Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity
Part of the results reproduced; minor but material deviations remained.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
▸Reproduction agent’s raw note
DROP (non_pipeline). PLoS ONE 2015 wet-lab mouse genetics/physiology paper (tissue-specific conditional Apoe knockouts; diet studies) by Wagner, Bartelt, Schlein, Heeren. Methods are entirely bench assays (Cre/loxP genetics, FPLC, qPCR/TaqMan, Western blot, ELISA, ALT, Tyloxapol VLDL secretion, 125I-TC turnover, H&E+ImageJ, Student's t-test) with NO bioinformatic/computational pipeline, NO sequencing/microarray/proteomics, NO code repository (own or third-party, so P16 does not apply), and NO public data accession. Data availability = 'all data within the paper and SI'; the SI is only two summary TIF figures (S1 food intake, S2 OGTT), both verified to resolve as valid TIFFs. Nothing pipeline-derived exists to reproduce, so no «our HPC» compute was run. Profiled the only deposited data (2 SI figures, grade D, delivers_promised=partial) and recorded 7 representative reported wet-lab claims with paper locations for audit. NOT attempted: re-deriving any reported number, because no raw/machine-readable data or code was deposited (a data-availability limitation, not evidence of fabrication). Honest, evidence-backed drop; no result forced or fabricated.
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Assessment versions
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v1 current initial assessmentassessed: 2026-06-18 ⛓ df07d296cf51
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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: sonnetThe study investigates whether the metabolic phenotypes seen in globally apoE-deficient mice (hypercholesterolemia and altered diet-induced obesity/adiposity) are attributable specifically to hepatocyte-derived or adipocyte-derived apoE, using a novel Cre-loxP conditional tissue-specific Apoe knockout mouse model.
- ★ Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia finding
- ★ Adipocyte-specific apoE deletion does not reproduce the lean/insulin-sensitive adipose phenotype seen in global Apoe-/- mice finding
- ★ A novel conditional (Cre-loxP) tissue-specific Apoe knockout mouse model was generated (Apoe ΔHep and Apoe ΔAT) resource
- ★ Apoe ΔHep mice show increased body/liver weight, hepatic steatosis, elevated ALT and inflammation markers on high-fat diet finding
- ★ Apoe ΔAT mice show no detectable metabolic phenotype on either HFD or WTD finding
- ★ Circulating plasma apoE is predominantly derived from hepatic production, not adipose tissue finding
- ★ VLDL organ-specific tissue uptake is disturbed in Apoe ΔHep mice while plasma VLDL clearance rate (half-life) is unaltered finding
- ★ ApoE produced by cell types other than hepatocytes or adipocytes likely explains the lean and insulin-sensitive phenotype of global Apoe-/- mice mechanism
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| real-time RT-PCR (TaqMan) | liver and white adipose tissue, mouse | Cre-loxP tissue-specific Apoe deletion | Apoe mRNA expression (ΔΔCt, normalized to Tbp) | TaqMan Gene Expression Assay, Applied Biosystems |
| Western blot | liver lysates, mouse | Apoe ΔHep knockout (Cre+ vs Cre-) | total apoE protein amount (34 kDa) | NuPAGE Bis-Tris gels, Invitrogen; apoE antibody, Santa Cruz |
| ELISA | plasma, mouse | diet (chow/HFD/WTD) x genotype | apoE plasma levels | — |
| FPLC lipoprotein profiling | pooled plasma, mouse | diet x genotype | cholesterol and apoE distribution across lipoprotein fractions | AKTA FPLC with S6-superose sizing columns, GE Healthcare |
| VLDL production assay (Tyloxapol injection) | plasma, mouse | diet (chow/WTD) x Apoe ΔHep genotype | VLDL triglyceride and cholesterol secretion rate | — |
| 125I-VLDL turnover/organ distribution assay | plasma and organs (liver, heart, fat pads, kidney, spleen, muscle), mouse | injection of 125I-labeled apoE-free VLDL tracer, Apoe ΔHep genotype | plasma decay (half-life) and organ-specific radioactivity uptake | 125I-tyramine cellubiose labeling |
| biochemical liver lipid quantification | liver homogenate, mouse | diet x genotype | triglyceride and cholesterol content normalized to protein | commercial kits, Roche |
| histology (H&E staining) | liver and epididymal WAT, mouse | diet x genotype | steatosis grade and adipocyte size distribution | ImageJ |
- ▲ Apoe ΔHep mice showed higher body weight on HFD compared to WT controls about 10%
- ▲ Liver mass increased in Apoe ΔHep mice on HFD
- ▲ Hepatic cholesterol elevated in Apoe ΔHep mice on both HFD and WTD; hepatic triglycerides unaltered by genotype
- ▲ Plasma ALT activity higher in Apoe ΔHep mice than WT on HFD 4-fold
- ▲ Plasma cholesterol increased in Apoe ΔHep mice on WTD, with increased TRL/remnant cholesterol by FPLC
- ▼ VLDL triglyceride secretion (post-Tyloxapol) was lower in Apoe ΔHep mice on both chow and WTD; VLDL cholesterol unchanged
- – Plasma half-life of 125I-VLDL was similar between genotypes, but organ-specific VLDL uptake/delivery differed
- – Apoe ΔAT mice showed no genotype-specific differences in body weight, tissue mass, adipocyte size, or oral glucose tolerance on HFD or WTD
- pvalue p<0.05 (significance threshold used for all Student's t-test comparisons)
- fold_change 4-fold (ALT plasma activity higher in Apoe ΔHep vs WT controls on HFD)
- other about 10% (higher body weight of Apoe ΔHep mice vs WT controls on HFD)
- count n≥8 (sample size for hepatic Apoe expression comparison in Apoe ΔHep mice (Fig 1B))
- count at least 10 generations (backcrossing of floxed Apoe mice onto C57BL6/J background)
- other 16 weeks (duration of dietary feeding (chow/HFD/WTD) before tissue harvest)
- other 0.5 g kg-1 body weight (intravenous Tyloxapol dose used for VLDL production assay)
- other 1 g/kg (oral glucose dose used for oral glucose tolerance test)
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.
