EdU+ proliferation | — |
| Low-input / bulk RNA-seq | FACS-sorted intimal CX3CR1+ MΦs from chimeric Ccl2MCΔ/Δ mice (MCRFP-rep Cx3cr1-MΦGFP-rep bone marrow); aortic intima/media of Ccl2SMC mice | MC/SMC-specific Ccl2 deletion; 20- or 14-week western diet | differentially expressed efferocytosis/M2-like and MΦ marker genes | — |
- ▼ Disruption of CCL2 signaling impaired perivascular macrophages' ability to reach laser microinjuries (delayed dendrite formation and time to injury).
- ▲ CCL2 addition enhanced macrophage survival in vitro under starvation stress.
- ▼ Perivascular CD68+ MΦ coverage in kidney microvasculature was reduced in Ccl2MCΔ/Δ vs control mice.
- – Reduced macrophage coverage was not explained by changes in proliferation (EdU+) or blood monocyte counts.
- – Perivascular MΦ clusters from Ccl2MCΔ/Δ mice showed lower homeostatic genes (Atf3, Dusp, Fos, Fkbp5, Ddit4, Cebpb, Jun) and enriched inflammatory transcripts (Syk, Irf8, Lst1).
- ▼ Intimal MΦs from atherosclerotic Ccl2MCΔ/Δ mice had reduced efferocytosis/M2-like genes (Cd36, Folr2, Clec4e, Pecam1) and MΦ markers (Adgre4, Fabp4).
- ▲ CCL2 and MIF were the most prominently expressed chemokines mediating SMC→MΦ interactions, mainly via the cSMC subset and the CCL2-CCR2 axis.
- ▼ Lung Zeb2hi interstitial MΦ cluster (maintaining tissue-specific identity) was reduced in Ccl2MCΔ/Δ lungs.
- count n = 17–37 individual cells from 3–4 mice/group (MΦ dendrite/injury-reaching imaging with CCL2 antibody)
- count n = 3 experiments (in vitro CCL2 macrophage survival assay)
- count n = 5–6 mice/group (kidney perivascular CD68+ MΦ coverage and blood monocyte counts)
- count n = 4/group (scRNA-seq of kidney and lung MΦs, Ccl2MCΔ/Δ vs Ccl2MC+/+)
- count n = 3–4 chimera mice (low-input RNA-seq of intimal Cx3cr1+ MΦs after 20 weeks western diet)
- count Ccl2SMC+/+ n = 11, Ccl2SMCΔ/Δ n = 10 (BCA plaque size/remodeling morphometry after 14 weeks western diet)
- count Ccl2SMC+/+ n = 3, Ccl2SMCΔ/Δ n = 4 (bulk intima/media RNA-seq)
- pvalue p < 0.05 (significance threshold across analyses (Student's t test, ANOVA, mixed-effects))
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.
The study combines in vivo/ex vivo imaging, in vitro assays, mouse genetic-deletion experiments, and single-cell/bulk/low-input RNA-seq. For quantitative comparisons between two groups (e.g., genotypes, treatments), two-tailed Student's t tests were used, while repeated/longitudinal measures (survival over time, plaque parameters across consecutive locations) were analyzed with repeated-measures two-way ANOVA or a mixed-effects model. Transcriptomic comparisons report differentially regulated genes using adjusted p-values, and results are generally shown as bar graphs of mean with SEM with significance flagged at p < 0.05.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Student's t test | Figures 1C, 1G, 1H, 1I (dendrite/injury time, perivascular MΦ content, proliferation, monocyte counts), 2I (chimera RNA-seq genes), 3H, 3K (ACTA2 and LGALS3 content) | n = 5–6 mice/group (1G, 1I); 17–37 cells from 3–4 mice/group (1C); 3–4 chimera mice (2I); 10–11 mice/group (3H, 3K) | not stated |
| Repeated measures two-way ANOVA | Figure 1F (peritoneal macrophage survival over time under CCL2 stimulation) | n = 3 experiments | not stated |
| Repeated measures two-way ANOVA or mixed-effects model | Figures 3F, 3G, 3I, 3J (plaque size, vascular remodeling, ACTA2 and LGALS3 area across three consecutive BCA locations) | Ccl2SMC+/+ n = 11, Ccl2SMCΔ/Δ n = 10 (3F/3G); n = 10–11/group (3I, 3J) | not stated |
| Differential expression analysis (adjusted p-value; method not named) | scRNA-seq volcano/violin plots (Figures 2C–2H), low-input RNA-seq (2I), bulk intima/media RNA-seq volcano plots (Figure 3M, axes Log2FC vs -Log10 adj. p-value) | n = 4/group (scRNA-seq 2A/2B); n = 3 vs n = 4 (bulk RNA-seq 3L/3M) | na |
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Two-group comparisons were analyzed with Student's t test.↳ Could also: A Mann-Whitney U (Wilcoxon rank-sum) test could also be applied, or normality/variance could be checked with a Welch's t test variant. — For the small per-group n common here (e.g., 3–6), a rank-based test makes no distributional assumption and a Welch correction accommodates unequal variances; either would complement the parametric result.
