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Arvind M, Pattnaik B, Gheware A, Prakash YS, Srivastava M, Agrawal A, Bhatraju NK. Plausible role of INPP4A dysregulation in idiopathic pulmonary fibrosis. Physiol Rep 2024; 12:e16032. [PMID: 38720166 PMCID: PMC11078778 DOI: 10.14814/phy2.16032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
INPP4A has been shown to be involved in the regulation of cell proliferation and apoptosis of multiple cell types including fibroblasts. Previous reports from our group have demonstrated the role of inositol polyphosphate 4-phosphatase Type I A (INPP4A) in these functions. Though existing evidences suggest a critical role for INPP4A in the maintenance of lung homeostasis, its role in chronic lung diseases is relatively under explored. In the current study, we made an attempt to understand the regulation of INPP4A in idiopathic pulmonary fibrosis (IPF). Through integration of relevant INPP4A gene expression data from public repositories with our results from in vitro experiments and mouse models, we show that INPP4A is altered in IPF. Interestingly, the direction of the change is dependent both on the disease stage and the region of the lung used. INPP4A was found to be upregulated when analyzed in lung sample representative of the whole lung, but was downregulated in the fibrotic regions of the lung. Similarly, INPP4A was found to be high, compared to controls, only in the early stage of the disease. Though the observed increase in INPP4A was found to be negatively correlated to physiological indices, FVC, and DLCO, of lung function, treatment with anti-INPP4A antibody worsened the condition in bleomycin treated mice. These contrasting results taken together are suggestive of a nuanced regulation of INPP4A in IPF which is dependent on the disease stage, cellular state and extent of fibrosis in the lung region being analyzed.
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Affiliation(s)
- Meghana Arvind
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Bijay Pattnaik
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Department of Pulmonary Critical Care and Sleep MedicineAll India Institute of Medical SciencesNew DelhiIndia
| | - Atish Gheware
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- Division of Pulmonary and Critical Care Medicine, Department of MedicineWashington University in St. LouisSt. LouisMissouriUSA
| | - Y. S. Prakash
- Department of Anaesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
| | - Mousami Srivastava
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Symbiosis Statistical Institute (SSI)Symbiosis International University (SIU)PuneMaharashtraIndia
| | - Anurag Agrawal
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- Trivedi School of BiosciencesAshoka UniversitySonipatHaryanaIndia
| | - Naveen Kumar Bhatraju
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Trivedi School of BiosciencesAshoka UniversitySonipatHaryanaIndia
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Abstract
Phosphoinositides (PIs) are phospholipids derived from phosphatidylinositol. PIs are regulated via reversible phosphorylation, which is directed by the opposing actions of PI kinases and phosphatases. PIs constitute a minor fraction of the total cellular lipid pool but play pleiotropic roles in multiple aspects of cell biology. Genetic mutations of PI regulatory enzymes have been identified in rare congenital developmental syndromes, including ciliopathies, and in numerous human diseases, such as cancer and metabolic and neurological disorders. Accordingly, PI regulatory enzymes have been targeted in the design of potential therapeutic interventions for human diseases. Recent advances place PIs as central regulators of membrane dynamics within functionally distinct subcellular compartments. This brief review focuses on the emerging role PIs play in regulating cell signaling within the primary cilium and in directing transfer of molecules at interorganelle membrane contact sites and identifies new roles for PIs in subcellular spaces.
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Affiliation(s)
- Elizabeth Michele Davies
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Christina Anne Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Harald Alfred Stenmark
- Department of Molecular Cell Biology, Institute for Cancer Research. The Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
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Ma XY, Wei L, Lei Z, Chen Y, Ding Z, Chen ZS. Recent progress on targeting leukemia stem cells. Drug Discov Today 2021; 26:1904-1913. [PMID: 34029689 DOI: 10.1016/j.drudis.2021.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/14/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
Leukemia is a type of malignant clonal disease of hematopoietic stem cells (HSCs). A small population of leukemic stem cells (LSCs) are responsible for the initiation, drug resistance, and relapse of leukemia. LSCs have the ability to form tumors after xenotransplantation in immunodeficient mice and appear to be common in most human leukemias. Therefore, the eradication of LSCs is an approach with the potential to improve survival or even to cure leukemia. Using recent research in the field of LSCs, we summarize the targeted therapy approaches for the removal of LSCs through surface markers including immune checkpoint molecules, pathways influencing LSC survival, or the survival microenvironment of LSCs. In addition, we introduce the survival microenvironment and survival regulation of LSCs.
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Affiliation(s)
- Xiang-Yu Ma
- School of Pharmacy, Weifang Medical University, Weifang 261053, PR China
| | - Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang 261053, PR China.
| | - Zining Lei
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Yanglu Chen
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, Shandong 250101, PR China
| | - Zhe-Sheng Chen
- School of Pharmacy, Weifang Medical University, Weifang 261053, PR China.
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McEwen GK, Alquezar-Planas DE, Dayaram A, Gillett A, Tarlinton R, Mongan N, Chappell KJ, Henning J, Tan M, Timms P, Young PR, Roca AL, Greenwood AD. Retroviral integrations contribute to elevated host cancer rates during germline invasion. Nat Commun 2021; 12:1316. [PMID: 33637755 PMCID: PMC7910482 DOI: 10.1038/s41467-021-21612-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Repeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the immediate repercussions of retroviral endogenisation on host health. Here we examine retroviral endogenisation during its earliest stages in the koala (Phascolarctos cinereus), a species undergoing germline invasion by koala retrovirus (KoRV) and affected by high cancer prevalence. We characterise KoRV integration sites (IS) in tumour and healthy tissues from 10 koalas, detecting 1002 unique IS, with hotspots of integration occurring in the vicinity of known cancer genes. We find that tumours accumulate novel IS, with proximate genes over-represented for cancer associations. We detect dysregulation of genes containing IS and identify a highly-expressed transduced oncogene. Our data provide insights into the tremendous mutational load suffered by the host during active retroviral germline invasion, a process repeatedly experienced and overcome during the evolution of vertebrate lineages.
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Affiliation(s)
- Gayle K McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Institute for Neurophysiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, QLD, Australia
| | - Rachael Tarlinton
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Nigel Mongan
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Keith J Chappell
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Joerg Henning
- School of Veterinary Science, University of Queensland, Brisbane, QLD, Australia
| | - Milton Tan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Peter Timms
- Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Paul R Young
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität, Berlin, Germany.
