FoxO transcription factors are required for hepatic HDL cholesterol clearance
The main result did not reproduce in this reproduction attempt. Where our recomputation produced values that differ from the published ones, those discrepancies are listed below. This is a single automated attempt — not peer review and not a finding of error or misconduct — and differences can also arise from data access, undocumented parameters or the computing environment. The verdict can be contested via “report an error”.
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 only indirectly comparable
- 🔴A deviation arose in the data or preprocessing
- 🟡A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡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
Predominantly a wet-lab mouse paper; only 2 pipeline-derived results in scope, both attempted on «our HPC». The microarray it 'queried' is not deposited with this paper but reused from Haeusler 2014 (GSE60527), which is open, complete (12 samples, balanced 2x2x3) and delivers what is promised. Reanalysis (GEOquery+limma) REPRODUCES the qualitative direction of the headline finding - Scarb1 and Lipc trend DOWN in L-FoxO1,3,4 livers - and the HOMER motif claim (137/346 FoxO motifs near Scarb1/Lipc, 'dozens' confirmed). However it is a PARTIAL, not clean 1:1: (a) the Scarb1/Lipc microarray changes are not statistically significant on their own (the paper's significance comes from qPCR, which is wet-lab/out-of-scope); (b) two genes the paper lists as unchanged - Abcg5 and Abcg8 - are in fact significantly reduced in the pooled genotype model (a real discrepancy, but analytical/power-related, not fabrication). NOT attempted (out of scope): qPCR, HDL-C/lipid assays, lipoprotein kinetics, selective CE uptake, SR-BI re-expression rescue, Westerns, histology, all mouse phenotyping. No fabrication indicated.
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Assessment versions
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v1 current initial assessment Score 49assessed: 2026-06-18 ⛓ 650fb67616e8
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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
- 2026-06-18
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-18no 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 study tests whether the insulin-repressible FoxO transcription factors in the liver mediate insulin's effect on HDL cholesterol, hypothesizing that hepatic FoxOs are required for HDL-C clearance and cholesterol homeostasis.
- ★ Mice with liver-specific triple FoxO knockout (L-FoxO1,3,4) have increased HDL cholesterol. finding
- ★ Hepatic FoxOs are required for cholesterol homeostasis and HDL-mediated reverse cholesterol transport to the liver. mechanism
- ★ Increased HDL-C in L-FoxO1,3,4 mice is associated with decreased expression of the HDL-C clearance factors SR-BI and hepatic lipase and defective hepatic selective uptake of HDL cholesteryl ester. mechanism
- ★ The HDL-C phenotype can be rescued by re-expression of SR-BI. finding
- L-FoxO1,3,4 mice have reduced hepatic glucose production. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| plasma HDL cholesterol measurement | liver-specific triple FoxO knockout (L-FoxO1,3,4) mice | liver-specific FoxO1,3,4 knockout | HDL cholesterol levels | — |
| gene/protein expression analysis | L-FoxO1,3,4 mouse liver | liver-specific FoxO1,3,4 knockout | expression of SR-BI and hepatic lipase | — |
| HDL cholesteryl ester selective uptake assay | L-FoxO1,3,4 mouse liver | liver-specific FoxO1,3,4 knockout | hepatic selective uptake of HDL cholesteryl ester | — |
| SR-BI re-expression rescue experiment | L-FoxO1,3,4 mice | SR-BI re-expression | HDL-C phenotype rescue | — |
- ▲ L-FoxO1,3,4 mice have increased HDL cholesterol
- ▼ Decreased expression of SR-BI and hepatic lipase in L-FoxO1,3,4 liver
- ▼ Defective hepatic selective uptake of HDL cholesteryl ester
- – Re-expression of SR-BI rescued the HDL-C phenotype
- ▼ L-FoxO1,3,4 mice have reduced hepatic glucose production
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The paper reports a mouse genetic study comparing liver-specific triple FoxO knockout (L-FoxO1,3,4) mice with controls to examine effects on HDL-C metabolism, SR-BI and hepatic lipase expression, and selective hepatic cholesteryl ester uptake. A rescue experiment involving SR-BI re-expression is also described. Specific statistical tests, sample sizes, and reporting conventions are not detailed in the text provided (abstract and metadata only; full methods and results sections were not included in the supplied text).
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| not stated | not stated — full methods/results text not supplied | — | not stated |
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The study compares a single knockout genotype against controls across multiple metabolic endpoints (HDL-C, SR-BI expression, hepatic lipase, cholesteryl ester uptake), which typically involves multiple separate tests.↳ Could also: A single mixed-model ANOVA or linear mixed model with genotype as a fixed effect and animal as a random effect, followed by a single multiplicity correction (e.g., Benjamini-Hochberg FDR) across all endpoints. — Controlling the family-wise error rate or FDR across multiple correlated outcomes reduces the probability of false positives and makes the inference across endpoints more coherent.
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The rescue experiment (SR-BI re-expression) introduces a three-group comparison (control, knockout, knockout + rescue), which is a common design in genetic mouse studies.↳ Could also: One-way ANOVA with a post-hoc test (e.g., Tukey HSD or Dunnett's test against the control group) applied to the three groups jointly. — A single ANOVA followed by a planned post-hoc comparison controls the familywise error rate across the three pairwise comparisons more explicitly than conducting separate t-tests.