This study used a conditional Cre-loxP mouse model to compare tissue-specific apoE-deficient mice (Apoe^ΔHep or Apoe^ΔAT) against floxed littermate controls across three dietary regimens (chow, HFD, WTD) for 16 weeks. All pairwise group comparisons were performed with unpaired Student's t-tests, with results expressed as mean ± SEM. Statistical significance was defined by p < 0.05, indicated by asterisks in figures; no multiplicity correction was stated despite numerous outcomes tested across conditions and genotypes.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Student's t-test (two-sample, unpaired) | Apoe mRNA expression in liver (Fig 1B) and WAT (Fig 1C) | n≥8 (liver); n≥6 (WAT) | not stated |
| Student's t-test (two-sample, unpaired) | ApoE plasma levels across diets (Fig 1E) | n≥3 to n≥8 per group per dietary condition | not stated |
| Student's t-test (two-sample, unpaired) | Body weight curves and tissue weights (liver, BAT, IngWAT, EpiWAT; Fig 2A–J) | n≥3 to n≥9 per group per diet | not stated |
| Student's t-test (two-sample, unpaired) | Hepatic TG and cholesterol, plasma ALT, OGTT, liver gene expression (Tnf, Cd68, Cxcl-2, Cxcl-10; Fig 3) | n≥4 to n≥8 per group per diet | not stated |
| Student's t-test (two-sample, unpaired) | Plasma total cholesterol and triglycerides across diets (Fig 4A,B) | n≥3 to n≥8 per group per diet | not stated |
| Student's t-test (two-sample, unpaired) | VLDL production (tyloxapol assay) and 125I-VLDL organ distribution (Fig 5A–D, 5H) | n≥5 to n≥8 per group | not stated |
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Multiple independent Student's t-tests were applied across many outcomes and dietary conditions without a stated multiplicity correction↳ Could also: A two-way ANOVA (genotype × diet) with a post-hoc correction (e.g., Tukey HSD or Bonferroni) could also have been applied to outcomes measured across all three diets — Two-way ANOVA directly models the genotype-by-diet interaction — a central question of the study — and an omnibus test with post-hoc correction controls the family-wise error rate across the simultaneous comparisons, making the inferential structure explicit
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FPLC lipoprotein profiles (Figs 4C–H, 5E–F) were generated from pooled plasma samples per group and no between-group statistics were applied to these profiles↳ Could also: Individual-sample FPLC profiling followed by area-under-curve or fraction-specific quantification could also support formal statistical comparison between genotypes — Pooling samples precludes estimation of within-group variability and formal hypothesis testing on fraction-specific cholesterol levels; individual profiles would allow the differences visible in the traces to be accompanied by confidence intervals or p-values
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Dispersion was reported as SEM throughout all figures↳ Could also: Standard deviation (SD) or 95% confidence intervals could also be used to represent spread — SEM reflects precision of the mean estimate and narrows mechanically with increasing n; SD describes the biological variability of individual animals and is often preferred for that purpose, while 95% CIs simultaneously convey both precision and inferential content — particularly informative for small group sizes (n≥3 to n≥9)
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Statistical significance was reported as binary asterisk notation (p<0.05) without exact p-values↳ Could also: Exact p-values (e.g., p=0.03, p=0.18) could also be reported for each comparison — Exact p-values allow readers to evaluate borderline results, support downstream meta-analyses, and distinguish a p=0.049 from a p=0.001 finding — a distinction obscured by the single-threshold asterisk system
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The Student's t-test (a parametric test) was used for all comparisons, including groups with the smallest stated sample sizes (n≥3 to n≥5)↳ Could also: A non-parametric alternative such as the Mann-Whitney U test could also be applied, particularly for the smallest group sizes where distributional assumptions are difficult to verify — With very small n the normality assumption underlying the t-test cannot be robustly assessed; non-parametric rank-based tests make fewer distributional assumptions, though they are generally less powerful when the normality assumption is met
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No a priori sample size justification or power calculation was reported↳ Could also: A power calculation based on a pilot estimate or published values for a primary outcome (e.g., plasma cholesterol difference) could also have been reported — Reporting a power calculation or the targeted effect size helps readers interpret null results — such as the absence of phenotype in Apoe^ΔAT mice — as having been adequately powered to detect a biologically relevant difference, rather than leaving the power of those negative findings uncertain
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope analysis — PMID 26695075
Title: Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity Authors: Wagner T, Bartelt A, Schlein C, Heeren J. Venue: PLoS ONE 2015 Dec 22;10(12):e0145102 · DOI 10.1371/journal.pone.0145102 · PMCID PMC4687855 Note: the operator («email») is a co-author of this paper.