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Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies. JOURNAL OF ONCOLOGY 2019; 2019:7239206. [PMID: 31467542 PMCID: PMC6699387 DOI: 10.1155/2019/7239206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023]
Abstract
The last two decades of genome-scale research revealed a complex molecular picture of acute myeloid leukemia (AML). On the one hand, a number of mutations were discovered and associated with AML diagnosis and prognosis; some of them were introduced into diagnostic tests. On the other hand, transcriptome studies, which preceded AML exome and genome sequencing, remained poorly translated into clinics. Nevertheless, gene expression studies significantly contributed to the elucidation of AML pathogenesis and indicated potential therapeutic directions. The power of transcriptomic approach lies in its comprehensiveness; we can observe how genome manifests its function in a particular type of cells and follow many genes in one test. Moreover, gene expression measurement can be combined with mutation detection, as high-impact mutations are often present in transcripts. This review sums up 20 years of transcriptome research devoted to AML. Gene expression profiling (GEP) revealed signatures distinctive for selected AML subtypes and uncovered the additional within-subtype heterogeneity. The results were particularly valuable in the case of AML with normal karyotype which concerns up to 50% of AML cases. With the use of GEP, new classes of the disease were identified and prognostic predictors were proposed. A plenty of genes were detected as overexpressed in AML when compared to healthy control, including KIT, BAALC, ERG, MN1, CDX2, WT1, PRAME, and HOX genes. High expression of these genes constitutes usually an unfavorable prognostic factor. Upregulation of FLT3 and NPM1 genes, independent on their mutation status, was also reported in AML and correlated with poor outcome. However, transcriptome is not limited to the protein-coding genes; other types of RNA molecules exist in a cell and regulate genome function. It was shown that microRNA (miRNA) profiles differentiated AML groups and predicted outcome not worse than protein-coding gene profiles. For example, upregulation of miR-10a, miR-10b, and miR-196b and downregulation of miR-192 were found as typical of AML with NPM1 mutation whereas overexpression of miR-155 was associated with FLT3-internal tandem duplication (FLT3-ITD). Development of high-throughput technologies and microarray replacement by next generation sequencing (RNA-seq) enabled uncovering a real variety of leukemic cell transcriptomes, reflected by gene fusions, chimeric RNAs, alternatively spliced transcripts, miRNAs, piRNAs, long noncoding RNAs (lncRNAs), and their special type, circular RNAs. Many of them can be considered as AML biomarkers and potential therapeutic targets. The relations between particular RNA puzzles and other components of leukemic cells and their microenvironment, such as exosomes, are now under investigation. Hopefully, the results of this research will shed the light on these aspects of AML pathogenesis which are still not completely understood.
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Phosphatidylinositol (3,4) bisphosphate-specific phosphatases and effector proteins: A distinct branch of PI3K signaling. Cell Signal 2015; 27:1789-98. [DOI: 10.1016/j.cellsig.2015.05.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/16/2015] [Accepted: 05/20/2015] [Indexed: 01/22/2023]
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Abstract
Animal models have been invaluable in the efforts to better understand and ultimately treat patients suffering from leukemia. While important insights have been gleaned from these models, limitations must be acknowledged. In this review, we will highlight the various animal models of leukemia and describe their contributions to the improved understanding and treatment of these cancers.
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Xie J, Erneux C, Pirson I. How does SHIP1/2 balance PtdIns(3,4)P2 and does it signal independently of its phosphatase activity? Bioessays 2013; 35:733-43. [PMID: 23650141 DOI: 10.1002/bies.201200168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The number of cellular events identified as being directly or indirectly modulated by phosphoinositides dramatically increased in the recent years. Part of the complexity results from the fact that the seven phosphoinositides play second messenger functions in many different areas of growth factors and insulin signaling, cytoskeletal organization, membrane dynamics, trafficking, or nuclear signaling. PtdIns(3,4)P2 is commonly reported as a product of the SH2 domain-containing inositol 5-phosphatases 1/2 (SHIP1 and SHIP2) that dephosphorylate PtdIns(3,4,5)P3 at the 5-position. Here we discuss recent interest in PtdIns(3,4)P2 signaling highlighting its involvement in key cellular mechanisms such as cell adhesion, migration, and cytoskeletal regulation. We question and discuss the involvement of SHIP2 either as a PI 5-phosphatase or as a scaffold protein in insulin signaling, cytoskeletal dynamics, and endocytosis of growth factor receptors.
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Affiliation(s)
- Jingwei Xie
- Department of Pathophysiology, China Medical University, Heping District, Shenyang Liaoning Province, China
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9
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Abstract
Phosphoinositide signalling molecules interact with a plethora of effector proteins to regulate cell proliferation and survival, vesicular trafficking, metabolism, actin dynamics and many other cellular functions. The generation of specific phosphoinositide species is achieved by the activity of phosphoinositide kinases and phosphatases, which phosphorylate and dephosphorylate, respectively, the inositol headgroup of phosphoinositide molecules. The phosphoinositide phosphatases can be classified as 3-, 4- and 5-phosphatases based on their specificity for dephosphorylating phosphates from specific positions on the inositol head group. The SAC phosphatases show less specificity for the position of the phosphate on the inositol ring. The phosphoinositide phosphatases regulate PI3K/Akt signalling, insulin signalling, endocytosis, vesicle trafficking, cell migration, proliferation and apoptosis. Mouse knockout models of several of the phosphoinositide phosphatases have revealed significant physiological roles for these enzymes, including the regulation of embryonic development, fertility, neurological function, the immune system and insulin sensitivity. Importantly, several phosphoinositide phosphatases have been directly associated with a range of human diseases. Genetic mutations in the 5-phosphatase INPP5E are causative of the ciliopathy syndromes Joubert and MORM, and mutations in the 5-phosphatase OCRL result in Lowe's syndrome and Dent 2 disease. Additionally, polymorphisms in the 5-phosphatase SHIP2 confer diabetes susceptibility in specific populations, whereas reduced protein expression of SHIP1 is reported in several human leukaemias. The 4-phosphatase, INPP4B, has recently been identified as a tumour suppressor in human breast and prostate cancer. Mutations in one SAC phosphatase, SAC3/FIG4, results in the degenerative neuropathy, Charcot-Marie-Tooth disease. Indeed, an understanding of the precise functions of phosphoinositide phosphatases is not only important in the context of normal human physiology, but to reveal the mechanisms by which these enzyme families are implicated in an increasing repertoire of human diseases.
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Loss-of-function of inositol polyphosphate-4-phosphatase reversibly increases the severity of allergic airway inflammation. Nat Commun 2012; 3:877. [PMID: 22673904 DOI: 10.1038/ncomms1880] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 05/02/2012] [Indexed: 01/09/2023] Open
Abstract
Inositol polyphosphate phosphatases regulate the magnitude of phosphoinositide-3 kinase signalling output. Although inositol polyphosphate-4-phosphatase is known to regulate phosphoinositide-3 kinase signalling, little is known regarding its role in asthma pathogenesis. Here we show that modulation of inositol polyphosphate-4-phosphatase alters the severity of asthma. Allergic airway inflammation in mice led to calpain-mediated degradation of inositol polyphosphate-4-phosphatase. In allergic airway inflammation models, preventing inositol polyphosphate-4-phosphatase degradation by inhibiting calpain activity, or overexpression of inositol polyphosphate-4-phosphatase in mouse lungs, led to attenuation of the asthma phenotype. Conversely, knockdown of inositol polyphosphate-4-phosphatase severely aggravated the allergic airway inflammation and the asthma phenotype. Interestingly, inositol polyphosphate-4-phosphatase knockdown in lungs of naive mice led to spontaneous airway hyper-responsiveness, suggesting that inositol polyphosphate-4-phosphatase could be vital in maintaining the lung homeostasis. We suggest that inositol polyphosphate-4-phosphatase has an important role in modulating inflammatory response in asthma, and thus, uncover a new understanding of the complex interplay between inositol signalling and asthma, which could provide alternative strategies in asthma management.
