Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36451813", "kind": "science-record", "revision": 4, "content_hash": "sha256:539ef39c5318257e96de3f45edb272cbda28ec08206d7db2b091196510d20e54", "created_at": "2026-11-01T19:00:55Z", "updated_at": "2026-11-01T22:50:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma.", "doi": "10.3389/fimmu.2022.1038927", "pmid": "36451813", "authors": ["Cong Liu", "Dingwei Liu", "Fangfei Wang", "Yang Liu", "Jun Xie", "Jinliang Xie", "Yong Xie"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Background: Colon adenocarcinoma (COAD) is a common digestive system malignancy with high mortality and poor prognosis. Accumulating evidence indicates that choline metabolism is closely related to tumorigenesis and development. However, the efficacy of choline metabolism-related signature in predicting patient prognosis, immune microenvironment and chemotherapy response has not been fully clarified.\nMethods: Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. Two choline metabolism-related genes (CHKB and PEMT) were identified by univariate and multivariate Cox regression analyses. TCGA-COAD was the training cohort, and GSE17536 was the validation cohort. Patients in the high- and low-risk groups were distinguished according to the optimal cutoff value of the risk score. A nomogram was used to assess the prognostic accuracy of the choline metabolism-related signature. Calibration curves, decision curve analysis (DCA), and clinical impact curve (CIC) were used to improve the clinical applicability of the prognostic signature. Gene Ontology (GO) and KEGG pathway enrichment analyses of DEGs in the high- and low-risk groups were performed. KEGG cluster analysis was conducted by the KOBAS-i database. The distribution and expression of CHKB and PEMT in various types of immune cells were analyzed based on single-cell RNA sequencing (scRNA-seq). The CIBERSORT and ESTIMATE algorithms evaluated tumor immune cell infiltration in the high- and low-risk groups. Evaluation of the half maximal inhibitory concentration (IC50) of common chemotherapeutic drugs based on the choline metabolism-related signature was performed. Small molecule compounds were predicted using the Connectivity Map (CMap) database. Molecular docking is used to simulate the binding conformation of small molecule compounds and key targets. By immunohistochemistry (IHC), Western blot, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) experiments, the expression levels of CHKB and PEMT in human, mouse, and cell lines were detected.\nResults: We constructed and validated a choline metabolism-related signature containing two genes (CHKB and PEMT). The overall survival (OS) of patients in the high-risk group was significantly worse than that of patients in the low-risk group. The nomogram could effectively and accurately predict the OS of COAD patients at 1, 3, and 5 years. The DCA curve and CIC demonstrate the clinical utility of the nomogram. scRNA-seq showed that CHKB was mainly distributed in endothelial cells, while PEMT was mainly distributed in CD4+ T cells and CD8+ T cells. In addition, multiple types of immune cells expressing CHKB and PEMT differed significantly. There were significant differences in the immune microenvironment, immune checkpoint expression and chemotherapy response between the two risk groups. In addition, we screened five potential small molecule drugs that targeted treatment for COAD. Finally, the results of IHC, Western blot, and qRT-PCR consistently showed that the expression of CHKB in human, mouse, and cell lines was elevated in normal samples, while PMET showed the opposite trend.\nConclusion: In conclusion, we constructed a choline metabolism-related signature in COAD and revealed its potential application value in predicting the prognosis, immune microenvironment, and chemotherapy response of patients, which may lay an important theoretical basis for future personalized precision therapy.", "claims": [{"id": "claim-method", "statement": "Two choline metabolism-related genes (CHKB and PEMT) were identified by univariate and multivariate Cox regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36451813", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Two choline metabolism-related genes (CHKB and PEMT) were identified by univariate and multivariate Cox regression analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36451813", "locator": "sections[33] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The prognostic nomogram achieved AUC values of 0.766, 0.78, and 0.724 for predicting 1-, 3-, and 5-year overall survival, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36451813", "locator": "sections[23] \"Development of a prognostic nomogram\" paragraph 2", "quote": "Our results showed that compared with other clinical features, the nomogram for predicting OS at 1, 3, and 5 years had the highest AUC values of 0.766, 0.78, and 0.724, respectively ( Figure 6D )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The prognostic nomogram achieved AUC values of 0.766, 0.78, and 0.724 for predicting 1-, 3-, and 5-year overall survival, respectively.", "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:36451813"], "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:GSE17536"], "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:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36451813", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1038927", "sha256": "sha256:0296bb90f80be122470082b5ce3c5dab5090948369415bb3179b50acae7b1493", "bytes": 78566, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1038927", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9701742", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . 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The CIBERSORT and ESTIMATE algo", "nalyzed based on single-cell RNA sequencing (scRNA-seq). The CIBERSORT and ESTIMATE algorithms eval", "strate the clinical utility of the nomogram. scRNA-seq showed that CHKB was mainly distributed in e"], "order_basis": "paper_text_order:1626", "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": 0.93, "evidence": ["une cells were analyzed based on single-cell RNA sequencing (scRNA-seq). The CIBERSORT and ESTIMATE algo"], "order_basis": "paper_text_order:1638", "id": "assay:2"}, {"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": ["small molecule compounds and key targets. By immunohistochemistry (IHC), Western blot, quantitative reverse tr", "ds and key targets. By immunohistochemistry (IHC), Western blot, quantitative reverse transcr", "treatment for COAD. Finally, the results of IHC, Western blot, and qRT-PCR consistently show", "n paraffin, and sliced at 4μm for subsequent IHC experiment. The study protocol and all proce"], "order_basis": "paper_text_order:2135", "id": "assay:3"}, {"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": ["key targets. By immunohistochemistry (IHC), Western blot, quantitative reverse transcription-polymera", "tment for COAD. Finally, the results of IHC, Western blot, and qRT-PCR consistently showed that the ex"], "order_basis": "paper_text_order:2164", "id": "assay:4"}, {"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": ["expression levels of CHKB and PEMT in human, mouse, and cell lines were detected. Results: We c", "showed that the expression of CHKB in human, mouse, and cell lines was elevated in normal sampl", "welve eight-weeks-old wild-type male C57BL/6 mice were purchased from the Department of Laboratory", "atory Animal Science of Nanchang University. Mice were reared in an environment with alternating da"], "order_basis": "paper_text_order:2310", "id": "assay:5"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e Science&Technology Co.,Ltd., WuHan). Other cell lines were cultured in RPIM-1640 medium (Gibco, USA) containing", "logy Co.,Ltd., WuHan). Other cell lines were cultured in RPIM-1640 medium (Gibco, USA) containing 10%", "ining 10% fetal bovine serum. All cells were cultured in an CO2 incubator (Thermo Fisher Scientific)", "ype Culture Collection, Shanghai. Caco-2 was cultured by Special medium for Caco-2 cells (Procell"], "order_basis": "paper_text_order:4767", "id": "assay:6"}, {"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": ["Two choline metabolism-related genes (CHKB and PEMT) were identified by univariate and multivariate Cox regression analyses."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}