High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myeloma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29861858", "kind": "science-record", "revision": 8, "content_hash": "sha256:d9823ae5450872693f6c20fa966534957aff6e11c324c82aebb7705296f26f4a", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:59:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myeloma.", "doi": "10.18632/oncotarget.25350", "pmid": "29861858", "authors": ["Soushi Ibata", "Masayoshi Kobune", "Shohei Kikuchi", "Masahiro Yoshida", "Shogo Miura", "Hiroto Horiguchi", "Kazuyuki Murase", "Satoshi Iyama", "Kohichi Takada", "Koji Miyanishi", "Junji Kato"], "journal": "Oncotarget", "year": 2018, "abstract": "Recent advances in plasma cell biology and molecularly-targeted therapy enable us to employ various types of drugs including immunomodulatory drugs, proteasome inhibitors, and immunotherapy. However, the optimal therapeutic strategies to introduce these drugs for heterogeneous patients with multiple myeloma (MM) have not yet been clarified. In the present study, we attempted to identify a new factor indicating poor prognosis in CD138+ myeloma cells using accumulated Gene Expression Omnibus (GEO) datasets from studies of MM and to assess the relationship between gene expression and survival using MAQC-II Project Myeloma (GSE24080). Five GEO datasets (GSE5900, GSE58133, GSE68871, GSE57317 and GSE16791) which were analyzed by the same microarray platform (GLP570) were combined into one MM database including various types of MM. However, we found that gene expression levels were quite heterogeneous. Hence, we focused on the differentially-expressed genes (DEGs) between newly-diagnosed MM and relapsed/refractory MM and found that the expression levels of more than 20 genes changed two-fold or more. Additionally, pathway analysis indicated that six pathways including Hippo signaling were significantly enriched. Then, we applied all DEGs and genes associated with core enrichment for GSE24080 to evaluate their involvement in disease prognosis. We found that nucleoporin 133 (NUP133) is an independent poor prognostic factor by Cox proportional hazard analysis. These results suggested that high expression of NUP133 could be useful when choosing the appropriate MM therapy and may be a new target of MM therapy.", "claims": [{"id": "claim-method", "statement": "The relationship between DEGs and OS were evaluated using the publicly accessible MAQC-II Project MM dataset (GSE24080) from the GEO using the Cox proportional hazard model provided from EZR [26].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29861858", "locator": "sections[11] \"Statistical analysis\" paragraph 3", "quote": "The relationship between DEGs and OS were evaluated using the publicly accessible MAQC-II Project MM dataset (GSE24080) from the GEO using the Cox proportional hazard model provided from EZR [26]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To assess the relationship between candidate genes and survival, we used another dataset, The MicroArray Quality Control (MAQC)-II Project MM dataset (GSE24080) (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080) [14]. In this dataset, gene expression profiling of highly-purified bone marrow plasma cells in NDMM (N = 559) was available. Moreover, this dataset was analyzed using an Affymetrix Human Genome U133 Plus 2.0 Array by which myeloma dataset #2 was also analyzed. Furthermore, supplementary data regarding clinical information such as survival time, the total number of deaths (N = 172), recurrence or progression (N = 249) and cytogenetic abnormalities of individual patients was included with this dataset. After all data of GSE24080 were downloaded and combined with clinical information, the relationship between all candidate genes and OS was analyzed using the Cox proportional hazard model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "To assess the relationship between candidate genes and survival, we used another dataset, The MicroArray Quality Control (MAQC)-II Project MM dataset (GSE24080) (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080) [14]."}, {"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "In this dataset, gene expression profiling of highly-purified bone marrow plasma cells in NDMM (N = 559) was available."}, {"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "Moreover, this dataset was analyzed using an Affymetrix Human Genome U133 Plus 2.0 Array by which myeloma dataset #2 was also analyzed."}, {"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "Furthermore, supplementary data regarding clinical information such as survival time, the total number of deaths (N = 172), recurrence or progression (N = 249) and cytogenetic abnormalities of individual patients was included with this dataset."}, {"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "After all data of GSE24080 were downloaded and combined with clinical information, the relationship between all candidate genes and OS was analyzed using the Cox proportional hazard model."