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Dyson JM, Fedele CG, Davies EM, Becanovic J, Mitchell CA. Phosphoinositide phosphatases: just as important as the kinases. Subcell Biochem 2012; 58:215-279. [PMID: 22403078 DOI: 10.1007/978-94-007-3012-0_7] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phosphoinositide phosphatases comprise several large enzyme families with over 35 mammalian enzymes identified to date that degrade many phosphoinositide signals. Growth factor or insulin stimulation activates the phosphoinositide 3-kinase that phosphorylates phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P(2)] to form phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P(3)], which is rapidly dephosphorylated either by PTEN (phosphatase and tensin homologue deleted on chromosome 10) to PtdIns(4,5)P(2), or by the 5-phosphatases (inositol polyphosphate 5-phosphatases), generating PtdIns(3,4)P(2). 5-phosphatases also hydrolyze PtdIns(4,5)P(2) forming PtdIns(4)P. Ten mammalian 5-phosphatases have been identified, which regulate hematopoietic cell proliferation, synaptic vesicle recycling, insulin signaling, and embryonic development. Two 5-phosphatase genes, OCRL and INPP5E are mutated in Lowe and Joubert syndrome respectively. SHIP [SH2 (Src homology 2)-domain inositol phosphatase] 2, and SKIP (skeletal muscle- and kidney-enriched inositol phosphatase) negatively regulate insulin signaling and glucose homeostasis. SHIP2 polymorphisms are associated with a predisposition to insulin resistance. SHIP1 controls hematopoietic cell proliferation and is mutated in some leukemias. The inositol polyphosphate 4-phosphatases, INPP4A and INPP4B degrade PtdIns(3,4)P(2) to PtdIns(3)P and regulate neuroexcitatory cell death, or act as a tumor suppressor in breast cancer respectively. The Sac phosphatases degrade multiple phosphoinositides, such as PtdIns(3)P, PtdIns(4)P, PtdIns(5)P and PtdIns(3,5)P(2) to form PtdIns. Mutation in the Sac phosphatase gene, FIG4, leads to a degenerative neuropathy. Therefore the phosphatases, like the lipid kinases, play major roles in regulating cellular functions and their mutation or altered expression leads to many human diseases.
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Affiliation(s)
- Jennifer M Dyson
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Rd, 3800, Clayton, Australia
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Retroviral integration mutagenesis in mice and comparative analysis in human AML identify reduced PTP4A3 expression as a prognostic indicator. PLoS One 2011; 6:e26537. [PMID: 22028901 PMCID: PMC3197662 DOI: 10.1371/journal.pone.0026537] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 09/28/2011] [Indexed: 12/05/2022] Open
Abstract
Acute myeloid leukemia (AML) results from multiple genetic and epigenetic aberrations, many of which remain unidentified. Frequent loss of large chromosomal regions marks haplo-insufficiency as one of the major mechanisms contributing to leukemogenesis. However, which haplo-insufficient genes (HIGs) are involved in leukemogenesis is largely unknown and powerful experimental strategies aimed at their identification are currently lacking. Here, we present a new approach to discover HIGs, using retroviral integration mutagenesis in mice in which methylated viral integration sites and neighbouring genes were identified. In total we mapped 6 genes which are flanked by methylated viral integration sites (mVIS). Three of these, i.e., Lrmp, Hcls1 and Prkrir, were up regulated and one, i.e., Ptp4a3, was down regulated in the affected tumor. Next, we investigated the role of PTP4A3 in human AML and we show that PTP4A3 expression is a negative prognostic indicator, independent of other prognostic parameters. In conclusion, our novel strategy has identified PTP4A3 to potentially have a role in AML, on one hand as a candidate HIG contributing to leukemogenesis in mice and on the other hand as a prognostic indicator in human AML.
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An evolutionarily conserved PTEN-C/EBPalpha-CTNNA1 axis controls myeloid development and transformation. Blood 2010; 115:4715-24. [PMID: 20371743 PMCID: PMC9728059 DOI: 10.1182/blood-2009-11-255778] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Loss of function of tumor suppressor genes, such as PTEN, CEBPAlpha, and CTNNA1 (encoding the alpha-catenin protein), has been found to play an essential role in leukemogenesis. However, whether these genes genetically interact remains largely unknown. Here, we show that PTEN-mammalian target of rapamycin signaling acts upstream to dictate the ratio of wild-type p42 C/EBPalpha to its dominant-negative p30 isoform, which critically determines whether p30 C/EBPalpha (lower p42/p30 ratio) or p42 C/EBPalpha (higher p42/p30 ratio) binds to the proximal promoter of the retained CTNNA1 allele. Binding of p30 C/EBPalpha recruits the polycomb repressive complex 2 to suppress CTNNA1 transcription through repressive H3K27me3 modification, whereas binding of p42 C/EBPalpha relieves this repression and promotes CTNNA1 expression through activating H3K4me3 modification. Loss of Pten function in mice and zebrafish induces myelodysplasia with abnormal invasiveness of myeloid progenitors accompanied by significant reductions in both wild-type C/EBPalpha and alpha-catenin protein. Importantly, frame-shift mutations in either PTEN or CEBPA were detected exclusively in the primary LICs with low CTNNA1 expression. This study uncovers a novel molecular pathway, PTEN-C/EBPalpha-CTNNA1, which is evolutionarily conserved and might be therapeutically targeted to eradicate LICs with low CTNNA1 expression.
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Taskesen E, Beekman R, de Ridder J, Wouters BJ, Peeters JK, Touw IP, Reinders MJT, Delwel R. HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics 2010; 11:275. [PMID: 20492700 PMCID: PMC2892465 DOI: 10.1186/1471-2105-11-275] [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] [Received: 11/24/2009] [Accepted: 05/21/2010] [Indexed: 12/02/2022] Open
Abstract
Background Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with increased signal intensity (as a result of hybridization of labeled DNA) in a region. Currently, no standard criteria are available to define these regions-of-interest as there is no single probe intensity cut-off level, different regions-of-interest can contain various numbers of probes, and can vary in genomic width. Furthermore, the chromosomal distance between neighboring probes can vary across the genome among different arrays. Results We have developed Hypergeometric Analysis of Tiling-arrays (HAT), and first evaluated its performance for tiling-array datasets from a Chromatin Immunoprecipitation study on chip (ChIP-on-chip) for the identification of genome-wide DNA binding profiles of transcription factor Cebpa (used for method comparison). Using this assay, we can refine the detection of regions-of-interest by illustrating that regions detected by HAT are more highly enriched for expected motifs in comparison with an alternative detection method (MAT). Subsequently, data from a retroviral insertional mutagenesis screen were used to examine the performance of HAT among different applications of tiling-array datasets. In both studies, detected regions-of-interest have been validated with (q)PCR. Conclusions We demonstrate that HAT has increased specificity for analysis of tiling-array data in comparison with the alternative method, and that it accurately detects regions-of-interest in two different applications of tiling-arrays. HAT has several advantages over previous methods: i) as there is no single cut-off level for probe-intensity, HAT can detect regions-of-interest at various thresholds, ii) it can detect regions-of-interest of any size, iii) it is independent of probe-resolution across the genome, and across tiling-array platforms and iv) it employs a single user defined parameter: the significance level. Regions-of-interest are detected by computing the hypergeometric-probability, while controlling the Family Wise Error. Furthermore, the method does not require experimental replicates, common regions-of-interest are indicated, a sequence-of-interest can be examined for every detected region-of-interest, and flanking genes can be reported.