What kind of study is this?
A wet-lab mouse genetics / metabolic physiology study. The authors generated a novel conditional (floxed) Apoe allele and used Cre/loxP to delete apoE tissue-specifically in hepatocytes (Apoe^ΔHep) or adipocytes (Apoe^ΔAT), then fed the mice experimental diets (chow / high-fat diet HFD / Western-type diet WTD) and phenotyped them.
Methods inventory (from Materials & Methods, PMC4687855)
| Technique | Output | Class |
|---|---|---|
| Cre/loxP, genotyping PCR, Southern blot | allele validation | wet-lab |
| Body weight curves, food intake | physiology | wet-lab |
| Oral glucose tolerance test (AccuChek) | glucose curves | wet-lab |
| Plasma cholesterol / triacylglyceride kits | concentrations | wet-lab |
| ELISA (apoE) | plasma apoE | wet-lab |
| ALT (Cobas Mira) | liver enzyme | wet-lab |
| FPLC (S6 Superose, ÄKTA) lipoprotein sizing | lipoprotein profiles | wet-lab |
| Tyloxapol VLDL secretion; ¹²⁵I-TC turnover | secretion/clearance rates | wet-lab |
| Hepatic lipid extraction + Lowry | tissue lipids | wet-lab |
| Real-time RT-PCR (TaqMan, ΔΔCt) | targeted gene expression | wet-lab |
| Western blot (apoE) | protein | wet-lab |
| H&E histology + ImageJ adipocyte sizing | morphometry | manual image analysis |
| Student's t-test (p<0.05) | significance | basic stats |
In scope vs out of scope (pipeline-derived results only)
Bioinformatic / computational-pipeline results in this paper: NONE.
- No high-throughput sequencing (RNA-seq/WGS/WES/ATAC), no microarray, no proteomics MS, no genome-wide assay, no alignment/quantification/DE pipeline.
- Gene expression is targeted qPCR (a handful of genes, ΔΔCt) — bench measurement, not a pipeline.
- The only "computational" step is ImageJ adipocyte-area measurement on H&E micrographs (manual ROI quantification). The source micrographs are not deposited, so even this is not reproducible from shipped data.
- Statistics are pairwise Student's t-tests — not a pipeline.
Every reported number is a wet-lab measurement on mice. There is no pipeline-derived computational result to reproduce.
Code & data availability
- Code: none. No repository, no scripts (own or third-party). The brief's P16 third-party-tool path does not apply — there is no computational analysis to re-run on the paper's data.
- Data availability statement (verbatim): "All relevant data are within the paper and its Supporting Information files."
- Public accession: none (no GEO/SRA/ENA/ArrayExpress/PRIDE/Zenodo).
- Supporting Information: two TIF figure images only —
- S1 Fig "Effect of tissue-specific Apoe deletion on food intake" (.s001, 231 634 B)
- S2 Fig "Effect of adipose tissue-specific deletion of apoE on oral glucose tolerance" (.s002, 377 770 B) No raw per-animal data tables, no spreadsheets — only summary figures.
Decision
DROP — drop_reason = non_pipeline (secondary: no_code, no_data_accession).
This is a text-mineable biomedical paper with no computational pipeline, no code
artifact, and no deposited machine-readable dataset; only summary figures of
wet-lab measurements are available. No «our HPC» compute is warranted. Per the brief,
drops are valid outcomes — recorded honestly with full evidence rather than forcing
a result.
No individual results have been recorded for this entry yet.
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.
PMID 26695075 is an all-wet-lab mouse genetics/physiology paper (PLoS ONE 2015, tissue-specific conditional Apoe knockouts) with no computational pipeline, no code, and no deposited machine-readable data — only two summary SI figures — so it was correctly dropped as non_pipeline. All reported endpoints are bench measurements that cannot be placed against any output (q1/q2 red on availability, not an authors' defect). No re-derivation was possible and no fabrication signal exists; overall yellow reflects a sound study with nothing computationally reproducible.
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Reproduction footprint
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