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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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2
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Siti Mariam I, Norhidayah R, Zulaikha AB, Nazihah MY, Rosline H, Kausar GA, Sarina S, Azlan H, Ankathil R. Differential prognostic impact of stratified additional chromosome abnormalities on disease progression among Malaysian chronic myeloid leukemia patients undergoing treatment with imatinib mesylate. Front Oncol 2022; 12:720845. [PMID: 36003793 PMCID: PMC9393706 DOI: 10.3389/fonc.2022.720845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of additional chromosome abnormalities (ACAs) in chronic myeloid leukemia (CML) patients during treatment with a tyrosine kinase inhibitor (TKI) regime is generally associated with resistance to treatment and a sign of disease progression to accelerated phase or blast phase. We report the type, frequency, and differential prognostic impact of stratified ACAs with treatment response in 251 Malaysian CML patients undergoing TKI therapy. ACAs were observed in 40 patients (15.9%) of which 7 patients (17.5%) showed ACAs at time of initial diagnosis whereas 33 patients (82.5%) showed ACAs during the course of IM treatment. In order to assess the prognostic significance, we stratified the CML patients with ACAs into four groups, group 1 (+8/+Ph), group 2 (hypodiploidy), group 3 (structural/complex abnormalities); group 4 (high-risk complex abnormalities), and followed up the disease outcome of patients. Group 1 and group 2 relatively showed good prognosis while patients in group 3 and group 4 had progressed or transformed to AP or blast phase with a median survival rate of 12 months after progression. Novel ACAs consisting of rearrangements involving chromosome 11 and chromosome 12 were found to lead to myeloid BP while ACAs involving the deletion of 7q or monosomy 7 led toward a lymphoid blast phase. There was no evidence of group 2 abnormalities (hypodiploidy) contributing to disease progression. Compared to group 1 abnormalities, CML patients with group 3 and group 4 abnormalities showed a higher risk for disease progression. We conclude that the stratification based on individual ACAs has a differential prognostic impact and might be a potential novel risk predictive system to prognosticate and guide the treatment of CML patients at diagnosis and during treatment.
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Affiliation(s)
- Ismail Siti Mariam
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Ramli Norhidayah
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Abu Bakar Zulaikha
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Mohd Yunus Nazihah
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Hassan Rosline
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Ghazali Anis Kausar
- Unit of Biostatstics and Research Methodology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Sulong Sarina
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Husin Azlan
- Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
- *Correspondence: Ravindran Ankathil,
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t(4;12)(q12;p13) ETV6-rearranged AML without eosinophilia does not involve PDGFRA: relevance for imatinib insensitivity. Blood Adv 2021; 6:818-827. [PMID: 34587239 PMCID: PMC8945303 DOI: 10.1182/bloodadvances.2021005280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022] Open
Abstract
Apparent ETV6-PDGFRA fusions identified by FISH analysis in t(4;12)(q12;p13) AML should be confirmed by sequencing. Sequence-confirmed ETV6-PDGFRA fusions have not been identified in patients with t(4;12)(q12;p13) AML without eosinophilia.
Acute myeloid leukemia (AML) with t(4;12)(q12;p13) translocation is rare and often associated with an aggressive clinical course and poor prognosis. Previous reports based on fluorescence in situ hybridization (FISH) analysis have suggested that ETV6::PDGFRA fusions are present in these patients, despite the absence of eosinophilia, which is typically found in other hematopoietic malignancies with PDGFRA-containing fusions. We first detected an ETV6-SCFD2 fusion by targeted RNA sequencing in a patient with t(4;12)(q12;p13) who had been diagnosed with an ETV6-PDGFRA fusion by FISH analysis but failed to respond to imatinib. We then retrospectively identified 4 additional patients with AML and t(4;12)(q12;p13) with apparent ETV6-PDGFRA fusions using chromosome and FISH analysis and applied targeted RNA sequencing to archival material. We again detected rearrangements between ETV6 and non-PDGFRA 4q12 genes, including SCFD2, CHIC2, and GSX2. None of the 3 patients who received imatinib based on the incorrect assumption of an ETV6-PDGFRA fusion responded. Our findings highlight the importance of using a sequencing-based assay to confirm the presence of targetable gene fusions, particularly in genomic regions, such as 4q12, with many clinically relevant genes that are too close to resolve by chromosome or FISH analysis. Finally, combining our data and review of the literature, we show that sequence-confirmed ETV6-PDGFRA fusions are typically found in eosinophilic disorders (3/3 cases), and patients with t(4;12)(q12;p13) without eosinophilia are found to have other 4q12 partners on sequencing (17/17 cases).