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Several figures apply multiple independent Student's t tests across related readouts and tissues.↳ Could also: A single ANOVA framework with a post-hoc multiplicity correction (e.g., Tukey HSD or Holm/Benjamini-Hochberg) could also be used across the family of comparisons. — A shared correction controls the family-wise or false-discovery rate across the set of related tests, which can be informative when many comparisons are reported together.
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Results are summarized as mean with SEM.↳ Could also: Showing SD, a 95% confidence interval, or plotting individual data points could also convey the data. — SD conveys the spread of the underlying observations and a CI conveys precision of the estimate; for small n these are often preferred and individual points show the full distribution.
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Significance is indicated relative to a p < 0.05 threshold (∗).↳ Could also: Reporting exact p-values alongside effect-size estimates (e.g., mean difference with CI, Cohen's d) could also accompany the threshold flags. — Exact p-values and effect sizes give readers the magnitude and precision of differences, supporting interpretation beyond a binary cutoff.
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RNA-seq differential expression is reported with adjusted p-values and a method/software not named in the text.↳ Could also: Naming the pipeline and correction method (e.g., DESeq2/edgeR/limma with Benjamini-Hochberg FDR) and stating the significance and fold-change thresholds could also be included. — Explicit tooling and threshold reporting aids reproducibility and clarifies the family over which multiplicity was controlled.
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Reanalyzed public scRNA-seq violin comparisons are calculated on cells with detectable expression of each gene.↳ Could also: A complementary analysis including zero/non-detected cells, or a model accounting for dropout (e.g., a zero-inflated or pseudobulk approach), could also be reported. — Including non-expressing cells or pseudobulk aggregation reflects expression frequency and can change inferred differences, offering a fuller view of the per-cluster expression.
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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CCL2 neutralization impairs perivascular macrophage dendrite extension and migration to sterile laser-injury sites in ear microvasculatureimaging mouse ear down 2023×1papers★ This paper is the founder (earliest)
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Mural cell-specific Ccl2 deletion reduces perivascular CD68+ macrophage density in kidney microvasculatureimaging mouse kidney down 2023×1papers★ This paper is the founder (earliest)
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Reduced perivascular macrophage coverage in Ccl2MCΔ/Δ kidney is not attributable to changes in macrophage proliferation or circulating monocyte countsimaging mouse kidney none 2023×1papers★ This paper is the founder (earliest)
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CCL2 promotes macrophage survival under nutrient starvation stress in vitroother mouse peritoneal macrophage up 2023×1papers★ This paper is the founder (earliest)
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Intimal macrophages from atherosclerotic Ccl2MCΔ/Δ mice show reduced efferocytosis and M2-like gene expression including Cd36, Folr2, and Clec4eRNA-seq mouse aorta down 2023×1papers★ This paper is the founder (earliest)
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CCL2 is the most prominently expressed SMC-derived chemokine mediating smooth muscle cell-to-macrophage interactions via the CCL2-CCR2 axis in coronary atherosclerosisscRNA-seq human coronary artery up 2023×1papers★ This paper is the founder (earliest)
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Mural cell Ccl2 deletion shifts perivascular kidney macrophages from a homeostatic (Atf3, Fos, Jun-high) to an inflammatory (Syk, Irf8, Lst1-high) transcriptional statescRNA-seq mouse kidney mixed 2023×1papers★ This paper is the founder (earliest)
