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pmid:40687236

Integrated single-cell and bulk RNA sequencing reveals prognostic and immunotherapy-associated myofibroblastic cancer-associated fibroblast subtypes in head and neck squamous cell carcinoma.

Translational cancer research · 2025 doi:10.21037/tcr-2025-649

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:40687236
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science-record
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2026-11-01T10:25:51Z
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2026-11-01T10:25:51Z
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corpus-assay-engine
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sep_to_sci_v1
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urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Integrated single-cell and bulk RNA sequencing reveals prognostic and immunotherapy-associated myofibroblastic cancer-associated fibroblast subtypes in head and neck squamous cell carcinoma.
doi
10.21037/tcr-2025-649
pmid
40687236
authors
null
journal
Translational cancer research
year
2025
abstract
null
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claim-1
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the headline numerical result the paper states for its main finding
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null
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null
tolerance
null
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null
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abstract
[1]
authors
experiment object · 8 fields
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partial
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the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
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read_published_estimate
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1
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Read the published estimate and its interval from the source
kind
other
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complete
blocked_on
null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40687236
outputs array · 1 item
[0]
the published estimate, its unit and its interval
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[1] object · 13 fields
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obtain_source_data
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2
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data-preparation
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The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
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[0]
the source data with its provenance
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[2] object · 13 fields
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run_analysis
order
3
name
Run the analysis programme
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state
blocked
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no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40687236
parameters object · 0 fields
inputs array · 0 items
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[0]
the registered result
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step:run_analysis input 'materials:the source data behind the published result in pmid:40687236' does not resolve to a declared asset
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xml
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10.21037/tcr-2025-649
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null
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Source read by the package builder: full_text.
structure object · 1 field
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full_text
gaps array · 1 item
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asset:source:pmid:40687236 not verified
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read_published_estimate
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xml
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source:pmid:40687236
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corpus_record_absent
review object · 5 fields
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partial
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{"parent_value":3,"unit":"identified CAF subclusters","evidence":"Among the three identified CAF subclusters, myCAFs showed the strongest association with patient prognosis and were enriched in pathways related to DNA repair, oxidative phosphorylation, and E2F targets.","target_result":"Three CAF subclusters were identified, with myCAFs showing the strongest association with patient prognosis.","number_stated":true}
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identified CAF subclusters
evidence
Among the three identified CAF subclusters, myCAFs showed the strongest association with patient prognosis and were enriched in pathways related to DNA repair, oxidative phosphorylation, and E2F targets.
target_result
Three CAF subclusters were identified, with myCAFs showing the strongest association with patient prognosis.
number_stated
true
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chars 6561-6764 of source sha256 40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54
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2026-10-31T15:23:13.229815+00:00
[1] object · 8 fields
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minimax_alt
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raw_response
<think>We need answer JSON only. Need parse task carefully. User asks find single numerical result replication of registered target has to reproduce. Registered target: headline numerical result paper states for main finding. Source seems abstract/results text but does not include numerical headline effect size. Need determine if any number attached to main finding. We must report headline number only, exact contiguous quote. If no number for registered target, false, parent_value 0, unit/evidence empty, target_result says what text states instead. Need identify source states qualitative main finding: myCAFs subtype most relevant to prognosis HNSCC, lower myCAF scores responded better immunotherapy, etc. Numerical results present (seven types, 11 clusters, three subtypes, PCA 30 dimensions resolution 0.3), but these aren't headline numerical result for main finding. Could perhaps target headline number be "three subtypes"? Yet registered target says "the headline numerical result the paper states for its main finding." They expect a numeric result, likely need identify if abstract has a value. Here abstract lacks effect sizes. We should say no number stated. target_result what text states instead. Evidence empty. Need exact quote? For no number no evidence required per instruction. target_result could quote qualitative result perhaps. They say "say in target_result what the text does state instead." Need perhaps exact wording: "the myCAFs were found to be the subtype most relevant to the prognosis of HNSCC..." and "patients with lower myCAF scores responded better to immunotherapy." Should target_result be concise. Unit empty. parent 0 number_stated false. Could "three" count as numerical result? Text states "The CAFs were then re-categorized into following three subtypes..." That's a number central perhaps headline result. But replication target asks "single numerical result that a replication of the registered target has to reproduce." Usually these benchmark prompts target specific parent metric from source, often source has sentence like "AUC = 0.XX". Registered target vague deliberately. We need assess. Main finding in this paper qualitative; numerical headline may be "myCAF subtype most relevant to prognosis", but no hazard ratio, P, AUC. Counts are methods/descriptive, not headline numerical result. So false. Need JSON valid. target_result perhaps: "The text states qualitatively that myCAFs were the subtype most relevant to HNSCC prognosis and that patients with lower myCAF scores responded better to immunotherapy; it gives no headline numerical result for that finding."</think> {"parent_value":0,"unit":"","evidence":"","target_result":"The myCAFs were the subtype most relevant to HNSCC prognosis, and patients with lower myCAF scores responded better to immunotherapy; no numerical result for this main finding is stated.","number_stated":false}
reading object · 6 fields
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The myCAFs were the subtype most relevant to HNSCC prognosis, and patients with lower myCAF scores responded better to immunotherapy; no numerical result for this main finding is stated.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:23:12.605762+00:00
agreement
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disagreements object · 4 fields
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minimax
The percentage of myofibroblast-like cancer-associated fibroblasts (myCAFs) was reduced in HNSCC following immunotherapy; no numerical percentage or effect size is stated in the supplied text.