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Affiliation(s)
- Erdogan Taskesen
- Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands
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15
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Kool J, Berns A. High-throughput insertional mutagenesis screens in mice to identify oncogenic networks. Nat Rev Cancer 2009; 9:389-99. [PMID: 19461666 DOI: 10.1038/nrc2647] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Retroviral insertional mutagenesis screens have been used for many years as a tool for cancer gene discovery. In recent years, completion of the mouse genome sequence as well as improved technologies for cloning and sequencing of retroviral insertions have greatly facilitated the retrieval of more complete data sets from these screens. The concomitant increase of the size of the screens allows researchers to address new questions about the genes and signalling networks involved in tumour development. In addition, the development of new insertional mutagenesis tools such as DNA transposons enables screens for cancer genes in tissues that previously could not be analysed by retroviral insertional mutagenesis.
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Affiliation(s)
- Jaap Kool
- Division of Molecular Genetics, The Cancer Genomics Centre, The Centre of Biomedical Genetics, Academic Medical Center, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
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Regulation of PI(3)K/Akt signalling and cellular transformation by inositol polyphosphate 4-phosphatase-1. EMBO Rep 2009; 10:487-93. [PMID: 19325558 DOI: 10.1038/embor.2009.28] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/08/2022] Open
Abstract
Akt is a crucial phosphoinositide 3-kinase (PI(3)K) effector that regulates cell proliferation and survival. PI(3)K-generated signals, PtdIns(3,4,5)P(3) and PtdIns(3,4)P(2), direct Akt plasma membrane engagement. Pathological Akt plasma membrane association promotes oncogenesis. PtdIns(3,4)P(2) is degraded by inositol polyphosphate 4-phosphatase-1 (4-ptase-1) forming PtdIns(3)P; however, the role of 4-ptase-1 in regulating the activation and function of Akt is unclear. In mouse embryonic fibroblasts lacking 4-ptase-1 ((-/-)MEFs), the Akt-pleckstrin homology (PH) domain was constitutively membrane-associated both in serum-starved and agonist-stimulated cells, in contrast to (+/+)MEFs, in which it was detected only at the plasma membrane following serum stimulation. Epidermal growth factor (EGF) stimulation resulted in increased Ser(473) and Thr(308)-Akt phosphorylation and activation of Akt-dependent signalling in (-/-)MEFs, relative to (+/+)MEFs. Significantly, loss of 4-ptase-1 resulted in increased cell proliferation and decreased apoptosis. SV40-transformed (-/-)MEFs showed increased anchorage-independent cell growth and formed tumours in nude mice. This study provides the first evidence, to our knowledge, that 4-ptase-1 controls the activation of Akt and thereby cell proliferation, survival and tumorigenesis.
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The gene encoding thioredoxin-interacting protein (TXNIP) is a frequent virus integration site in virus-induced mouse leukemia and is overexpressed in a subset of AML patients. Leuk Res 2009; 33:1367-71. [PMID: 19327827 DOI: 10.1016/j.leukres.2009.02.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/23/2009] [Accepted: 02/25/2009] [Indexed: 11/23/2022]
Abstract
Thioredoxin-interacting protein (TXNIP) is involved in reactive oxygen species-induced stress responses. In a screen for novel disease genes in murine leukemia virus (MLV)-induced mouse leukemias, we identified Txnip as a frequent target for proviral integration. Ectopic TXNIP expression inhibited the proliferation of myeloid progenitor cells. TXNIP transcript and protein levels were significantly elevated in human AML blasts of certain patients, particularly those harboring translocation t(8;21). Nucleotide sequencing revealed no abnormalities in the TXNIP coding region in AML. These findings suggest that deregulated TXNIP expression contributes to MLV-induced murine leukemia as well as human AML.
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18
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Fujino Y, Ohno K, Tsujimoto H. Molecular pathogenesis of feline leukemia virus-induced malignancies: Insertional mutagenesis. Vet Immunol Immunopathol 2008; 123:138-43. [DOI: 10.1016/j.vetimm.2008.01.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Touw IP, Erkeland SJ. Retroviral insertion mutagenesis in mice as a comparative oncogenomics tool to identify disease genes in human leukemia. Mol Ther 2008; 15:13-9. [PMID: 17164770 DOI: 10.1038/sj.mt.6300040] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Retroviral insertion mutagenesis has recently received much attention because of its adverse effects in the application of retroviral vector-based gene therapy, resulting in leukemia in certain patients. At the same time, retroviral mutagenesis in mice is being considered a powerful forward genetic strategy to identify disease genes involved in cancer. The publication of the mouse genome sequence and the development of high-throughput genomic approaches have given a further boost to this rapidly evolving field. The increasing numbers of new potential oncogenes identified in retroviral screens have given a valuable basis for a better understanding of cancer related pathways in mice. Important challenges that now lie ahead of us are (i) to determine the relevance and causal relationship of these genes with various types of human cancer (ii) to develop strategies to identify tumor suppressor genes on a large scale, (iii) to place the disease genes into regulatory networks to better understand their role in the complex pathogenesis of cancer, and (iv) to determine their value for diagnosis refinement and therapeutic target intervention in human disease. In this review, we will give a brief update of the current state-of-the-art and thoughts concerning these issues. We will specifically focus on the value of employing retroviral insertion mutagenesis in mice and gene expression profiling in man in the context of acute myeloid leukemia.
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Affiliation(s)
- Ivo P Touw
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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20
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Heuzé ML, Lamsoul I, Moog-Lutz C, Lutz PG. Ubiquitin-mediated proteasomal degradation in normal and malignant hematopoiesis. Blood Cells Mol Dis 2008; 40:200-10. [DOI: 10.1016/j.bcmd.2007.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 07/11/2007] [Indexed: 01/10/2023]
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21
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Mutation of C/EBPalpha predisposes to the development of myeloid leukemia in a retroviral insertional mutagenesis screen. Blood 2008; 111:4309-21. [PMID: 18212247 DOI: 10.1182/blood-2007-06-097790] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The CCAAT enhancer binding protein alpha (C/EBPalpha) is an important myeloid tumor suppressor that is frequently mutated in human acute myeloid leukemia (AML). We have previously shown that mice homozygous for the E2F repression-deficient Cebpa(BRM2) allele develop nonfatal AML with long latency and incomplete penetrance, suggesting that accumulation of secondary mutations is necessary for disease progression. Here, we use SRS19-6-driven retroviral insertional mutagenesis to compare the phenotypes of leukemias arising in Cebpa(+/+), Cebpa(+/BRM2), and Cebpa(BRM2/BRM2) mice, with respect to disease type, latency of tumor development, and identity of the retroviral insertion sites (RISs). Both Cebpa(+/BRM2) and Cebpa(BRM2/BRM2) mice preferentially develop myeloid leukemias, but with differing latencies, thereby demonstrating the importance of gene dosage. Determination of RISs led to the identification of several novel candidate oncogenes, some of which may collaborate specifically with the E2F repression-deficient allele of Cebpa. Finally, we used an in silico pathway analysis approach to extract additional information from single RISs, leading to the identification of signaling pathways which were preferentially deregulated in a disease- and/or genotype-specific manner.
