Transcriptomic and functional analysis of ANGPTL4 overexpression in pancreatic cancer nominates targets that reverse chemoresistance.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36747689", "kind": "science-record", "revision": 4, "content_hash": "sha256:871ff60f33f820ce13e3e20a5bd51b0c9be94b981d0d297dd3c934b3f1582a3e", "created_at": "2026-11-01T19:01:19Z", "updated_at": "2026-11-01T22:51:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic and functional analysis of ANGPTL4 overexpression in pancreatic cancer nominates targets that reverse chemoresistance.", "doi": "10.21203/rs.3.rs-2444404/v1", "pmid": "36747689", "authors": ["Emily R Gordon", "Carter A Wright", "Mikayla James", "Sara J Cooper"], "journal": "Research square", "year": 2023, "abstract": "Background Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers based on five-year survival rates. Genes contributing to chemoresistance represent novel therapeutic targets that can improve treatment response. Increased expression of ANGPTL4 in tumors correlates with poor outcomes in pancreatic cancer. Methods We used statistical analysis of publicly available gene expression data (TCGA-PAAD) to test whether expression of ANGPTL4 and its downstream targets, ITGB 4 and APOL1 , were correlated with patient survival. We measured the impact of ANGPTL4 overexpression in a common pancreatic cancer cell line, MIA PaCa-2 cells, using CRISPRa for overexpression and DsiRNA for knockdown. We characterized global gene expression changes associated with high levels of ANGPTL4 and response to gemcitabine treatment using RNA-sequencing. Gemcitabine dose response curves were calculated on modified cell lines by measuring cell viability with CellTiter-Glo (Promega). Impacts on cell migration were measured using a time course scratch assay. Results We show that ANGPTL4 overexpression leads to in vitro resistance to gemcitabine and reduced survival times in patients. Overexpression of ANGPTL4 induces transcriptional signatures of tumor invasion and metastasis, proliferation and differentiation, and inhibition of apoptosis. Analyses revealed an overlapping signature of genes associated with both ANGPTL4 activation and gemcitabine response. Increased expression of the genes in this signature in patient PDAC tissues was significantly associated with shorter patient survival. We identified 42 genes that were both co-regulated with ANGPTL4 and were responsive to gemcitabine treatment. ITGB4 and APOL1 were among these genes. Knockdown of either of these genes in cell lines overexpressing ANGPTL4 reversed the observed gemcitabine resistance and inhibited cellular migration associated with epithelial to mesenchymal transition (EMT) and ANGPTL4 overexpression. Conclusions These data suggest that ANGPTL4 promotes EMT and regulates the genes APOL1 and ITGB4 . Importantly, we show that inhibition of both targets reverses chemoresistance and decreases migratory potential. Our findings have revealed a novel pathway regulating tumor response to treatment and suggest relevant therapeutic targets in pancreatic cancer.", "claims": [{"id": "claim-method", "statement": "We compared the patients with the lowest and highest quartile of average gene expression and performed survival analysis. Survival curves and analyses were generated using the “ggplot2”, “survminer”, and “survival” R packages. P values generated are log rank values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36747689", "locator": "sections[12] \"Overall Survival Analysis (OS)\" paragraph 2", "quote": "We compared the patients with the lowest and highest quartile of average gene expression and performed survival analysis. Survival curves and analyses were generated using the “ggplot2”, “survminer”, and “survival” R packages. P values generated are log rank values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data generated in this study are available in Gene Expression Omnibus (GEO) at GSE207359. Clinical data and RNA-sequencing data for TCGA-PAAD (PDAC) samples were retrieved on 04/01/2020 using the GDC Data Portal (https://portal.gdc.cancer.gov/projects/TCGA-PAAD). Our analyses included 178 samples in this cohort that had matched clinical and RNA sequencing data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36747689", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The RNA-seq data generated in this study are available in Gene Expression Omnibus (GEO) at GSE207359. Clinical data and RNA-sequencing data for TCGA-PAAD (PDAC) samples were retrieved on 04/01/2020 using the GDC Data Portal (https://portal.gdc.cancer.gov/projects/TCGA-PAAD). Our analyses included 178 samples in this cohort that had matched clinical and RNA sequencing data."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:36747689"], "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:GSE207359"], "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:GSE207359"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36747689", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21203/rs.3.rs-2444404/v1", "sha256": "sha256:d1f93c4e712673183a1cd0854128f8d7b83a77052db012e5ae2789aacd0eacee", "bytes": 37593, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21203/rs.3.rs-2444404/v1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9900996", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE207359", "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=GSE207359", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE207359", "version": null, "note": "The RNA-seq data generated in this study are available in Gene Expression Omnibus (GEO) at GSE207359. Clinical data and RNA-sequencing