1
|
Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020. [PMID: 33033246 DOI: 10.1038/s41467-020-18875-x.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
Collapse
Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain. .,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain.,Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
| |
Collapse
|
2
|
Martinez-Lage M, Torres-Ruiz R, Puig-Serra P, Moreno-Gaona P, Martin MC, Moya FJ, Quintana-Bustamante O, Garcia-Silva S, Carcaboso AM, Petazzi P, Bueno C, Mora J, Peinado H, Segovia JC, Menendez P, Rodriguez-Perales S. In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells. Nat Commun 2020; 11:5060. [PMID: 33033246 PMCID: PMC7544871 DOI: 10.1038/s41467-020-18875-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Fusion oncogenes (FOs) are common in many cancer types and are powerful drivers of tumor development. Because their expression is exclusive to cancer cells and their elimination induces cell apoptosis in FO-driven cancers, FOs are attractive therapeutic targets. However, specifically targeting the resulting chimeric products is challenging. Based on CRISPR/Cas9 technology, here we devise a simple, efficient and non-patient-specific gene-editing strategy through targeting of two introns of the genes involved in the rearrangement, allowing for robust disruption of the FO specifically in cancer cells. As a proof-of-concept of its potential, we demonstrate the efficacy of intron-based targeting of transcription factors or tyrosine kinase FOs in reducing tumor burden/mortality in in vivo models. The FO targeting approach presented here might open new horizons for the selective elimination of cancer cells.
Collapse
Affiliation(s)
- M Martinez-Lage
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - R Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain.
| | - P Puig-Serra
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - P Moreno-Gaona
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - M C Martin
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - F J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - O Quintana-Bustamante
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - S Garcia-Silva
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - A M Carcaboso
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - P Petazzi
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - C Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
| | - J Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, 08950, Barcelona, Spain
| | - H Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - J C Segovia
- Differentiation and Cytometry Unit, Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), 28040, Madrid, Spain
- Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), 28040, Madrid, Spain
| | - P Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, 08036, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, 08010, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - S Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
| |
Collapse
|
3
|
Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment. Nat Commun 2018; 9:3169. [PMID: 30093669 PMCID: PMC6085350 DOI: 10.1038/s41467-018-05707-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Targeting specific protein–protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibition. A potential solution to these problems is to select intracellular antibody fragments to block PPIs, use these antibody fragments for target validation in disease models and finally derive small molecules overlapping the antibody-binding site. Here, we explore this strategy using an anti-mutant RAS antibody fragment as a competitor in a small-molecule library screen for identifying RAS-binding compounds. The initial hits are optimized by structure-based design, resulting in potent RAS-binding compounds that interact with RAS inside the cells, prevent RAS-effector interactions and inhibit endogenous RAS-dependent signalling. Our results may aid RAS-dependent cancer drug development and demonstrate a general concept for developing small compounds to replace intracellular antibody fragments, enabling rational drug development to target validated PPIs. Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells.
Collapse
|
4
|
Werner H, Meisel-Sharon S, Bruchim I. Oncogenic fusion proteins adopt the insulin-like growth factor signaling pathway. Mol Cancer 2018; 17:28. [PMID: 29455671 PMCID: PMC5817802 DOI: 10.1186/s12943-018-0807-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/05/2018] [Indexed: 02/08/2023] Open
Abstract
The insulin-like growth factor-1 receptor (IGF1R) has been identified as a potent anti-apoptotic, pro-survival tyrosine kinase-containing receptor. Overexpression of the IGF1R gene constitutes a typical feature of most human cancers. Consistent with these biological roles, cells expressing high levels of IGF1R are expected not to die, a quintessential feature of cancer cells. Tumor specific chromosomal translocations that disrupt the architecture of transcription factors are a common theme in carcinogenesis. Increasing evidence gathered over the past fifteen years demonstrate that this type of genomic rearrangements is common not only among pediatric and hematological malignancies, as classically thought, but may also provide a molecular and cytogenetic foundation for an ever-increasing portion of adult epithelial tumors. In this review article we provide evidence that the mechanism of action of oncogenic fusion proteins associated with both pediatric and adult malignancies involves transactivation of the IGF1R gene, with ensuing increases in IGF1R levels and ligand-mediated receptor phosphorylation. Disrupted transcription factors adopt the IGF1R signaling pathway and elicit their oncogenic activities via activation of this critical regulatory network. Combined targeting of oncogenic fusion proteins along with the IGF1R may constitute a promising therapeutic approach.
Collapse
Affiliation(s)
- Haim Werner
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel. .,Yoran Institute for Human Genome Research, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Shilhav Meisel-Sharon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ilan Bruchim
- Department of Obstetrics and Gynecology, Hillel Yaffe Medical Center, Hadera 38100, affiliated with the Technion Institute of Technology, Haifa, Israel
| |
Collapse
|
5
|
Sharon SM, Pozniak Y, Geiger T, Werner H. TMPRSS2-ERG fusion protein regulates insulin-like growth factor-1 receptor (IGF1R) gene expression in prostate cancer: involvement of transcription factor Sp1. Oncotarget 2016; 7:51375-51392. [PMID: 27285981 PMCID: PMC5239482 DOI: 10.18632/oncotarget.9837] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/22/2016] [Indexed: 01/12/2023] Open
Abstract
Prostate cancer is a major health issue in the Western world. The most common gene rearrangement in prostate cancer is the TMPRSS2-ERG fusion, which results in aberrant expression of the transcription factor ERG. The insulin-like growth factor-1 receptor (IGF1R) plays a key role in cell growth and tumorigenesis, and is overexpressed in most malignancies, including prostate cancer. In this study we show that TMPRSS2-ERG mediates its tumorigenic effects through regulation of IGF1R gene expression. Silencing of T-ERG in VCaP cells resulted in downregulation of both IGF1R and Sp1, a critical IGF1R regulator. Co-immunoprecipitation assays revealed a physical interaction between transcription factors ERG and Sp1, with potential relevance in IGF1R gene regulation. In addition, transactivation of the IGF1R gene by ERG was mediated at the level of transcription, as indicated by results of promoter assays. To identify new co-activators of the TMPRSS2-ERG fusion protein we performed mass spectrometry-based proteomic analyses. Among other interactors, we identified AP-2 complex subunit mu (AP2M1) and caveolin-1 (CAV1) in association with ERG in cell nuclei. These proteins play a mechanistic role in IGF1R internalization. Our analyses are consistent with a potential novel function of TMPRSS2-ERG as a major regulator of IGF1R gene expression. Results may impinge upon ongoing efforts to target the IGF1R in the clinics.
Collapse
Affiliation(s)
- Shilhav Meisel Sharon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim Werner
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Yoran Institute for Human Genome Research, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
6
|
Igarashi H, Koizumi K, Kaneko R, Ikeda K, Egawa R, Yanagawa Y, Muramatsu SI, Onimaru H, Ishizuka T, Yawo H. A Novel Reporter Rat Strain That Conditionally Expresses the Bright Red Fluorescent Protein tdTomato. PLoS One 2016; 11:e0155687. [PMID: 27195805 PMCID: PMC4873025 DOI: 10.1371/journal.pone.0155687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/03/2016] [Indexed: 01/28/2023] Open
Abstract
Despite the strength of the Cre/loxP recombination system in animal models, its application in rats trails that in mice because of the lack of relevant reporter strains. Here, we generated a floxed STOP tdTomato rat that conditionally expresses a red fluorescent protein variant (tdTomato) in the presence of exogenous Cre recombinase. The tdTomato signal vividly visualizes neurons including their projection fibers and spines without any histological enhancement. In addition, a transgenic rat line (FLAME) that ubiquitously expresses tdTomato was successfully established by injecting intracytoplasmic Cre mRNA into fertilized ova. Our rat reporter system will facilitate connectome studies as well as the visualization of the fine structures of genetically identified cells for long periods both in vivo and ex vivo. Furthermore, FLAME is an ideal model for organ transplantation research owing to improved traceability of cells/tissues.
