Aberrant gene expression pattern in the glycolysis-cholesterol synthesis axis is linked with immune infiltration and prognosis in prostate cancer: A bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36316896", "kind": "science-record", "revision": 3, "content_hash": "sha256:59b4fabf4b17946e10aae163435694284c5054ee5f3c2f26a829c40c36c8f11a", "created_at": "2026-11-01T18:15:44Z", "updated_at": "2026-11-01T21:29:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Aberrant gene expression pattern in the glycolysis-cholesterol synthesis axis is linked with immune infiltration and prognosis in prostate cancer: A bioinformatics analysis.", "doi": "10.1097/MD.0000000000031416", "pmid": "36316896", "authors": ["Yiwen Yuan", "Jukun Song", "Qinghua Wu"], "journal": "Medicine", "year": 2022, "abstract": "Aberrant lipid metabolism is an early event in tumorigenesis and has been found in a variety of tumor types, especially prostate cancer (PCa). Therefore, We hypothesize that PCa can be stratified into metabolic subgroups based on glycolytic and cholesterogenic related genes, and the different subgroups are closely related to the immune microenvironment. Bioinformatics analysis of genomic, transcriptomic, and clinical data from a comprehensive cohort of PCa patients was performed. Datasets included the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) dataset, GSE70768, our previously published PCa cohort. The unsupervised cluster analysis was employed to stratify PCa samples based on the expression of metabolic-related genes. Four molecular subtypes were identified, named Glycolytic, Cholesterogenic, Mixed, and Quiescent. Each metabolic subtype has specific features. Among the 4 subtypes, the cholesterogenic subtype exhibited better median survival, whereas patients with high expression of glycolytic genes showed the shortest survival. The mitochondrial pyruvate carriers (MPC) 1 exhibited expression difference between PCa metabolic subgroups, but not for MPCs 2. Glycolytic subtypes had lower immune cell scores, while Cholesterogenic subgroups had higher immune cell scores. Our results demonstrated that metabolic classifications based on specific glycolytic and cholesterol-producing pathways provide new biological insights into previously established subtypes and may guide develop personalized therapies for unique tumor metabolism characteristics.", "claims": [{"id": "claim-method", "statement": "The survival rate of 4 PCa subtypes was compared using the Kaplan–Meier curves and Log-rank tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36316896", "locator": "sections[6] \"2.4. Survival analysis\" paragraph 2", "quote": "The survival rate of 4 PCa subtypes was compared using the Kaplan–Meier curves and Log-rank tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36316896", "locator": "sections[27] \"(untitled)\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four molecular subtypes were identified, named Glycolytic, Cholesterogenic, Mixed, and Quiescent.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36316896", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Four molecular subtypes were identified, named Glycolytic, Cholesterogenic, Mixed, and Quiescent."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four molecular subtypes were identified, named Glycolytic, Cholesterogenic, Mixed, and Quiescent.", "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:36316896"], "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:GSE70768"], "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:GSE70768"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36316896", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000031416", "sha256": "sha256:1eb342f980b11102581585214fca5013a021a1200321145fb34cf3ffd0c5ed57", "bytes": 39966, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000031416", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9622640", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE70768", "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=GSE70768", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70768", "version": null, "note": "The datasets generated during and/or analyzed during the current study are publicly available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are publicly