Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33789676", "kind": "science-record", "revision": 8, "content_hash": "sha256:fe3684c6583e2627435ac5cf10b0a7a49996e3e6ea58dfcd18cc4d9d9b2f71f9", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:46:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing.", "doi": "10.1186/s12935-021-01881-4", "pmid": "33789676", "authors": ["Wei Zheng", "Wangzhong Ye", "Zijie Wu", "Xinyi Huang", "Yuanji Xu", "Qinyan Chen", "Zhizhong Lin", "Yanyu Chen", "Penggang Bai", "Chuanben Chen"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: Early diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging. Therefore, we explored the pathogenetic roles and associated mechanisms of exosomes in plasma of patients with early-stage NPC.\nMETHODS: Exosomes in plasma were extracted by ultra-high-speed centrifugation. Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples.\nRESULTS: Western blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes.\nCONCLUSIONS: We identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.", "claims": [{"id": "claim-method", "statement": "The DESeq2 R package (1.26.0) was used to identify the DEmiRNAs between NPC and normal group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33789676", "locator": "sections[8] \"DEmiRNA\" paragraph 2", "quote": "The DESeq2 R package (1.26.0) was used to identify the DEmiRNAs between NPC and normal group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated (GSE163867) and/or analyzed during the current study are available in the [GEO] repository, [http://www.ncbi.nlm.nih.gov/geo] [49]. Reference Other datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33789676", "locator": "sections[32] \"notes\" paragraph 1", "quote": "The datasets generated (GSE163867) and/or analyzed during the current study are available in the [GEO] repository, [http://www.ncbi.nlm.nih.gov/geo] [49]. Reference Other datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33789676"], "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:GSE118720"], "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:GSE118720"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33789676", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-01881-4", "sha256": "sha256:cc71c7a99a2a2bea91f8daed1d4dfd5f9b7836b7a9778d9f5a1bec4e1b31c743", "bytes": 37778, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-01881-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8011216", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE118720", "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=GSE118720", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118720", "version": null, "note": "The datasets generated (GSE163867) and/or analyzed during the current study are available in the [GEO] repository, [http://www.ncbi.nlm.nih.gov/geo] [49]. 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Reference Other datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3336949", "GSM3336950", "GSM3336951", "GSM3336952", "GSM3336953", "GSM3336954", "GSM3336955", "GSM3336956", "GSM3336957", "GSM3336958", "GSM3336959"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "miRNA-Seq profiling of nasopharyngeal carcinoma (NPC) and normal control samples", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE12452", "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=GSE12452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12452", "version": null, "note": "The datasets generated (GSE163867) and/or analyzed during the current study are available in the [GEO] repository, [http://www.ncbi.nlm.nih.gov/geo] [49]. 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