Collapse
Affiliation(s)
- Hiroyuki Igarashi
- Department of Physiology and Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
- Tohoku University Division for Interdisciplinary Advanced Research and Education, Sendai, Miyagi, Japan
| | - Kyo Koizumi
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi, Japan
| | - Ryosuke Kaneko
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
- Bioresource center, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Keiko Ikeda
- Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Ryo Egawa
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi, Japan
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Shin-ichi Muramatsu
- Division of Neurology, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
- Center for Gene & Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Onimaru
- Department of Physiology, Showa University School of Medicine, Shinagawa, Tokyo, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi, Japan
| | - Hiromu Yawo
- Department of Physiology and Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Miyagi, Japan
| |
Collapse
|
7
|
Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA. Neoplasia 2013; 14:1087-96. [PMID: 23226102 DOI: 10.1593/neo.121342] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/16/2012] [Accepted: 09/30/2012] [Indexed: 12/15/2022] Open
Abstract
mRNA chimeras from chromosomal translocations often play a role as transforming oncogenes. However, cancer transcriptomes also contain mRNA chimeras that may play a role in tumor development, which arise as transcriptional or post-transcriptional events. To identify such chimeras, we developed a deterministic screening strategy for long-range sequence analysis. High-throughput, long-read sequencing was then performed on cDNA libraries from major tumor histotypes and corresponding normal tissues. These analyses led to the identification of 378 chimeras, with an unexpectedly high frequency of expression (≈2 x 10(-5) of all mRNA). Functional assays in breast and ovarian cancer cell lines showed that a large fraction of mRNA chimeras regulates cell replication. Strikingly, chimeras were shown to include both positive and negative regulators of cell growth, which functioned as such in a cell-type-specific manner. Replication-controlling chimeras were found to be expressed by most cancers from breast, ovary, colon, uterus, kidney, lung, and stomach, suggesting a widespread role in tumor development.
Collapse
|
8
|
Zhang L, Mitani Y, Caulin C, Rao PH, Kies MS, Saintigny P, Zhang N, Weber RS, Lippman SM, El-Naggar AK. Detailed genome-wide SNP analysis of major salivary carcinomas localizes subtype-specific chromosome sites and oncogenes of potential clinical significance. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 182:2048-57. [PMID: 23583282 DOI: 10.1016/j.ajpath.2013.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/04/2013] [Accepted: 02/11/2013] [Indexed: 01/31/2023]
Abstract
The molecular genetic alterations underlying the development and diversity of salivary gland carcinomas are largely unknown. To characterize these events, comparative genomic hybridization analysis was performed, using a single-nucleotide polymorphism microarray platform, of 60 fresh-frozen specimens that represent the main salivary carcinoma types: mucoepidermoid carcinoma (MEC), adenoid cystic carcinoma (ACC), and salivary duct carcinoma (SDC). The results were correlated with the clinicopathologic features and translocation statuses to characterize the genetic alterations. The most commonly shared copy number abnormalities (CNAs) in all types were losses at chromosomes 6q23-26 and the 9p21 region. Subtype-specific CNAs included a loss at 12q11-12 in ACC and a gain at 17q11-12 in SDC. Focal copy number losses included 1p36.33-p36-22 in ACC, 9p13.2 in MEC, and 3p12.3-q11-2, 6q21-22.1, 12q14.1, and 12q15 in SDC. Tumor-specific amplicons were identified at 11q23.3 (PVRL1) in ACC, 11q13.3 (NUMA1) in MEC, and 6p21.1 (CCND3), 9p13.2 (PAX5), 12q15 (CNOT2/RAB3IP), 12q21.1 (GLIPR1L1), and 17q12 (ERBB2/CCL4) in SDC. A comparative CNA analysis of fusion-positive and fusion-negative ACCs and MECs revealed relatively lower CNAs in fusion-positive tumors than in fusion-negative tumors in both tumor types. An association between CNAs and high grade and advanced stage was observed in MECs only. These findings support the pathogenetic segregation of these entities and define novel chromosomal sites for future identification of biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Lim B, Jun HJ, Kim AY, Kim S, Choi J, Kim J. The TFG-TEC fusion gene created by the t(3;9) translocation in human extraskeletal myxoid chondrosarcomas encodes a more potent transcriptional activator than TEC. Carcinogenesis 2012; 33:1450-8. [PMID: 22581839 DOI: 10.1093/carcin/bgs164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The t(3;9)(q11-q12;q22) translocation associated with human extraskeletal myxoid chondrosarcomas results in a chimeric molecule in which the N-terminal domain (NTD) of the TFG (TRK-fused gene) is fused to the TEC (Translocated in Extraskeletal Chondrosarcoma) gene. Little is known about the biological function of TFG-TEC. Because the NTDs of TFG-TEC and TEC are structurally different, and the TFG itself is a cytoplasmic protein, the functional consequences of this fusion in extraskeletal myxoid chondrosarcomas were examined. The results showed that the chimeric gene encoded a nuclear protein that bound DNA with the same sequence specificity as the parental TEC protein. Comparison of the transactivation properties of TFG-TEC and TEC indicated that the former has higher transactivation activity for a known target reporter containing TEC-binding sites. Additional reporter assays for TFG (NTD) showed that the TGF (NTD) of TFG-TEC induced a 12-fold increase in the activation of luciferase from a reporter plasmid containing GAL4 binding sites when fused to the DNA-binding domain of GAL4, indicating that the TFG (NTD) of the TFG-TEC protein has intrinsic transcriptional activation properties. Finally, deletion analysis of the functional domains of TFG (NTD) indicated that the PB1 (Phox and Bem1p) and SPYGQ-rich region of TFG (NTD) were capable of activating transcription and that full integrity of TFG (NTD) was necessary for full transactivation. These results suggest that the oncogenic effect of the t(3;9) translocation may be due to the TFG-TEC chimeric protein and that fusion of the TFG (NTD) to the TEC protein produces a gain-of-function chimeric product.
Collapse
Affiliation(s)
- Bobae Lim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University Seoul 121-742, Korea
| | | | | | | | | | | |
Collapse
|
10
|
Mitani Y, Rao PH, Futreal PA, Roberts DB, Stephens PJ, Zhao YJ, Zhang L, Mitani M, Weber RS, Lippman SM, Caulin C, El-Naggar AK. Novel chromosomal rearrangements and break points at the t(6;9) in salivary adenoid cystic carcinoma: association with MYB-NFIB chimeric fusion, MYB expression, and clinical outcome. Clin Cancer Res 2011; 17:7003-14. [PMID: 21976542 PMCID: PMC3225955 DOI: 10.1158/1078-0432.ccr-11-1870] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To investigate the molecular genetic heterogeneity associated with the t(6:9) in adenoid cystic carcinoma (ACC) and correlate the findings with patient clinical outcome. EXPERIMENTAL DESIGN Multimolecular and genetic techniques complemented with massive pair-ended sequencing and single-nucleotide polymorphism array analyses were used on tumor specimens from 30 new and 52 previously analyzed fusion transcript-negative ACCs by reverse transcriptase PCR (RT-PCR). MYB mRNA expression level was determined by quantitative RT-PCR. The results of 102 tumors (30 new and 72 previously reported cases) were correlated with the clinicopathologic factors and patients' survival. RESULTS The FISH analysis showed 34 of 82 (41.5%) fusion-positive tumors and molecular techniques identified fusion transcripts in 21 of the 82 (25.6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene. Massive pair-end sequencing of a subset of tumors confirmed the proximal translocation to an NFIB sequence and led to the identification of a new fusion gene (NFIB-AIG1) in one of the tumors. Overall, MYB-NFIB gene fusion rate by FISH was in 52.9% whereas fusion transcript forming incidence was 38.2%. Significant statistical association between the 5' MYB transcript expression and patient survival was found. CONCLUSIONS We conclude that: (i) t(6;9) results in complex genetic and molecular alterations in ACC, (ii) MYB-NFIB gene fusion may not always be associated with chimeric transcript formation, (iii) noncanonical MYB-NFIB gene fusions occur in a subset of tumors, (iv) high MYB expression correlates with worse patient survival.
