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Coudray A, Battenhouse AM, Bucher P, Iyer VR. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PeerJ 2018; 6:e5362. [PMID: 30083469 PMCID: PMC6074801 DOI: 10.7717/peerj.5362] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of somatic mutations. However there has been little systematic evaluation of the utility of RNA-seq for identifying somatic mutations. Here, we develop and evaluate a pipeline for processing RNA-seq data from glioblastoma multiforme (GBM) tumors in order to identify somatic mutations. The pipeline entails the use of the STAR aligner 2-pass procedure jointly with MuTect2 from genome analysis toolkit (GATK) to detect somatic variants. Variants identified from RNA-seq data were evaluated by comparison against the COSMIC and dbSNP databases, and also compared to somatic variants identified by exome sequencing. We also estimated the putative functional impact of coding variants in the most frequently mutated genes in GBM. Interestingly, variants identified by RNA-seq alone showed better representation of GBM-related mutations cataloged by COSMIC. RNA-seq-only data substantially outperformed the ability of WES to reveal potentially new somatic mutations in known GBM-related pathways, and allowed us to build a high-quality set of somatic mutations common to exome and RNA-seq calls. Using RNA-seq data in parallel with WES data to detect somatic mutations in cancer genomes can thus broaden the scope of discoveries and lend additional support to somatic variants identified by exome sequencing alone.
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Affiliation(s)
- Alexandre Coudray
- School of Life Sciences, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Anna M Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Philipp Bucher
- School of Life Sciences, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX, USA
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2
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Olar A, Goodman LD, Wani KM, Boehling NS, Sharma DS, Mody RR, Gumin J, Claus EB, Lang FF, Cloughesy TF, Lai A, Aldape KD, DeMonte F, Sulman EP. A gene expression signature predicts recurrence-free survival in meningioma. Oncotarget 2018; 9:16087-16098. [PMID: 29662628 PMCID: PMC5882319 DOI: 10.18632/oncotarget.24498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/01/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Meningioma is the most common primary brain tumor and has a variable risk of local recurrence. While World Health Organization (WHO) grade generally correlates with recurrence, there is substantial within-grade variation of recurrence risk. Current risk stratification does not accurately predict which patients are likely to benefit from adjuvant radiation therapy (RT). We hypothesized that tumors at risk for recurrence have unique gene expression profiles (GEP) that could better select patients for adjuvant RT. METHODS We developed a recurrence predictor by machine learning modeling using a training/validation approach. RESULTS Three publicly available AffymetrixU133 gene expression datasets (GSE9438, GSE16581, GSE43290) combining 127 primary, non-treated meningiomas of all grades served as the training set. Unsupervised variable selection was used to identify an 18-gene GEP model (18-GEP) that separated recurrences. This model was validated on 62 primary, non-treated cases with similar grade and clinical variable distribution as the training set. When applied to the validation set, 18-GEP separated recurrences with a misclassification error rate of 0.25 (log-rank p=0.0003). 18-GEP was predictive for tumor recurrence [p=0.0008, HR=4.61, 95%CI=1.89-11.23)] and was predictive after adjustment for WHO grade, mitotic index, sex, tumor location, and Simpson grade [p=0.0311, HR=9.28, 95%CI=(1.22-70.29)]. The expression signature included genes encoding proteins involved in normal embryonic development, cell proliferation, tumor growth and invasion (FGF9, SEMA3C, EDNRA), angiogenesis (angiopoietin-2), cell cycle regulation (CDKN1A), membrane signaling (tetraspanin-7, caveolin-2), WNT-pathway inhibitors (DKK3), complement system (C1QA) and neurotransmitter regulation (SLC1A3, Secretogranin-II). CONCLUSIONS 18-GEP accurately stratifies patients with meningioma by recurrence risk having the potential to guide the use of adjuvant RT.