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Bellet MM, Stincardini C, Costantini C, Gargaro M, Pieroni S, Castelli M, Piobbico D, Sassone-Corsi P, Della-Fazia MA, Romani L, Servillo G. The Circadian Protein PER1 Modulates the Cellular Response to Anticancer Treatments. Int J Mol Sci 2021; 22:ijms22062974. [PMID: 33804124 PMCID: PMC8001324 DOI: 10.3390/ijms22062974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 01/30/2023] Open
Abstract
The circadian clock driven by the daily light–dark and temperature cycles of the environment regulates fundamental physiological processes and perturbations of these sophisticated mechanisms may result in pathological conditions, including cancer. While experimental evidence is building up to unravel the link between circadian rhythms and tumorigenesis, it is becoming increasingly apparent that the response to antitumor agents is similarly dependent on the circadian clock, given the dependence of each drug on the circadian regulation of cell cycle, DNA repair and apoptosis. However, the molecular mechanisms that link the circadian machinery to the action of anticancer treatments is still poorly understood, thus limiting the application of circadian rhythms-driven pharmacological therapy, or chronotherapy, in the clinical practice. Herein, we demonstrate the circadian protein period 1 (PER1) and the tumor suppressor p53 negatively cross-regulate each other’s expression and activity to modulate the sensitivity of cancer cells to anticancer treatments. Specifically, PER1 physically interacts with p53 to reduce its stability and impair its transcriptional activity, while p53 represses the transcription of PER1. Functionally, we could show that PER1 reduced the sensitivity of cancer cells to drug-induced apoptosis, both in vitro and in vivo in NOD scid gamma (NSG) mice xenotransplanted with a lung cancer cell line. Therefore, our results emphasize the importance of understanding the relationship between the circadian clock and tumor regulatory proteins as the basis for the future development of cancer chronotherapy.
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Affiliation(s)
- Marina Maria Bellet
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
- Correspondence: (M.M.B.); (G.S.); Tel.: +39-0755858238 (M.M.B.); +39-0755858110 (G.S.)
| | - Claudia Stincardini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Stefania Pieroni
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Marilena Castelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Danilo Piobbico
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, CA 92617, USA;
| | - Maria Agnese Della-Fazia
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
| | - Giuseppe Servillo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.S.); (C.C.); (M.G.); (S.P.); (M.C.); (D.P.); (M.A.D.-F.); (L.R.)
- Correspondence: (M.M.B.); (G.S.); Tel.: +39-0755858238 (M.M.B.); +39-0755858110 (G.S.)
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Zhang L, Wang M, Wang Z, Zeng Z, Wen L, Xu Y, Yao L, Cen J, Li H, Pan J, Sun A, Wu D, Chen S, Ma L, Yang X. Identification of a novel ETV6 truncated fusion gene in myeloproliferative neoplasm, unclassifiable with t(4;12)(q12;p13). Ann Hematol 2020; 99:2445-2447. [PMID: 32734549 DOI: 10.1007/s00277-020-04207-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/27/2020] [Indexed: 11/26/2022]
MESH Headings
- Abnormal Karyotype
- Aged
- Bone Marrow/pathology
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/ultrastructure
- Chromosomes, Human, Pair 4/genetics
- Chromosomes, Human, Pair 4/ultrastructure
- Diagnosis, Differential
- Exons/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Male
- Myeloproliferative Disorders/diagnosis
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/pathology
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogene Proteins c-ets/genetics
- RNA, Long Noncoding/genetics
- Repressor Proteins/genetics
- Translocation, Genetic
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Ling Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Man Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Zheng Wang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Zhao Zeng
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Lijun Wen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yi Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Li Yao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Jiannong Cen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Jinlan Pan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Aining Sun
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China
| | - Liang Ma
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China.
| | - Xiaofei Yang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China.