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the publicly accessible GEO MAQC-II Project Myeloma dataset (GSE24080) and Cox proportional hazard analysis, the study found that high NUP133 expression was an independent poor prognostic factor in newly diagnosed multiple myeloma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29861858", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found that nucleoporin 133 (NUP133) is an independent poor prognostic factor by Cox proportional hazard analysis."}, {"asset": "source:pmid:29861858", "locator": "sections[5] \"Identification of a new poor prognostic factor in patients with MM\" paragraph 2", "quote": "After all data of GSE24080 were downloaded and combined with clinical information, the relationship between all candidate genes and OS was analyzed using the Cox proportional hazard model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using the publicly accessible GEO MAQC-II Project Myeloma dataset (GSE24080) and Cox proportional hazard analysis, the study found that high NUP133 expression was an independent poor prognostic factor in newly diagnosed multiple myeloma.", "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:29861858"], "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. 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In this dataset, gene expression profiling of highly-purified bone marrow plasma cells in NDMM (N = 559) was available. Moreover, this dataset was analyzed using an Affymetrix Human Genome U133 Plus 2.0 Array by which myeloma dataset #2 was also analyzed. Furthermore, supplementary data regarding clinical information such as survival time, the total number of deaths (N = 172), recurrence or progression (N = 249) and cytogenetic abnormalities of individual patients was included with this dataset. After all data of GSE24080 were downloaded and combined with clinical information, the relationship between all candidate genes and OS was analyzed using the Cox proportional hazard model.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To assess the relationship between candidate genes and survival, we used another dataset, The MicroArray Quality Control (MAQC)-II Project MM dataset (GSE24080) (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080) [14]. In this dataset, gene expression profiling of highly-purified bone marrow plasma cells in NDMM (N = 559) was available. Moreover, this dataset was analyzed using an Affymetrix Human Genome U133 Plus 2.0 Array by which myeloma dataset #2 was also analyzed. Furthermore, supplementary data regarding clinical information such as survival time, the total number of deaths (N = 172), recurrence or progression (N = 249) and cytogenetic abnormalities of individual patients was included with this dataset. 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SIGNALING_BY_HIPPO", "16", "1.5587571", "0.027290449"], ["2. REGULATION_OF_IFNA_SIGNALING", "24", "1.5417559", "0.025477707"], ["3. LIGAND_GATED_ION_CHANNEL_TRANSPORT", "20", "1.5310737", "0.014403292"], ["4. KERATAN_SULFATE_KERATIN_METABOLISM", "26", "1.5274918", "0.029045643"], ["5. KERATAN_SULFATE_ BIOSYNTHESIS", "22", "1.4906782", "0.04158004"], ["6. 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analysis of the relationship between gene expression and OS by Cox proportional hazard model using the publicly accessible MAQC-II Project MM dataset (GSE24080)", "rows": [["Gene symbol", "Hazard ratio (95% CI)", "P value"], ["CSNK1A1P1", "1.118 (0.943–1.325)", "0.2001"], ["GABRA2", "0.934 (0.725–1.204)", "0.5977"], ["GABRA4", "1.048 (0.890–1.235)", "0.5715"], ["GABRA5", "1.037 (0.925–1.163)", "0.5300"], ["GABRB1", "0.975 (0.841–1.130)", "0.7314"], ["GABRG2", "1.242 (1.048–1.471)", "0.0125*"], ["GABRG3", "1.045 (0.830–1.315)", "0.7108"], ["GABRR1", "0.892 (0.726–1.095)", "0.2731"], ["GLRA1", "1.208 (1.011–1.444)", "0.0374*"], ["GLRA3", "0.985 (0.817–1.187)", "0.8699"], ["GLRB", "0.978 (0.800–1.194)", "0.8244"], ["IFNA1", "1.102 (0.973–1.249)", "0.1249"], ["IFNA4", "1.465 (1.076–1.997)", "0.0155*"], ["IFNA5", "0.909 (0.692–1.195)", "0.4947"], ["IFNA6", "0.953 (0.836–1.086)", "0.4658"], ["IFNA7", "0.971 (0.834–1.130)", "0.7016"], ["IFNA8", "0.996 (0.886–1.119)", "0.9459"], ["IFNA10", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE24080"], "resolved_accessions": ["GSE24080"], "statements": ["To assess the relationship between candidate genes and survival, we used another dataset, The MicroArray Quality Control (MAQC)-II Project MM dataset (GSE24080) (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24080) [14]. In this dataset, gene expression profiling of highly-purified bone marrow plasma cells in NDMM (N = 559) was available. Moreover, this dataset was analyzed using an Affymetrix Human Genome U133 Plus 2.0 Array by which myeloma dataset #2 was also analyzed. Furthermore, supplementary data regarding clinical information such as survival time, the total number of deaths (N = 172), recurrence or progression (N = 249) and cytogenetic abnormalities of individual patients was included with this dataset. After all data of GSE24080 were downloaded and combined with clinical information, the relationship between all candidate genes and OS was analyzed using the Cox proportional hazard model."], "basis": "The paper names GSE24080 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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