Circulating exosomal PCAT1 as a complement of carcinoembryonic antigen for early colorectal cancer diagnosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39640681", "kind": "science-record", "revision": 3, "content_hash": "sha256:d57e9dfb4fb6698e4e850286e735c0fced09047b7cd0f853149394446d204e7b", "created_at": "2026-11-01T20:29:55Z", "updated_at": "2026-11-01T22:13:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Circulating exosomal PCAT1 as a complement of carcinoembryonic antigen for early colorectal cancer diagnosis.", "doi": "10.1016/j.heliyon.2024.e39264", "pmid": "39640681", "authors": ["Jinghe Cao", "Wei Chao", "Jiansheng Zhang", "Jiajia Mao", "Jianchao Zeng", "Delan Luo", "Shishun Huang", "Jiashu Li", "Baoyu He", "Hongli Pan"], "journal": "Heliyon", "year": 2024, "abstract": "Backgrounds: Given the global prevalence of colorectal cancer (CRC), advancements in prompt and accurate diagnosis are crucial. Long non-coding RNAs (lncRNAs) in serum exosomes are emerging as potential diagnostic biomarkers. This study evaluated the feasibility of using serum exosomal lncRNAs for early-stage CRC diagnosis in clinical practice.\nMethods: Candidate serum exosomal lncRNAs were identified through an integrated analysis of two GEO datasets (GSE100206 and GSE100063) containing non-coding RNA expression profiles in serum exosomes. Exosomes isolated from participants' serum were validated using transmission electron microscopy (TEM) and immunoblotting. The expression levels of serum exosomal PCAT1 were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Diagnostic accuracy was assessed using receiver operating characteristic (ROC) analysis.\nResults: Serum exosomal PCAT1 levels were evaluated in 150 CRC patients, 66 patients with benign colorectal lesions, and 128 healthy controls. ROC analysis demonstrated high diagnostic efficacy of serum exosomal PCAT1 for CRC. Notably, the predictive performance was sufficient to distinguish early-stage CRC patients. Additionally, the diagnostic value was significant for CRC patients with low serum carcinoembryonic antigen (CEA) levels. Measuring serum exosomal PCAT1 could complement CEA assessment, enhancing CRC diagnostic accuracy.\nConclusions: Serum exosomal PCAT1 can complement CEA assessment, aiding in early CRC diagnosis and helping to differentiate the disease, especially in patients with low CEA levels.", "claims": [{"id": "claim-method", "statement": "Diagnostic metrics, including the area under the ROC curve, specificity, sensitivity, positive predictive value, negative predictive value, and likelihood ratio, were calculated through ROC curve analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39640681", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Diagnostic metrics, including the area under the ROC curve, specificity, sensitivity, positive predictive value, negative predictive value, and likelihood ratio, were calculated through ROC curve analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39640681", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PCAT1 outperformed CEA in terms of AUC, specificity, and sensitivity in CRC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39640681", "locator": "sections[10] \"Validation of diagnostic potential of circulating exosomal PCAT1 in two independent cohorts\" paragraph 2", "quote": "Notably, PCAT1 outperformed CEA in terms of AUC, specificity, and sensitivity in CRC patients (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PCAT1 outperformed CEA in terms of AUC, specificity, and sensitivity in CRC patients.", "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:39640681"], "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:GSE100063"], "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:GSE100063"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39640681", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e39264", "sha256": "sha256:5c95134d5fe1080cbf0d4c73a8e50990cb45acc2c3ac66689133a79b4c65dbad", "bytes": 28396, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e39264", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11620264", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100063", "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=GSE100063", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100063", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2670728", "GSM2670729", "GSM2670730", "GSM2670731", "GSM2670732", "GSM2670733", "GSM2670734", "GSM2670735", "GSM2670736", "GSM2670737", "GSM2670738", "GSM2670739"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with colorectal carcinoma", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE100206", "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=GSE100206", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100206", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2674606", "GSM2674607", "GSM2674608", "GSM2674609", "GSM2674610", "GSM2674611", "GSM2674612", "GSM2674613", "GSM2674614", "GSM2674615", "GSM2674616", "GSM2674617", "GSM2674618", "GSM2674619", "GSM2674620", "GSM2674621", "GSM2674622", "GSM2674623", "GSM2674624", "GSM2674625", "GSM2674626", "GSM2674627", "GSM2674628", "GSM2674629", "GSM2674630", "GSM2674631", "GSM2674632", "GSM2674633", "GSM2674634", "GSM2674635", "GSM2674636", "GSM2674637"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of normal persons", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE100063 not downloaded", "asset:data:geo:GSE100063 licence not read", "asset:data:geo:GSE100206 not downloaded", "asset:data:geo:GSE100206 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "PCA"}}, {"id": "method-2", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}, {"id": "method-4", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Diagnostic metrics, including the area under the ROC curve, specificity, sensitivity, positive predictive value, negative predictive value, and likelihood ratio, were calculated through ROC curve analysis."}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE100206", "GSE100063"], "resolved_accessions": ["GSE100206", "GSE100063"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE100206, GSE100063 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:39640681", "data:geo:GSE100063"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100063"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:41:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8434, "completion_tokens": 1592, "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:39640681", "type": "paper", "label": "pmid:39640681"}, {"id": "source:pmid:39640681", "type": "manuscript", "label": "PMID 39640681 full text"}, {"id": "data:geo:GSE100063", "type": "dataset", "label": "GEO GSE100063"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39640681", "type": "paper", "label": "pmid:39640681"}, {"id": "source:pmid:39640681", "type": "manuscript", "label": "PMID 39640681 full text"}, {"id": "data:geo:GSE100063", "type": "dataset", "label": "GEO GSE100063"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39640681", "type": "extraction", "used": ["source:pmid:39640681"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100063", "type": "accession_resolution", "used": ["data:geo:GSE100063"], "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:39640681", "parent_hash": "sha256:84188f2a3702592984e0be259c3c6ff378b076608a87c08c648c43ca2b7ba018", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE100063 licence not read", "asset:data:geo:GSE100063 not downloaded", "asset:data:geo:GSE100206 licence not read", "asset:data:geo:GSE100206 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["g transmission electron microscopy (TEM) and immunoblotting. The expression levels of serum exosomal PCA", "es of serum exosomes (scale bar = 100 nm). E Western blot analysis detected exosomal markers (CD63, CD", "ients with low CEA levels. TEM (Fig. 2d) and Western blot analyses (Fig. 2e) validated the exosomes is"], "order_basis": "paper_text_order:719", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["w (CEAL) early-stage CRC patients using SYBR-qPCR and TaqMan-qPCR. H Diagnostic performance of", "tage CRC patients using SYBR-qPCR and TaqMan-qPCR. H Diagnostic performance of serum PCAT1 for", "Comparison and correlation of data from SYBR-qPCR and TaqMan-qPCR methods.Fig. 2 We then analy", "orrelation of data from SYBR-qPCR and TaqMan-qPCR methods.Fig. 2 We then analyzed PCAT1 expres"], "order_basis": "paper_text_order:4944", "id": "assay:2"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["PCA"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}