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Jovčevska I, Zupanec N, Kočevar N, Cesselli D, Podergajs N, Stokin CL, Myers MP, Muyldermans S, Ghassabeh GH, Motaln H, Ruaro ME, Bourkoula E, Turnšek TL, Komel R. TRIM28 and β-actin identified via nanobody-based reverse proteomics approach as possible human glioblastoma biomarkers. PLoS One 2014; 9:e113688. [PMID: 25419715 PMCID: PMC4242679 DOI: 10.1371/journal.pone.0113688] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/27/2014] [Indexed: 01/23/2023] Open
Abstract
Malignant gliomas are among the rarest brain tumours, and they have the worst prognosis. Grade IV astrocytoma, known as glioblastoma multiforme (GBM), is a highly lethal disease where the standard therapies of surgery, followed by radiation and chemotherapy, cannot significantly prolong the life expectancy of the patients. Tumour recurrence shows more aggressive form compared to the primary tumour, and results in patient survival from 12 to 15 months only. Although still controversial, the cancer stem cell hypothesis postulates that cancer stem cells are responsible for early relapse of the disease after surgical intervention due to their high resistance to therapy. Alternative strategies for GBM therapy are thus urgently needed. Nanobodies are single-domain antigen-binding fragments of heavy-chain antibodies, and together with classical antibodies, they are part of the camelid immune system. Nanobodies are small and stable, and they share a high degree of sequence identity to the human heavy chain variable domain, and these characteristics offer them advantages over classical antibodies or antibody fragments. We first immunised an alpaca with a human GBM stem-like cell line prepared from primary GBM cultures. Next, a nanobody library was constructed in a phage-display vector. Using nanobody phage-display technology, we selected specific GBM stem-like cell binders through a number of affinity selections, using whole cell protein extracts and membrane protein-enriched extracts from eight different GBM patients, and membrane protein-enriched extracts from two established GBM stem-like cell lines (NCH644 and NCH421K cells). After the enrichment, periplasmic extract ELISA was used to screen for specific clones. These nanobody clones were recloned into the pHEN6 vector, expressed in Escherichia coli WK6, and purified using immobilised metal affinity chromatography and size-exclusion chromatography. Specific nanobody:antigen pairs were obtained and mass spectrometry analysis revealed two proteins, TRIM28 and β-actin, that were up-regulated in the GBM stem-like cells compared to the controls.
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Affiliation(s)
- Ivana Jovčevska
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Neja Zupanec
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Kočevar
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Daniela Cesselli
- Department of Medical and Biological Sciences (DSMB), University of Udine, Udine, Italy
| | - Neža Podergajs
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology (NIB), Ljubljana, Slovenia
| | - Clara Limbaeck Stokin
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Michael P. Myers
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Structural Biology Research Center, VIB, Brussels, Belgium
| | - Gholamreza Hassanzadeh Ghassabeh
- Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Nanobody Service Facility, VIB, Brussels, Belgium
| | - Helena Motaln
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology (NIB), Ljubljana, Slovenia
| | | | - Evgenia Bourkoula
- Department of Medical and Biological Sciences (DSMB), University of Udine, Udine, Italy
| | - Tamara Lah Turnšek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology (NIB), Ljubljana, Slovenia
| | - Radovan Komel
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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102
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Ludvigsen M, Kamper P, Hamilton-Dutroit SJ, Bendix K, Møller MB, d'Amore FA, Honoré B. Relationship of intratumoural protein expression patterns to age and Epstein-Barr virus status in classical Hodgkin lymphoma. Eur J Haematol 2014; 95:137-49. [DOI: 10.1111/ejh.12463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Maja Ludvigsen
- Department of Biomedicine; Aarhus University; Aarhus Denmark
| | - Peter Kamper
- Department of Haematology; Aarhus University Hospital; Aarhus Denmark
| | | | - Knud Bendix
- Institute of Pathology; Aarhus University Hospital; Aarhus Denmark
| | | | | | - Bent Honoré
- Department of Biomedicine; Aarhus University; Aarhus Denmark
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103
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Deregulation of serum microRNA expression is associated with cigarette smoking and lung cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:364316. [PMID: 25386559 PMCID: PMC4217347 DOI: 10.1155/2014/364316] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 02/05/2023]
Abstract
Lung cancer is the leading cause of cancer-related death and cigarette smoking is the main risk factor for lung cancer. Circulating microRNAs (miRNAs) are considered potential biomarkers of various cancers, including lung cancer. However, it is unclear whether changes in circulating miRNAs are associated with smoking and smoking-related lung cancer. In this study, we determined the serum miRNA profiles of 10 nonsmokers, 10 smokers, and 10 lung-cancer patients with miRCURY LNA microRNA arrays. The differentially expressed miRNAs were then confirmed in a larger sample. We found that let-7i-3p and miR-154-5p were significantly downregulated in the sera of smokers and lung-cancer patients, so the serum levels of let-7i-3p and miR-154-5p are associated with smoking and smoking-related lung cancer. The areas under receiver operating characteristic curves for let-7i-3p and miR-154-5p were approximately 0.892 and 0.957, respectively. In conclusion, our results indicate that changes in serum miRNAs are associated with cigarette smoking and lung cancer and that let-7i-3p and miR-154-5p are potential biomarkers of smoking-related lung cancer.