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Affiliation(s)
- Adriana Olar
- Medical University of South Carolina & Hollings Cancer Center, Departments of Pathology and Laboratory Medicine & Neurosurgery, Charleston, SC, USA
| | - Lindsey D. Goodman
- Neurosciences Graduate Group, Perlman School of Medicine, University of Pennsylvania, Department of Biology, Philadelphia, PA, USA
| | - Khalida M. Wani
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, TX, USA
| | | | - Devi S. Sharma
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Reema R. Mody
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Joy Gumin
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Elizabeth B. Claus
- Brigham and Women’s Hospital, Harvard Medical School, Department of Neurosurgery, Boston, MA, USA
- School of Public Health, Yale University, Department of Biostatistics, New Haven, CT, USA
| | - Frederick F. Lang
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Timothy F. Cloughesy
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Albert Lai
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Kenneth D. Aldape
- MacFeeters-Hamilton Brain Tumour Centre, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Franco DeMonte
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Erik P. Sulman
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center, Departments of Radiation Oncology and Genomic Medicine, Houston, TX, USA
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3
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Mäkelä K, Helén P, Haapasalo H, Paavonen T. Complement activation in astrocytomas: deposition of C4d and patient outcome. BMC Cancer 2012; 12:565. [PMID: 23199209 PMCID: PMC3517746 DOI: 10.1186/1471-2407-12-565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 11/28/2012] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND C4d is a cleavage product of complement component C4 and is considered to serve as a marker for the site of complement activation. In this study C4d staining of grade I-IV astrocytic tumors was studied to explore if there is an association between complement activation and the grade of tumor, or patient survival. METHODS Tissue micro-array samples of 102 astrocytomas were stained immunohistochemically. The material consisted of 9 pilocytic astrocytomas and 93 grade II-IV astrocytomas, of which 67 were primary resections and 26 recurrent tumors. The intensity of C4d staining as well as extent of C4d and CD34 staining were evaluated. The intensity of C4d staining was scored semiquantitatively. The extent of the staining was counted morphometrically with a point counting grid yielding a percent of C4d and CD34 positive area of the sample. RESULTS The intensity and extent of C4d staining increased in grade II-IV diffusely infiltrating astrocytoma tumors in line with the malignancy grade (p = 0.034 and p = 0.016, respectively, Kruskal-Wallis test). However, C4d positive tumor area percentages were higher in grade I pilocytic astrocytomas than in grade II-IV diffusely infiltrating astrocytomas (p = 0.041, Mann-Whitney test). There was a significant correlation between CD34 positive and C4d positive endothelial area fraction in diffusely infiltrating astrocytomas (p < 0.001, Pearson correlation). In these tumors, the increasing intensity of C4d staining was also associated with worsened patient outcome (p = 0.014, log-rank test). CONCLUSION The worsening of patient outcome and malignant progression of tumor cells seem to be connected to microenvironmental changes evoked by chronically activated complement.
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Affiliation(s)
- Katri Mäkelä
- Department of Pathology, University of Tampere Medical School, Tampere, Finland
- University of Tampere, School of Medicine, Biokatu 6, Tampere 33520, Finland
| | - Pauli Helén
- Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- Department of Pathology, University of Tampere Medical School, Tampere, Finland
- Department of Pathology, Fimlab laboratories, Tampere University Hospital, Tampere, Finland
| | - Timo Paavonen
- Department of Pathology, University of Tampere Medical School, Tampere, Finland
- Department of Pathology, Fimlab laboratories, Tampere University Hospital, Tampere, Finland
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Domingues PH, Teodósio C, Ortiz J, Sousa P, Otero A, Maillo A, Bárcena P, García-Macias MC, Lopes MC, de Oliveira C, Orfao A, Tabernero MD. Immunophenotypic identification and characterization of tumor cells and infiltrating cell populations in meningiomas. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:1749-61. [PMID: 22982440 DOI: 10.1016/j.ajpath.2012.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/12/2012] [Accepted: 07/06/2012] [Indexed: 11/27/2022]
Abstract
Meningiomas are primary tumors of the central nervous system composed of both neoplastic and other infiltrating cells. We determined the cellular composition of 51 meningioma samples by multiparameter flow cytometric (MFC) immunophenotyping and investigated the potential relationship between mRNA and protein expression levels of neoplastic cells. For immunophenotypic, morphologic, and cytogenetic characterization of individual cell populations, a large panel of markers was used together with phagocytic/endocytic functional assays and MFC sorting. Overall, our results revealed coexistence of CD45(-) neoplastic cells and CD45(+) immune infiltrating cells in all meningiomas. Infiltrating cells included tissue macrophages, with an HLA-DR(+)CD14(+)CD45(+)CD68(+)CD16(-/+)CD33(-/+) phenotype and high phagocytic/endocytic activity, and a small proportion of cytotoxic lymphocytes (mostly T CD8(+) and natural killer cells). Tumor cells expressed multiple cell adhesion proteins, tetraspanins, HLA-I/HLA-DR molecules, complement regulatory proteins, cell surface ectoenzymes, and growth factor receptors. Noteworthy, the relationship between mRNA and protein levels was variable, depending on the proteins evaluated and the level of infiltration by immune cells. In summary, our results indicate that MFC immunophenotyping provides a reliable tool for the characterization of the patterns of protein expression of different cell populations coexisting in meningioma samples, with a more accurate measure of gene expression profiles of tumor cells at the functional/protein level than conventional mRNA microarray, independently of the degree of infiltration of the tumor by immune cells.