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22
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Sørensen AB, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS. Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virus. Retrovirology 2007; 4:46. [PMID: 17617899 PMCID: PMC1936429 DOI: 10.1186/1742-4690-4-46] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 07/06/2007] [Indexed: 01/25/2023] Open
Abstract
Background Mutations of an alternative splice donor site located within the gag region has previously been shown to broaden the pathogenic potential of the T-lymphomagenic gammaretrovirus Moloney murine leukemia virus, while the equivalent mutations in the erythroleukemia inducing Friend murine leukemia virus seem to have no influence on the disease-inducing potential of this virus. In the present study we investigate the splice pattern as well as the possible effects of mutating the alternative splice sites on the oncogenic properties of the B-lymphomagenic Akv murine leukemia virus. Results By exon-trapping procedures we have identified a novel gammaretroviral exon, resulting from usage of alternative splice acceptor (SA') and splice donor (SD') sites located in the capsid region of gag of the B-cell lymphomagenic Akv murine leukemia virus. To analyze possible effects in vivo of this novel exon, three different alternative splice site mutant viruses, mutated in either the SA', in the SD', or in both sites, respectively, were constructed and injected into newborn inbred NMRI mice. Most of the infected mice (about 90%) developed hematopoietic neoplasms within 250 days, and histological examination of the tumors showed that the introduced synonymous gag mutations have a significant influence on the phenotype of the induced tumors, changing the distribution of the different types as well as generating tumors of additional specificities such as de novo diffuse large B cell lymphoma (DLBCL) and histiocytic sarcoma. Interestingly, a broader spectrum of diagnoses was made from the two single splice-site mutants than from as well the wild-type as the double splice-site mutant. Both single- and double-spliced transcripts are produced in vivo using the SA' and/or the SD' sites, but the mechanisms underlying the observed effects on oncogenesis remain to be clarified. Likewise, analyses of provirus integration sites in tumor tissues, which identified 111 novel RISs (retroviral integration sites) and 35 novel CISs (common integration sites), did not clearly point to specific target genes or pathways to be associated with specific tumor diagnoses or individual viral mutants. Conclusion We present here the first example of a doubly spliced transcript within the group of gammaretroviruses, and we show that mutation of the alternative splice sites that define this novel RNA product change the oncogenic potential of Akv murine leukemia virus.
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Affiliation(s)
- Annette Balle Sørensen
- Department of Molecular Biology, University of Aarhus, Denmark
- The State and University Library, Universitetsparken, DK-8000 Aarhus C, Denmark
| | - Anders H Lund
- Department of Molecular Biology, University of Aarhus, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Sandra Kunder
- Institute of Pathology, GSF-National Research Center for Environment and Health, Neuherberg, Germany
| | | | - Jörg Schmidt
- Department of Comparative Medicine GSF-National Research Center for Environment and Health, Neuherberg, Germany
| | | | - Matthias Wabl
- Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, CA, USA
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23
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Voisin V, Rassart E. Complete genome sequences of the two viral variants of the Graffi MuLV: Phylogenetic relationship with other murine leukemia retroviruses. Virology 2007; 361:335-47. [PMID: 17208267 DOI: 10.1016/j.virol.2006.10.045] [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] [Received: 08/17/2006] [Revised: 10/03/2006] [Accepted: 10/28/2006] [Indexed: 11/15/2022]
Abstract
A detailed phylogenetic analysis of two variants of the Graffi murine retrovirus, GV-1.2 and GV-1.4, showed that they are closely related to SRS 19-6 and Moloney MuLVs. Two stretches of sequence testify to the divergence between Graffi and SRS 19-6 MuLVs, one corresponding to a recombination event of Graffi MuLV with a xenotropic virus. Moloney MuLV was found more distant, particularly in the GAG region. Our study encompasses every class of MuLVs (ecotropic, amphotropic, xenotropic, polytropic) with some focus on exogenous ecotropic viruses and further adds to previous phylogenetic studies. Graffi, SRS 19-6, Moloney, Friend and Rauscher MuLVs form a cluster that appears to share a common ancestor with the Casitas-amphotropic and -ecotropic MuLVs but are more distant to the Akv-type and xenotropic MuLVs. The analysis also revealed that the ENV region of HEMV, the prototype of the MuLV ancestor, was closely related to the corresponding region of Cas-Br-E.
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Affiliation(s)
- Véronique Voisin
- Laboratoire de biologie moléculaire, Département des sciences biologiques, Université du Québec à Montréal, Case Postale 8888 Succursale Centre-ville, Montréal, Canada H3C-3P8
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24
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Erkeland SJ, Aarts LH, Irandoust M, Roovers O, Klomp A, Valkhof M, Gits J, Eyckerman S, Tavernier J, Touw IP. Novel role of WD40 and SOCS box protein-2 in steady-state distribution of granulocyte colony-stimulating factor receptor and G-CSF-controlled proliferation and differentiation signaling. Oncogene 2006; 26:1985-94. [PMID: 17001306 DOI: 10.1038/sj.onc.1210004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Signals induced by granulocyte colony-stimulating factor (G-CSF), the major cytokine involved in neutrophil development, are tightly controlled by ligand-induced receptor internalization. Truncated G-CSF receptors (G-CSF-Rs) that fail to internalize show sustained proliferation and defective differentiation signaling. Steady-state forward routing also determines cell surface levels of cytokine receptors, but mechanisms controlling this are poorly understood. Here, we show that WD40 and suppressor of cytokine signaling (SOCS) box protein-2 (Wsb-2), an SOCS box-containing WD40 protein with currently unknown function, binds to the COOH-terminal region of G-CSF-R. Removal of this region did not affect internalization, yet resulted in increased membrane expression of G-CSF-R and enhanced proliferation signaling at the expense of differentiation induction. Conversely, Wsb-2 binding to the G-CSF-R reduced its cell surface expression and inhibited proliferation signaling. These effects depended on the SOCS box involved in ubiquitylation and on cytosolic lysines of G-CSF-R and imply a major role for ubiquitylation through the G-CSF-R C-terminus in forward routing of the receptor. Importantly, the Wsb-2 gene is commonly disrupted by virus integrations in mouse leukemia. We conclude that control of forward routing of G-CSF-R is essential for a balanced response of myeloid progenitors to G-CSF and suggest that disturbance of this balance may contribute to myeloid leukemia.
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Affiliation(s)
- S J Erkeland
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
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25
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Martín-Hernández J, Balle Sørensen A, Pedersen FS. Non-identical patterns of proviral insertions around host transcription units in lymphomas induced by different strains of murine leukemia virus. Virology 2006; 353:193-9. [PMID: 16790256 DOI: 10.1016/j.virol.2006.05.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/15/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
In a small sample of 57 retrovirus integration sites (RISs) isolated from 23 end-stage lymphomas induced in NMRI mice by the B-lymphotropic Akv wt or an enhancer mutant hereof, Akv1-99, we identified 14 novel RISs and defined 9 novel CISs (common insertion sites). Moreover, when comparing with RISs from tumors induced by the T-lymphomagenic SL3-3, we observed that SL3-3 targets RefSeq promoter regions with a significantly higher frequency than Akv/Akv1-99 and in an orientation-dependent way. Altogether, our results strongly emphasize the importance of host genetic background and virus type for retroviral insertion mutagenesis screens and suggest that different types of MLV may favor specific genomic regions and orientations in order exert optimal effect on target gene expression during lymphoma induction and development.