Collapse
Affiliation(s)
- Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Falzarano SM, Zhou M, Carver P, Tsuzuki T, Simmerman K, He H, Magi-Galluzzi C. ERG gene rearrangement status in prostate cancer detected by immunohistochemistry. Virchows Arch 2011; 459:441-7. [PMID: 21773753 DOI: 10.1007/s00428-011-1128-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/07/2011] [Accepted: 04/20/2011] [Indexed: 11/30/2022]
Abstract
TMPRSS2-ERG, the most common gene fusion in prostate cancer, is associated with expression of a truncated protein product of the oncogene ERG. A novel anti-ERG monoclonal antibody has been recently characterized. We investigated the correlation between ERG rearrangement assessed by fluorescence in situ hybridization (FISH) and ERG expression detected by immunohistochemistry in a large cohort of patients treated with radical prostatectomy for clinically localized prostate cancer. Thirteen tissue microarrays comprising 305 tumors and a subset of 112 samples of nonneoplastic prostatic tissue were assessed for ERG rearrangement status by FISH and for ERG expression by immunohistochemistry. Accuracy of ERG detection by immunohistochemistry in predicting ERG status as assessed by FISH (criterion standard) was calculated in terms of sensitivity, specificity, positive and negative predictive values. Of 305 tumor foci, 103 (34%) showed ERG rearrangement by FISH. ERG was detected by immunohistochemistry in 100 (33%) cases, 99 of which were FISH positive. ERG detection by immunohistochemistry demonstrated a sensitivity and specificity of 96% and 99%, respectively, with positive and negative predictive values of 99% and 98%, respectively. None of the 112 samples of nonneoplastic prostatic tissue was rearranged by FISH or showed any ERG expression. In conclusion, ERG detection by immunohistochemistry in prostate cancer was highly predictive of ERG rearrangement as assessed by FISH in a large cohort of prostatectomy patients. Given the high yield and the easier task of performing immunohistochemistry vs. FISH, ERG assessment by immunohistochemistry may be useful for characterizing ERG status in prostate cancer.
Collapse
|
12
|
Kim S, Lim B, Kim J. EWS-Oct-4B, an alternative EWS-Oct-4 fusion gene, is a potent oncogene linked to human epithelial tumours. Br J Cancer 2010; 102:436-46. [PMID: 20051954 PMCID: PMC2816667 DOI: 10.1038/sj.bjc.6605516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Characterisation of EWS-Oct-4 translocation fusion product in bone and soft-tissue tumours revealed a chimeric gene resulting from an in-frame fusion between EWS (Ewing's sarcoma gene) exons 1-6 and Oct-4 exons 1-4. Recently, an alternative form of the fusion protein between the EWS and Oct-4 genes, named EWS-Oct-4B, was reported in two types of epithelial tumours, a hidradenoma of the skin and a mucoepidermoid carcinoma of the salivary glands. As the N-terminal and POU domains of the EWS-Oct-4 and EWS-Oct-4B proteins are not structurally identical, we decided to investigate the functional consequences of the EWS-Oct-4B fusion. METHODS In this report, we have characterised the EWS-Oct-4B fusion protein. To investigate how the EWS-Oct-4B protein contributes to tumourigenesis in human cancers, we analysed its DNA-binding activity, subcellular localisation, transcriptional activation behaviour, and oncogenic properties. RESULTS We found that this new chimeric gene encodes a nuclear protein that binds DNA with the same sequence specificity as the parental Oct-4 protein or the fusion EWS-Oct-4 protein. We show that the nuclear localisation signal of EWS-Oct-4B is dependent on the POU DNA-binding domain, and we identified a cluster of basic amino acids, (269)RKRKR(273), in the POU domain that specifically mediates the nuclear localisation of EWS-Oct-4B. Comparison of the properties of EWS-Oct-4B and EWS-Oct-4 indicated that EWS-Oct-4B is a less-potent transcriptional activator of a reporter construct carrying the Oct-4-binding sites. Deletion analysis of the functional domains of EWS-Oct-4B revealed that the EWS N-terminal domain (NTD)(B), POU, and C-terminal domain (CTD) are necessary for its full transactivation potential. Despite its reduced activity as a transcriptional activator, EWS-Oct-4B regulated the expression of fgf-4 (fibroblast growth factor-4) and nanog, which are potent mitogens, as well as of Oct-4 downstream target genes, the promoters of which contain potential Oct-4-binding sites. Finally, ectopic expression of EWS-Oct-4B in Oct-4-null ZHBTc4 ES cells resulted in increased tumourigenic growth potential in nude mice. CONCLUSION These results suggest that the oncogenic effect of the t(6;22) translocation is due to the EWS-Oct-4B chimeric protein, and that alternative fusion of the EWS amino terminal domain to the Oct-4 DNA-binding domain produces another transforming chimeric product in human epithelial tumours.
Collapse
Affiliation(s)
- S Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, Korea
| | | | | |
Collapse
|
13
|
Hegyi H, Buday L, Tompa P. Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PLoS Comput Biol 2009; 5:e1000552. [PMID: 19888473 PMCID: PMC2768585 DOI: 10.1371/journal.pcbi.1000552] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 09/30/2009] [Indexed: 12/22/2022] Open
Abstract
Chromosomal translocations, which often generate chimeric proteins by fusing segments of two distinct genes, represent the single major genetic aberration leading to cancer. We suggest that the unifying theme of these events is a high level of intrinsic structural disorder, enabling fusion proteins to evade cellular surveillance mechanisms that eliminate misfolded proteins. Predictions in 406 translocation-related human proteins show that they are significantly enriched in disorder (43.3% vs. 20.7% in all human proteins), they have fewer Pfam domains, and their translocation breakpoints tend to avoid domain splitting. The vicinity of the breakpoint is significantly more disordered than the rest of these already highly disordered fusion proteins. In the unlikely event of domain splitting in fusion it usually spares much of the domain or splits at locations where the newly exposed hydrophobic surface area approximates that of an intact domain. The mechanisms of action of fusion proteins suggest that in most cases their structural disorder is also essential to the acquired oncogenic function, enabling the long-range structural communication of remote binding and/or catalytic elements. In this respect, there are three major mechanisms that contribute to generating an oncogenic signal: (i) a phosphorylation site and a tyrosine-kinase domain are fused, and structural disorder of the intervening region enables intramolecular phosphorylation (e.g., BCR-ABL); (ii) a dimerisation domain fuses with a tyrosine kinase domain and disorder enables the two subunits within the homodimer to engage in permanent intermolecular phosphorylations (e.g., TFG-ALK); (iii) the fusion of a DNA-binding element to a transactivator domain results in an aberrant transcription factor that causes severe misregulation of transcription (e.g. EWS-ATF). Our findings also suggest novel strategies of intervention against the ensuing neoplastic transformations. Chromosomal translocations generate chimeric proteins by fusing segments of two distinct genes and are frequently associated with cancer. The proteins involved are large and fairly heterogeneous in sequence and typically have only a few dispersed structural domains connected by long uncharacterized regions. It has never been studied from a structural perspective how these chimeras survive losing significant portions of the original proteins and acquire new oncogenic functions. By analyzing a collection of 406 human translocation proteins we show here that the answer to both questions lies to a large extent in the high level of structural disorder in the fusion partner proteins (on average, they are twice as disordered as all human proteins). The translocation breakpoints usually avoid globular domains. In rare cases when a globular domain is truncated by the fusion, it happens at a location in the domain where the hydrophobicity exposed by the split is favorable (i.e., not too high). Disorder on average is significantly higher in the vicinity of the breakpoint than in the rest of the fusion proteins. Disorder also plays a pivotal role in the acquired oncogenic function by bringing distant/disparate fusion segments together that enables novel intra- and/or intermolecular interactions.