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Affiliation(s)
- Patrícia H Domingues
- Centre for Neurosciences and Cell Biology, Faculty of Pharmacy, University of Coimbra, Portugal
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5
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Abstract
Cancer cells need to interact synergistically with their surrounding microenvironment to form a neoplasm and to progress further to colonize distant organs. The microenvironment can exert profound epigenetic effects on cells through cell-derived interactions between cells, or through cell-derived factors deposited into the microenvironment. Tumor progression implies immune-escaping and triggers several processes that synergistically induce a cooperation among transformed and stromal cells, that compete for space and resources such as oxygen and nutrients. Therefore, the extra cellular milieu and tissue microenvironment heterotypic interactions cooperate to promote tumor growth, angiogenesis, and cancer cell motility, through elevated secretion of pleiotropic cytokines and soluble factors. Clusterin (CLU), widely viewed as an enigmatic protein represents one of the numerous cellular factors sharing the intracellular information with the microenvironment and it has also a systemic diffusion, tightly joining the "In and the Out" of the cell with a still debated variety of antagonistic functions. The multiplicity of names for CLU is an indication of the complexity of the problem and could reflect, on one hand its multifunctionality, or alternatively could mask a commonality of function. The posited role for CLU, further supported as a cytoprotective prosurvival chaperone-like molecule, seems compelling, in contrast its tumor suppressor function, as a guide of the guardians of the genome (DNA-repair proteins Ku70/80, Bax cell death inducer), could really reflect the balanced expression of its different forms, most certainly depending on the intra- and extracellular microenvironment cross talk. The complicated balance of cytokines network and the regulation of CLU forms production in cancer and stromal cells undoubtedly represent a potential link among adaptative responses, genomic stability, and bystander effect after oxidative stresses and damage. This review focuses on the tumor-microenvironment interactions strictly involved in controlling local cancer growth, invasion, and distant metastases that play a decisive role in the regulation of CLU different forms expression and release. In addition, we focus on the pleiotropic action of the extracellular form of this protein, sCLU, that may play a crucial role in redirecting stromal changes, altering intercellular communications binding cell surface receptors and contributing to influence the secretion of chemokines in paracrine and autocrine fashion. Further elucidation of CLU functions inside and outside ("in and out") of cancer cell are warranted for a deeper understanding of the interplay between tumor and stroma, suggesting new therapeutic cotargeting strategies.
