A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36275722", "kind": "science-record", "revision": 3, "content_hash": "sha256:31e4e100ace5243f2999731f2e19a418cb614db59dbf07998a78579a490a4a9d", "created_at": "2026-11-01T18:15:40Z", "updated_at": "2026-11-01T21:29:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis.", "doi": "10.3389/fimmu.2022.1022420", "pmid": "36275722", "authors": ["Liang Chen", "Xueming Zhang", "Qixiang Zhang", "Tao Zhang", "Jiaheng Xie", "Wei Wei", "Ying Wang", "Hongzhu Yu", "Hongkun Zhou"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Background: As a tumor type with high mortality and poor therapeutic effect, the pathogenesis of pancreatic cancer is still unclear. It is necessary to explore the significance of necroptosis in pancreatic cancer.\nMethods: Pancreatic cancer transcriptome data were obtained from the TCGA database, ICGC database, and GSE85916 in the GEO database. The TCGA cohort was set as a training cohort, while the ICGC and GSE85916 cohort were set as the validation cohorts. Single-cell sequencing data of pancreatic cancer were obtained from GSE154778 in the GEO database. The genes most associated with necroptosis were identified by weighted co-expression network analysis and single-cell sequencing analysis. COX regression and Lasso regression were performed for these genes, and the prognostic model was established. By calculating risk scores, pancreatic cancer patients could be divided into NCPTS_high and NCPTS_low groups, and survival analysis, immune infiltration analysis, and mutation analysis between groups were performed. Cell experiments including gene knockdown, CCK-8 assay, clone formation assay, transwell assay and wound healing assay were conducted to explore the role of the key gene EPS8 in pancreatic cancer. PCR assays on clinical samples were further used to verify EPS8 expression.\nResults: We constructed the necroptosis-related signature in pancreatic cancer using single-cell sequencing analysis and transcriptome analysis. The calculation formula of risk score was as follows: NCPTS = POLR3GL * (-0.404) + COL17A1 * (0.092) + DDIT4 * (0.007) + PDE4C * (0.057) + CLDN1 * 0.075 + HMGA2 * 0.056 + CENPF * 0.198 +EPS8 * 0.219. Through this signature, pancreatic cancer patients with different cohorts can be divided into NCPTS_high and NCPTS_low group, and the NCPTS_high group has a significantly poorer prognosis. Moreover, there were significant differences in immune infiltration level and mutation level between the two groups. Cell assays showed that in CAPAN-1 and PANC-1 cell lines, EPS8 knockdown significantly reduced the viability, clonogenesis, migration and invasion of pancreatic cancer cells. Clinical PCR assay of EPS8 expression showed that EPS8 expression was significantly up-regulated in pancreatic cancer (*P<0.05).\nConclusion: Our study can provide a reference for the diagnosis, treatment and prognosis assessment of pancreatic cancer.", "claims": [{"id": "claim-method", "statement": "Univariate COX analysis was first performed to identify necroptosis genes associated with prognosis (P <0.05). Subsequently, LASSO regression and tenfold cross-validation were used to further identify the key genes affecting patient outcomes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36275722", "locator": "sections[8] \"Construction and evaluation of the prognostic model\" paragraph 2", "quote": "Univariate COX analysis was first performed to identify necroptosis genes associated with prognosis (P <0.05). Subsequently, LASSO regression and tenfold cross-validation were used to further identify the key genes affecting patient outcomes."}], "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 authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36275722", "locator": "sections[29] \"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 authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The eight-gene necroptosis-related prognostic signature separated pancreatic cancer patients into NCPTS_high and NCPTS_low groups, with significantly poorer prognosis in the NCPTS_high group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36275722", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Through this signature, pancreatic cancer patients with different cohorts can be divided into NCPTS_high and NCPTS_low group, and the NCPTS_high group has a significantly poorer prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The eight-gene necroptosis-related prognostic signature separated pancreatic cancer patients into NCPTS_high and NCPTS_low groups, with significantly poorer prognosis in the NCPTS_high group.", "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:36275722"], "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:GSE154778"], "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:GSE154778"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36275722", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.1022420", "sha256": "sha256:2f3814ecae6b5e7fae997db6f41e7882c8013df6c421ee6d6f10b066c03aac2c", "bytes": 41068, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.1022420", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9585241", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE154778", "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=GSE154778", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE154778", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "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. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4679532", "GSM4679533", "GSM4679534", "GSM4679535", "GSM4679536", "GSM4679537", "GSM4679538", "GSM4679539", "GSM4679540", "GSM4679541", "GSM4679542", "GSM4679543", "GSM4679544", "GSM4679545", "GSM4679546", "GSM4679547"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues", "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:GSE85916", "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=GSE85916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE85916", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.", "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. Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2287304", "GSM2287305", "GSM2287306", "GSM2287307", "GSM2287308", "GSM2287309", "GSM2287310", "GSM2287311", "GSM2287312", "GSM2287313", "GSM2287314", "GSM2287315", "GSM2287316", "GSM2287317", "GSM2287318", "GSM2287319", "GSM2287320", "GSM2287321", "GSM2287322", "GSM2287323", "GSM2287324", "GSM2287325", "GSM2287326", "GSM2287327", "GSM2287328", "GSM2287329", "GSM2287330", "GSM2287331", "GSM2287332", "GSM2287333", "GSM2287334", "GSM2287335", "GSM2287336", "GSM2287337", "GSM2287338", "GSM2287339", "GSM2287340", "GSM2287341", "GSM2287342", "GSM2287343", "GSM2287344", "GSM2287345", "GSM2287346", "GSM2287347", "GSM2287348", "GSM2287349", "GSM2287350", "GSM2287351", "GSM2287352", "GSM2287353", "GSM2287354", "GSM2287355", "GSM2287356", "GSM2287357", "GSM2287358", "GSM2287359", "GSM2287360", "GSM2287361", "GSM2287362", "GSM2287363", "GSM2287364", "GSM2287365", "GSM2287366", "GSM2287367", "GSM2287368", "GSM2287369", "GSM2287370", "GSM2287371", "GSM2287372", "GSM2287373", "GSM2287374", "GSM2287375", "GSM2287376", "GSM2287377", "GSM2287378", "GSM2287379", "GSM2287380", "GSM2287381", "GSM2287382", "GSM2287383"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Patients with human resected pancreatic cancer", "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:GSE154778 not downloaded", "asset:data:geo:GSE154778 licence not read", "asset:data:geo:GSE85916 not downloaded", "asset:data:geo:GSE85916 licence not read"]}, "analysis": {"state": "partial", "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": 0.7, "band": "medium", "quote": "COX regression"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-3", "family": null, "specific": null, "label": "Univariate Cox analysis followed by LASSO regression with tenfold cross-validation", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Univariate COX analysis was first performed to identify necroptosis genes associated with prognosis (P <0.05). Subsequently, LASSO regression and tenfold cross-validation were used to further identify the key genes affecting patient outcomes."}}], "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": ["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": ["GSE85916", "GSE154778"], "resolved_accessions": ["GSE85916", "GSE154778"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE85916, GSE154778 in 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:36275722", "data:geo:GSE154778"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE154778"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:12:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11605, "completion_tokens": 1382, "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:36275722", "type": "paper", "label": "pmid:36275722"}, {"id": "source:pmid:36275722", "type": "manuscript", "label": "PMID 36275722 full text"}, {"id": "data:geo:GSE154778", "type": "dataset", "label": "GEO GSE154778"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36275722", "type": "paper", "label": "pmid:36275722"}, {"id": "source:pmid:36275722", "type": "manuscript", "label": "PMID 36275722 full text"}, {"id": "data:geo:GSE154778", "type": "dataset", "label": "GEO GSE154778"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36275722", "type": "extraction", "used": ["source:pmid:36275722"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE154778", "type": "accession_resolution", "used": ["data:geo:GSE154778"], "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:36275722", "parent_hash": "sha256:e1fe7a6472530ffc5865fcada823b63c73a15a6a2f9de5004ddf554656e275d9", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE154778 licence not read", "asset:data:geo:GSE154778 not downloaded", "asset:data:geo:GSE85916 licence not read", "asset:data:geo:GSE85916 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e performed. Cell experiments including gene knockdown, CCK-8 assay, clone formation assay, transwe", "that in CAPAN-1 and PANC-1 cell lines, EPS8 knockdown significantly reduced the viability, clonoge"], "order_basis": "paper_text_order:1144", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": [". Cell experiments including gene knockdown, CCK-8 assay, clone formation assay, transwell assa"], "order_basis": "paper_text_order:1155", "id": "assay:2"}, {"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": 0.7, "evidence": ["COX regression"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}