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Zhang J, Yan S, Li R, Wang G, Kang S, Wang Y, Hou W, Wang C, Tian W. CRMarker: A manually curated comprehensive resource of cancer RNA markers. Int J Biol Macromol 2021; 174:263-269. [PMID: 33529633 DOI: 10.1016/j.ijbiomac.2021.01.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/06/2021] [Accepted: 01/28/2021] [Indexed: 01/08/2023]
Abstract
Biomolecular markers have extremely important value for cancer research and treatment. However, as far as we know, there are still no searchable and predictable resources focusing on multiple classes of RNA molecular markers in cancers. Herein, we developed CRMarker, a manually curated comprehensive repository of cancer RNA markers. In the current release, CRMarker v1.1 consists of 5489 "known" cancer RNA markers based on 8756 valid publications in PubMed, including 2878 mRNAs (genes), 1314 miRNAs, 1097 lncRNAs and 200 circRNAs, and involving two functional molecules (diagnosis and prognosis), 21 organisms and 154 cancers. The search results provided by the database are comprehensive, including 11 items such as RNA molecule expression and risk level, type of tissue or sample, cancer subtype, reference type, etc. Moreover, CRMarker also provides more than 18,000 potential cancer RNA markers, which are predicted based on "guilt-by-association" analysis of the above-mentioned "known" RNA markers and three molecular interaction networks, and survival analysis of 18 gene expression data sets with survival data. CRMarker v1.1 has a friendly interface and is freely available online at http://crmarker.hnnu.edu.cn/. We aim to build a comprehensive platform that is convenient for cancer researchers and clinicians to inquire and retrieve.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China; Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, PR China; Key Laboratory of Industrial Dust Prevention and Control & Occupational Health and Safety, Ministry of Education, Huainan, PR China; Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, PR China.
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China
| | - Ruoyu Li
- School of Computer Science, Huainan Normal University, Huainan, PR China
| | - Gangyuan Wang
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China
| | - Siyong Kang
- School of Computer Science, Huainan Normal University, Huainan, PR China
| | - Ying Wang
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China
| | - Wenmin Hou
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China
| | - Chenrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan 232001, PR China
| | - Weidong Tian
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, PR China.
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Polati R, Brandi J, Dalai I, Zamò A, Cecconi D. Tissue proteomics of splenic marginal zone lymphoma. Electrophoresis 2015; 36:1612-21. [PMID: 25873066 DOI: 10.1002/elps.201400329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 03/27/2015] [Accepted: 04/02/2015] [Indexed: 12/20/2022]
Abstract
Splenic marginal zone lymphoma (SMZL) is a rare chronic B lymphoproliferative disease, whose molecular pathogenesis has still not been well established. For the first time, a proteomic approach was undertaken to analyse the protein profiles of SMZL tissue. 1D and 2D Western blot, immunohistochemical analysis, and functional data mining were also performed in order to validate results, investigate protein species specific regulation, classify proteins, and explore their potential relationships. We demonstrated that SMZL is characterized by modulation of protein species related to energetic metabolism and apoptosis pathways. We also reported specific protein species (such as biliverdin reductase A, manganese superoxide dismutase, beta-2 microglobulin, growth factor receptor-bound protein 2, acidic leucine-rich nuclear phosphoprotein 32 family member A, and Set nuclear oncogene) directly involved in NF-kB and BCR pathways, as well as in chromatin remodelling and cytoskeleton. Our findings shed new light on SMZL pathogenesis and provide a basis for the future development of novel biomarkers. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD001124.
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Affiliation(s)
- Rita Polati
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Jessica Brandi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Irene Dalai
- Department of Pathology and Diagnostics, Pathological Anatomy, University of Verona, Verona, Italy
| | - Alberto Zamò
- Department of Pathology and Diagnostics, Pathological Anatomy, University of Verona, Verona, Italy
| | - Daniela Cecconi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
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Drexler HG, Ehrentraut S, Nagel S, Eberth S, MacLeod RAF. Malignant hematopoietic cell lines: in vitro models for the study of primary mediastinal B-cell lymphomas. Leuk Res 2014; 39:18-29. [PMID: 25480038 DOI: 10.1016/j.leukres.2014.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/30/2014] [Accepted: 11/05/2014] [Indexed: 11/27/2022]
Abstract
Primary mediastinal B-cell lymphoma (PMBL) is a highly aggressive disease with a unique set of biological, clinical, morphological, immunological and in particular genetic features that in the molecular era of defining lymphomas clearly distinguishes it as a separate entity from other diffuse large B-cell lymphomas (DLBCL). A precise molecular diagnosis of PMBL can be achieved by gene expression profiling. The signature gene expression profile of PMBL is more closely related to classic Hodgkin lymphoma (cHL) than to other DLBCL subgroups. A number of common genetic aberrations in PMBL and cHL further underscore their close relationship. To investigate the pathobiology of lymphomas in depth, many groups have turned to cell lines that are suitable models facilitating molecular studies and providing unique insights. For the purposes of the current perspective, we focus on four bona fide PMBL-derived cell lines (FARAGE, KARPAS-1106, MEDB-1, U-2940) that we identified and validated as such through hierarchical cluster analysis among a large collection of leukemia-lymphoma cell lines. These gene expression profiles showed that the four PMBL cell lines represent a distinct entity and are most similar to cHL cell lines, confirming derivation from a related cell type. A validated cell line resource for PMBL should assist those seeking druggable targets in this entity. This review aims to provide a comprehensive overview of the currently available cellular models for the study of PMBL.
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Affiliation(s)
- Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Dept. Human and Animal Cell Lines, Braunschweig, Germany.
| | - Stefan Ehrentraut
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Dept. Human and Animal Cell Lines, Braunschweig, Germany
| | - Stefan Nagel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Dept. Human and Animal Cell Lines, Braunschweig, Germany
| | - Sonja Eberth
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Dept. Human and Animal Cell Lines, Braunschweig, Germany
| | - Roderick A F MacLeod
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Dept. Human and Animal Cell Lines, Braunschweig, Germany
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van Krieken JH. New developments in the pathology of malignant lymphoma: a review of the literature published from August to November 2009. J Hematop 2009; 2:245-51. [PMID: 20309432 PMCID: PMC2798938 DOI: 10.1007/s12308-009-0052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- J. Han van Krieken
- Department of Pathology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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