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Affiliation(s)
- Sabina Pucci
- Department of Biopathology, Institute of Anatomic Pathology, University of Rome Tor Vergata, 00133 Rome, Italy
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6
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Keller A, Ludwig N, Backes C, Romeike BFM, Comtesse N, Henn W, Steudel WI, Mawrin C, Lenhof HP, Meese E. Genome wide expression profiling identifies specific deregulated pathways in meningioma. Int J Cancer 2009; 124:346-51. [PMID: 19003955 DOI: 10.1002/ijc.23942] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Genome-wide expression signatures improve the understanding of tumor biology. We performed expression profiling of 24 meningioma including 8 of each WHO grade and 2 dura controls analyzing 55.000 transcripts including 18.300 known genes. We compared expression in meningioma vs. dura, expression of low grade (WHO I) vs. higher-grade (WHO II and WHO III) tumors and expression of meningothelial and syncytial meningioma vs. fibroblastic meningioma. Overall expression was significantly decreased in meningioma compared to dura and in meningothelial and syncytial compared to fibroblastic meningioma. Gene expression was exemplarily confirmed by immunohistochemistry using independent samples. Applying our statistical gene set analysis toolkit "GeneTrail", we identified significantly deregulated biochemical pathways using Kyoto encyclopedia of genes and genomes and Transpath databases. Kyoto encyclopedia of genes and genomes pathways with decreased expression in meningioma included cell adhesion molecules (p<0.0001) and cytokine-cytokine receptor interactions (p<0.0001). Pathways with increased expression included several metabolic pathways. Extended expression profiling by a novel statistical gene set enrichment identified pathways that have previously not been associated with meningioma.
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Affiliation(s)
- Andreas Keller
- Center for Bioinformatics, Saarland University, Building E.1.1, Saarbrücken 66041, Germany
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7
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Allen C, Paraskevakou G, Liu C, Iankov ID, Msaouel P, Zollman P, Myers R, Peng KW, Russell SJ, Galanis E. Oncolytic measles virus strains in the treatment of gliomas. Expert Opin Biol Ther 2008; 8:213-20. [PMID: 18194077 DOI: 10.1517/14712598.8.2.213] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Recurrent gliomas have a dismal outcome despite use of multimodality treatment including surgery, radiation therapy and chemotherapy. OBJECTIVE In this article the authors discuss potential applications of oncolytic measles virus strains as novel antitumor agents in the treatment of gliomas. METHODS Important aspects of measles virus development as an anticancer therapeutic agent including engineering, retargeting and combination studies with other therapeutic modalities are discussed. The translational process that led to the first clinical trial of an engineered measles virus derivative in patients with recurrent glioblastoma multiforme is also described. RESULTS/CONCLUSIONS Oncolytic measles virus strains hold promise as novel antitumor agents in the treatment of gliomas.
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Affiliation(s)
- Cory Allen
- Mayo Clinic, Molecular Medicine Department, 200 First Street SW, Rochester, MN 55905, USA
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8
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Yan J, Allendorf DJ, Li B, Yan R, Hansen R, Donev R. The Role of Membrane Complement Regulatory Proteins in Cancer Immunotherapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008. [DOI: 10.1007/978-0-387-78952-1_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ravindranath NMH, Shuler C. Expression of complement restriction factors (CD46, CD55 & CD59) in head and neck squamous cell carcinomas. J Oral Pathol Med 2007; 35:560-7. [PMID: 16968237 DOI: 10.1111/j.1600-0714.2006.00466.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Tumor cells can escape complement-dependent cytotoxicity (CDC) by expressing complement restriction factors (CRFs), CD46, CD55 and CD59. CRF-expression in non-neoplastic mucosa of the head and neck was compared with biopsies of the head and neck squamous cell carcinoma (HNSCC) and cell lines derived from oral squamous cell carcinomas (OSCC). METHODS Normal mucosa and HNSCC tumor tissue (poor, moderate, or well differentiated) specimens were immunostained with anti-CRF monoclonal antibodies. Immunostaining of the OSCC cell lines (SCC12 and SCC71) was examined under laser scan fluorescence microscopy. RESULTS CD46, CD55 and CD59 were highly expressed in HNSCC cells including T1/T2N0M0 stages. The CRF expression was much lower or absent in non-neoplastic squamous epithelia or in the submucosa of both normal and tumor tissues. CONCLUSIONS Enhanced staining of tumor tissues at stages T1/T2 indicates that the CRFs are overexpressed by primary tumors before metastasis to either lymph nodes or organs (N0M0 stage) suggesting that CRFs are formed early during tumorigenesis.
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Affiliation(s)
- Naren M H Ravindranath
- Center for Craniofacial Molecular Biology, University of Southern California, Health Sciences Campus, Los Angeles, CA, USA.