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6
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Biswas A, Rajesh Y, Mitra P, Mandal M. ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors. Biochim Biophys Acta Rev Cancer 2020; 1874:188389. [PMID: 32659251 DOI: 10.1016/j.bbcan.2020.188389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
ETV6 (translocation-Ets-leukemia virus) gene is a transcriptional repressor mainly involved in haematopoiesis and maintenance of vascular networks and has developed to be a major oncogene with the potential ability of forming fusion partners with many other genes with carcinogenic consequences. ETV6 fusions function primarily by constitutive activation of kinase activity of the fusion partners, modifications in the normal functions of ETV6 transcription factor, loss of function of ETV6 or the partner gene and activation of a proto-oncogene near the site of translocation. The role of ETV6 fusion gene in tumorigenesis has been well-documented and more variedly found in haematological malignancies. However, the role of the ETV6 oncogene in solid tumors has also risen to prominence due to an increasing number of cases being reported with this malignancy. Since, solid tumors can be well-targeted, the diagnosis of this genre of tumors based on ETV6 malignancy is of crucial importance for treatment. This review highlights the important ETV6 associated fusions in solid tumors along with critical insights as to existing and novel means of targeting it. A consolidation of novel therapies such as immune, gene, RNAi, stem cell therapy and protein degradation hitherto unused in the case of ETV6 solid tumor malignancies may open further therapeutic avenues.
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Affiliation(s)
- Angana Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Yetirajam Rajesh
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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7
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Frenkel-Morgenstern M. Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras. Methods Mol Biol 2020; 2079:27-40. [PMID: 31728960 DOI: 10.1007/978-1-4939-9904-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chimeric RNA moieties typically consist of exons from two genes expressed from different genomic locations and produced by chromosomal translocations, trans-splicing or transcription errors. Recent advances in next-generation sequencing procedures have opened new horizons for identification of novel chimeric transcripts in various diseases in a personalized manner. Here we describe the detailed computational procedures to identify chimeric transcripts using RNA-seq reads. Moreover, we elaborate on the domain-domain co-occurrence method to detect alterations in chimeric protein-protein interaction (ChiPPI) networks produced by chimeric RNA that are translated to chimeric proteins.
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8
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Chronic myelomonocytic leukemia with ETV6-ABL1 rearrangement and SMC1A mutation. Cancer Genet 2019; 238:31-36. [DOI: 10.1016/j.cancergen.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/18/2019] [Accepted: 07/06/2019] [Indexed: 12/16/2022]
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9
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Badar T, Johnson L, Trifilo K, Wang H, Kudlow BA, Padron E, Pappenhausen PR, Hussaini MO. Detection of Novel t(12;17)(p12;p13) in Relapsed Refractory Acute Myeloid Leukemia by Anchored Multiplex PCR(AMP)-based Next-Generation Sequencing. Appl Immunohistochem Mol Morphol 2019; 27:e28-e31. [PMID: 28187034 DOI: 10.1097/pai.0000000000000477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although several technologies can be used to detect gene fusions, anchored multiplex PCR next-generation sequencing (AMP-NGS) offers the advantage of novel fusion detection and the ability to multiplex multitudinous genes. We applied AMP-NGS technology in the evaluation of a 56-year-old gentleman with myelodysplastic syndrome transformed acute myeloid leukemia (AML). Patient was initially diagnosed with low-risk myelodysplastic syndrome-refractory cytopenias and multilineage dysplasia (MDS-RCMD), progressed to AML after failing hypomethylating agent therapy. At progression patients had normal cytogenetics but NGS profiling showed ETV6 c.416_417del CT frame shift and U2AF1 S34F mutations. Patient attains brief remission of 2 months after induction chemotherapy and then he was refractory to 2 salvage chemotherapy regimens. Reassessment after failing second salvage, identified t(12;17)(p13;p13)[20] by karyotype. It was postulated that the 12p13 locus might represent a new rearrangement of ETV6. AMP-NGS confirmed involvement of the ETV6 with discovery of a novel fusion partner, HIC1. The detection of the novel fusion partners was supported by the breakpoints originally observed by karyotype. This discovery of ETV6-HIC1 gene fusion by AMP-NGS technology provided new insight into a leukemogenic pathway in AML. Future use of this technology can serve as an adjunct tool in workup of patients with AML and can also help in formulating therapeutic strategies.