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104
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Baraitser-Winter cerebrofrontofacial syndrome: delineation of the spectrum in 42 cases. Eur J Hum Genet 2014; 23:292-301. [PMID: 25052316 DOI: 10.1038/ejhg.2014.95] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 04/05/2014] [Accepted: 04/30/2014] [Indexed: 11/08/2022] Open
Abstract
Baraitser-Winter, Fryns-Aftimos and cerebrofrontofacial syndrome types 1 and 3 have recently been associated with heterozygous gain-of-function mutations in one of the two ubiquitous cytoplasmic actin-encoding genes ACTB and ACTG1 that encode β- and γ-actins. We present detailed phenotypic descriptions and neuroimaging on 36 patients analyzed by our group and six cases from the literature with a molecularly proven actinopathy (9 ACTG1 and 33 ACTB). The major clinical anomalies are striking dysmorphic facial features with hypertelorism, broad nose with large tip and prominent root, congenital non-myopathic ptosis, ridged metopic suture and arched eyebrows. Iris or retinal coloboma is present in many cases, as is sensorineural deafness. Cleft lip and palate, hallux duplex, congenital heart defects and renal tract anomalies are seen in some cases. Microcephaly may develop with time. Nearly all patients with ACTG1 mutations, and around 60% of those with ACTB mutations have some degree of pachygyria with anteroposterior severity gradient, rarely lissencephaly or neuronal heterotopia. Reduction of shoulder girdle muscle bulk and progressive joint stiffness is common. Early muscular involvement, occasionally with congenital arthrogryposis, may be present. Progressive, severe dystonia was seen in one family. Intellectual disability and epilepsy are variable in severity and largely correlate with CNS anomalies. One patient developed acute lymphocytic leukemia, and another a cutaneous lymphoma, indicating that actinopathies may be cancer-predisposing disorders. Considering the multifaceted role of actins in cell physiology, we hypothesize that some clinical manifestations may be partially mutation specific. Baraitser-Winter cerebrofrontofacial syndrome is our suggested designation for this clinical entity.
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105
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Liu PF, Wang YH, Cao YW, Jiang HP, Yang XC, Wang XS, Niu HT. Far from resolved: stromal cell-based iTRAQ research of muscle-invasive bladder cancer regarding heterogeneity. Oncol Rep 2014; 32:1489-96. [PMID: 25050759 DOI: 10.3892/or.2014.3340] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/04/2014] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to globally characterize the cancer stroma expression profile of muscle-invasive bladder cancer in different metastatic risk groups and to discuss the decisive role of biological pathway change in cancer heterogeneity. Laser capture microdissection was employed to harvest purified muscle-invasive bladder cancer stromal cells derived from 30 clinical samples deriving from 3 different metastatic risk groups. Isobaric tags for relative and absolute quantitation (iTRAQ) and two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) were used to identify the differentially expressed proteins. Subsequently, the differentially expressed proteins were further analyzed by bioinformatics tools. After completing the above tasks, the proteins of interest were further compared with the published litterature. We identified 1,049 differentially expressed proteins by paired comparison (high risk vs. median, low risk and normal groups; median risk vs. low risk and normal groups, low risk vs. normal group; a total of 6 comparisons). A total of 510,549,548 proteins as significantly altered (ratio fold-change≥1.5 or ≤0.667 between the metastatic potential risk group and the normal group) were presented in the low/median/high metastatic risk group, respectively. Pathway analysis revealed that the differentially expressed proteins were mainly located in the Kyoto Encyclopedia of Genes and Genomes pathways, including focal adhesion pathway, systemic lupus erythematosus pathway and ECM-receptor interaction pathway. In addition, several proteins such as EXOC4, MYH10 and MMP-9 may serve as candidate biomarkers of muscle-invasive bladder cancer. Our study confirmed that stromal cells, an important part of the cancer tissue, are pivotal for regulating the heterogeneity of cancer. Common changes in biological pathways determined the malignant phenotype of muscle-invasive bladder cancer, and biomarker discovery should take into account both neoplastic cells and their corresponding stromata.
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Affiliation(s)
- Peng-Fei Liu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Yong-Hua Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Yan-Wei Cao
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Hai-Ping Jiang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Xue-Cheng Yang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Xin-Sheng Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
| | - Hai-Tao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao 266101, P.R. China
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106
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FFPE tissue as a feasible source for gene expression analysis--a comparison of three reference genes and one tumor marker. Pathol Res Pract 2013; 209:784-9. [PMID: 24156825 DOI: 10.1016/j.prp.2013.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/05/2013] [Accepted: 09/19/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND Formalin-fixation, paraffin-embedding is the standard processing technique for tumor tissue in modern pathology. New techniques such as cryo-conservation allow rapid fixation and long-time storage but come along with increased costs and enlarged storage complexity. However, formalin-fixed, paraffin-embedded (FFPE) tissue is available in a large quantity, making it the ideal material for retrospective studies. The following study was designed to investigate the influence of formalin-fixation on the quality of mRNA and applicability of FFPE-derived mRNA for gene expression analysis. Three potential reference genes for pulmonary tumors with neuroendocrine differentiation were included and tested for their robust expression. MATERIALS AND METHODS Eighty specimens collected from 2005 to 2012 at the Institute of Pathology and Neuropathology at the University Hospital Essen were analyzed for their gene expression by using TaqMan(®) gene expression assays on demand (AoD). Three distinct potential reference genes (ACTB, GAPDH, HPRT1) were evaluated for their expression, and a proteasome subunit (PSMA1) was included in the analysis as tumor marker and functioned as an internal technical control. CONCLUSION For GAPDH and ACTB, a highly significant correlation and consistent expression between the investigated entities was found, making them reliable reference genes for further research. Additionally, the feasibility for a FFPE tissue-based gene expression analysis was verified by showing that the mRNA quality is sufficient. When standardized FFPE preparation is performed carefully, sufficient mRNA can be isolated for reliable and successful gene expression analysis. That provides the basis the door for large, retrospective studies that correlate molecular and clinical follow-up data.
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