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Ravindranath NMH, Shuler C. Cell-surface density of complement restriction factors (CD46, CD55, and CD59): oral squamous cell carcinoma versus other solid tumors. ACTA ACUST UNITED AC 2006; 103:231-9. [PMID: 17234541 DOI: 10.1016/j.tripleo.2006.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 05/17/2006] [Accepted: 05/30/2006] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Complement restriction factors (CD46, membrane cofactor; CD55, decay accelerating factor; and CD59, protectin) are overexpressed on tumor cells, and they enable tumor cells to escape from complement-dependent and antibody-mediated killing. Cell-surface density of complement restriction factors (CRFs) on oral squamous cell carcinoma (OSCC) is compared with that found on other solid tumors (breast, pancreas, colon carcinomas, and melanoma) to understand the significance of their diversity. STUDY DESIGN The cell-surface expression of CRFs on tumor cells was confirmed with confocal laser scan fluorescent microscopy. Cell suspension enzyme-linked immunosorbent assay (cs-ELISA), which measures the density of cell-surface antigens, was utilized to study CRFs on the cell surface of tumor cells (OSCC, 2 cell lines; breast, 5 cell lines; pancreas, 3 cell lines; colon, 3 cell lines; and melanoma, 9 cell lines). RESULTS Confocal laser scan fluorescent microscopy confirmed the expression of CD46, CD55, and CD59 on the cell surface of OSCC cell lines SCC12 and SCC71. The relative densities of cell-surface expression obtained from cs-ELISAs of CRFs on OSCCs are as follows: CD59 > CD55 > CD46. The relative densities of the 3 CRFs in breast and pancreatic carcinomas were similar to those found in OSCCs, whereas the profile of CRFs in melanoma (CD59 > CD55 < CD46) and colon cancer (CD46 > CD55 > CD59) were different. CONCLUSIONS These findings indicate diverse strategies adopted by tumor types to resist antibody-mediated complement-dependent cytotoxicity; possibly the factors (exogenous and endogenous) in their respective microenvironments may play a role in the diversity.
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Affiliation(s)
- Naren M H Ravindranath
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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11
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Greer KA, Higgins MA, Cox ML, Ryan TP, Berridge BR, Kashtan CE, Lees GE, Murphy KE. Gene expression analysis in a canine model of X-linked Alport syndrome. Mamm Genome 2006; 17:976-90. [PMID: 16964446 DOI: 10.1007/s00335-005-0179-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 04/21/2006] [Indexed: 12/23/2022]
Abstract
Chronic kidney disease (CKD) often culminates in renal failure as a consequence of progressive interstitial fibrosis and is an important cause of illness and death in dogs. Identification of disease biomarkers and gene expression changes will yield valuable information regarding the specific biological pathways involved in disease progression. Toward these goals, gene expression changes in the renal cortex of dogs with X-linked Alport syndrome (XLAS) were examined using microarray technology. Extensive changes in inflammatory, metabolic, immune, and extracellular matrix biology were revealed in affected dogs. Statistical analysis showed 133 genes that were robustly induced or repressed in affected animals relative to age-matched littermates. Altered expression of numerous major histocompatibility complex (MHC) molecules suggests that the immune system plays a significant role in XLAS. Increased expression of COL4A1 and TIMP-1 at the end stage of disease supports the suggestion that expression increases in association with progression of fibrosis and confirms an observation of increased COL4A1 protein expression. Clusterin may function as one of the primary defenses of the renal cortex against progressive injury in dogs with XLAS, as demonstrated here by increased CLU gene expression. Cellular mechanisms that function during excess oxidative stress might also act to deter renal damage, as evidenced by alterations in gene expression of SOD1, ACO1, FDXR, and GPX1. This investigation provides a better understanding of interstitial fibrosis pathogenesis, and potential biomarkers for early detection, factors that are essential to discovering more effective treatments thereby reducing clinical illness and death due to CKD.