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Mural cell Ccl2 deletion reduces the Zeb2-high tissue-resident interstitial macrophage cluster in lungscRNA-seq mouse lung down 2023×1papers★ This paper is the founder (earliest)
Citation network
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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-37652021
Paper: Pekayvaz et al., Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation. Immunity 2023. PMID 37652021 · PMCID PMC10588993 · DOI 10.1016/j.immuni.2023.08.002
Link triage (harvested links vs. what the paper actually says)
The BRIEF's harvested artifacts are mostly mis-harvests and were verified against the paper text before any compute:
- Code link
github.com/mjoppich/poreSTAT— FALSE POSITIVE. poreSTAT is co-author M. Joppich's Oxford Nanopore fast5 analysis framework ("work in progress", JS/Python, numpy/h5py). It is unrelated to this paper's scRNA-seq / bulk RNA-seq analyses. The paper text contains no GitHub URL and no code-availability statement; the link was associated by author-name harvesting, not cited by the paper. → effectivelyno_codefor the paper's own pipelines. - Resource availability (verbatim): "Materials are available upon request from the
lead author." The paper's own sequencing data is on-request, not deposited under a
public accession. →
data_restrictedfor all own-data results. GSE131780— this is an EXTERNAL public dataset (Wirka et al. 2019, Nat Med SuperSeries; human/mouse smooth-muscle-cell scRNA-seq), which the paper reanalyzed. The human coronary subseries GSE131778 ships a processed count matrix (GSE131778_human_coronary_scRNAseq_wirka_et_al_GEO.txt.gz, 21.8 MB) → public & obtainable. This is the one reproducible surface.
IN SCOPE (pipeline-derived, public data, reproducible)
| Result | Figure | Pipeline | Data |
|---|---|---|---|
| Chemokine/cytokine expression across human mural-cell (MC/SMC) clusters; CCL2 most prominently expressed chemokine, MIF robust, CXCL9 comparably low | Fig 1D–E | scRNA-seq clustering (Seurat + SCTransform) on the reanalyzed external dataset | GSE131778 processed matrix (public) |
This is the 80% target: a clearly-stated, pinnable claim derivable from a public matrix with the named standard pipeline (Seurat). We reproduce the qualitative ranking (which chemokine dominates MC clusters; CXCL9 low) rather than exact UMAP coordinates.
OUT OF SCOPE (not attempted — recorded, not dropped silently)
- Mouse scRNA-seq of kidney/lung macrophages (Ccl2^MCΔ/Δ vs control) — own data, on-request →
data_restricted. - Low-input RNA-seq of intimal CX3CR1+ macrophages — own data, on-request →
data_restricted. - Bulk RNA-seq of intima/media — own data, on-request →
data_restricted. - All wet-lab, imaging (Imaris/QuPath), flow cytometry, histology — non-pipeline / out of scope.
Why this scoping
The paper's own computational results cannot be reproduced (data on-request, no code shipped). The only honest, fully public reproducible result is the reanalysis of the external Wirka et al. human coronary scRNA-seq underlying Fig 1D–E. We attempt exactly that and grade it provisionally; a human reviewer decides the final match.
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.
Only Fig 1D-E (a reanalysis of the external public dataset GSE131778) was reproducible: CCL2 ranks 1/23 (5.58, 3.6x CXCL12) and CXCL9 ranks 20/23 (0.0027), cleanly confirming the headline 'CCL2 most prominent / CXCL9 low'; the co-claim that MIF is 'robustly expressed' reproduces only partially (rank 8/23, mid-pack). Deviations are on our side (Seurat 5.5.0 vs 4.0.4, data-driven clustering, self-defined mural-cell set) plus a data-availability wall — the paper's own sequencing data is on-request and the shipped code link is a false positive, so the bulk of the paper is untestable rather than wrong. Nothing is fabrication-suspect; the reproducible surface is solid with explainable deviations, hence an overall yellow.
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.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
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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.