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Mouse metabolic phenotyping studies of this type routinely measure outcomes (e.g., plasma cholesterol) that may not be normally distributed, particularly at small sample sizes typical of genetic mouse work.↳ Could also: Non-parametric alternatives such as the Mann-Whitney U (for two-group comparisons) or Kruskal-Wallis test with Dunn's post-hoc (for three groups) could also be applied. — Non-parametric tests do not assume normality and can be more appropriate when n per group is small (e.g., ≤8), as is common in transgenic mouse studies; they provide an independent check on parametric results.
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Gene expression outcomes (SR-BI, hepatic lipase mRNA/protein) are likely compared between genotypes, a context where specialized tools are sometimes used.↳ Could also: For mRNA quantification by RT-qPCR, a ΔΔCt-based analysis with appropriate reference gene normalization and reporting of efficiency-corrected fold-changes with 95% CIs would also be standard. — Reporting fold-changes with confidence intervals alongside p-values conveys both the magnitude and precision of expression differences, aiding biological interpretation.
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Results in studies of this type are frequently summarized with SEM to represent group means.↳ Could also: SD or 95% CIs around the mean could also be used to summarize spread. — SD describes the variability of individual animals (biologically interpretable), while 95% CIs convey estimation uncertainty; both are often preferred over SEM for small-n animal studies because SEM can visually understate biological variability.
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The study uses a complete gene knockout to establish that FoxOs are required for hepatic HDL clearance.↳ Could also: A dose-response or graded knockdown design (e.g., heterozygous knockouts or inducible partial suppression) could also characterize the relationship between FoxO activity and HDL-C. — Graded designs can reveal whether the phenotype is linearly related to FoxO dosage or threshold-dependent, providing additional mechanistic resolution beyond the binary knockout comparison.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — PMID 29408809
Paper: Lee SX, Heine M, Schlein C, … Haeusler RA. FoxO transcription factors are required for hepatic HDL cholesterol clearance. J Clin Invest. 2018;128(4):1615-1626. DOI 10.1172/JCI94230 · PMCID PMC5873864.
NOTE: the user/operator («email», Christian Schlein) is a co-author.
Nature of the study
Predominantly a wet-lab mouse-physiology study: liver-specific triple FoxO knockout (L-FoxO1,3,4), plasma HDL-C, lipoprotein kinetics, selective CE uptake, SR-BI re-expression rescue, qPCR, Western blots. The bulk of the figures are wet-lab and out of scope for computational reproduction.
In-scope pipeline-derived (computational) results
R1 — Microarray query (CORE, clearly reproducible)
The authors "queried microarrays from livers of L-FoxO1,3,4 mice" for HDL-metabolism genes. Reported result:
- Scarb1 (SR-BI) and Lipc (hepatic lipase): reduced in L-FoxO1,3,4 livers.
- No change in HDL synthesis / biliary-excretion genes: Abca1, Apoa1, Apoa2, Lcat, Apoe, Abcg5, Abcg8.
The microarray is not deposited with this paper; it is the L-FoxO1,3,4 liver microarray from the prior Haeusler-lab paper (Haeusler et al., Nat Commun 2014; Integrated control of hepatic lipogenesis vs glucose production requires FoxO TFs), deposited as GEO GSE60527 (GPL6096, Affymetrix Mouse Exon 1.0 ST; 12 samples = WT vs TKO × fast 22h / refed 4h × 3). 1:1 reproduction = re-derive genotype effect (KO−WT) for the 9 named genes from GSE60527. Pipeline: GEOquery → limma differential expression.
R2 — HOMER motif analysis (harder; attempted)
"motif analysis using HOMER … identified dozens of FoxO consensus sequences in and near Scarb1 and Lipc" using "the entire mouse gene sequences of Scarb1 and Lipc (including introns) plus 50 kb upstream of each TSS" (Supplemental Fig. 8A–C). Pipeline: extract mm10 regions → HOMER FoxO motif scan → count consensus matches.
Out of scope (wet-lab / manual / not pipeline-derived)
qPCR (Fig 2A,B), HDL-C and lipid measurements, lipoprotein turnover/kinetics, selective cholesteryl-ester uptake assays, adenoviral SR-BI re-expression rescue, Western blots, histology, all mouse phenotyping. Not attempted.
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 two pipeline-derived results were in scope and the reused microarray (GSE60527) is fully public and complete, so data identity is clean. The headline direction reproduces (Scarb1/Lipc trend down; 137/346 FoxO motifs confirm 'dozens'), but neither reaches microarray significance — the paper's significance rests on out-of-scope qPCR — and two genes called 'unchanged' (Abcg5 adj.P=0.016, Abcg8 adj.P=0.008) are in fact significantly reduced. The discrepancies sit on the analysis/statistics side and are plausibly driven by our self-chosen pooled model and low power (n=3/group), not by the authors or by fabrication; all values are derivable from the shared data. Overall a solid, direction-consistent partial reproduction with explainable deviations.
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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.