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MESH Headings
- Animals
- Enhancer Elements, Genetic
- Leukemia Virus, Murine/genetics
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, B-Cell/virology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell/virology
- Mice
- Mice, Inbred Strains
- Mutagenesis, Insertional
- Proviruses/genetics
- Retroviridae/genetics
- Transcription, Genetic
- Virus Integration/genetics
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Affiliation(s)
- Javier Martín-Hernández
- Department of Molecular Biology, University of Aarhus, C.F. Moellers Alle, Build. 130, DK-8000 Aarhus C, Denmark
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26
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Voisin V, Barat C, Hoang T, Rassart E. Novel insights into the pathogenesis of the Graffi murine leukemia retrovirus. J Virol 2006; 80:4026-37. [PMID: 16571819 PMCID: PMC1440465 DOI: 10.1128/jvi.80.8.4026-4037.2006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 01/25/2006] [Indexed: 11/20/2022] Open
Abstract
The Graffi murine leukemia virus (MuLV) was isolated in 1954 by Arnold Graffi, who characterized it as a myeloid leukemia-inducing retrovirus. He and his team, however, soon observed the intriguing phenomenon of hematological diversification, which corresponded to a decrease of myeloid leukemias and an increase of other types of leukemias. Recently, we derived two different molecular clones corresponding to ecotropic nondefective genomes that were named GV-1.2 and GV-1.4. The induced leukemias were classified as myeloid based on morphological analysis of blood smears. In this study, we further characterized the two variants of the Graffi murine retrovirus, GV-1.2 and GV-1.4, in three different strains of mice. We show that the Graffi MuLV is a multipotent retrovirus capable of inducing both lymphoid (T- and B-cell) and nonlymphoid (myeloid, erythroid, megakaryocytic) leukemia. Many of these are very complex with concomitant expression of different hematopoietic lineages. Interestingly, a high percentage of megakaryocytic leukemias, a type of leukemia rarely observed with MuLVs, arise in the FVB/n strain of mice. The genetic backgrounds of the different strains of mice influence greatly the results. Furthermore, the enhancer region, different for GV-1.2 and GV-1.4, plays a pivotal role in the disease specificity: GV-1.2 induces more lymphoid leukemias, and GV-1.4 induces more nonlymphoid ones.
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MESH Headings
- Animals
- Enhancer Elements, Genetic
- Flow Cytometry
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/pathogenicity
- Leukemia, B-Cell/immunology
- Leukemia, B-Cell/pathology
- Leukemia, Experimental/pathology
- Leukemia, Megakaryoblastic, Acute/immunology
- Leukemia, Megakaryoblastic, Acute/pathology
- Leukemia, Myeloid/immunology
- Leukemia, Myeloid/pathology
- Leukemia, T-Cell/immunology
- Leukemia, T-Cell/pathology
- Mice
- Mice, Inbred BALB C
- Retroviridae Infections/pathology
- Terminal Repeat Sequences
- Tumor Virus Infections/pathology
- Virus Latency
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Affiliation(s)
- Véronique Voisin
- Laboratoire de Biologie Moléculaire, Département des Sciences Biologiques, Université du Québec à Montréal, Case Postale 8888 Succ. Centre-ville, Montréal, Canada H3C-3P8
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27
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Erkeland SJ, Verhaak RGW, Valk PJM, Delwel R, Löwenberg B, Touw IP. Significance of murine retroviral mutagenesis for identification of disease genes in human acute myeloid leukemia. Cancer Res 2006; 66:622-6. [PMID: 16423987 DOI: 10.1158/0008-5472.can-05-2908] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Retroviral insertion mutagenesis is considered a powerful tool to identify cancer genes in mice, but its significance for human cancer has remained elusive. Moreover, it has recently been debated whether common virus integrations are always a hallmark of tumor cells and contribute to the oncogenic process. Acute myeloid leukemia (AML) is a heterogeneous disease with a variable response to treatment. Recurrent cytogenetic defects and acquired mutations in regulatory genes are associated with AML subtypes and prognosis. Recently, gene expression profiling (GEP) has been applied to further risk stratify AML. Here, we show that mouse leukemia genes identified by retroviral insertion mutagenesis are more frequently differentially expressed in distinct subclasses of adult and pediatric AML than randomly selected genes or genes located more distantly from a virus integration site. The candidate proto-oncogenes showing discriminative expression in primary AML could be placed in regulatory networks mainly involved in signal transduction and transcriptional control. Our data support the validity of retroviral insertion mutagenesis in mice for human disease and indicate that combining these murine screens for potential proto-oncogenes with GEP in human AML may help to identify critical disease genes and novel pathogenetic networks in leukemia.
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Affiliation(s)
- Stefan J Erkeland
- Department of Hematology, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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28
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Yamashita N, Osato M, Huang L, Yanagida M, Kogan SC, Iwasaki M, Nakamura T, Shigesada K, Asou N, Ito Y. Haploinsufficiency of Runx1/AML1 promotes myeloid features and leukaemogenesis in BXH2 mice. Br J Haematol 2006; 131:495-507. [PMID: 16281942 DOI: 10.1111/j.1365-2141.2005.05793.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Haploinsufficiency of RUNX1/AML1 is associated with familial platelet disorder with a predisposition to acute myeloid leukaemia (FPD/AML), but the causal relationship remains to be addressed experimentally. Mice heterozygous for the Runx1 null mutation, Runx1+/-, are considered to be genetically comparable with human FPD/AML patients but do not develop spontaneous leukaemia. To induce additional genetic alterations, retroviral insertional mutagenesis was employed with the use of BXH2 mice, which develop myeloid leukaemia because of the random integration of retrovirus present in the mouse. Heterozygous disruption of Runx1 in BXH2 mice resulted in a shortening of the latency period of leukaemia. In addition, BXH2-Runx1+/- mice exhibited more marked myeloid features than control mice. Moreover, the c-Kit gene, mutated in human RUNX leukaemias, was recurrently activated in BXH2-Runx1+/- mice, and a colony-forming assay revealed synergism between the Runx1+/- status and c-KIT overexpression. In conclusion, the BXH2-Runx1+/- system is a promising mouse model to investigate the mechanism of leukaemogenesis in FPD/AML.
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29
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Chen E, Lim MS, Rosic-Kablar S, Liu J, Jolicoeur P, Dubé ID, Hough MR. Dysregulated expression of mitotic regulators is associated with B-cell lymphomagenesis in HOX11-transgenic mice. Oncogene 2006; 25:2575-87. [PMID: 16407851 DOI: 10.1038/sj.onc.1209285] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dysregulated expression of the homeobox gene, HOX11 is a frequent etiologic event in T-cell acute lymphoblastic leukemias. HOX11-transgenic mice (IgHmu-HOX11Tg)-expressing HOX11 in the B-cell compartment develop B-cell lymphomas with extended latency. The latency suggests that additional genetic events are required prior to the onset of malignant lymphoma. We report the identification of 17 HOX11 collaborating genes, revealed through their propensity to be targeted in a proviral insertional mutagenesis screen. Seven integrations disrupted genes in mitotic spindle checkpoint control, suggesting that cells with elevated HOX11 expression are especially sensitive to dysregulation of chromosome segregation during mitosis. IgHmu-HOX11Tg primary B-lymphocyte cultures exposed to the aneugenic agents, colchicine and colcemid, exhibited increased incidences of chromosome missegregation as assessed by cytokinesis-block micronucleus assays. Additionally, IgHmu-HOX11Tg cultures were shown to exhibit aberrant bypass of spindle checkpoint arrest, as assessed by the increased presence of cycling cells determined by assessment of DNA content and by BrdU immunolabelling. Western immunoblotting revealed elevated expression of the mitotic effector molecules, cyclin A, cyclin B1 and cdc20 in IgHmu-HOX11Tg cultures. Moreover, spontaneously arising lymphoid neoplasms in IgHmu-HOX11Tg mice frequently exhibit aberrant expression of mitotic regulators, concomitant with increased development of micronuclei, abnormal mitotic checkpoint control and increased incidences of abnormal karyotypes when expanded in culture. Collectively, these findings indicate that abnormal regulation of spindle checkpoint control as a result of HOX11 overexpression leads to a heightened predisposition for development of aneuploidy, contributing to oncogenesis.