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Affiliation(s)
- Kimberly A Greer
- Department of Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4467, USA
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12
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Ulasov IV, Tyler MA, Zheng S, Han Y, Lesniak MS. CD46 Represents a Target for Adenoviral Gene Therapy of Malignant Glioma. Hum Gene Ther 2006; 17:556-64. [PMID: 16716112 DOI: 10.1089/hum.2006.17.556] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Malignant gliomas remain refractory to adenovirus serotype 5 (Ad5) gene therapy because of the lack of the primary adenoviral receptor, the coxsackie-adenovirus receptor (CAR), on tumor cells. To bypass the dependence on CAR, we investigated the expression of adenovirus serotype 3 (Ad3) receptor, or CD46, on glioma cells. First, we analyzed the expression of CD46 by RT-PCR on primary and passaged glioma cells. We then performed immunofluorescence studies to examine protein expression of CAR and CD46 on the same tumor lines. Finally, we constructed a replication-defective Ad vector that binds to CD46 and contains a luciferase transgenic cassette in place of the deleted E1 region: Ad5/3 (containing tail/shaft domain of Ad5 and knob domain of Ad3). These vectors were analyzed in vitro and in vivo against malignant glioma and compared with wild-type Ad5 or control vector Ad3/5 (containing tail of Ad5, shaft of Ad3, and knob of Ad5). The chimeric vector Ad5/3 showed a significant increase in the transduction efficiency of glioma tumor cells. At the same time, blocking the CD46 receptor caused a 65% inhibition of adenoviral infection when using Ad5/3. Taken together, these results indicate that CD46 is overexpressed by malignant glioma. Retargeting to the Ad3 receptor enhances gene transfer and offers a novel target for gene therapy of malignant brain tumors.
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Affiliation(s)
- Ilya V Ulasov
- Division of Neurosurgery, University of Chicago, IL 60637, USA
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Wrobel G, Roerig P, Kokocinski F, Neben K, Hahn M, Reifenberger G, Lichter P. Microarray‐based gene expression profiling of benign, atypical and anaplastic meningiomas identifies novel genes associated with meningioma progression. Int J Cancer 2004; 114:249-56. [PMID: 15540215 DOI: 10.1002/ijc.20733] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To identify gene expression profiles associated with human meningiomas of different World Health Organization (WHO) malignancy grades, we analyzed 30 tumors (13 benign meningiomas, WHO grade I; 12 atypical meningiomas, WHO grade II; 5 anaplastic meningiomas, WHO grade III) for the expression of 2,600 genes using cDNA-microarray technology. Receiver operator curve (ROC) analysis with a cutoff value of 45% selection probability identified 37 genes with decreased and 27 genes with increased expression in atypical and anaplastic meningiomas, compared to benign meningiomas. Supervised classification of the tumors did not reveal specific expression patterns representative of each WHO grade. However, anaplastic meningiomas could be distinguished from benign meningiomas by differential expression of a distinct set of genes, including several ones associated with cell cycle regulation and proliferation. Investigation of potential correlations between microarray expression data and genomic aberrations, detected by comparative genomic hybridization (CGH), demonstrated that losses on chromosomes 10 and 14 were associated with distinct expression profiles, including increased expression of several genes related to the insulin-like growth factor (IGF) (IGF2, IGFBP3 and AKT3) or wingless (WNT) (CTNNB1, CDK5R1, ENC1 and CCND1) pathways. Taken together, our microarray-based expression profiling revealed interesting novel candidate genes and pathways that may contribute to meningioma progression.
