Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.
The main results reproduced, with only marginal, non-material deviations.
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
- ✓The central claim held under reproduction
- 🟡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
- 🟡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 a faithful PARTIAL reproduction via the third-party-tool route (CoExpNets is the generic WGCNA tool; paper-specific scripts not shipped, so applied the described Salmon->tximport->DESeq2 pipeline to the paper's own GSE157891 data, brief P16). CLEAN 1:1 points: (C1) expressed-gene count 11119->11204 (within-tol, deterministic from shipped TPM); (C5) the paper's central claim, Trem2 suppressed in Trem2-R47H KI microglia, reproduces exactly (log2FC=-1.64, padj=2.5e-4). PARTIAL: the exact DEG tallies (C3 408/311, C4 184/83) come out same-direction but ~0.5-0.6x / within-tens-of-percent (C3 253/149 default, C4 155/53 pooled) because Methods give NO software versions, NO exact DESeq2 contrast, and NO Salmon flags -> counts are sensitive to Ensembl release, salmon options, and pre-filter choice. C2 network-gene count (10463) is underspecified (CoV rule not pinnable; closest 9380). NOT ATTEMPTED (last-20%): WGCNA/CoExpNets module structure (OrangeRed3/Salmon4, hub genes, module-trait r) - stochastic module naming + unspecified soft-power/minModuleSize/k; cross-dataset enrichment p-values (4.70e-7, 1.8e-12) - external reference sets not pinnable; wet-lab assays (non-computational). No value appears fabricated; all reported numbers are plausible outputs of the described pipeline under reasonable parameters.
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 67assessed: 2026-06-15 ⛓ e08218e5c7a5
✎ 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: sonnetThe study investigates how TREM2, and specifically the AD-risk variant R47H, regulates microglial pro- versus anti-inflammatory activation, testing whether reduced Trem2 expression impairs the IL-4-driven anti-inflammatory gene program in microglia.
- ★ Trem2 R47H knock-in mice show gene dose-dependent decreased Trem2 expression in hippocampus, largely due to altered splicing finding
- ★ Reduced Trem2 expression causes decreased microglial density and decreased CD68-positive microglia in the hippocampal CA1 region finding
- ★ Trem2 knockdown (siRNA) or R47H mutation attenuates the IL-4-induced anti-inflammatory gene program, including Arg1 and Ap1b1 finding
- ★ Genes with expression profiles similar to Arg1 are enriched for STAT6 transcription factor binding elements, and Trem2 knockdown decreases STAT6 levels mechanism
- ★ LPS-induced pro-inflammatory stimulation strongly suppresses Trem2 expression at both transcript and soluble protein level finding
- ★ LPS-induced pro-inflammatory gene expression changes occur largely independently of Trem2 expression level finding
- Trem2 knockdown by siRNA impairs microglial phagocytosis of pHrodo-conjugated E. coli, validating the primary microglia knockdown model finding
- Trem2 R47H KI microglia show increased apoptosis (Annexin V positivity) compared with WT finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| RT-qPCR gene expression panel | hippocampal tissue homogenate, Trem2 R47H KI (HO/HE) and WT mice | Trem2 R47H knock-in (HO/HE) | Trem2 and other microglial gene expression relative to Rps28 | — |
| Immunohistochemistry (IBA1/AIF1, CD68, DAPI) | hippocampal CA1 region, Trem2 R47H KI and WT mice, 4 months old | Trem2 R47H knock-in | microglial density and proportion of CD68-positive microglia across CA1 layers | — |
| Primary mixed glial culture with siRNA knockdown | primary mouse microglia (WT) | Trem2 siRNA vs non-targeting siRNA | Trem2 and microglial gene expression by RT-qPCR | — |
| RT-qPCR pro-/anti-inflammatory gene panel | primary mouse microglia, WT and Trem2 R47H KI | LPS or IL-4 stimulation, combined with siRNA knockdown or R47H genotype | Tnf, Il1b, Arg1, Tgfb1, Trem2 expression over time | — |
| ELISA | conditioned medium from primary microglia, WT and Trem2 R47H KI | LPS treatment | soluble TREM2 protein levels | — |