data for TCGA-PAAD (PDAC) samples were retrieved on 04/01/2020 using the GDC Data Portal (https://portal.gdc.cancer.gov/projects/TCGA-PAAD). Our analyses included 178 samples in this cohort that had matched clinical and RNA sequencing data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study are available in Gene Expression Omnibus (GEO) at GSE207359. Clinical data and RNA-sequencing data for TCGA-PAAD (PDAC) samples were retrieved on 04/01/2020 using the GDC Data Portal (https://portal.gdc.cancer.gov/projects/TCGA-PAAD). Our analyses included 178 samples in this cohort that had matched clinical and RNA sequencing data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6284923", "GSM6284924", "GSM6284925", "GSM6284926", "GSM6284927", "GSM6284928", "GSM6284929", "GSM6284930", "GSM6284931", "GSM6284932", "GSM6284933", "GSM6284934", "GSM6284935", "GSM6284936", "GSM6284937", "GSM6284938", "GSM6284939", "GSM6284940", "GSM6284941", "GSM6284942", "GSM6284943", "GSM6284944", "GSM6284945", "GSM6284946", "GSM6284947", "GSM6284948", "GSM6284949", "GSM6284950", "GSM6284951", "GSM6284952", "GSM6284953", "GSM6284954", "GSM6284955", "GSM6284956", "GSM6284957", "GSM6284958", "GSM6284959", "GSM6284960", "GSM6284961", "GSM6284962", "GSM6284963", "GSM6284964", "GSM6284965", "GSM6284966", "GSM6284967", "GSM6284968", "GSM6284969", "GSM6284970"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Transcriptomic and functional analysis of ANGPTL4 overexpression in pancreatic cancer nominates targets that reverse chemoresistance", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE207359 not downloaded", "asset:data:geo:GSE207359 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We compared the patients with the lowest and highest quartile of average gene expression and performed survival analysis. Survival curves and analyses were generated using the “ggplot2”, “survminer”, and “survival” R packages. P values generated are log rank values."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "log rank"}}, {"id": "method-3", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "DESeq2"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE207359"], "resolved_accessions": ["GSE207359"], "statements": ["The RNA-seq data generated in this study are available in Gene Expression Omnibus (GEO) at GSE207359. Clinical data and RNA-sequencing data for TCGA-PAAD (PDAC) samples were retrieved on 04/01/2020 using the GDC Data Portal (https://portal.gdc.cancer.gov/projects/TCGA-PAAD). Our analyses included 178 samples in this cohort that had matched clinical and RNA sequencing data."], "basis": "The paper names GSE207359 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": ["survival_km"], "assets": ["source:pmid:36747689", "data:geo:GSE207359"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE207359"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:26:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10896, "completion_tokens": 1721, "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:36747689", "type": "paper", "label": "pmid:36747689"}, {"id": "source:pmid:36747689", "type": "manuscript", "label": "PMID 36747689 full text"}, {"id": "data:geo:GSE207359", "type": "dataset", "label": "GEO GSE207359"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36747689", "type": "paper", "label": "pmid:36747689"}, {"id": "source:pmid:36747689", "type": "manuscript", "label": "PMID 36747689 full text"}, {"id": "data:geo:GSE207359", "type": "dataset", "label": "GEO GSE207359"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36747689", "type": "extraction", "used": ["source:pmid:36747689"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE207359", "type": "accession_resolution", "used": ["data:geo:GSE207359"], "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:36747689", "parent_hash": "sha256:7bdd3810b3ffa347e002f5f9cd511c9018f4d061e03b750e035dbe59d142c3c7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE207359 licence not read", "asset:data:geo:GSE207359 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": 0.99, "evidence": ["Transcriptomic and functional analysis of ANGPTL4 overexpre", "and response to gemcitabine treatment using RNA-sequencing. Gemcitabine dose response curves were calcu", "in R (version 3.6.1 and R version 4.1.2 for RNAseq analysis). The following R packages and soft"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["ng CRISPRa for overexpression and DsiRNA for knockdown. We characterized global gene expression cha", "ent. ITGB4 and APOL1 were among these genes. Knockdown of either of these genes in cell lines overe"], "order_basis": "paper_text_order:784", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ation and differentiation, and inhibition of apoptosis. Analyses revealed an overlapping signature", "cell lines by measuring cell viability with CellTiter-Glo (Promega). Impacts on cell migration wer"], "order_basis": "paper_text_order:1048", "id": "assay:3"}, {"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": ["% FBS, and 0.5% Penicillin-Streptomycin. All cell lines were maintained at 37°C and 5% CO2. Cells were cryopreserved", "-CRL-1420), and Panc-1 (ATCC #CRL-1469) were cultured in D10 media: DMEM (Lonza #12-614Q) supplemente"], "order_basis": "paper_text_order:2563", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We compared the patients with the lowest and highest quartile of average gene expression and performed survival analysis. Survival curves and analyses were generated using the “ggplot2”, “survminer”, and “survival” R packages. P values generated are log rank values."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}