minimax_alt
The supplied text does not state a numerical effect estimate for the main finding; it reports that myCAFs showed the strongest association with HNSCC patient prognosis, among three identified CAF subtypes.
decisive
false
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minimax array · 9 items
[0]
Integrated single-cell and bulk RNA sequencing
[1]
Principal component analysis
[2]
DoRothEA transcription-factor analysis
[3]
scMetabolism metabolic-activity analysis
[4]
Univariate and multivariate analyses
[5]
Seurat immune-cell-modulation analysis
[6]
clusterProfiler pathway analysis
[7]
Kaplan-Meier survival analysis
[8]
Log-rank test
minimax_alt array · 10 items
[0]
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[1]
Seurat
[2]
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[3]
SingleR
[4]
DoRothEA
[5]
scMetabolism
[6]
Univariate and multivariate analyses
[7]
clusterProfiler
[8]
Cancer Therapeutics Response Portal (CTRP)
[9]
PRISM Repurposing datasets
decisive
false
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minimax
Wilcoxon test
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decisive
true
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minimax_alt
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decisive_fields
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null
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evidence object · 1 field
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source_resolution
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null
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null
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minimax_alt
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step:run_analysis blocked on no owned computational capability is bound to this experiment
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step:run_analysis input 'materials:the source data behind the published result in pmid:40687236' does not resolve to a declared asset
[12]
targets
Complete file
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["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40687236"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "69d67f51a9305a333c12d56770054499c5ce997b2e121161dcb6ad953ee508da", "source_hash": "40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54", "raw_response_sha256": "sha256:88b371349277b025e1c93e356e6dc0e691dd8b2c673af85475970082834fd4c1", "raw_response_chars": 5382}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "01052ac80903486c022dc0f0d4355ef6c1813565c78a2831b04557cfa3fb2fa9", "source_hash": "40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54", "raw_response_sha256": "sha256:64f298ef6eaf50bd1eb2a4a6ad17ec2c7fbdbd24ca1ec3ef0a776f913979ff82", "raw_response_chars": 61501}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "1b36fbbfb2a180e444efc9016af82e33dc7b13efcdadb6485842ae654c61cd54", "source_hash": "40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54", "raw_response": "{\"parent_value\":3,\"unit\":\"identified CAF subclusters\",\"evidence\":\"Among the three identified CAF subclusters, myCAFs showed the strongest association with patient prognosis and were enriched in pathways related to DNA repair, oxidative phosphorylation, and E2F targets.\",\"target_result\":\"Three CAF subclusters were identified, with myCAFs showing the strongest association with patient prognosis.\",\"number_stated\":true}", "reading": {"parent_value": 3, "unit": "identified CAF subclusters", "evidence": "Among the three identified CAF subclusters, myCAFs showed the strongest association with patient prognosis and were enriched in pathways related to DNA repair, oxidative phosphorylation, and E2F targets.", "target_result": "Three CAF subclusters were identified, with myCAFs showing the strongest association with patient prognosis.", "number_stated": true, "source_locator": "chars 6561-6764 of source sha256 40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54"}, "recorded_at": "2026-10-31T15:23:13.229815+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e1662d246ec69b0cfc4ac973ef8e309092fddb3cdc95654859f3a32b31491568", "source_hash": "40b537d9cd759d518d47ab97d355290175e2bb620f72856bce5559c3e2732d54", "raw_response": "<think>We need answer JSON only. Need parse task carefully. User asks find single numerical result replication of registered target has to reproduce. Registered target: headline numerical result paper states for main finding. Source seems abstract/results text but does not include numerical headline effect size. Need determine if any number attached to main finding. We must report headline number only, exact contiguous quote. If no number for registered target, false, parent_value 0, unit/evidence empty, target_result says what text states instead.