Low TYROBP expression predicts poor prognosis in multiple myeloma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38549127", "kind": "science-record", "revision": 3, "content_hash": "sha256:138807c55d1211f153da7db0a8ddf4a16854b6eed497ebd4a07f6e338bcc300f", "created_at": "2026-11-01T19:20:30Z", "updated_at": "2026-11-01T22:11:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Low TYROBP expression predicts poor prognosis in multiple myeloma.", "doi": "10.1186/s12935-024-03304-6", "pmid": "38549127", "authors": ["Hong Luo", "Chengyun Pan", "Li Wang", "Lin Zheng", "Shuyun Cao", "Xiuying Hu", "Tianzhen Hu", "Naiqin Zhao", "Qin Shang", "Jishi Wang"], "journal": "Cancer cell international", "year": 2024, "abstract": "BACKGROUND: Multiple myeloma (MM) is the second most common refractory hematologic cancer. Searching for new targets and prognostic markers for MM is significant.\nMETHODS: GSE39754, GSE6477 and GSE24080 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in MM versus healthy people from GSE39754 and GSE6477 were screened using limma package, and MM-related module genes were chosen with the use of Weighted gene co-expression network analysis (WGCNA), and the two were intersected using ggVennDiagram for obtaining MM-related DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. Then, protein-protein interactions (PPI) analysis in String database was used to obtain hub genes, while prognosis was analyzed by survival package in GSE24080. Receiver operating characteristic (ROC) curve was adopted for evaluating diagnostic value of hub genes. Besides, univariable/multivariable Cox regression were employed to screen independent prognostic biomarkers. Gene set enrichment analysis (GSEA) was used to find possible mechanism. Finally, western-blotting and reverse transcription-polymerase chain reaction (RT-PCR) verify TYROBP expression within MM and healthy people. We performed cell adhesion and transwell assays for investigating TYROBP function in MM cell adhesion and migration.\nRESULTS: Through differential analyses, 92 MM-related DEGs were obtained. 10 hub genes were identified by PPI and CytoHubba. Their diagnostic and prognostic significance was analyzed. Down-regulation of genes like TYROBP, ELANE, MNDA, and MPO related to dismal MM prognosis. Upon univariable/multivariable Cox regression, TYROBP independently predicted MM prognosis. GSEA pathway was enriched, indicating that TYROBP expression affected MM development via cell adhesion molecular pathway. Upon Western-blotting and RT-PCR assays, TYROBP expression among MM patients decreased relative to healthy donors. Cell adhesion and transwell migration assays revealed increased MM cell adhesion and decreased migration upon TYROBP up-regulation.\nCONCLUSION: In summary, TYROBP is a potential prognostic marker for MM.", "claims": [{"id": "claim-method", "statement": "Besides, univariable/multivariable Cox regression were employed to screen independent prognostic biomarkers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38549127", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Besides, univariable/multivariable Cox regression were employed to screen independent prognostic biomarkers."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Some data underlying this article are available in NCBI-GEO (http://www.ncbi.nlm.nih.gov/geo). The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. The data underlying this article are available in the article and in its online supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38549127", "locator": "sections[30] \"Availability of data and materials\" paragraph 2", "quote": "Some data underlying this article are available in NCBI-GEO (http://www.ncbi.nlm.nih.gov/geo). The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. The data underlying this article are available in the article and in its online supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In summary, TYROBP is a potential prognostic marker for MM.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38549127", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In summary, TYROBP is a potential prognostic marker for MM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In summary, TYROBP is a potential prognostic marker for MM.", "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:38549127"], "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:GSE24080"], "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:GSE24080"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38549127", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-024-03304-6", "sha256": "sha256:93a3801260cf787d6ab766e45cf73cd2bdc4a3156a46abb7460ee417036c0e8a", "bytes": 41172, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-024-03304-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10979612", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE24080", "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=GSE24080", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE24080", "version": null, "note": "Some data underlying this article are available in NCBI-GEO (http://www.ncbi.nlm.nih.gov/geo). The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. The data underlying this article are available in the article and in its online supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some data underlying this article are available in NCBI-GEO (http://www.ncbi.nlm.nih.gov/geo). The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. 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The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. The data underlying this article are available in the article and in its online supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Some data underlying this article are available in NCBI-GEO (http://www.ncbi.nlm.nih.gov/geo). The datasets were derived from sources in the public domain: GSE39754: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39754; GSE6477: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6477; GSE24080: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080. Others are incorporated into the article and its online supplementary material. 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The data underlying this article are available in the article and in its online supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM148911", "GSM148912", "GSM148914", "GSM148915", "GSM148916", "GSM148917", "GSM148918", "GSM148919", "GSM148920", "GSM148921", "GSM148922", "GSM148923", "GSM148924", "GSM148925", "GSM148926", "GSM148927", "GSM148928", "GSM148929", "GSM148930", "GSM148931", "GSM148932", "GSM148933", "GSM148934", "GSM148935", "GSM148936", "GSM148937", "GSM148938", "GSM148939", "GSM148940", "GSM148941", "GSM148942", "GSM148943", "GSM148944", "GSM148945", "GSM148946", "GSM148947", "GSM148948", "GSM148949", "GSM148950", "GSM148951", "GSM148952", "GSM148953", "GSM148954", "GSM148955", "GSM148956", "GSM148957", "GSM148958", "GSM148959", "GSM148960", "GSM148961", "GSM148962", "GSM148963", "GSM148964", "GSM148965", "GSM148966", "GSM148967", "GSM148968", "GSM148969", "GSM148970", "GSM148971", "GSM148972", "GSM148973", 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