Collapse
Affiliation(s)
- Hedi Hegyi
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University Medical School, Budapest, Hungary
| | - Peter Tompa
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
| |
Collapse
|
14
|
Lee J, Kim J, Kang I, Kim H, Han YM, Kim J. The EWS-Oct-4 fusion gene encodes a transforming gene. Biochem J 2007; 406:519-26. [PMID: 17564582 PMCID: PMC2049031 DOI: 10.1042/bj20070243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The t(6;22)(p21;q12) translocation associated with human bone and soft-tissue tumours results in a chimaeric molecule fusing the NTD (N-terminal domain) of the EWS (Ewing's sarcoma) gene to the CTD (C-terminal domain) of the Oct-4 (octamer-4) embryonic gene. Since the N-terminal domains of EWS and Oct-4 are structurally different, in the present study we have assessed the functional consequences of the EWS-Oct-4 fusion. We find that this chimaeric gene encodes a nuclear protein which binds DNA with the same sequence specificity as the parental Oct-4 protein. Comparison of the transactivation properties of EWS-Oct-4 and Oct-4 indicates that the former has higher transactivation activity for a known target reporter gene containing Oct-4 binding. Deletion analysis of the functional domains of EWS-Oct-4 indicates that the EWS (NTD), the POU domain and the CTD of EWS-Oct-4 are necessary for full transactivation potential. EWS-Oct-4 induced the expression of fgf-4 (fibroblast growth factor 4) and nanog, which are potent mitogens as well as Oct-4 downstream target genes whose promoters contain potential Oct-4-binding sites. Finally, ectopic expression of EWS-Oct-4 in Oct-4-null ZHBTc4 ES (embryonic stem) cells resulted in increased tumorigenic growth potential in nude mice. These results suggest that the oncogenic effect of the t(6;22) translocation is due to the EWS-Oct-4 chimaeric protein and that fusion of the EWS NTD to the Oct-4 DNA-binding domain produces a transforming chimaeric product.
Collapse
MESH Headings
- Animals
- Cell Transformation, Neoplastic
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 6/genetics
- DNA-Binding Proteins
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation
- Humans
- Mice
- Mice, Nude
- Octamer Transcription Factor-3/genetics
- Octamer Transcription Factor-3/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Oncogenes/physiology
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Sarcoma, Ewing
- Translocation, Genetic
Collapse
Affiliation(s)
- Jungwoon Lee
- *Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Ja Young Kim
- *Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - In Young Kang
- *Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Hye Kyoung Kim
- *Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Yong-Mahn Han
- †Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
| | - Jungho Kim
- *Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-742, South Korea
- To whom correspondence should be addressed (email )
| |
Collapse
|
15
|
Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res 2007; 6:1899-916. [PMID: 17391015 PMCID: PMC2588346 DOI: 10.1021/pr060393m] [Citation(s) in RCA: 193] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.
Collapse
Affiliation(s)
- Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- CORRESPONDING AUTHOR FOOTNOTE: Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
| |
Collapse
|
16
|
Harrison CJ, Griffiths M, Moorman F, Schnittger S, Cayuela JM, Shurtleff S, Gottardi E, Mitterbauer G, Colomer D, Delabesse E, Castéras V, Maroc N. A multicenter evaluation of comprehensive analysis of MLL translocations and fusion gene partners in acute leukemia using the MLL FusionChip device. ACTA ACUST UNITED AC 2007; 173:17-22. [PMID: 17284365 DOI: 10.1016/j.cancergencyto.2006.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 09/07/2006] [Indexed: 10/23/2022]
Abstract
Rearrangements of the MLL gene are significant in acute leukemia. Among the most frequent translocations are t(4;11)(q21;q23) and t(9;11)(p22;q23), which give rise to the MLL-AFF1 and MLL-MLLT3 fusion genes (alias MLL-AF4 and MLL-AF9) in acute lymphoblastic and acute myeloid leukemia, respectively. Current evidence suggests that determining the MLL status of acute leukemia, including precise identification of the partner gene, is important in defining appropriate treatment. This underscores the need for accurate detection methods. A novel molecular diagnostic device, the MLL FusionChip, has been successfully used to identify MLL fusion gene translocations in acute leukemia, including the precise breakpoint location. This study evaluated the performance of the MLL FusionChip within a routine clinical environment, comprising nine centers worldwide, in the analysis of 21 control and 136 patient samples. It was shown that the assay allowed accurate detection of the MLL fusion gene, regardless of the breakpoint location, and confirmed that this multiplex approach was robust in a global multicenter trial. The MLL FusionChip was shown to be superior to other detection methods. The type of molecular information provided by MLL FusionChip gave an indication of the appropriate primers to design for disease monitoring of MLL patients following treatment.
Collapse
MESH Headings
- Acute Disease
- Adult
- Child
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 9
- Histone-Lysine N-Methyltransferase
- Humans
- In Situ Hybridization, Fluorescence
- Infant
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oligonucleotide Array Sequence Analysis/instrumentation
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins, Fusion/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Translocation, Genetic
Collapse
Affiliation(s)
- Christine J Harrison
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, MP 822 Duthie Building, Southampton General Hospital, Southampton SO16 6YD, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Soft tissue tumours represent a heterogeneous group of mesenchymal lesions and their classification continues to evolve as a result of incorporating advances in cytogenetic and molecular techniques. In the last decade traditional diagnostic approaches were supplemented with a significant number of reliable molecular diagnostic tools, detecting tumour type-specific genetic alterations. In addition, the successful application of some of these techniques to formalin-fixed paraffin-embedded tissue made it possible to subject a broader range of clinical material to molecular analysis. Thus, molecular genetics has already become an integral part of the work-up in some tumours, such as paediatric small blue round cell tumours, which demonstrate characteristic translocations. Several lines of evidence suggest that sarcomas can be divided into two major genetic groups: (i) sarcomas with specific genetic alterations and usually simple karyotypes, such as reciprocal chromosomal translocations (e.g. FUS-DDIT3 in myxoid liposarcoma) and specific oncogenic mutations (e.g. KIT mutation in gastrointestinal stromal tumours); and (i) sarcomas with non-specific genetic alterations and complex unbalanced karyotypes. Some of these genetic abnormalities, including chromosomal numerical changes, translocations, gene amplifications or large deletions can be apparent at the cytogenetic level (karyotyping, fluorescence in situ hybridization), while others, such as small deletions, insertions or point mutations, require molecular genetic techniques (polymerase chain reaction and sequence analysis). This review focuses on the applicability of genetic testing in the diagnosis and prognosis of soft tissue sarcomas, and gives a realistic appraisal of the ancillary role of molecular techniques, including its advantages and limitations.