\n\nNeed identify source states qualitative main finding: myCAFs subtype most relevant to prognosis HNSCC, lower myCAF scores responded better immunotherapy, etc. Numerical results present (seven types, 11 clusters, three subtypes, PCA 30 dimensions resolution 0.3), but these aren't headline numerical result for main finding. Could perhaps target headline number be \"three subtypes\"? Yet registered target says \"the headline numerical result the paper states for its main finding.\" They expect a numeric result, likely need identify if abstract has a value. Here abstract lacks effect sizes. We should say no number stated. target_result what text states instead. Evidence empty. Need exact quote? For no number no evidence required per instruction. target_result could quote qualitative result perhaps. They say \"say in target_result what the text does state instead.\" Need perhaps exact wording: \"the myCAFs were found to be the subtype most relevant to the prognosis of HNSCC...\" and \"patients with lower myCAF scores responded better to immunotherapy.\" Should target_result be concise. Unit empty. parent 0 number_stated false.\n\nCould \"three\" count as numerical result? Text states \"The CAFs were then re-categorized into following three subtypes...\" That's a number central perhaps headline result. But replication target asks \"single numerical result that a replication of the registered target has to reproduce.\" Usually these benchmark prompts target specific parent metric from source, often source has sentence like \"AUC = 0.XX\". Registered target vague deliberately. We need assess. Main finding in this paper qualitative; numerical headline may be \"myCAF subtype most relevant to prognosis\", but no hazard ratio, P, AUC. Counts are methods/descriptive, not headline numerical result. So false.\n\nNeed JSON valid. target_result perhaps: \"The text states qualitatively that myCAFs were the subtype most relevant to HNSCC prognosis and that patients with lower myCAF scores responded better to immunotherapy; it gives no headline numerical result for that finding.\"</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The myCAFs were the subtype most relevant to HNSCC prognosis, and patients with lower myCAF scores responded better to immunotherapy; no numerical result for this main finding is stated.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The myCAFs were the subtype most relevant to HNSCC prognosis, and patients with lower myCAF scores responded better to immunotherapy; no numerical result for this main finding is stated.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:23:12.605762+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "The percentage of myofibroblast-like cancer-associated fibroblasts (myCAFs) was reduced in HNSCC following immunotherapy; no numerical percentage or effect size is stated in the supplied text.", "minimax_alt": "The supplied text does not state a numerical effect estimate for the main finding; it reports that myCAFs showed the strongest association with HNSCC patient prognosis, among three identified CAF subtypes.", "decisive": false}, "analysis_methods": {"minimax": ["Integrated single-cell and bulk RNA sequencing", "Principal component analysis", "DoRothEA transcription-factor analysis", "scMetabolism metabolic-activity analysis", "Univariate and multivariate analyses", "Seurat immune-cell-modulation analysis", "clusterProfiler pathway analysis", "Kaplan-Meier survival analysis", "Log-rank test"], "minimax_alt": ["Integrated single-cell and bulk RNA sequencing (RNA-seq) analysis", "Seurat", "Principal component analysis (PCA)", "SingleR", "DoRothEA", "scMetabolism", "Univariate and multivariate analyses", "clusterProfiler", "Cancer Therapeutics Response Portal (CTRP)", "PRISM Repurposing datasets"], "decisive": false}, "statistical_method": {"minimax": "Wilcoxon test", "minimax_alt": "Kaplan-Meier curves and the log-rank test", "decisive": true}, "number_stated": {"minimax": true, "minimax_alt": false, "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:318f27cef1fe5a05b04573b07f1a7ec6215f06c94cc0eef60673bfb204d4da11", "type": "sep_package", "label": "SEP v1 package for pmid:40687236"}], "activities": [{"id": "activity:conversion:pmid:40687236", "type": "conversion", "used": ["package:318f27cef1fe5a05b04573b07f1a7ec6215f06c94cc0eef60673bfb204d4da11"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "c96234e0-b75d-40b1-8bd4-ac0fe7c7e59c", "parent_hash": "318f27cef1fe5a05b04573b07f1a7ec6215f06c94cc0eef60673bfb204d4da11", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40687236 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40687236' does not resolve to a declared asset", "targets"]}