Exosomal transcript cargo and functional correlation with HNSCC patients' survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39272022", "kind": "science-record", "revision": 4, "content_hash": "sha256:f22b72195f8cb570264144342c1be103e13a5fc7151c4a56bf986a9252dc13a6", "created_at": "2026-11-01T20:29:26Z", "updated_at": "2026-11-01T22:55:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exosomal transcript cargo and functional correlation with HNSCC patients' survival.", "doi": "10.1186/s12885-024-12759-9", "pmid": "39272022", "authors": ["Joni Yadav", "Apoorva Chaudhary", "Tanya Tripathi", "Divya Janjua", "Udit Joshi", "Nikita Aggarwal", "Arun Chhokar", "Chetkar Chandra Keshavam", "Anna Senrung", "Alok Chandra Bharti"], "journal": "BMC cancer", "year": 2024, "abstract": "BACKGROUND: HPV status in a subset of HNSCC is linked with distinct treatment outcomes. Present investigation aims to elucidate the distinct clinicopathological features of HPV-positive and HPV-negative HNSCC and investigate their association with the HNSCC patient survival.\nMATERIALS AND METHODS: The total RNA of exosomes from HPV-positive (93VU147T) and HPV-negative (OCT-1) HNSCC cells was isolated, and the transcripts were estimated using Illumina HiSeq X. The expression of altered transcripts and their clinical relevance were further analyzed using publicly available cancer transcriptome data from The Cancer Genome Atlas (TCGA).\nRESULTS: Transcriptomic analyses identified 3785 differentially exported transcripts (DETs) in HPV-positive exosomes compared to HPV-negative exosomes. DETs that regulate the protein machinery, cellular redox potential, and various neurological disorder-related pathways were over-represented in HPV-positive exosomes. TCGA database revealed the clinical relevance of altered transcripts. Among commonly exported abundant transcripts, SGK1 and MAD1L1 showed high expression, which has been correlated with poor survival in HNSCC patients. In the top 20 DETs of HPV-negative exosomes, high expression of FADS3, SGK3, and TESK2 correlated with poor survival of the HNSCC patients in the TCGA database.\nCONCLUSION: Overall, our study demonstrates that HPV-positive and HPV-negative cells' exosomes carried differential transcripts cargo that may be related to pathways associated with neurological disorders. Additionally, the altered transcripts identified have clinical relevance, correlating with patient survival in HNSCC, thereby highlighting their potential as biomarkers and as therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Differential analysis was conducted using DESeq2 [34].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39272022", "locator": "sections[17] \"Differential transcript abundance analysis\" paragraph 2", "quote": "Differential analysis was conducted using DESeq2 [34]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets used and or/analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39272022", "locator": "sections[40] \"notes\" paragraph 1", "quote": "The data sets used and or/analyzed during the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Transcriptomic analyses identified 3785 differentially exported transcripts (DETs) in HPV-positive exosomes compared to HPV-negative exosomes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39272022", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Transcriptomic analyses identified 3785 differentially exported transcripts (DETs) in HPV-positive exosomes compared to HPV-negative exosomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Transcriptomic analyses identified 3785 differentially exported transcripts (DETs) in HPV-positive exosomes compared to HPV-negative exosomes.", "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:39272022"], "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. 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