Overexpressed PRAME is a potential immunotherapy target in sarcoma subtypes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28630682", "kind": "science-record", "revision": 6, "content_hash": "sha256:e03953fafc7b0de49a33cff61962c95d9053f93eb78c2c6d6e87b36f7fd624b4", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Overexpressed PRAME is a potential immunotherapy target in sarcoma subtypes.", "doi": "10.1186/s13569-017-0077-3", "pmid": "28630682", "authors": ["Jason Roszik", "Wei-Lien Wang", "John A Livingston", "Christina L Roland", "Vinod Ravi", "Cassian Yee", "Patrick Hwu", "Andrew Futreal", "Alexander J Lazar", "Shreyaskumar R Patel", "Anthony P Conley"], "journal": "Clinical sarcoma research", "year": 2017, "abstract": "BACKGROUND: PRAME (preferentially expressed antigen in melanoma), a member of the cancer-testis antigen family, has been shown to have increased expression in solid tumors, including sarcoma, and PRAME-specific therapies are currently in development for other cancers such as melanoma.\nMETHODS: To map the landscape of PRAME expression in sarcoma, we used publicly available data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) projects and determined which sarcoma subtypes and subsets are associated with increased PRAME expression. We also analyzed how PRAME expression correlates with survival and expression of markers related to antigen presentation and T cell function. Furthermore, tumor and normal tissue expression comparisons were performed using data from the genotype-tissue expression (GTEx) project.\nRESULTS: We found that uterine carcinosarcoma highly overexpresses the PRAME antigen, and synovial sarcomas and multifocal leiomyosarcomas also show high expressions suggesting that PRAME may be an effective target of immunotherapies of these tumors. However, we also discovered that PRAME expression negatively correlates with genes involved in antigen presentation, and in synovial sarcoma MHC class I antigen presentation deficiencies are also present, potentially limiting the efficacy of immunotherapies of this malignancy.\nCONCLUSIONS: We determined that uterine carcinosarcoma, synovial sarcoma, and leiomyosarcoma patients would potentially benefit from PRAME-specific immunotherapies. Tumor escape through loss of antigen presentation needs to be further studied.", "claims": [{"id": "claim-method", "statement": "For comparisons of two groups we performed two-tailed Student’s t-tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28630682", "locator": "sections[5] \"Statistical analyses\" paragraph 2", "quote": "For comparisons of two groups we performed two-tailed Student’s t-tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We used publicly available data as described in the “Methods”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28630682", "locator": "sections[14] \"ack\" paragraph 1", "quote": "We used publicly available data as described in the “Methods”."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Headline result: uterine carcinosarcoma highly overexpressed PRAME, while synovial sarcoma and multifocal leiomyosarcoma also showed high PRAME expression, suggesting potential benefit from PRAME-specific immunotherapies. The paper analyzed publicly available TCGA and CCLE data and examined PRAME associations with survival and antigen-presentation/T-cell markers; the listed sections do not specify the statistical test used.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28630682", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We found that uterine carcinosarcoma highly overexpresses the PRAME antigen, and synovial sarcomas and multifocal leiomyosarcomas also show high expressions suggesting that PRAME may be an effective target of immunotherapies of these tumors."}, {"asset": "source:pmid:28630682", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "To map the landscape of PRAME expression in sarcoma, we used publicly available data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) projects and determined which sarcoma subtypes and subsets are associated with increased PRAME expression."}, {"asset": "source:pmid:28630682", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We also analyzed how PRAME expression correlates with survival and expression of markers related to antigen presentation and T cell function."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Headline result: uterine carcinosarcoma highly overexpressed PRAME, while synovial sarcoma and multifocal leiomyosarcoma also showed high PRAME expression, suggesting potential benefit from PRAME-specific immunotherapies. The paper analyzed publicly available TCGA and CCLE data and examined PRAME associations with survival and antigen-presentation/T-cell markers; the listed sections do not specify the statistical test used.", "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:28630682"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28630682", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13569-017-0077-3", "sha256": "sha256:0231c1c4c23d464686cedc8994bb5f19abee7753987849767b408cae94d53dec", "bytes": 17392, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13569-017-0077-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5471883", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Two-tailed Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For comparisons of two groups we performed two-tailed Student’s t-tests."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Two-tailed Student’s t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["We used publicly available data as described in the “Methods”."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28630682"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:38Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 36607, "completion_tokens": 5519, "cached_tokens": 1824}}, "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:28630682", "type": "paper", "label": "pmid:28630682"}, {"id": "source:pmid:28630682", "type": "manuscript", "label": "PMID 28630682 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28630682", "type": "paper", "label": "pmid:28630682"}, {"id": "source:pmid:28630682", "type": "manuscript", "label": "PMID 28630682 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28630682", "type": "extraction", "used": ["source:pmid:28630682"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:28630682", "parent_hash": "sha256:b347995f461268bcd4c58303abe864c222c854c5a15ebf72b4823697ec69612c", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["ses were performed using microarray and also RNA-sequencing data. The TPM unit was used for RNA-seq, and", "A-sequencing data. The TPM unit was used for RNA-seq, and in the case of microarray we used RMA-n", "e available. When comparing expressions from RNA sequencing from the TCGA and GTEx databases, we used th", "found to be most suitable unit for comparing RNA sequencing data [13]. For the analysis of PRAME express"], "order_basis": "paper_text_order:1920", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["CLE expression analyses were performed using microarray and also RNA-sequencing data. The TPM unit w", "nit was used for RNA-seq, and in the case of microarray we used RMA-normalized data, which is calcul"], "order_basis": "paper_text_order:2410", "id": "assay:2"}]}