Collapse
Affiliation(s)
- C R Antonescu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
| |
Collapse
|
18
|
Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genes Dev 2006; 16:394-404. [PMID: 16461635 PMCID: PMC1415204 DOI: 10.1101/gr.4247306] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 11/30/2005] [Indexed: 11/24/2022]
Abstract
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is well established that solid tumor genomes accumulate a large number of genome rearrangements during tumorigenesis. End Sequence Profiling (ESP) maps and clones genome breakpoints associated with all types of genome rearrangements elucidating the structural organization of tumor genomes. Here we extend the ESP methodology in several directions using the breast cancer cell line MCF-7. First, targeted ESP is applied to multiple amplified loci, revealing a complex process of rearrangement and co-amplification in these regions reminiscent of breakage/fusion/bridge cycles. Second, genome breakpoints identified by ESP are confirmed using a combination of DNA sequencing and PCR. Third, in vitro functional studies assign biological function to a rearranged tumor BAC clone, demonstrating that it encodes anti-apoptotic activity. Finally, ESP is extended to the transcriptome identifying four novel fusion transcripts and providing evidence that expression of fusion genes may be common in tumors. These results demonstrate the distinct advantages of ESP including: (1) the ability to detect all types of rearrangements and copy number changes; (2) straightforward integration of ESP data with the annotated genome sequence; (3) immortalization of the genome; (4) ability to generate tumor-specific reagents for in vitro and in vivo functional studies. Given these properties, ESP could play an important role in a tumor genome project.
Collapse
Affiliation(s)
- Stanislav Volik
- Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Nam CH, Rabbitts TH. The role of LMO2 in development and in T cell leukemia after chromosomal translocation or retroviral insertion. Mol Ther 2005; 13:15-25. [PMID: 16260184 DOI: 10.1016/j.ymthe.2005.09.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 09/21/2005] [Accepted: 09/21/2005] [Indexed: 01/23/2023] Open
Abstract
Chromosomal translocations are primary events in the development of leukemias, representing at least one genetic feature of the putative cancer stem cell. Studies of genes influenced by chromosomal translocations have yielded a vast amount of information about how cancer is initiated and maintained. In particular, acute leukemias have demonstrated that chromosomal translocations often involve transcription regulators that function by interacting with proteins and by controlling cell fate in the aberrant setting of the developing cancer cell. As a quintessential chromosomal translocation gene product, LMO2 has many properties that typify this class of molecule. In addition to its involvement in chromosomal translocations, the LMO2 gene was inadvertently activated in an X-SCID gene therapy trial by retroviral insertion. New molecular therapies targeted directly at the LMO2 protein could have major impact as adjuncts to existing therapies or as therapeutics in their own right. In this review, we outline the current knowledge about LMO2 and some possible routes to develop reagents that might be possible macromolecular drugs in the future.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Endothelium, Vascular/physiology
- Genetic Therapy
- Hematopoiesis
- Humans
- LIM Domain Proteins
- Leukemia, T-Cell/genetics
- Leukemia, T-Cell/metabolism
- Metalloproteins/genetics
- Metalloproteins/physiology
- Mice
- Mice, Transgenic
- Multiprotein Complexes/physiology
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Proto-Oncogene Proteins
- Retroviridae/genetics
- Transcription, Genetic
- Translocation, Genetic/genetics
- Translocation, Genetic/physiology
Collapse
Affiliation(s)
- Chang-Hoon Nam
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | | |
Collapse
|
20
|
Wan W, Albom MS, Lu L, Quail MR, Becknell NC, Weinberg LR, Reddy DR, Holskin BP, Angeles TS, Underiner TL, Meyer SL, Hudkins RL, Dorsey BD, Ator MA, Ruggeri BA, Cheng M. Anaplastic lymphoma kinase activity is essential for the proliferation and survival of anaplastic large-cell lymphoma cells. Blood 2005; 107:1617-23. [PMID: 16254137 DOI: 10.1182/blood-2005-08-3254] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The roles of aberrant expression of constitutively active ALK chimeric proteins in the pathogenesis of anaplastic large-cell lymphoma (ALCL) have been well defined; nevertheless, the notion that ALK is a molecular target for the therapeutic modulation of ALK+ ALCL has not been validated thus far. Select fused pyrrolocarbazole (FP)-derived small molecules with ALK inhibitory activity were used as pharmacologic tools to evaluate whether functional ALK is essential for the proliferation and survival of ALK+ ALCL cells in culture. These compounds inhibited interleukin 3 (IL-3)-independent proliferation of BaF3/NPM-ALK cells in an ALK inhibition-dependent manner and significantly blocked colony formation in agar of mouse embryonic fibroblast (MEF) cells harboring NPM-ALK. Inhibition of NPM-ALK phosphorylation in the ALK+ ALCL-derived cell lines resulted in significant inhibition of cell proliferation and induction of apoptotic-cell death, while having marginal effects on the proliferation and survival of K562, an ALK- leukemia cell line. ALK inhibition resulted in cell-cycle G1 arrest and inactivation of ERK1/2, STAT3, and AKT signaling pathways. Potent and selective ALK inhibitors may have therapeutic application for ALK+ ALCL and possibly other solid and hematologic tumors in which ALK activation is implicated in their pathogenesis.
Collapse
Affiliation(s)
- Weihua Wan
- Oncology, Cephalon Inc, 145 Brandywine Pkwy, West Chester, PA 19380, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Mitelman F, Mertens F, Johansson B. Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders. Genes Chromosomes Cancer 2005; 43:350-66. [PMID: 15880352 DOI: 10.1002/gcc.20212] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Chromosome abnormalities have been reported in more than 46,000 benign and malignant neoplastic disorders, leading to the identification of numerous recurrent abnormalities. A substantial number of recurrent balanced aberrations (RBAs), in particular, reciprocal translocations, occur with remarkable specificity in association with clinical and tumor characteristics. This information has become increasingly important both in basic cancer research, as a means to identify pathogenetically important genes, and clinically, as a diagnostic and prognostic instrument. Knowledge of the frequencies of such aberrations thus is of theoretical as well as practical value. However, it is unknown to what extent the data available in the literature reflect reality. A large proportion of the published cases, at least 40%, are biased, in the sense that they were reported because of a specific or unusual karyotypic feature. We have systematically ascertained all RBAs and present data on the frequencies of these abnormalities and their molecular genetic consequences among unselected patients, that is, those studied as part of investigations of consecutive series of individuals with a particular neoplastic disorder. The salient features of the present study are: (1) published data clearly overestimate the prevalence of individual RBAs in most tumor types as well as the proportion of patients having such aberrations. In fact, several well-known published RBAs are not recurrent or have not even been seen among unselected patients, and in no tumor entity, except for chronic myeloid leukemia, does the frequency of unselected cytogenetically abnormal neoplasms with RBAs exceed 35%; (2) the proportions of unselected cases characterized by RBAs among those tumor entities in which at least one RBA has been identified vary considerably both within and among hematologic malignancies, malignant lymphomas, and solid tumors; and (3) the molecular consequences of a substantial proportion, ranging from 19% in hematologic malignancies to 65% in epithelial tumors, of the most common RBAs in unselected patients remain to be clarified.
Collapse
Affiliation(s)
- Felix Mitelman
- Department of Clinical Genetics, University Hospital, Lund, Sweden.
| | | | | |
Collapse
|
22
|
Daser A, Rabbitts TH. The versatile mixed lineage leukaemia gene MLL and its many associations in leukaemogenesis. Semin Cancer Biol 2005; 15:175-88. [PMID: 15826832 DOI: 10.1016/j.semcancer.2005.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The marked association of abnormalities of chromosome 11 long arm, band q23, with human leukaemia led to the identification of the 11q23 gene called MLL (or HTRX, HRX, TRX1, ALL-1). MLL can become fused with one of a remarkable panoply of genes from other chromosome locations in individual leukaemias, leading to either acute myeloid or lymphoid tumours (hence the name MLL for mixed lineage leukaemia). The unusual finding that a single protein could be involved in both myeloid and lymphoid malignancies and that the truncated protein could do so as a fusion with very disparate partners has prompted studies to define the molecular role of MLL-fusions in leukaemogenesis and to the development of MLL-controlled mouse models of leukaemogenesis. These studies have defined MLL-fusion proteins as regulators of gene expression, controlling such elements as HOX genes, and have indicated a variety of mechanisms by which MLL-fusion proteins contribute to leukaemogenesis.