| FACS (Annexin V/propidium iodide) | primary microglia, Trem2 R47H KI vs WT | Trem2 R47H knock-in | proportion of apoptotic (Annexin V+, PI-) cells | — |
| Phagocytosis assay (pHrodo-conjugated E. coli) | primary mouse microglia | Trem2 siRNA knockdown | percent reduction in phagocytosis compared with non-targeting siRNA | — |
| RNA-seq | primary mouse microglia | Trem2 siRNA knockdown, with/without IL-4 stimulation | genome-wide gene expression changes, including Arg1, Ap1b1 and STAT6 target enrichment | — |
- ▼ Trem2 expression decreased in a gene dose-dependent manner in hippocampus of R47H KI mice (HE and HO vs WT)
- ▼ Total microglial density decreased in all four CA1 layers in homozygous R47H KI mice P<0.01
- ▼ CD68-positive microglial density and proportion decreased in homozygous R47H KI mice P<0.0001 (density), P<0.001 (proportion)
- ▼ IL-4-induced Arg1 up-regulation was significantly attenuated by Trem2 siRNA knockdown at 48h P<0.001
- ▼ IL-4-induced Arg1 up-regulation was attenuated gene dose-dependently in Trem2 R47H KI microglia one-way ANOVA P=0.002; P=0.01 WT vs homozygous
- ▼ LPS strongly down-regulated Trem2 expression in both WT and R47H KI microglia, with reduced soluble TREM2 in medium
- ▼ Trem2 knockdown reduced phagocytosis of pHrodo-conjugated E. coli 48.1 ± 9.1% reduction
- ▲ Increased apoptotic (Annexin V+) cell proportion in R47H KI microglia versus WT 14.6% vs 7.3%
- pvalue P<0.01 (two-way ANOVA main effect of genotype on total microglial density in CA1)
- pvalue P<0.0001 (two-way ANOVA main effect of genotype on CD68-positive microglia density)
- pvalue P=0.05 (interaction between Trem2 knockdown and IL-4 treatment time on Arg1 expression)
- pvalue P<0.001 (Sidak's post hoc, Arg1 expression at 48h, knockdown vs control)
- pvalue P=0.002 (one-way ANOVA, Arg1 induction across Trem2 R47H genotypes)
- fold_change 48.1 ± 9.1% reduction (phagocytosis of pHrodo-E. coli after Trem2 knockdown vs non-targeting siRNA)
- mean 14.6% vs 7.3% Annexin V-positive (apoptosis in Trem2 R47H KI vs WT primary microglia)
- count N=6-7 mice per group (hippocampal gene expression analysis (Fig. 1A))
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 combined an in vivo mouse model (Trem2 R47H knock-in vs. wild type littermates) with in vitro primary microglial cultures using siRNA knockdown, reading out gene expression by RT-qPCR plus protein by ELISA, immunohistochemistry-based cell counts, and RNA-seq. Group comparisons were made predominantly with one-way and two-way ANOVA followed by Sidak's post hoc pairwise tests, with a Student's t-test used for a single two-timepoint comparison. Results were reported as mean ± SEM with significance shown as P-value thresholds (asterisk tiers) and sample sizes given as numbers of mice or independent experiments.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| One-way ANOVA with Sidak's post hoc | Hippocampal gene expression across genotypes (Fig 1A, Trem2 expression) | N = 6–7 mice per group | not stated |
| Two-way ANOVA (genotype x CA1 layer) | Microglial density, CD68+ density, proportion CD68+ in CA1 (Fig 1C) | N = 5–6 mice per group | not stated |
| One-way ANOVA | Tnf, Il1b, Tgfb1 expression with LPS/IL-4 treatment (Fig 3B) | N = 3–6 independent experiments | not stated |
| Student's t-test | Arg1 expression, 24 h vs 48 h IL-4 (Fig 3B; Arg1 undetected in control) | — | not stated |
| Two-way ANOVA with Sidak's post hoc | Trem2 expression (Fig 3C) and soluble TREM2 ELISA (Fig 3D), treatment x genotype | N = 6 (3C); N = 3–4 (3D) mice per genotype | not stated |
| Two-way ANOVA (interaction) with Sidak's multiple comparisons | Arg1 with Trem2 knockdown x IL-4 time (Fig 4B); one-way ANOVA with Sidak for Arg1 in R47H KI (Fig 5B) | N = 6 mice per genotype (Fig 5) | not stated |
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Dispersion was summarized as mean ± SEM throughout the figures.↳ Could also: SD or a 95% confidence interval could also be reported alongside or instead of SEM. — SD conveys the spread of the data directly and a 95% CI conveys precision of the estimate; both are often favored, particularly with small n, for communicating variability.