available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1817707", "GSM1817708", "GSM1817709", "GSM1817710", "GSM1817711", "GSM1817712", "GSM1817713", "GSM1817714", "GSM1817715", "GSM1817716", "GSM1817717", "GSM1817718", "GSM1817719", "GSM1817720", "GSM1817721", "GSM1817722", "GSM1817723", "GSM1817724", "GSM1817725", "GSM1817726", "GSM1817727", "GSM1817728", "GSM1817729", "GSM1817730", "GSM1817731", "GSM1817732", "GSM1817733", "GSM1817734", "GSM1817735", "GSM1817736", "GSM1817737", "GSM1817738", "GSM1817739", "GSM1817740", "GSM1817741", "GSM1817742", "GSM1817743", "GSM1817744", "GSM1817745", "GSM1817746", "GSM1817747", "GSM1817748", "GSM1817749", "GSM1817750", "GSM1817751", "GSM1817752", "GSM1817753", "GSM1817754", "GSM1817755", "GSM1817756", "GSM1817757", "GSM1817758", "GSM1817759", "GSM1817760", "GSM1817761", "GSM1817762", "GSM1817763", "GSM1817764", "GSM1817765", "GSM1817766", "GSM1817767", "GSM1817768", "GSM1817769", "GSM1817770", "GSM1817771", "GSM1817772", "GSM1817773", "GSM1817774", "GSM1817775", "GSM1817776", "GSM1817777", "GSM1817778", "GSM1817779", "GSM1817780", "GSM1817781", "GSM1817782", "GSM1817783", "GSM1817784", "GSM1817785", "GSM1817786", "GSM1817787", "GSM1817788", "GSM1817789", "GSM1817790", "GSM1817791", "GSM1817792", "GSM1817793", "GSM1817794", "GSM1817795", "GSM1817796", "GSM1817797", "GSM1817798", "GSM1817799", "GSM1817800", "GSM1817801", "GSM1817802", "GSM1817803", "GSM1817804", "GSM1817805", "GSM1817806", "GSM1817807", "GSM1817808", "GSM1817809", "GSM1817810", "GSM1817811", "GSM1817812", "GSM1817813", "GSM1817814", "GSM1817815", "GSM1817816", "GSM1817817", "GSM1817818", "GSM1817819", "GSM1817820", "GSM1817821", "GSM1817822", "GSM1817823", "GSM1817824", "GSM1817825", "GSM1817826", "GSM1817827", "GSM1817828", "GSM1817829", "GSM1817830", "GSM1817831", "GSM1817832", "GSM1817833", "GSM1817834", "GSM1817835", "GSM1817836", "GSM1817837", "GSM1817838", "GSM1817839", "GSM1817840", "GSM1817841", "GSM1817842", "GSM1817843", "GSM1817844", "GSM1817845", "GSM1817846", "GSM1817847", "GSM1817848", "GSM1817849", "GSM1817850", "GSM1817851", "GSM1817852", "GSM1817853", "GSM1817854", "GSM1817855", "GSM1817856", "GSM1817857", "GSM1817858", "GSM1817859", "GSM1817860", "GSM1817861", "GSM1817862", "GSM1817863", "GSM1817864", "GSM1817865", "GSM1817866", "GSM1817867", "GSM1817868", "GSM1817869", "GSM1817870", "GSM1817871", "GSM1817872", "GSM1817873", "GSM1817874", "GSM1817875", "GSM1817876", "GSM1817877", "GSM1817878", "GSM1817879", "GSM1817880", "GSM1817881", "GSM1817882", "GSM1817883", "GSM1817884", "GSM1817885", "GSM1817886", "GSM1817887", "GSM1817888", "GSM1817889", "GSM1817890", "GSM1817891", "GSM1817892", "GSM1817893", "GSM1817894", "GSM1817895", "GSM1817896", "GSM1817897", "GSM1817898", "GSM1817899", "GSM1817900", "GSM1817901", "GSM1817902", "GSM1817903", "GSM1817904", "GSM1817905"], "sample_count": 199, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Prostate cancer stratification using molecular profiles [CamCap ExpressionArray]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE70768 not downloaded", "asset:data:geo:GSE70768 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The survival rate of 4 PCa subtypes was compared using the Kaplan–Meier curves and Log-rank tests."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "PCA"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_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": ["GSE70768"], "resolved_accessions": ["GSE70768"], "statements": ["The datasets generated during and/or analyzed during the current study are publicly available."], "basis": "The paper names GSE70768 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": ["logrank_test"], "assets": ["source:pmid:36316896", "data:geo:GSE70768"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE70768"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:13:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11925, "completion_tokens": 1493, "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:36316896", "type": "paper", "label": "pmid:36316896"}, {"id": "source:pmid:36316896", "type": "manuscript", "label": "PMID 36316896 full text"}, {"id": "data:geo:GSE70768", "type": "dataset", "label": "GEO GSE70768"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36316896", "type": "paper", "label": "pmid:36316896"}, {"id": "source:pmid:36316896", "type": "manuscript", "label": "PMID 36316896 full text"}, {"id": "data:geo:GSE70768", "type": "dataset", "label": "GEO GSE70768"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36316896", "type": "extraction", "used": ["source:pmid:36316896"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE70768", "type": "accession_resolution", "used": ["data:geo:GSE70768"], "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:36316896", "parent_hash": "sha256:b54cf9c535ed25067ce71c092c62d53b502c8dae9d0690734125a9f8d5c69c40", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE70768 licence not read", "asset:data:geo:GSE70768 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The survival rate of 4 PCa subtypes was compared using the Kaplan–Meier curves and Log-rank tests."], "order_basis": "analysis_only", "id": "assay:1"}]}