Collapse
Affiliation(s)
- A Daser
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB22QH, UK
| | | |
Collapse
|
23
|
Racanicchi S, Maccherani C, Liberatore C, Billi M, Gelmetti V, Panigada M, Rizzo G, Nervi C, Grignani F. Targeting fusion protein/corepressor contact restores differentiation response in leukemia cells. EMBO J 2005; 24:1232-42. [PMID: 15729358 PMCID: PMC556397 DOI: 10.1038/sj.emboj.7600593] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Accepted: 02/01/2005] [Indexed: 01/05/2023] Open
Abstract
The AML1/ETO and PML/RARalpha leukemia fusion proteins induce acute myeloid leukemia by acting as transcriptional repressors. They interact with corepressors, such as N-CoR and SMRT, that recruit a multiprotein complex containing histone deacetylases on crucial myeloid differentiation genes. This leads to gene repression contributing to generate a differentiation block. We expressed in leukemia cells containing PML/RARalpha and AML1/ETO N-CoR protein fragments derived from fusion protein/corepressor interaction surfaces. This blocks N-CoR/SMRT binding by these fusion proteins, and disrupts the repressor protein complex. In consequence, the expression of genes repressed by these fusion proteins increases and differentiation response to vitamin D3 and retinoic acid is restored in previously resistant cells. The alteration of PML/RARalpha-N-CoR/SMRT connections triggers proteasomal degradation of the fusion protein. The N-CoR fragments are biologically effective also when directly transduced by virtue of a protein transduction domain. Our data indicate that fusion protein activity is permanently required to maintain the leukemia phenotype and show the route to developing a novel therapeutic approach for leukemia, based on its molecular pathogenesis.
Collapse
Affiliation(s)
- Serena Racanicchi
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Chiara Maccherani
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Concetta Liberatore
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Monia Billi
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Vania Gelmetti
- Dipartimento di Istologia ed Embriologia Medica, Università di Roma ‘La Sapienza', Roma, Italy
- Parco Bio-Medico Scientifico San Raffaele di Roma, Roma, Italy
| | - Maddalena Panigada
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Giovanni Rizzo
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
| | - Clara Nervi
- Dipartimento di Istologia ed Embriologia Medica, Università di Roma ‘La Sapienza', Roma, Italy
- Parco Bio-Medico Scientifico San Raffaele di Roma, Roma, Italy
| | - Francesco Grignani
- Patologia Generale and Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, Perugia, Italy
- Medicina Interna e Scienze Oncologiche, Dipartimento di Medicina Clinica e Sperimentale, Perugia University, Policlinico Monteluce, 06100 Perugia, Italy. Tel.: +39 075 572 6264; Fax: +39 075 578 3444; E-mail:
| |
Collapse
|
24
|
Kawaguchi S, Wada T, Ida K, Sato Y, Nagoya S, Tsukahara T, Kimura S, Sahara H, Ikeda H, Shimozawa K, Asanuma H, Torigoe T, Hiraga H, Ishii T, Tatezaki SI, Sato N, Yamashita T. Phase I vaccination trial of SYT-SSX junction peptide in patients with disseminated synovial sarcoma. J Transl Med 2005; 3:1. [PMID: 15647119 PMCID: PMC545052 DOI: 10.1186/1479-5876-3-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Accepted: 01/12/2005] [Indexed: 12/26/2022] Open
Abstract
Background Synovial sarcoma is a high-grade malignant tumor of soft tissue, characterized by the specific chromosomal translocation t(X;18), and its resultant SYT-SSX fusion gene. Despite intensive multimodality therapy, the majority of metastatic or relapsed diseases still remain incurable, thus suggesting a need for new therapeutic options. We previously demonstrated the antigenicity of SYT-SSX gene-derived peptides by in vitro analyses. The present study was designed to evaluate in vivo immunological property of a SYT-SSX junction peptide in selected patients with synovial sarcoma. Methods A 9-mer peptide (SYT-SSX B: GYDQIMPKK) spanning the SYT-SSX fusion region was synthesized. Eligible patients were those (i) who have histologically and genetically confirmed, unresectable synovial sarcoma (SYT-SSX1 or SYT-SSX2 positive), (ii) HLA-A*2402 positive, (iii) between 20 and 70 years old, (iv) ECOG performance status between 0 and 3, and (v) who gave informed consent. Vaccinations with SYT-SSX B peptide (0.1 mg or 1.0 mg) were given subcutaneously six times at 14-day intervals. These patients were evaluated for DTH skin test, adverse events, tumor size, tetramer staining, and peptide-specific CTL induction. Results A total of 16 vaccinations were carried out in six patients. The results were (i) no serious adverse effects or DTH reactions, (ii) suppression of tumor progression in one patient, (iii) increases in the frequency of peptide-specific CTLs in three patients and a decrease in one patient, and (iv) successful induction of peptide-specific CTLs from four patients. Conclusions Our findings indicate the safety of the SYT-SSX junction peptide in the use of vaccination and also give support to the property of the peptide to evoke in vivo immunological responses. Modification of both the peptide itself and the related protocol is required to further improve the therapeutic efficacy.
Collapse
Affiliation(s)
- Satoshi Kawaguchi
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takuro Wada
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazunori Ida
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuriko Sato
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Nagoya
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tomohide Tsukahara
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Sigeharu Kimura
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroeki Sahara
- Marine Biomedical Institute, Sapporo Medical University School of Medicine, Rishirifuji, Japan
| | - Hideyuki Ikeda
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kumiko Shimozawa
- Cancer Vaccine Laboratory, Innovation Plaza Hokkaido, Japan Science and Technology Corporation, Sapporo, Japan
| | - Hiroko Asanuma
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroaki Hiraga
- Division of Orthopedics, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Takeshi Ishii
- Division of Orthopaedic Surgery, Chiba Cancer Center Hospital, Chiba, Japan
| | | | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toshihiko Yamashita
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
25
|
Forster A, Pannell R, Drynan L, Cano F, Chan N, Codrington R, Daser A, Lobato N, Metzler M, Nam CH, Rodriguez S, Tanaka T, Rabbitts T. Chromosomal translocation engineering to recapitulate primary events of human cancer. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2005; 70:275-82. [PMID: 16869763 DOI: 10.1101/sqb.2005.70.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mouse models of human cancers are important for understanding determinants of overt disease and for "preclinical" development of rational therapeutic strategies; for instance, based on macrodrugs. Chromosomal translocations underlie many human leukemias, sarcomas, and epithelial tumors. We have developed three technologies based on homologous recombination in mouse ES cells to mimic human chromosome translocations. The first, called the knockin method, allows creation of fusion genes like those typical of translocations of human leukemias and sarcomas. Two new conditional chromosomal translocation mimics have been developed. The first is a method for generating reciprocal chromosomal translocations de novo using Cre-loxP recombination (translocator mice). In some cases, there is incompatible gene orientation and the translocator model cannot be applied. We have developed a different model (invertor mice) for these situations. This method consists of introducing an inverted cDNA cassette into the intron of a target gene and bringing the cassette into the correct transcriptional orientation by Cre-loxP recombination. We describe experiments using the translocator model to generate MLL-mediated neoplasias and the invertor method to generate EWS-ERG-mediated cancer. These methods mimic the situation found in human chromosome translocations and provide the framework for design and study of human chromosomal translocations in mice.