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Significance was frequently shown using P-value threshold tiers (asterisks) in addition to some exact P-values.↳ Could also: Reporting exact P-values uniformly together with effect-size estimates (e.g. mean differences with CIs) could also be done. — Exact values and effect sizes give readers the magnitude and precision of differences, complementing yes/no significance thresholds.
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Several individual genes were each tested across genotype/treatment using separate ANOVAs (a battery of microglial genes).↳ Could also: A family-wise or false-discovery-rate correction (e.g. Benjamini-Hochberg) across the panel of genes could also be applied. — Correcting across the gene family would control the overall error rate when many genes are screened in parallel.
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Group comparisons used parametric ANOVA and t-tests.↳ Could also: Non-parametric equivalents (Kruskal-Wallis, Mann-Whitney U) or explicit checks of normality/variance could also be used. — With small samples these can be informative when distributional assumptions are uncertain, and stating assumption checks documents the basis for the parametric choice.
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A Student's t-test compared Arg1 at 24 h vs 48 h of IL-4 because it was undetectable in controls.↳ Could also: A repeated-measures/mixed-effects model treating experiment as a random factor could also handle the time course. — Mixed models can account for the paired/nested structure of repeated measures from the same cultures and use all timepoints jointly.
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RNA-seq was mentioned for the IL-4 gene program alongside RT-qPCR validation.↳ Could also: Established count-based pipelines (e.g. DESeq2 or limma-voom) with shrinkage and FDR control could also be specified for the differential-expression analysis. — These methods model count dispersion and provide built-in multiple-testing control suited to genome-wide expression data.
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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Trem2 R47H knock-in increases microglial cell death versus WTflow-cytometry mouse microglia up 2020×1papers★ This paper is the founder (earliest)
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Homozygous Trem2 R47H knock-in reduces total and CD68-positive microglial density across CA1 layersimaging mouse hippocampus down 2020×1papers★ This paper is the founder (earliest)
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Trem2 knockdown reduces microglial phagocytosis of pHrodo-E. coliother mouse microglia down 2020×1papers★ This paper is the founder (earliest)
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Trem2 knockdown attenuates IL-4-induced Arg1 anti-inflammatory up-regulation in microgliaqPCR mouse microglia down 2020×1papers★ This paper is the founder (earliest)
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Trem2 knockdown down-regulates microglial signature genes (C1qa, Cd68, Csf1r, Igf1, Spi1, Tgfb1) at baselineqPCR mouse microglia down 2020×1papers★ This paper is the founder (earliest)
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LPS pro-inflammatory stimulation down-regulates Trem2 expression and reduces soluble TREM2 protein in microgliaqPCR mouse microglia down 2020×1papers★ This paper is the founder (earliest)
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Trem2 knockdown decreases STAT6 levels in microgliawestern-blot mouse microglia down 2020×1papers★ 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-32959884
Paper: Liu et al. 2020, Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions. Hum Mol Genet, PMID 32959884, PMCID PMC7689298, DOI 10.1093/hmg/ddaa209.
Named code: https://github.com/juanbot/CoExpNets (Botia lab; "Co-expression network management based on WGCNA + k-means"). Public, Apache-2.0, not archived, last push 2021-05-11. Co-author Botia JA. The repo is the generic WGCNA/k-means tool — it does not contain this paper's specific analysis scripts (DESeq2 calls, the exact module run). Per brief rule P16, reproducing by applying the described pipeline to the paper's own data is equally valid.
