Transcription Factor MAFB as a Prognostic Biomarker for the Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36077342", "kind": "science-record", "revision": 4, "content_hash": "sha256:ce2489fc4e8d7c171f092386f1fd9261aecd1cbf5273c710671b64e3a17e44b6", "created_at": "2026-11-01T18:15:18Z", "updated_at": "2026-11-01T22:07:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcription Factor MAFB as a Prognostic Biomarker for the Lung Adenocarcinoma.", "doi": "10.3390/ijms23179945", "pmid": "36077342", "authors": ["Omar Samir", "Naohiro Kobayashi", "Teppei Nishino", "Mennatullah Siyam", "Manoj Kumar Yadav", "Yuri Inoue", "Satoru Takahashi", "Michito Hamada"], "journal": "International journal of molecular sciences", "year": 2022, "abstract": "MAFB is a basic leucine zipper (bZIP) transcription factor specifically expressed in macrophages. We have previously identified MAFB as a candidate marker for tumor-associated macrophages (TAMs) in human and mouse models. Here, we analyzed single-cell sequencing data of patients with lung adenocarcinoma obtained from the GEO database (GSE131907). Analyzed data showed that general macrophage marker CD68 and macrophage scavenger receptor 1 (CD204) were expressed in TAM and lung tissue macrophage clusters, while transcription factor MAFB was expressed specifically in TAM clusters. Clinical records of 120 patients with lung adenocarcinoma stage I (n = 57), II (n = 21), and III (n = 42) were retrieved from Tsukuba Human Tissue Biobank Center (THB) in the University of Tsukuba Hospital, Japan. Tumor tissues from these patients were extracted and stained with anti-human MAFB antibody, and then MAFB-positive cells relative to the tissue area (MAFB+ cells/tissue area) were morphometrically quantified. Our results indicated that higher numbers of MAFB+ cells significantly correlated to increased local lymph node metastasis (nodal involvement), high recurrence rate, poor pathological stage, increased lymphatic permeation, higher vascular invasion, and pleural infiltration. Moreover, increased amounts of MAFB+ cells were related to poor overall survival and disease-free survival, especially in smokers. These data indicate that MAFB may be a suitable prognostic biomarker for smoker lung cancer patients.", "claims": [{"id": "claim-method", "statement": "The correlations between the grade of MAFB+ cells density and the clinicopathological factors were evaluated through Fisher’s exact test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36077342", "locator": "sections[12] \"4.4. Statistical Analysis\" paragraph 2", "quote": "The correlations between the grade of MAFB+ cells density and the clinicopathological factors were evaluated through Fisher’s exact test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. All source code is available from our GitHub page (https://github.com/Teppei-Nishino/TAM, accessed on 30 August 2022)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36077342", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. All source code is available from our GitHub page (https://github.com/Teppei-Nishino/TAM, accessed on 30 August 2022))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36077342"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE131907"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE131907"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36077342", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms23179945", "sha256": "sha256:41b7419abeb3f255534794eeceb05c43974c5f368927f885f916ec29a8743e20", "bytes": 41521, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms23179945", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9456510", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE131907", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131907", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE131907", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. All source code is available from our GitHub page (https://github.com/Teppei-Nishino/TAM, accessed on 30 August 2022)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. All source code is available from our GitHub page (https://github.com/Teppei-Nishino/TAM, accessed on 30 August 2022)).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3827114", "GSM3827115", "GSM3827116", "GSM3827117", "GSM3827118", "GSM3827119", "GSM3827120", "GSM3827121", "GSM3827122", "GSM3827123", "GSM3827124", "GSM3827125", "GSM3827126", "GSM3827127", "GSM3827128", "GSM3827129", "GSM3827130", "GSM3827131", "GSM3827132", "GSM3827133", "GSM3827134", "GSM3827135", "GSM3827136", "GSM3827137", "GSM3827138", "GSM3827139", "GSM3827140", "GSM3827141", "GSM3827142", "GSM3827143", "GSM3827144", "GSM3827145", "GSM3827146", "GSM3827147", "GSM3827148", "GSM3827149", "GSM3827150", "GSM3827151", "GSM3827152", "GSM3827153", "GSM3827154", "GSM3827155", "GSM3827156", "GSM3827157", "GSM3827158", "GSM3827159", "GSM3827160", "GSM3827161", "GSM3827162", "GSM3827163", "GSM3827164", "GSM3827165", "GSM3827166", "GSM3827167", "GSM3827168", "GSM3827169", "GSM3827170", "GSM3827171"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Single cell RNA sequencing of lung adenocarcinoma", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE131907 not downloaded", "asset:data:geo:GSE131907 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Welch"}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-5", "family": null, "specific": null, "label": "Fisher’s exact test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The correlations between the grade of MAFB+ cells density and the clinicopathological factors were evaluated through Fisher’s exact test."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE131907"], "resolved_accessions": ["GSE131907"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. All source code is available from our GitHub page (https://github.com/Teppei-Nishino/TAM, accessed on 30 August 2022))."], "basis": "The paper names GSE131907 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["welch_t"], "assets": ["source:pmid:36077342", "data:geo:GSE131907"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE131907"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:04:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12893, "completion_tokens": 1561, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36077342", "type": "paper", "label": "pmid:36077342"}, {"id": "source:pmid:36077342", "type": "manuscript", "label": "PMID 36077342 full text"}, {"id": "data:geo:GSE131907", "type": "dataset", "label": "GEO GSE131907"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36077342", "type": "paper", "label": "pmid:36077342"}, {"id": "source:pmid:36077342", "type": "manuscript", "label": "PMID 36077342 full text"}, {"id": "data:geo:GSE131907", "type": "dataset", "label": "GEO GSE131907"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36077342", "type": "extraction", "used": ["source:pmid:36077342"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE131907", "type": "accession_resolution", "used": ["data:geo:GSE131907"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:36077342", "parent_hash": "sha256:005681dcbed53db0b9b217e7098f9cccef84f95a377b339210c9316c0cf312ce", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE131907 licence not read", "asset:data:geo:GSE131907 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["r-associated macrophages (TAMs) in human and mouse models. Here, we analyzed single-cell sequen", "ces MAFB expression in lung macrophages in a mouse model [10]. Therefore, we decided to analyze wheth", "ces MAFB expression in lung macrophages in a mouse model [10]. Therefore, we decided to analyze"], "order_basis": "paper_text_order:244", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["B+ cells density. (A) Representative data of immunohistochemical analysis of human lung adenocarcinomas with", "and 2019 (Table S1). The cancer tissues were immunostained using an anti-MAFB antibody, and the number"], "order_basis": "paper_text_order:2271", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Welch"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}