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Affiliation(s)
- Gunnar Wrobel
- Division of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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14
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Rushmere NK, Knowlden JM, Gee JMW, Harper ME, Robertson JF, Morgan BP, Nicholson RI. Analysis of the level of mRNA expression of the membrane regulators of complement, CD59, CD55 and CD46, in breast cancer. Int J Cancer 2004; 108:930-6. [PMID: 14712499 DOI: 10.1002/ijc.11606] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have examined the relative mRNA expression of the complement (C) regulatory proteins CD59, CD55 and CD46 in RNA isolated from 50 primary breast cancer specimens using a semiquantitative RT-PCR approach. Having normalized the mRNA expression levels of the C regulators relative to actin, we subsequently correlated their expression with estrogen receptor (ER) and various clinical, pathologic and biochemical features of the disease. CD59 and CD46 were detected in all clinical biopsies, while CD55 mRNA was detected in the majority of samples. The comparative levels of expression between the 3 regulators analyzed, using Spearman rank correlation test, revealed a significant association (p = 0.01; r = 0.36) between CD46 and CD59. CD46 exhibited the most striking pattern of association, with increased levels of expression being associated with ER-positive samples and lower levels of expression associated with a loss of differentiation and epidermal growth factor receptor positivity. Application of Spearman rank correlation test revealed CD46 expression was significantly associated with expression of ER at the level of protein (p = 0.031; r = 0.31) and mRNA (p < 0.001; r = 0.52). CD46 expression also correlated with insulin-like growth factor receptor-positive samples using Spearman rank correlation test (p = 0.016; r = 0.34), but negatively associated with tumor samples either exhibiting histologic grade 3 when compared to grades 1 or 2 or displaying elevated levels of inflammatory cell infiltrate. Immunohistochemical analysis of a limited series (n = 8) of paraffin-embedded breast cancers indicated that the level of CD46 protein expression directly associates with that of the mRNA and, where prominent, is localized in the tumor epithelial cell population, including at the plasma membrane. These data provide new information on expression of these important regulators in breast cancer and suggest that CD46 should be evaluated as a novel prognostic indicator.
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Affiliation(s)
- Neil K Rushmere
- Complement Biology Group, Department of Medical Biochemistry, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, Wales, UK.
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Matsuda A, Itoh Y, Koshikawa N, Akizawa T, Yana I, Seiki M. Clusterin, an abundant serum factor, is a possible negative regulator of MT6-MMP/MMP-25 produced by neutrophils. J Biol Chem 2003; 278:36350-7. [PMID: 12860995 DOI: 10.1074/jbc.m301509200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MT6-MMP/MMP-25 is the latest member of the membrane-type matrix metalloproteinase (MT-MMP) subgroup in the MMP family and is expressed in neutrophils and some brain tumors. The proteolytic activity of MT6-MMP has been studied using recombinant catalytic fragments and shown to degrade several components of the extracellular matrix. However, the activity is possibly modulated further by the C-terminal hemopexin-like domain, because some MMPs are known to interact with other proteins through this domain. To explore the possible function of this domain, we purified a recombinant MT6-MMP with the hemopexin-like domain as a soluble form using a Madin-Darby canine kidney cell line as a producer. Mature and soluble MT6-MMP processed at the furin motif was purified as a 45-kDa protein together with a 46-kDa protein having a single cleavage in the hemopexin-like domain. Interestingly, 73- and 70-kDa proteins were co-purified with the soluble MT6-MMP by forming stable complexes. They were identified as clusterin, a major component of serum, by N-terminal amino acid sequencing. MT1-MMP that also has a hemopexin-like domain did not form a complex with clusterin. MT6-MMP forming a complex with clusterin was detected in human neutrophils as well. The enzyme activity of the soluble MT6-MMP was inactive in the clusterin complex. Purified clusterin was inhibitory against the activity of soluble MT6-MMP. On the other hand, it had no effect on the activities of MMP-2 and soluble MT1-MMP. Because clusterin is an abundant protein in the body fluid in tissues, it may act as a negative regulator of MT6-MMP in vivo.
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Affiliation(s)
- Akira Matsuda
- Division of Cancer Cell Research, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
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Wakimoto H, Johnson PR, Knipe DM, Chiocca EA. Effects of innate immunity on herpes simplex virus and its ability to kill tumor cells. Gene Ther 2003; 10:983-90. [PMID: 12756419 DOI: 10.1038/sj.gt.3302038] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Several clinical trials have or are being performed testing the safety and efficacy of different strains of oncolytic viruses (OV) for malignant cancers. OVs represent either naturally occurring or genetically engineered strains of viruses that exhibit relatively selective replication in tumor cells. Several types of OV have been derived from herpes simplex virus 1 (HSV1). Tumor oncolysis depends on the processes of initial OV infection of tumor, followed by subsequent propagation of OV within the tumor itself. The role of the immune responses in these processes has not been extensively studied. On the contrary, effects of the immune response on the processes of wild-type HSV1 infection and propagation in the central nervous system have been studied and described in detail. The first line of defense against a wild-type HSV1 infection in both naive and immunized individuals is provided by innate humoral (complement, cytokines, chemokines) and cellular (macrophages, neutrophils, NK cells, gammadelta T cells, and interferon-producing cells) responses. These orchestrate the lysis of virions and virus-infected cells as well as provide a link to effective adaptive immunity. The role of innate defenses in curtailing the oncolytic effect of genetically engineered HSV has only recently been studied, but several of the same host responses appear to be operative in limiting anticancer effects by the replicating virus. The importance of this knowledge lies in finding avenues to modulate such initial innate responses, in order to allow for increased oncolysis of tumors while minimizing host toxicity.