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MESH Headings
- Animals
- B-Lymphocytes/metabolism
- B-Lymphocytes/virology
- Bromodeoxyuridine/metabolism
- Cdc20 Proteins
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cyclin A/genetics
- Cyclin A/metabolism
- Cyclin B/genetics
- Cyclin B/metabolism
- Cyclin B1
- Disease Models, Animal
- Female
- Gene Expression Regulation, Neoplastic
- Genes, cdc
- Homeodomain Proteins/genetics
- Humans
- Immunoglobulin Heavy Chains/genetics
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Mutagenesis, Insertional
- Proviruses/genetics
- RNA, Messenger/metabolism
- Retroviridae/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Spindle Apparatus/metabolism
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Affiliation(s)
- E Chen
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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30
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Uren AG, Kool J, Berns A, van Lohuizen M. Retroviral insertional mutagenesis: past, present and future. Oncogene 2005; 24:7656-72. [PMID: 16299527 DOI: 10.1038/sj.onc.1209043] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Retroviral insertion mutagenesis screens in mice are powerful tools for efficient identification of oncogenic mutations in an in vivo setting. Many oncogenes identified in these screens have also been shown to play a causal role in the development of human cancers. Sequencing and annotation of the mouse genome, along with recent improvements in insertion site cloning has greatly facilitated identification of oncogenic events in retrovirus-induced tumours. In this review, we discuss the features of retroviral insertion mutagenesis screens, covering the mechanisms by which retroviral insertions mutate cellular genes, the practical aspects of insertion site cloning, the identification and analysis of common insertion sites, and finally we address the potential for use of somatic insertional mutagens in the study of nonhaematopoietic and nonmammary tumour types.
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Affiliation(s)
- A G Uren
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam
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31
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Rasmussen MH, Sørensen AB, Morris DW, Dutra JC, Engelhard EK, Wang CL, Schmidt J, Pedersen FS. Tumor model-specific proviral insertional mutagenesis of the Fos/Jdp2/Batf locus. Virology 2005; 337:353-64. [PMID: 15913695 DOI: 10.1016/j.virol.2005.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 04/05/2005] [Accepted: 04/22/2005] [Indexed: 11/29/2022]
Abstract
Retroviral activation of the AP-1/ATF super family member Jdp2 was recently reported to be a common event in M-MLV-induced T cell lymphoma in p27-null C57x129 mice as compared to wild type-inoculated mice but has not been found important in other models. On the basis of retroviral tag retrieval from 1190 individual Akv- and SL3-3-induced lymphomas, we here report that insertional mutagenesis into the 250-kb Fos/Jdp2/Batf locus is associated with SL3-3 MLV-induced T but not Akv-induced B cell lymphomas of NMRI and SWR mice. Integration pattern and clonality analyses suggest that Jdp2 participates in SL3-3-induced tumorigenesis distinctly as compared to the M-MLV setting. Northern blot analysis showed Jdp2 to be alternatively spliced in various normal tissues as well as MLV-induced lymphomas. Interestingly, in some tumors, proviral insertion seems to activate different mRNA sub-species. Whereas elevated mRNA levels of the Fos gene could not be correlated with provirus presence, in one case, Northern blot analysis as well as quantitative real-time PCR indicated proviral activation of the AP-1 super family member Batf, a gene not previously reported to be a target of insertional mutagenesis. A novel integration cluster between Jdp2 and Batf apparently did not influence the expression level of either gene, underscoring the importance of addressing expression effects to identify target genes of insertion. Altogether, such distinct insertion patterns point to different mechanism of activation of specific proto-oncogenes and are consequently of importance for the understanding of proviral activation mechanisms as well as the specific role of individual oncogenes in tumor development.
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MESH Headings
- 3T3 Cells
- Animals
- Basic-Leucine Zipper Transcription Factors
- DNA, Neoplasm/genetics
- DNA, Neoplasm/isolation & purification
- Disease Models, Animal
- Genes, fos
- Leukemia Virus, Murine/genetics
- Lymphoma, B-Cell/genetics
- Mice
- Mice, Inbred Strains
- Mutagenesis, Insertional
- Polymerase Chain Reaction
- Proviruses/genetics
- RNA, Messenger/genetics
- RNA, Viral/genetics
- Repressor Proteins/genetics
- Retroviridae/genetics
- Thymus Gland/virology
- Transcription Factors/genetics
- Tumor Cells, Cultured
- Virus Latency
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Affiliation(s)
- M H Rasmussen
- Department of Molecular Biology, University of Aarhus, C. F. Mollers Allé, Building 130, DK-8000 Aarhus C, Denmark
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32
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Lowther W, Wiley K, Smith GH, Callahan R. A new common integration site, Int7, for the mouse mammary tumor virus in mouse mammary tumors identifies a gene whose product has furin-like and thrombospondin-like sequences. J Virol 2005; 79:10093-6. [PMID: 16014973 PMCID: PMC1181551 DOI: 10.1128/jvi.79.15.10093-10096.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel common integration site for the mouse mammary tumor virus (MMTV) was identified (designated Int7) in five independently arising mouse mammary tumors. The insertion sites all cluster within a 1-kb region that is 2 to 3 kb 5' of the transcription initiation site of a gene, 2610028F08RIK, whose gene product contains furin-like and thrombospondin-like sequences. Expression of Int7 is normally very low or silent during various stages of mammary gland development, but MMTV integration at this site results in the activation of high steady-state levels of expression of the gene. These five tumors were also found to have two or three additional viral insertions, which in each case occurred flanking a member of either the Wnt and/or FGF gene family. Reverse transcriptase PCR results demonstrated that each of the viral insertions led to elevated expression of the presumed target flanking genes.
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Affiliation(s)
- William Lowther
- Mammary Biology and Tumorigenesis Laboratory, National Cancer Institute, Bethesda, MD 20892, USA
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van den Akker E, Vankan-Berkhoudt Y, Valk PJM, Löwenberg B, Delwel R. The common viral insertion site Evi12 is located in the 5'-noncoding region of Gnn, a novel gene with enhanced expression in two subclasses of human acute myeloid leukemia. J Virol 2005; 79:5249-58. [PMID: 15827139 PMCID: PMC1082726 DOI: 10.1128/jvi.79.9.5249-5258.2005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The leukemia and lymphoma disease locus Evi12 was mapped to the noncoding region of a novel gene, Gnn (named for Grp94 neighboring nucleotidase), that is located immediately upstream of the Grp94/Tra1 gene on mouse chromosome 10. The Gnn gene is conserved in mice and humans. Expression of fusion constructs between GFP and Gnn cDNA isoforms in HEK-293 cells showed that Gnn proteins are located mainly in the cytoplasm. Immunoblotting experiments demonstrated the presence of multiple Gnn protein isoforms in most organs, with the lowest levels of expression of the protein detected in bone marrow and spleen. The Evi12-containing leukemia cell line NFS107 showed high levels of expression of a approximately 150-kDa Gnn isoform (Gnn107) that was not observed in control cell lines. Overexpression may be due to the viral insertion in Evi12. The Gnn107 protein is probably encoded by a Gnn cDNA isoform that is expressed exclusively in NFS107 cells and that includes sequences of TU12B1-TY, a putative protein with homology to 5'-nucleotidase enzymes. Interestingly, using Affymetrix gene expression data of a cohort of 285 patients with acute myeloid leukemia (AML), we found that GNN/TU12B1-TY expression was specifically increased in two AML clusters. One cluster consisted of all AML patients with a t(8;21) translocation, and the second cluster consisted of AML patients with a normal karyotype carrying a FLT3 internal tandem duplication. These findings suggest that we identified a novel proto-oncogene that may be causally linked to certain types of human leukemia.