Collapse
Affiliation(s)
- A Forster
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Maroc N, Morel A, Beillard E, De La Chapelle AL, Fund X, Mozziconacci MJ, Dupont M, Cayuela JM, Gabert J, Koki A, Fert V, Hermitte F. A diagnostic biochip for the comprehensive analysis of MLL translocations in acute leukemia. Leukemia 2004; 18:1522-30. [PMID: 15322560 DOI: 10.1038/sj.leu.2403439] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reciprocal rearrangements of the MLL gene are among the most common chromosomal abnormalities in both Acute Lymphoblastic and Myeloid Leukemia. The MLL gene, located on the 11q23 chromosomal band, is involved in more than 40 recurrent translocations. In the present study, we describe the development and validation of a biochip-based assay designed to provide a comprehensive molecular analysis of MLL rearrangements when used in a standard clinical pathology laboratory. A retrospective blind study was run with cell lines (n=5), and MLL positive and negative patient samples (n=31), to evaluate assay performance. The limits of detection determined on cell line data were 10(-1), and the precision studies yielded 100% repeatability and 98% reproducibility. The study shows that the device can detect frequent (AF4, AF6, AF10, ELL or ENL) as well as rare partner genes (AF17, MSF). The identified fusion transcripts can then be used as molecular phenotypic markers of disease for the precise evaluation of minimal residual disease by RQ-PCR. This biochip-based molecular diagnostic tool allows, in a single experiment, rapid and accurate identification of MLL gene rearrangements among 32 different fusion gene (FG) partners, precise breakpoint positioning and comprehensive screening of all currently characterized MLL FGs.
Collapse
Affiliation(s)
- N Maroc
- IPSOGEN SAS, Case 923, 163, Av. de Luminy, Marseille Cedex 9, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Ida K, Kawaguchi S, Sato Y, Tsukahara T, Nabeta Y, Sahara H, Ikeda H, Torigoe T, Ichimiya S, Kamiguchi K, Wada T, Nagoya S, Hiraga H, Kawai A, Ishii T, Araki N, Myoui A, Matsumoto S, Ozaki T, Yoshikawa H, Yamashita T, Sato N. Crisscross CTL induction by SYT-SSX junction peptide and its HLA-A*2402 anchor substitute. THE JOURNAL OF IMMUNOLOGY 2004; 173:1436-43. [PMID: 15240740 DOI: 10.4049/jimmunol.173.2.1436] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To investigate the effects of anchor substitutions in SYT-SSX junction peptide, an HLA-A24 anchor residue (position 9) of the SYT-SSX B peptide (GYDQIMPKK) was substituted to more favorable residues according to the HLA-A24-binding motif. Among four substitutes constructed, a substitute with isoleucine (termed K9I peptide) most apparently enhanced the affinity for HLA-A24 molecule. Subsequent in vitro CTL induction analysis using PBMCs of 15 HLA-A24(+) synovial sarcoma patients revealed that the original B peptide allowed to induce synovial sarcoma-specific CTLs from 7 patients (47%), whereas such CTLs were inducible from 12 patients (80%) with K9I peptide. Moreover, the extent of cytotoxicity against HLA-A24(+) synovial sarcoma cell lines was higher in K9I peptide-induced CTLs than B peptide-induced CTLs. Influence of anchor substitution on peptide/TCR interaction was evaluated by cytotoxicity assays against autologous cells and tetramer analysis. CTLs induced from a synovial sarcoma patient using K9I peptide did not lyse autologous PHA blasts or EBV-infected B cells. In vitro stimulations of PBMCs from 5 HLA-A24(+) synovial sarcoma patients with K9I peptide increased the frequency of T cells reacting with both HLA-A24/K9I peptide tetramer and HLA-A24/B peptide tetramer. In contrast, the frequency of T cells reacting with HLA/HIV-derived peptide tetramer remained low. These findings support the validity in design of anchor residue substitution in SYT-SSX fusion gene-derived peptide, and provide a potential clue to the current stagnation in vaccination trials of fusion gene-derived natural junction peptides.
Collapse
Affiliation(s)
- Kazunori Ida
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 2004; 36:331-4. [PMID: 15054488 DOI: 10.1038/ng1335] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 02/11/2004] [Indexed: 12/17/2022]
Abstract
Cytogenetic aberrations have been reported in 45,000 human neoplasms. Structural balanced rearrangements are associated with distinct tumor subtypes with remarkable specificity and have been essential for identifying genes involved in tumorigenesis. All balanced rearrangements that have been characterized molecularly act by deregulating a gene in one of the breakpoints or by creating a fusion gene. Because most recurrent aberrations and rearranged genes have been found in hematological disorders, whereas numerous genomic imbalances have been identified in solid tumors, it has become generally accepted that there are pathogenetic differences between these neoplasms. We here show that in every tumor type, the numbers of recurrent balanced chromosome abnormalities, fusion genes and genes rearranged as a consequence of balanced aberrations are simply a function of the number of cases with an abnormal karyotype. Hence, there may not be any fundamental tissue-specific differences in the genetic mechanisms by which neoplasia is initiated.
Collapse
Affiliation(s)
- Felix Mitelman
- Department of Clinical Genetics, University Hospital, SE-221 85 Lund, Sweden.
| | | | | |
Collapse
|
29
|
Sato Y, Endo H, Ajiki T, Hakamata Y, Okada T, Murakami T, Kobayashi E. Establishment of Cre/LoxP recombination system in transgenic rats. Biochem Biophys Res Commun 2004; 319:1197-202. [PMID: 15194493 DOI: 10.1016/j.bbrc.2004.04.204] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Indexed: 10/26/2022]
Abstract
The rat has offered an important animal model in biomedical research including surgical procedure. However, advanced genetic manipulation has progressed less far in the rat than in the mouse. Here we report the Cre/LoxP transgenic rat system, demonstrating conditional chromosomal translocation both in the fertilization and adult stage, spatio-temporal gene controlling by catheter-based adenoviral gene transfer, and muscular fusion events in the limb transplant. Taking advantage of the larger body size of the rat than the mouse, this rat system provides a potential value to evaluate biomedical and therapeutic significance for gene therapy and regenerative medicine.
Collapse
Affiliation(s)
- Yuki Sato
- Division of Organ Replacement Research, Center for Molecular Medicine, Jichi Medical School, Tochigi 329-0498, Japan
| | | | | | | | | | | | | |
Collapse
|
30
|
Martinez-Mancilla M, Zafra G, Reynoso-Gómez E, Martinez-Avalos A, Rivera-Luna R, Gariglio P. A closer look at specific therapeutic strategies in leukemia. Leuk Lymphoma 2004; 45:1767-73. [PMID: 15223634 DOI: 10.1080/10428190410001683741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Leukemia-associated fusion genes are detected in a significant proportion of newly diagnosed cases, where genes encoding transcription factors are usually found at one of the breakpoints. Activated fusion proteins, such as PML-RARalpha and AML1-ETO, have been shown to inhibit cellular differentiation by recruitment of nuclear corepressor complexes, which maintain local histone deacetylase (HDAC) in a variety of hematologic lineage-specific gene promoters. This HDAC-dependent transcriptional repression appears as a common pathway in the development of leukemia and could represent an important target for new therapeutic agents. On the other hand, the Bcr-Abl oncoprotein shows high tyrosine kinase activity and deregulates signal transduction pathways involved normally in both apoptosis and proliferation. This aberrant activity is affected by signal transduction inhibitors (STIs), which block or prevent the oncogenic pathway. In this review, we present a closer look at our understanding of both the reversible transcriptional repression controlled by HDAC and the deregulated Bcr-Abl signal transduction. In addition, the application of low molecular weight drugs for human leukemia treatment based in this knowledge results in durable clinical remission and acceptable risk of toxic effects that should increase the cure rate. We hope that this review will provide timely information to the readers.