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Affiliation(s)
- H Wakimoto
- Molecular Neuro-Oncology Laboratories, Neurosurgery Service, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
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Lymar ES, Clark AM, Reeves R, Griswold MD. Clusterin gene in rat sertoli cells is regulated by a core-enhancer element. Biol Reprod 2000; 63:1341-51. [PMID: 11058537 DOI: 10.1095/biolreprod63.5.1341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Clusterin is a ubiquitous glycoprotein that is promiscuously expressed at a low basal level but can be highly induced by a variety of stress conditions. In contrast, in some secretory cells associated with tissue-fluid interfaces such as the Sertoli cells in the testis, clusterin demonstrates high constitutive expression. In this study, we address the mechanisms that regulate the constitutive expression of the clusterin gene by using primary cultures of immature rat Sertoli cells. We have identified a region of the rat clusterin gene promoter that activated transcription only in Sertoli cells and that mapped between positions -426 and -311. Sequence analysis of this region revealed a high concentration of potential regulatory elements. Using gel-shift assays combined with hydroxyl radical footprinting, we identified the elements recognized by the Sertoli cell nuclear factors. Comparison of the interactions with this region of the nuclear factors from different cell types demonstrated that recognition of the core-enhancer element is specific for the Sertoli cells, and in vitro, the core region was recognized by the transcription factor CBF. Transient transfections showed that a core enhancer is responsible for more than a half of the total promoter activity and is an essential element for the cell-specific activity of the Sertoli-specific region. In addition to the core enhancer, tandem Sp1 sites are also required for maximal activity of this region.
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Affiliation(s)
- E S Lymar
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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Thorsteinsson L, O'Dowd GM, Harrington PM, Johnson PM. The complement regulatory proteins CD46 and CD59, but not CD55, are highly expressed by glandular epithelium of human breast and colorectal tumour tissues. APMIS 1998; 106:869-78. [PMID: 9808413 DOI: 10.1111/j.1699-0463.1998.tb00233.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three of the proteins protecting cells from autologous lysis by complement are: membrane cofactor protein (MCP; CD46), an inhibitor of the membrane attack complex formation (CD59), and decay accelerating factor (DAF; CD55). We have investigated the expression of these proteins in breast and colorectal carcinoma by immunohistochemistry and immunoblotting of breast tissue for CD46. CD46 was consistently and strongly expressed in the epithelial compartment in 26/28 ductal carcinomas of the breast, 9/9 fibroadenomas, and 9/11 cases of control non-neoplastic breast tissue. CD59 showed a similar degree of expression in the fibroadenomas (9/9), but was less strongly expressed in carcinomatous (22/28) and control (5/11) tissues. In marked contrast, no CD55 expression was detected in tissue from 15 ductal carcinomas. Immunoblotting of breast tissue for CD46 showed the same size of the molecule as for lymphocytes. It had however considerably stronger expression in tumour tissue than in non-neoplastic tissue. CD46 and CD59 were either lacking or only weakly expressed in the epithelial component of control colorectal mucosa: 2/15 and 5/15, respectively. In contrast, tissue samples from colorectal adenocarcinomas showed clear staining for both CD59 (10/18) and, more markedly, CD46 (15/18). There was no association between the pattern or intensity of CD46 and CD59 expression and tumour differentiation. As the complement regulatory proteins CD46 and CD59 are also strongly expressed by trophoblast at the feto-maternal tissue interface, these results support the concept that similar mechanisms are employed both by the genetically dissimilar fetus and certain tumours to evade immune attack by their host.
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Affiliation(s)
- L Thorsteinsson
- Cancer Tissue Bank Research Centre, and Department of Immunology, University of Liverpool, England
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