Activated autophagy of innate immune cells during the early stages of major trauma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36713435", "kind": "science-record", "revision": 3, "content_hash": "sha256:6075557b7601841c71ba101ab546d2df9a4fa8504912c6e3b3099d069096af69", "created_at": "2026-11-01T19:01:16Z", "updated_at": "2026-11-01T22:08:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Activated autophagy of innate immune cells during the early stages of major trauma.", "doi": "10.3389/fimmu.2022.1090358", "pmid": "36713435", "authors": ["Deng Chen", "Cong Zhang", "Jialiu Luo", "Hai Deng", "Jingzhi Yang", "Shunyao Chen", "Peidong Zhang", "Liming Dong", "Teding Chang", "Zhao-Hui Tang"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Background: Trauma-induced immune dysfunction has been a major barrier to achieving reduced mortality, which is poorly understood. Autophagy is a crucial catabolic mechanism of immune cells during times of stress. Few studies have investigated the immune regulatory effects induced by autophagy after trauma. Here, we use single-cell transcriptomics analysis in a major trauma cohort to demonstrate the dominant role of autophagy in innate immune cells during the early stages of major trauma.\nMethod: Single-cell transcriptional profiling of peripheral blood mononuclear cells (PBMCs) was performed, which were sampled from three control participants and five major trauma patients within 6 hours of injury. In detail, after single-cell RNA-sequence data processing, cell type annotation and cluster marker identification were performed. A genetic toolbox with 604 autophagy-related genes was used to monitor the autophagy levels in immune cells. In addition, all transcriptome RNA sequencing data obtained from PBMCs in a cohort of 167 major trauma patients were downloaded from gene expression omnibus (GEO) datasets (GSE36809). Key deregulated biological processes and important autophagic hub genes involved in immune cells were identified by weighted gene co-expression network analysis and gene ontology enrichment analysis.\nResults: A total of 20,445 differentially expressed genes were identified and five co-expression modules were constructed. Enrichment analysis indicated that activated autophagy is the most important biological process during the early stages of major trauma, and JMY (autophagy-related genes) were identified as hub genes. The single-cell transcriptional profiling of PBMCs demonstrated that all components of adaptive immune cells were significantly decreased, whereas components of innate immune cells (monocytes and neutrophils) were significantly increased in major trauma patients compared with control participants. Activated autophagy was detected in monocytes and neutrophils by monitoring the dynamic transcriptional signature of the autophagy-related genetic toolbox. Biological process analysis shows that antigen uptake, processing presentation, and major histocompatibility complex (MHC) class II protein complex assembly pathways were up-regulated in autophagy-positive monocytes, whereas antigen processing and presentation of endogenous antigen and type I interferon signaling pathways were up-regulated in autophagy-positive neutrophils during the early stages of major trauma.\nConclusion: Our study demonstrated that autophagy is a biological process crucial to the development of immune disorders in the early stages of major trauma. Furthermore, the results of our study generated a comprehensive single-cell immune landscape for major trauma patients, in which we determined that autophagy profoundly affects the main functions of innate immune cells and provides insight into the cellular basis of immune dysregulation after major trauma.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis (WGCNA) was performed to categorize DEGs into different gene modules, and 5 gene modules were randomly assigned color labels ( Figure 1D ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36713435", "locator": "sections[16] \"Autophagy: an essential biological process in immune cells’ response to trauma\" paragraph 5", "quote": "Weighted gene co-expression network analysis (WGCNA) was performed to categorize DEGs into different gene modules, and 5 gene modules were randomly assigned color labels ( Figure 1D )."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE197522.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36713435", "locator": "sections[25] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE197522."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Autophagy was significantly activated in monocytes and neutrophils during the early stages of major trauma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36713435", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study demonstrated that autophagy is a biological process crucial to the development of immune disorders in the early stages of major trauma."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Autophagy was significantly activated in monocytes and neutrophils during the early stages of major trauma.", "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:36713435"], "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:GSE197552"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE197552"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36713435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1090358", "sha256": "sha256:ecbbc84c340e7b4261e4ae72f80c933a4d5d2f18b834bb20ed8bcbf8c06b554e", "bytes": 47679, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1090358", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9879135", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE197552", "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=GSE197552", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE197552", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE197522.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE197522.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5920479", "GSM5920480", "GSM5920481", "GSM5920482", "GSM5920483", "GSM5920484", "GSM5920485", "GSM5920486", "GSM5920487", "GSM5920488", "GSM5920489", "GSM5920490"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "TRPS1 impairs myogenic differentiation in embryonal rhabdomyosarcoma", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE36809", "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=GSE36809", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36809", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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categorize DEGs into different gene modules, and 5 gene modules were randomly assigned color labels ( Figure 1D )."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE36809", "GSE197552"], "resolved_accessions": ["GSE36809", "GSE197552"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE197522."], "basis": "The paper names GSE36809, GSE197552 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36713435", "data:geo:GSE197552"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE197552"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:25:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11620, "completion_tokens": 1441, "cached_tokens": 264}}, "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:36713435", "type": "paper", "label": "pmid:36713435"}, {"id": "source:pmid:36713435", "type": "manuscript", "label": "PMID 36713435 full text"}, {"id": "data:geo:GSE197552", "type": "dataset", "label": "GEO GSE197552"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36713435", "type": "paper", "label": "pmid:36713435"}, {"id": "source:pmid:36713435", "type": "manuscript", "label": "PMID 36713435 full text"}, {"id": "data:geo:GSE197552", "type": "dataset", "label": "GEO GSE197552"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36713435", "type": "extraction", "used": ["source:pmid:36713435"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE197552", "type": "accession_resolution", "used": ["data:geo:GSE197552"], "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:36713435", "parent_hash": "sha256:1cad0f90e67ac75a2913c6f41000a5892bde568ca13635208b2ebe7e307f2de1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE197552 licence not read", "asset:data:geo:GSE197552 not downloaded", "asset:data:geo:GSE36809 licence not read", "asset:data:geo:GSE36809 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["uced by autophagy after trauma. Here, we use single-cell transcriptomics analysis in a major trauma cohort to demonst", "e buffer solution (PBS) at room temperature. Single-cell RNA-seq data processing Raw data were aligned to the", "lity of the datasets. To perform comparative scRNA-seq analysis across experimental conditions, the", "analysis across experimental conditions, the scRNA-seq integration procedure was commenced by findi"], "order_basis": "paper_text_order:361", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["immune cells. In addition, all transcriptome RNA sequencing data obtained from PBMCs in a cohort of 167", "ution (PBS) at room temperature. Single-cell RNA-seq data processing Raw data were aligned to the", "phagy after trauma. Here, we use single-cell transcriptomics analysis in a major trauma cohort to demonst", "agy levels in immune cells. In addition, all transcriptome RNA sequencing data obtained from PBMCs in a"], "order_basis": "paper_text_order:373", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}