Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36187916", "kind": "science-record", "revision": 3, "content_hash": "sha256:c40e0fc6b6faa07957670dbfc85a7fdf2c23bbae621e8bb79a8d904230cdb29e", "created_at": "2026-11-01T18:15:29Z", "updated_at": "2026-11-01T21:29:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.", "doi": "10.1016/j.csbj.2022.08.066", "pmid": "36187916", "authors": ["Deze Zhao", "Xianyu Liu", "Yunhan Shan", "JiaJia Li", "Weifang Cui", "Jun Wang", "Junjie Jiang", "Qun Xie", "Chunfang Zhang", "Chaojun Duan"], "journal": "Computational and structural biotechnology journal", "year": 2022, "abstract": "Background: There are currently no treatments targeting the immune microenvironment (TME) as an extension of immunotherapy. Our research aims to provide guidance for the development of immune-related mRNA vaccines and the identification of immune subtypes for vaccine treatment in lung adenocarcinoma (LUAD).\nMethods: HTRNA-Seq and single cell RNA-seq data were obtained from The Cancer Genome Atlas (TCGA) and Gene-Expression Omnibus (GEO, GSE87340, GSE140343, GSE148071) databases. Immune checkpoints (ICP) were used as criteria to differentiate immune subtypes and immune resistance score (IRS) system is constructed by ssGSEA to judge the immune microenvironment status of patients.\nResults: Two overexpressed tumor-specific antigens, including ZC3H12D and TXNDC5, were found to be associated with both disease-free survival (DFS) and overall survival (OS). In addition, the expression of two genes correlated with antigen-presenting cell (APC) infiltration and tumor purity. Subsequently, the immune subtype of the patient was defined by constructing an IRS scoring system. The lower the IRS, the stronger the immune response in the TME. This result was verified in external datasets and at the single-cell level.\nConclusions: ZC3H12D and TXNDC5 are potential tumor-specific antigens for developing mRNA vaccines in LUAD. Importantly, patients with low IRS are more suitable for the use of immunotherapy and vaccines. Our research enhances understanding of TME features and guides more effective immunotherapy strategies.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression was performed based on OS to find prognosis related ICGs. Then, enrichment score (ES) of risk ICGs (HR > 1) and protect ICGs (HR < 1) was calculated using single sample gene set enrichment analysis (ssGSEA) in the R package ‘GSVA’.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36187916", "locator": "sections[6] \"Identification of immune subtypes\" paragraph 2", "quote": "Univariate Cox regression was performed based on OS to find prognosis related ICGs. Then, enrichment score (ES) of risk ICGs (HR > 1) and protect ICGs (HR < 1) was calculated using single sample gene set enrichment analysis (ssGSEA) in the R package ‘GSVA’."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36187916", "locator": "sections[17] \"Data availability\" paragraph 2", "quote": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ZC3H12D and TXNDC5 are potential tumor-specific antigens for developing mRNA vaccines in LUAD, and patients with low IRS are more suitable for immunotherapy and vaccines.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36187916", "locator": "sections[0] \"Abstract\" paragraph 7", "quote": "ZC3H12D and TXNDC5 are potential tumor-specific antigens for developing mRNA vaccines in LUAD. Importantly, patients with low IRS are more suitable for the use of immunotherapy and vaccines. Our research enhances understanding of TME features and guides more effective immunotherapy strategies."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ZC3H12D and TXNDC5 are potential tumor-specific antigens for developing mRNA vaccines in LUAD, and patients with low IRS are more suitable for immunotherapy and vaccines.", "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:36187916"], "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:GSE140343"], "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:GSE140343"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36187916", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.csbj.2022.08.066", "sha256": "sha256:984041a768f8ed2ed96b869eb60945d8b0cfadaaefa3b95393647a29510f5891", "bytes": 35984, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.csbj.2022.08.066", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9483806", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE140343", "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=GSE140343", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE140343", "version": null, "note": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4159498", "GSM4159499", "GSM4159500", "GSM4159501", "GSM4159502", "GSM4159503", "GSM4159504", "GSM4159505", "GSM4159506", "GSM4159507", "GSM4159508", "GSM4159509", "GSM4159510", "GSM4159511", "GSM4159512", "GSM4159513", "GSM4159514", "GSM4159515", "GSM4159516", "GSM4159517", "GSM4159518", "GSM4159519", "GSM4159520", "GSM4159521", "GSM4159522", "GSM4159523", "GSM4159524", "GSM4159525", "GSM4159526", "GSM4159527", "GSM4159528", "GSM4159529", "GSM4159530", "GSM4159531", "GSM4159532", "GSM4159533", "GSM4159534", "GSM4159535", "GSM4159536", "GSM4159537", "GSM4159538", "GSM4159539", "GSM4159540", "GSM4159541", "GSM4159542", "GSM4159543", "GSM4159544", "GSM4159545", "GSM4159546", "GSM4159547", "GSM4159548", "GSM4423295", "GSM4423296", "GSM4423297", "GSM4423298", "GSM4423299", "GSM4423300", "GSM4423301", "GSM4423302", "GSM4423303", "GSM4423304", "GSM4423305", "GSM4423306", "GSM4423307", "GSM4423308", "GSM4423309", "GSM4423310", "GSM4423311", "GSM4423312", "GSM4423313", "GSM4423314", "GSM4423315", "GSM4423316", "GSM4423317", "GSM4423318", "GSM4423319", "GSM4423320", "GSM4423321", "GSM4423322", "GSM4423323", "GSM4423324", "GSM4423325", "GSM4423326", "GSM4423327", "GSM4423328", "GSM4423329", "GSM4423330", "GSM4423332", "GSM4423333", "GSM4423334", "GSM4423335", "GSM4423336", "GSM4423337", "GSM4423338", "GSM4423339", "GSM4423340", "GSM4423341", "GSM4423342", "GSM4423343", "GSM4423344"], "sample_count": 100, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Gene expression profile of clinical LUAD tumors and their paired non-cancerous adjacent tissues by RNA-seq analysis", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE148071", "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=GSE148071", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148071", "version": null, "note": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4453576", "GSM4453577", "GSM4453578", "GSM4453579", "GSM4453580", "GSM4453581", "GSM4453582", "GSM4453583", "GSM4453584", "GSM4453585", "GSM4453586", "GSM4453587", "GSM4453588", "GSM4453589", "GSM4453590", "GSM4453591", "GSM4453592", "GSM4453593", "GSM4453594", "GSM4453595", "GSM4453596", "GSM4453597", "GSM4453598", "GSM4453599", "GSM4453600", "GSM4453601", "GSM4453602", "GSM4453603", "GSM4453604", "GSM4453605", "GSM4453606", "GSM4453607", "GSM4453608", "GSM4453609", "GSM4453610", "GSM4453611", "GSM4453612", "GSM4453613", "GSM4453614", "GSM4453615", "GSM4453616", "GSM4453617"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Comprehensive Profiling of Cancer Cells and Their Microenvironment in Advanced NSCLC", "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:GSE87340", "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=GSE87340", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87340", "version": null, "note": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2328306", "GSM2328307", "GSM2328308", "GSM2328309", "GSM2328310", "GSM2328311", "GSM2328312", "GSM2328313", "GSM2328314", "GSM2328315", "GSM2328316", "GSM2328317", "GSM2328318", "GSM2328319", "GSM2328320", "GSM2328321", "GSM2328322", "GSM2328323", "GSM2328324", "GSM2328325", "GSM2328326", "GSM2328327", "GSM2328328", "GSM2328329", "GSM2328330", "GSM2328331", "GSM2328332", "GSM2328333", "GSM2328334", "GSM2328335", "GSM2328336", "GSM2328337", "GSM2328338", "GSM2328339", "GSM2328340", "GSM2328341", "GSM2328342", "GSM2328343", "GSM2328344", "GSM2328345", "GSM2328346", "GSM2328347", "GSM2328348", "GSM2328349", "GSM2328350", "GSM2328351", "GSM2328352", "GSM2328353", "GSM2328354", "GSM2328355", "GSM2328356", "GSM2328357", "GSM2328358", "GSM2328359"], "sample_count": 54, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE140343 not downloaded", "asset:data:geo:GSE140343 licence not read", "asset:data:geo:GSE148071 not downloaded", "asset:data:geo:GSE148071 licence not read", "asset:data:geo:GSE87340 not downloaded", "asset:data:geo:GSE87340 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Univariate Cox regression was performed based on OS to find prognosis related ICGs. Then, enrichment score (ES) of risk ICGs (HR > 1) and protect ICGs (HR < 1) was calculated using single sample gene set enrichment analysis (ssGSEA) in the R package ‘GSVA’."}}], "targets": [], "gaps": []}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE87340", "GSE140343", "GSE148071"], "resolved_accessions": ["GSE87340", "GSE140343", "GSE148071"], "statements": ["The HTRNA-Seq, simple nucleotide variation, copy number variation data and related clinical information and single cell RNA sequencing data were described in method section “Data Extraction and Pre-processing”. All analyses were performed in R software. Specific content is explained in each section of Methods."], "basis": "The paper names GSE87340, GSE140343, GSE148071 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": ["cox_ph"], "assets": ["source:pmid:36187916", "data:geo:GSE140343"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE140343"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:07:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9310, "completion_tokens": 1736, "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:36187916", "type": "paper", "label": "pmid:36187916"}, {"id": "source:pmid:36187916", "type": "manuscript", "label": "PMID 36187916 full text"}, {"id": "data:geo:GSE140343", "type": "dataset", "label": "GEO GSE140343"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36187916", "type": "paper", "label": "pmid:36187916"}, {"id": "source:pmid:36187916", "type": "manuscript", "label": "PMID 36187916 full text"}, {"id": "data:geo:GSE140343", "type": "dataset", "label": "GEO GSE140343"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36187916", "type": "extraction", "used": ["source:pmid:36187916"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE140343", "type": "accession_resolution", "used": ["data:geo:GSE140343"], "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:36187916", "parent_hash": "sha256:1158afb53e0ca0219d21ca8b422fdc91db57e256a50dbe67e4d5d000e8a70684", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE140343 licence not read", "asset:data:geo:GSE140343 not downloaded", "asset:data:geo:GSE148071 licence not read", "asset:data:geo:GSE148071 not downloaded", "asset:data:geo:GSE87340 licence not read", "asset:data:geo:GSE87340 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["a (LUAD). Methods: HTRNA-Seq and single cell RNA-seq data were obtained from The Cancer Genome At"], "order_basis": "paper_text_order:417", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate Cox regression was performed based on OS to find prognosis related ICGs. Then, enrichment score (ES) of risk ICGs (HR > 1) and protect ICGs (HR < 1) was calculated using single sample gene set enrichment analysis (ssGSEA) in the R package ‘GSVA’."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}