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MESH Headings
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 17/genetics
- Frameshift Mutation
- High-Throughput Nucleotide Sequencing
- Humans
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Middle Aged
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Polymerase Chain Reaction
- Proto-Oncogene Proteins c-ets/genetics
- Proto-Oncogene Proteins c-ets/metabolism
- Recurrence
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Translocation, Genetic
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Talha Badar
- Department of Internal Medicine, Brandon Regional Hospital, Brandon
| | | | | | | | | | - Eric Padron
- Department of Hematopathology and Laboratory Medicine, Moffitt Cancer Center, Tampa, FL
| | | | - Mohammad O Hussaini
- Department of Hematopathology and Laboratory Medicine, Moffitt Cancer Center, Tampa, FL
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10
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Rasighaemi P, Ward AC. ETV6 and ETV7: Siblings in hematopoiesis and its disruption in disease. Crit Rev Oncol Hematol 2017; 116:106-115. [PMID: 28693791 DOI: 10.1016/j.critrevonc.2017.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/05/2017] [Accepted: 05/28/2017] [Indexed: 01/07/2023] Open
Abstract
ETV6 (TEL1) and ETV7 (TEL2) are closely-related members of the ETS family of transcriptional regulators. Both ETV6 and ETV7 have been demonstrated to play key roles in hematopoiesis, particularly with regard to maintenance of hematopoietic stem cells and control of lineage-specific differentiation, with evidence of functional interactions between both proteins. ETV6 has been strongly implicated in the molecular etiology of a number of hematopoietic diseases, including as a tumor suppressor, an oncogenic fusion partner, and an important regulator of thrombopoiesis, but recent evidence has also identified ETV7 as a potential oncogene in certain malignancies. This review provides an overview of ETV6 and ETV7 and their contribution to both normal and disrupted hematopoiesis. It also highlights the key clinical implications of the growing knowledge base regarding ETV6 abnormalities with respect to prognosis and treatment.
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Affiliation(s)
- Parisa Rasighaemi
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, 3216, Australia.
| | - Alister C Ward
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, 3216, Australia.
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11
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Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY. NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res 2015; 44:e29. [PMID: 26442529 PMCID: PMC4756807 DOI: 10.1093/nar/gkv1013] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
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Affiliation(s)
- Trees-Juen Chuang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chan-Shuo Wu
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Chen
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yuan Hung
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tai-Wei Chiang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Min-Yu Yang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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12
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Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A. ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Res 2014; 43:D68-75. [PMID: 25414346 PMCID: PMC4383979 DOI: 10.1093/nar/gku1199] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes. The ChiTaRS 2.1 database of chimeric transcripts and RNA-Seq data (http://chitars.bioinfo.cnio.es/) is the second version of the ChiTaRS database and includes improvements in content and functionality. Chimeras from eight organisms have been collated including novel sense–antisense (SAS) chimeras resulting from the slippage of the sense and anti-sense intragenic regions. The new database version collects more than 29 000 chimeric transcripts and indicates the expression and tissue specificity for 333 entries confirmed by RNA-seq reads mapping the chimeric junction sites. User interface allows for rapid and easy analysis of evolutionary conservation of fusions, literature references and experimental data supporting fusions in different organisms. More than 1428 cancer breakpoints have been automatically collected from public databases and manually verified to identify their correct cross-references, genomic sequences and junction sites. As a result, the ChiTaRS 2.1 collection of chimeras from eight organisms and human cancer breakpoints extends our understanding of the evolution of chimeric transcripts in eukaryotes as well as their functional role in carcinogenic processes.
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Affiliation(s)
- Milana Frenkel-Morgenstern
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Alessandro Gorohovski
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Dunja Vucenovic
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Lorena Maestre
- Monoclonal Antibodies Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Alfonso Valencia
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
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13
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Giguère A, Hébert J. Identification of a novel fusion gene involving RUNX1 and the antisense strand of SV2B in a BCR-ABL1-positive acute leukemia. Genes Chromosomes Cancer 2013; 52:1114-22. [PMID: 24123676 DOI: 10.1002/gcc.22105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/29/2013] [Indexed: 11/07/2022] Open
Abstract
RUNX1, a key regulator of hematopoiesis, is frequently mutated or implicated in chromosomal translocations in acute leukemia. About half of RUNX1 translocations remain uncharacterized at the molecular level. We describe here one such event, a t(15;21)(q26.1;q22) translocation identified in an adult patient diagnosed with a t(9;22)(q34;q11.2)-positive acute leukemia. This previously unreported rearrangement yields a fusion of RUNX1 with the antisense strand of the SV2B gene, a new translocation partner of RUNX1, resulting in the expression of out-of-frame mRNA chimeric transcripts and the production of putative truncated RUNX1 isoforms. The t(15;21) translocation also dissociates the P1 promoter of RUNX1 from its open reading frame, reducing RUNX1 expression levels in the patient's leukemic cells. Our data suggest that RUNX1 haploinsufficiency collaborates with the BCR-ABL1 oncogene in this leukemia. The description of this atypical gene fusion is an important addition to the characterization of the pathogenomic mechanisms leading to RUNX1 structural and functional alterations. Furthermore, our data strongly suggests that inadequate dosage of this gene plays an essential role in leukemogenesis.