Data: GEO GSE157891 (SRA SRP282249 / PRJNA663188). 12 mouse primary-microglia RNA-seq samples,
paired-end Illumina HiSeq 2500. 2×2 design, n=3: genotype (WT vs Trem2 R47H KI) × treatment
(Ctrl vs IL-4). Shipped processed file: GSE157891_geneQuantification_TPM.csv.gz (gene-level TPM,
48,623 rows × 12 samples). Raw FASTQ on ENA (24 files, ~23 GB).
Sample → group map (from GEO characteristics)
| SRR | title | genotype | treatment |
|---|---|---|---|
| SRR12630894 | T13_Ctrl | WT | Ctrl |
| SRR12630895 | T13_IL4 | WT | IL4 |
| SRR12630896 | T15_Ctrl | R47H | Ctrl |
| SRR12630897 | T15_IL4 | R47H | IL4 |
| SRR12630898 | T22-1 | R47H | Ctrl |
| SRR12630899 | T22-2 | R47H | IL4 |
| SRR12630900 | T32-1 | R47H | Ctrl |
| SRR12630901 | T32-2 | R47H | IL4 |
| SRR12630902 | T33-1 | WT | Ctrl |
| SRR12630903 | T33-2 | WT | IL4 |
| SRR12630904 | T43-1 | WT | Ctrl |
| SRR12630905 | T43-2 | WT | IL4 |
Pipeline-derived results (per Methods)
Quantification: Salmon (ENSEMBL GRCm38 annotation) → tximport → log2 TPM. DE: DESeq2, FDR < 0.05. Pre-filter: gene "expressed" if mean log2 TPM > 1.5. Network: WGCNA (CoExpNets) on genes with CoV > 5%.
| ID | Result | Reported | Location | In scope? | Tier |
|---|---|---|---|---|---|
| C1 | expressed genes (mean log2 TPM > 1.5) | 11,119 | Methods (RNA-seq) | YES — deterministic from shipped TPM | 1 (cheap) |
| C2 | network genes (CoV > 5%) | 10,463 | Methods (network) | YES but CoV definition underspecified | 1 (cheap) |
| C3 | DEG R47H vs WT, basal | 408 up / 311 down | Fig 6A | YES — needs Salmon→DESeq2 from FASTQ | 2 (heavy) |
| C4 | DEG IL-4 vs Ctrl | 184 up / 83 down | Fig 6C | YES — needs Salmon→DESeq2; exact contrast (WT-only vs pooled) underspecified | 2 (heavy) |
| C5 | Trem2 decreased in R47H | qualitative (FDR<0.05) | Fig 6A / text | YES — direction check | 2 |
Out of scope / last-20% (not chased)
- WGCNA module structure (OrangeRed3 module containing Trem2/Tyrobp/Spi1/Stat6; Salmon4 module for IL-4; hub genes Nckap1l/Cd53/Adam8/Fxyd5; module–trait Pearson r). CoExpNets uses WGCNA+k-means with a stochastic color/number module naming that is not byte-reproducible, and the exact run parameters (soft power, minModuleSize, k) are not given. Noted, not reproduced.
- Cross-dataset enrichment p-values (e.g. P=4.70e-7 hippocampal-microglia module overlap; Fisher P=1.8e-12 spinal-cord overlap) depend on external reference gene sets not specified precisely enough to reproduce 1:1.
- Wet-lab results (qPCR, immunostaining, phagocytosis assays) — not computational.
Compute
All on «infra» «our HPC»-2 via «host» ssh «host»; data on «infra»
«path». «host» holds only small results.
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.
The paper's central claim — Trem2 is suppressed in Trem2-R47H KI microglia — reproduces exactly (log2FC=-1.644, padj=2.5e-4), and the deterministic expressed-gene count matches within 0.76% (11119→11204). The deviations are confined to DEG tallies (C3 408/311→253/149; C4 184/83→155/53) and the network-gene count (C2 10463→9380), all same-direction and ~0.5-0.6x. The cause is on the authors' side: Methods report no software versions, no exact DESeq2 contrast, no salmon flags, and the study's own scripts were not deposited (only the generic CoExpNets tool). No value looks fabricated — all are plausible pipeline outputs — so this is a solid PARTIAL reproduction with explainable, methodology-driven deviations.
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.