One-Week Dynamic Changes in Cardiac Proteomes After Cardiac Radioablation in Experimental Rat Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35837601", "kind": "science-record", "revision": 4, "content_hash": "sha256:647d09d5439979258f1f19ae7db965e4af400ff0241e6502bd9670da94c6002e", "created_at": "2026-11-01T18:14:54Z", "updated_at": "2026-11-01T22:07:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "One-Week Dynamic Changes in Cardiac Proteomes After Cardiac Radioablation in Experimental Rat Model.", "doi": "10.3389/fcvm.2022.898222", "pmid": "35837601", "authors": ["Byoung Hyuck Kim", "Jin Woo Jung", "Dohyun Han", "Myung-Jin Cha", "Ji Hyun Chang"], "journal": "Frontiers in cardiovascular medicine", "year": 2022, "abstract": "Background: Recently, stereotactic ablative radiotherapy (SABR) has been adopted to non-invasively treat catheter ablation-refractory ventricular tachycardia (VT). VT episodes have been dramatically reduced after SABR, within weeks; however the underlying mechanisms of these clinical effects and potential mediators of early anti-arrhythmic effect remain unclear.\nMethods: In this study, cardiac tissue was harvested from non-irradiated control (0 Gy), conventional irradiated control (2 Gy), and radioablative test (25 Gy) rat groups after 3 and 7 days of irradiation. The samples were proteomically analyzed to identify the differentially expressed proteins (DEP) between different groups. Validation experiments were performed similar to validation in profiling where Data independent acquisition and parallel reaction monitoring methods were used. Data are available via ProteomeXchange with identifier PXD030878.\nResults: Functional enrichment analysis of 25 Gy sample showed that among the downregulated proteins, \"intracellular signal transduction\" and \"cell to cell adhesion\" proteins were significantly affected at day 3 while \"Ras protein signal transduction,\" \"GTPase regulation,\" and \"actin filament-based process\" proteins were majorly affected at day 7. GO analysis demonstrated that most of the upregulated proteins belonged to the classes \"cellular stress response,\" \"endomembranal organization,\" or \"endoplasmic reticulum stress response\" at day 3. At day 7, 42 proteins, mainly associated with response to drug, organic substance, or radiation, were specifically upregulated in 25 Gy. DEP analysis of cardiac conduction showed Ryr2 and Cav1 upregulation and Cacna2d2, Gja3, Scnb2, and Kcnn3 downregulation in the 25 Gy group compared to 0 Gy. In validation experiments, four proteins (Gsta1, Myot, Ephx1, and Capg) were repeatedly detected with 25 Gy-specific patterns at day 7.\nConclusions: 25 Gy single fractional irradiation induces considerable cardiac proteome changes within the first 7 days, distinct from 2 Gy. Several candidate proteins displayed 25 Gy-specific changes and were related to oxidative stress-induced innate response or cardiac remodeling processes. Future studies should explore the specific role of these proteins upon cardiac radioablation.", "claims": [{"id": "claim-method", "statement": "After normalization, we performed multiple sample test; the ANOVA test and student t-test for protein expression changes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35837601", "locator": "sections[10] \"Statistical Analyses\" paragraph 2", "quote": "After normalization, we performed multiple sample test; the ANOVA test and student t-test for protein expression changes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ebi.ac.uk/pride/archive/, PXD030878", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35837601", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ebi.ac.uk/pride/archive/, PXD030878"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Pairwise t-tests identified 200 differentially expressed proteins in the 25 Gy group at day 3 and 166 at day 7.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35837601", "locator": "sections[15] \"Pairwise Dose Group Comparison by t-Test\" paragraph 2", "quote": "At day 3, 200 proteins were differentially expressed after 25 Gy, of which 169 did not overlap with DEPs in control vs. 2 Gy (Figure 4C)."}, {"asset": "source:pmid:35837601", "locator": "sections[15] \"Pairwise Dose Group Comparison by t-Test\" paragraph 2", "quote": "At day 7, 166 proteins were differentially expressed after 25 Gy, of which 133 did not overlap with changes after 2 Gy (Figure 4D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Pairwise t-tests identified 200 differentially expressed proteins in the 25 Gy group at day 3 and 166 at day 7.", "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:35837601"], "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:PXD030878"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD030878"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35837601", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2022.898222", "sha256": "sha256:334602f6838c6f04ea723e3b05d559f3175e71b7784e1fe2969c6e87b997fdb2", "bytes": 53753, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2022.898222", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9273889", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030878", "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=PXD030878", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030878", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ebi.ac.uk/pride/archive/, PXD030878", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ebi.ac.uk/pride/archive/, PXD030878", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "In-depth quantitative proteomic analysis of rat cardiac tissue for exploring potential mediators of early cardiac reaioablation effect", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD030878 not downloaded", "asset:data:geo:PXD030878 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After normalization, we performed multiple sample test; the ANOVA test and student t-test for protein expression changes."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "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"}}, {"id": "method-4", "family": "clustering", "specific": "kmeans", "label": "Clustering", "dsl_operations": ["kmeans_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "K-means"}}, {"id": "method-5", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Hierarchical Clustering"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_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": ["PXD030878"], "resolved_accessions": ["PXD030878"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ebi.ac.uk/pride/archive/, PXD030878"], "basis": "The paper names PXD030878 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35837601", "data:geo:PXD030878"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD030878"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:55:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14685, "completion_tokens": 1131, "cached_tokens": 128}}, "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:35837601", "type": "paper", "label": "pmid:35837601"}, {"id": "source:pmid:35837601", "type": "manuscript", "label": "PMID 35837601 full text"}, {"id": "data:geo:PXD030878", "type": "dataset", "label": "GEO PXD030878"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35837601", "type": "paper", "label": "pmid:35837601"}, {"id": "source:pmid:35837601", "type": "manuscript", "label": "PMID 35837601 full text"}, {"id": "data:geo:PXD030878", "type": "dataset", "label": "GEO PXD030878"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35837601", "type": "extraction", "used": ["source:pmid:35837601"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD030878", "type": "accession_resolution", "used": ["data:geo:PXD030878"], "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:35837601", "parent_hash": "sha256:afe1f6493c98c704a4701e22713e0cc22eaf0aea814deacaf5fa2cbe76104271", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD030878 licence not read", "asset:data:geo:PXD030878 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"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": ["After Cardiac Radioablation in Experimental Rat Model.", "ntrol (2 Gy), and radioablative test (25 Gy) rat groups after 3 and 7 days of irradiation. Th", "ts aged 9–10 weeks were used for this study. Rats were housed at room temperature under a 12-h ligh", "ACUC No. 18-0245-S1A0). Male wild type Lewis rats aged 9–10 weeks were used for this study. Ra"], "order_basis": "paper_text_order:46", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["4Detailed dose group comparison scheme after LC-MS/MS analysis. The differentially expressed prote", "1Overall experimental scheme of quantitative proteomic analysis.Click here for additional data file"], "order_basis": "paper_text_order:9006", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After normalization, we performed multiple sample test; the ANOVA test and student t-test for protein expression changes."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}