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Affiliation(s)
- Amélie Giguère
- Quebec Leukemia Cell Bank and Hematology-Oncology Division, Maisonneuve-Rosemont Hospital, 5415 L'Assomption Blvd., Montréal H1T 2M4, Canada; Department of Medicine, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal H3C 3J7, Canada
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14
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Sugimoto T, Tomita A, Abe A, Iriyama C, Kiyoi H, Naoe T. Chimeric antisense RNA derived from chromosomal translocation modulates target gene expression. Haematologica 2012; 97:1278-80. [PMID: 22491739 PMCID: PMC3409828 DOI: 10.3324/haematol.2011.057869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Takumi Sugimoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Akihiro Tomita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akihiro Abe
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Hematology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Chisako Iriyama
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Tomoki Naoe
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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15
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De Braekeleer E, Douet-Guilbert N, Morel F, Le Bris MJ, Basinko A, De Braekeleer M. ETV6 fusion genes in hematological malignancies: a review. Leuk Res 2012; 36:945-61. [PMID: 22578774 DOI: 10.1016/j.leukres.2012.04.010] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/13/2012] [Accepted: 04/16/2012] [Indexed: 01/01/2023]
Abstract
Translocations involving band 12p13 are one of the most commonly observed chromosomal abnormalities in human leukemia and myelodysplastic syndrome. Their frequently result in rearrangements of the ETV6 gene. At present, 48 chromosomal bands have been identified to be involved in ETV6 translocations, insertions or inversions and 30 ETV6 partner genes have been molecularly characterized. The ETV6 protein contains two major domains, the HLH (helix-loop-helix) domain, encoded by exons 3 and 4, and the ETS domain, encoded by exons 6 through 8, with in between the internal domain encoded by exon 5. ETV6 is a strong transcriptional repressor, acting through its HLH and internal domains. Five potential mechanisms of ETV6-mediated leukemogenesis have been identified: constitutive activation of the kinase activity of the partner protein, modification of the original functions of a transcription factor, loss of function of the fusion gene, affecting ETV6 and the partner gene, activation of a proto-oncogene in the vicinity of a chromosomal translocation and dominant negative effect of the fusion protein over transcriptional repression mediated by wild-type ETV6. It is likely that ETV6 is frequently involved in leukemogenesis because of the large number of partners with which it can rearrange and the several pathogenic mechanisms by which it can lead to cell transformation.
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Affiliation(s)
- Etienne De Braekeleer
- Laboratoire d'Histologie, Embryologie et Cytogénétique, Université de Brest, Brest, France
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16
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Yang MY, Yang WC, Lin PM, Hsu JF, Hsiao HH, Liu YC, Tsai HJ, Chang CS, Lin SF. Altered expression of circadian clock genes in human chronic myeloid leukemia. J Biol Rhythms 2011; 26:136-48. [PMID: 21454294 DOI: 10.1177/0748730410395527] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian clock genes use transcriptional-translational feedback loops to control circadian rhythms. Recent studies have demonstrated that expression of some circadian clock genes displays daily oscillation in peripheral tissues including peripheral blood and bone marrow. Circadian rhythms regulate various functions of human body, and the disruption of circadian rhythm has been associated with cancer development and tumor progression. However, the direct links between aberrant circadian clock gene expression and human disorders remain largely unknown. In this study, comparisons were made between the expression profiles of 9 circadian clock genes from peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells (PMNs) from 18 healthy volunteers. Peripheral blood (PB) total leukocytes from 54 healthy volunteers and 95 patients with chronic myeloid leukemia (CML) were also investigated. Similar expression profiles of all 9 circadian clock genes were observed in PBMCs and PMNs of healthy individuals. In PB total leukocytes of healthy individuals, the daily pattern of PER1, PER2, PER3, CRY1, CRY2, and CKIε expression level peaked at 0800 h, and BMAL1 peaked at 2000 h. Daily pattern expression of these 7 genes was disrupted in newly diagnosed pre-imatinib mesylate-treated and blast crisis-phase patients with CML. Partial daily pattern gene expression recoveries were observed in patients with CML with complete cytogenetic response and major molecular response. The expression of CLOCK and TIM did not show a time-dependent variation among the healthy and patients with CML. These results indicate a possible association of the disrupted daily patterns of circadian clock gene expression with the pathogenesis of CML.