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Affiliation(s)
- Eric van den Akker
- Department of Hematology, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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Nielsen AA, Sørensen AB, Schmidt J, Pedersen FS. Analysis of wild-type and mutant SL3-3 murine leukemia virus insertions in the c-myc promoter during lymphomagenesis reveals target site hot spots, virus-dependent patterns, and frequent error-prone gap repair. J Virol 2005; 79:67-78. [PMID: 15596802 PMCID: PMC538719 DOI: 10.1128/jvi.79.1.67-78.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The murine leukemia retrovirus SL3-3 induces lymphomas in the T-cell compartment of the hematopoetic system when it is injected into newborn mice of susceptible strains. Previously, our laboratory reported on a deletion mutant of SL3-3 that induces T-cell tumors faster than the wild-type virus (S. Ethelberg, A. B. Sorensen, J. Schmidt, A. Luz, and F. S. Pedersen, J. Virol. 71:9796-9799, 1997). PCR analyses of proviral integrations in the promoter region of the c-myc proto-oncogene in lymphomas induced by wild-type SL3-3 [SL3-3(wt)] and the enhancer deletion mutant displayed a difference in targeting frequency into this locus. We here report on patterns of proviral insertions into the c-myc promoter region from SL3-3(wt), the faster variant, as well as other enhancer variants from a total of approximately 250 tumors. The analysis reveals (i) several integration site hot spots in the c-myc promoter region, (ii) differences in integration patterns between SL3-3(wt) and enhancer deletion mutant viruses, (iii) a correlation between tumor latency and the number of proviral insertions into the c-myc promoter, and (iv) a [5'-(A/C/G)TA(C/G/T)-3'] integration site consensus sequence. Unexpectedly, about 12% of the sequenced insertions were associated with point mutations in the direct repeat flanking the provirus. Based on these results, we propose a model for error-prone gap repair of host-provirus junctions.
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MESH Headings
- Animals
- Animals, Newborn
- Base Sequence
- Consensus Sequence
- DNA Repair
- Enhancer Elements, Genetic
- Female
- Gene Deletion
- Genes, myc
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/pathogenicity
- Leukemia, Experimental/pathology
- Leukemia, Experimental/virology
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell/virology
- Male
- Mice
- Molecular Sequence Data
- Mutation
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-myc/genetics
- Proviruses/genetics
- Retroviridae Infections/pathology
- Retroviridae Infections/virology
- Tumor Virus Infections/pathology
- Tumor Virus Infections/virology
- Virus Integration/genetics
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Tyybäkinoja A, Saarinen-Pihkala U, Elonen E, Knuutila S. Amplified, lost, and fused genes in 11q23-25 amplicon in acute myeloid leukemia, an array-CGH study. Genes Chromosomes Cancer 2005; 45:257-64. [PMID: 16283618 DOI: 10.1002/gcc.20288] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene amplifications occur rarely in hematologic neoplasms. We characterized two cases of acute myeloid leukemia (AML) with marker chromosomes and 11q23-25 amplicons. Case 1 was a 14-year-old male with an additional ring of chromosome 11 material as the sole karyotypic abnormality, as determined by G-banding and multicolor fluorescence in situ hybridization. Standard comparative genomic hybridization (CGH) showed amplification in 11q23-qter. However, the MLL gene, in 11q23, was not amplified by FISH. Case 2 was a 38-year-old male with the G-banding karyotype 51,XY,+8,+19,+3mar and with 11q22-qter amplification by standard CGH. This patient also had the MLL-LARG fusion gene. We used microarray-based CGH (array-CGH) to characterize the amplicons. In case 1, the amplified region in 11q24.3-25 (5.5 Mb) was continuous, and MLL was not amplified, as expected. In case 2, the amplicon was divided into two distinct parts, in 11q23.3 (1.2 Mb) and in 11q23.3-25 (13.3 Mb). It contained a loss ( approximately 1 Mb) in 11q23.3, and the amplicon breakpoint was in the middle of MLL. Although the amplicon size varied, the patients had a common amplified region in 11q24-25 that comprised 14 genes. Expression microarray of case 1 revealed that three of these genes, FLI1, NFRKB, and SNX19, were also overexpressed. The results indicate that the 11q24-q25 region may harbor new candidate oncogenes. In addition, the complex amplicon of case 2 suggests some intriguing chromosomal mechanisms.
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Affiliation(s)
- Anne Tyybäkinoja
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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van de Geijn GJM, Gits J, Touw IP. Distinct activities of suppressor of cytokine signaling (SOCS) proteins and involvement of the SOCS box in controlling G-CSF signaling. J Leukoc Biol 2004; 76:237-44. [PMID: 15107455 DOI: 10.1189/jlb.0104041] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Granulocyte-colony stimulating factor (G-CSF) induces proliferation of myeloid progenitor cells and controls their differentiation into mature neutrophils. Signal transducer and activator of transcription (STAT) proteins STAT3 and STAT5 are activated by G-CSF and play distinct roles in neutrophil development. Suppressor of cytokine signaling (SOCS) proteins are induced by STATs and inhibit signaling through various negative-feedback mechanisms. SOCS proteins can compete with docking of signaling substrates to receptors, interfere with Janus tyrosine kinase activity, and target proteins for proteasomal degradation. The latter process is mediated through the conserved C-terminal SOCS box. We determined the role of various SOCS proteins in controlling G-CSF responses and investigated the involvement of the SOCS box therein. We show that SOCS1 and SOCS3, but not CIS and SOCS2, inhibited G-CSF-induced STAT activation in human embryo kidney 293 cells. In myeloid 32D cells, SOCS1 and SOCS3 are induced by G-CSF. However, relative to interleukin-3-containing cultures, during G-CSF-induced neutrophilic differentiation, SOCS3 expression was further elevated, while SOCS1 levels remained constant. SOCS box deletion mutants of SOCS1 and SOCS3 were severely hampered in their abilities to inhibit STAT activation and to efficiently suppress colony formation by primary myeloid progenitors in response to G-CSF. These data demonstrate the importance of the SOCS box for the inhibitory effects of SOCS proteins on G-CSF signaling and show that among the different SOCS family members, SOCS3 is the major negative regulator of G-CSF responses during neutrophilic differentiation.
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Affiliation(s)
- Gert-Jan M van de Geijn
- Institute of Hematology, Erasmus University Medical Center, Room Ee 1330c, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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