Collapse
Affiliation(s)
- M Martinez-Mancilla
- Depto de Genética y Biología Molecular, CINVESTAV-IPN, Av. Instituto Politécnico Nacional No 2508, Col San Pedro Zacatenco, 07360 México D. F
| | | | | | | | | | | |
Collapse
|
31
|
Zhang Z, Zhang Y, Shi B, Deng W, Zhao Y, Chen R. Detecting chimeric 5′/3′UTRs with cross-chromosomal splicing by bioinformatics. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
32
|
Lee HJ, Kim S, Pelletier J, Kim J. Stimulation of hTAFII68 (NTD)-mediated transactivation by v-Src. FEBS Lett 2004; 564:188-98. [PMID: 15094065 DOI: 10.1016/s0014-5793(04)00314-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 03/05/2004] [Accepted: 03/11/2004] [Indexed: 12/17/2022]
Abstract
The three genes hTAF(II)68, EWS, and TLS (called the TET family) encode related RNA binding proteins containing an RNA recognition motif and three glycine-, arginine-, and proline-rich regions in the C-terminus and a degenerated repeat containing the consensus sequence Ser-Tyr-Gly-Gln-Ser in the N-terminus. In many human cancers, the N-terminal portion of hTAF(II)68, EWS, or TLS is fused to the DNA binding domain of one of several transcription factors including Fli-1, ERG, ETV1, E1AF, WT1, ATF-1, CHOP, or TEC. We have recognized the presence of several potential tyrosine phosphorylation sites within the amino-terminal domain of hTAF(II)68 and have investigated the potential effects of cytoplasmic signaling on hTAF(II)68 function. Herein, we find that hTAF(II)68 is phosphorylated on tyrosine residue(s) by ectopic expression of v-Src protein tyrosine kinase in vitro and in vivo. The hTAF(II)68 protein can associated with the SH3 domains of several cell signaling proteins, including v-Src protein tyrosine kinase. We also document that full-length v-Src can stimulate hTAF(II)68-mediated transcriptional activation, whereas deletion mutants of v-Src are unable to exert this effect. In addition, cellular Src activity appears important for hTAF(II)68 function since hTAF(II)68-mediated transactivation is reduced in a dose-dependent fashion by ectopic overexpression of a dominant-negative mutant of Src. Taken together, our results suggest that the biological activities of hTAF(II)68 are linked to the cytoplasmic Src signal transduction pathway.
Collapse
Affiliation(s)
- Hye Jin Lee
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul 121-743, South Korea
| | | | | | | |
Collapse
|
33
|
Johansson B, Mertens F, Mitelman F. Clinical and biological importance of cytogenetic abnormalities in childhood and adult acute lymphoblastic leukemia. Ann Med 2004; 36:492-503. [PMID: 15513300 DOI: 10.1080/07853890410018808] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Among the approximately 7,000 cytogenetically abnormal childhood and adult B- and T-lineage acute lymphoblastic leukemias (ALL) published to date, numerous recurring chromosomal aberrations and abnormality patterns have been identified, and it has been clearly shown that the cytogenetic features often correlate closely with specific morphologic, immunophenotypic, and clinical parameters. Thus, karyotypic investigations are now routinely performed for diagnostic and prognostic purposes in ALL, with the chromosomal abnormalities/cytogenetic patterns playing a major role for proper risk assessment and choice of treatment. At the same time, the cytogenetic analyses have resulted in the identification of more than 70 different genes, located at the breakpoints of ALL-associated structural chromosomal abnormalities, that are causally implicated in the leukemogenic process. Hence, the genetic studies have also improved our understanding of the mechanisms of leukemogenesis. However, the almost staggering amount of cytogenetic information presently available has made it increasingly difficult to obtain a general overview of the clinical and biological importance of karyotypic patterns in ALL. Here, we summarize and review the cytogenetic features of childhood and adult ALL, with emphasis on their molecular genetic consequences and their clinical impact.
Collapse
Affiliation(s)
- Bertil Johansson
- Deaprtment of Clinical Genetics, Lund University Hospital, Sweden.
| | | | | |
Collapse
|
34
|
Abstract
Chromosome translocations are often early or initiating events in leukaemogenesis, occurring prenatally in most cases of childhood leukaemia. Although these genetic changes are necessary, they are usually not sufficient to cause leukaemia. How, when and where do translocations arise? And can these insights aid our understanding of the natural history, pathogenesis and causes of leukaemia?
Collapse
Affiliation(s)
- Mel F Greaves
- LRF Centre for Cell and Molecular Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.
| | | |
Collapse
|
35
|
Tanaka T, Lobato MN, Rabbitts TH. Single domain intracellular antibodies: a minimal fragment for direct in vivo selection of antigen-specific intrabodies. J Mol Biol 2003; 331:1109-20. [PMID: 12927545 DOI: 10.1016/s0022-2836(03)00836-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a major need in target validation and therapeutic applications for molecules that can interfere with protein function inside cells. Intracellular antibodies (intrabodies) can bind to specific targets in cells but isolation of intrabodies is currently difficult. Intrabodies are normally single chain Fv fragments comprising variable domains of the immunoglobulin heavy (VH) and light chains (VL). We now demonstrate that single VH domains have excellent intracellular properties of solubility, stability and expression within the cells of higher organisms and can exhibit specific antigen recognition in vivo. We have used this intracellular single variable domain (IDab) format, based on a previously characterised intrabody consensus scaffold, to generate diverse intrabody libraries for direct in vivo screening. IDabs were isolated using two distinct antigens and affinities of isolated IDabs ranged between 20 nM and 200 nM. Moreover, IDabs selected for binding to the RAS protein could inhibit RAS-dependent oncogenic transformation of NIH3T3 cells. The IDab format is therefore ideal for in vivo intrabody use. This approach to intrabodies obviates the need for phage antibody libraries, avoids the requirement for production of antigen in vitro and allows for direct selection of intrabodies in vivo.
Collapse
Affiliation(s)
- Tomoyuki Tanaka
- MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK
| | | | | |
Collapse
|
36
|
Chung GTY, Yamada Y, Pannell R, Forster A, Rabbitts TH. The hepatitis C virus internal ribosome entry site facilitates efficient protein synthesis in blood vessel endothelium during tumour angiogenesis. Nucleic Acids Res 2003; 31:e46. [PMID: 12682381 PMCID: PMC153758 DOI: 10.1093/nar/gng046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The development of gene delivery systems for therapeutic use involves vectors (often retrovirus or adenovirus) which typically encode one target protein, but the use of internal ribosome entry sites (IRES) can confer the ability to express more than one protein from bi- or polycistronic mRNAs. IRES elements can display tissue-specific expression, so it is necessary to determine suitable IRES for specific clinical applicability. Blood vessel endothelial cells are important clinically since many different conditions involve neo-vascularisation (angiogenesis). We have demonstrated that the viral hepatitis C IRES element is a powerful mediator of protein synthesis in angiogenesis, such as found in solid tumours. Homologous recombination was used to introduce IRES-lacZ sequences into the Lmo2 gene, which is expressed in endothelial cells. beta-Galactosidase expression was determined during vascular remodelling in mouse embryos and in sprouting endothelium during growth of solid tumours, and showed that the hepatitis C IRES is used efficiently for protein synthesis in endothelial cells. This IRES element can provide the means to express two or more therapeutic genes in blood vessel endothelium in clinical conditions, such as cancer, which depend on angiogenesis.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Binding Sites/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Embryo, Mammalian/cytology
- Embryo, Mammalian/metabolism
- Endothelium, Vascular/metabolism
- Female
- Hepacivirus/genetics
- Hepacivirus/metabolism
- LIM Domain Proteins
- Lac Operon/genetics
- Male
- Metalloproteins/genetics
- Metalloproteins/physiology
- Mice
- Mice, Inbred C57BL
- Neoplasm Transplantation
- Neoplasms, Experimental/blood supply
- Neoplasms, Experimental/pathology
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Plasmids/genetics
- Protein Biosynthesis
- Ribosomes/metabolism
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Grace T Y Chung
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | | | | | | | | |
Collapse
|