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Affiliation(s)
- Ming-Yu Yang
- College of Medicine, Chang Gung University-Kaohsiung Division, Kaohsiung County, Taiwan
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17
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Abstract
The circadian clock is an endogenous time keeping system shared by most organisms. In mammals, a master pacemaker in the hypothalamus orchestrates temporal alignment of behavior and physiology by transmitting daily signals to multiple clocks in peripheral tissues. Disruption of this communication has a profound affect on human health and has been linked to diverse pathogenic conditions, including cancer. At the center of the molecular circadian machinery is a set of clock genes, generating rhythmic oscillations on a cellular level. In the past several years, research from different fields has revealed the complexity and ubiquitous nature of circadian regulation, uncovering intriguing associations between clock components and cellular pathways implicated in tumorigenesis. In this review, we discuss the emerging role of circadian genes in hematological and hormone-related malignancies. These new insights suggest that manipulating circadian biology as a way to fight cancer, as well as, other life threatening diseases is within the realm of possibility.
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Affiliation(s)
- Sigal Gery
- Cedars-Sinai Medical Center, Division of Hematology/Oncology,UCLA School of Medicine, Los Angeles, CA, USA
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18
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19
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Shadan FF. Circadian tempo: A paradigm for genome stability? Med Hypotheses 2007; 68:883-91. [PMID: 17092657 DOI: 10.1016/j.mehy.2006.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 07/25/2006] [Accepted: 08/11/2006] [Indexed: 11/16/2022]
Abstract
Circadian clocks are molecular time-keeping systems that underlie daily biological rhythms in anticipation of the changing light and dark cycles. These clocks mediate daily rhythms in physiology and behavior that are thought to confer an adaptive advantage for organisms. It is hypothesized that cell cycle checkpoints are gated to an intrinsic circadian clock to protect DNA from diurnal exposure to mutagens (e.g.; UV radiation peaks with daylight and dissolved genotoxins that fluctuate with feeding periods). It is proposed that DNA replication arrest in response to genotoxic stress is a likely basis for the evolution of circadian-gated DNA replication. This protective mechanism is highly conserved and can be traced along the evolutionary time-line to the early prokaryotes, unicellular eukaryotes and viruses. Peak DNA repair capacity is normally synchronous to the crest of mutagenic stress as they oscillate with respect to time. Mutator phenotypes with increased vulnerability to genotoxic stress may therefore develop when the circadian pattern of cell cycle control, DNA repair or apoptotic response are phase-shifted relative to the rhythm of mutagenic stress. The accumulating mutations would lead to accelerated aging, genome instability and neoplasia. The proposed model delineates areas of research with potentially profound implications for carcinogenesis.
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Affiliation(s)
- Farhad F Shadan
- The Scripps Research Institute and Scripps Clinic, La Jolla, CA 92037, USA.
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20
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Panagopoulos I, Strömbeck B, Isaksson M, Heldrup J, Olofsson T, Johansson B. Fusion of ETV6 with an intronic sequence of the BAZ2A gene in a paediatric pre-B acute lymphoblastic leukaemia with a cryptic chromosome 12 rearrangement. Br J Haematol 2006; 133:270-5. [PMID: 16643428 DOI: 10.1111/j.1365-2141.2006.06020.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ETV6 at 12p13 is rearranged in a variety of haematological malignancies and solid tumours, with more than 20 different partners having been reported. These fusions result in either chimeric proteins or activation of the partner gene. However, there are a few examples of abnormalities resulting in truncated and, most likely, unproductive ETV6 proteins, suggesting that haploinsufficiency of ETV6 and/or the partner is leukaemogenic. We present a novel ETV6 rearrangement, identified in a paediatric pre-B acute lymphoblastic leukaemia. Fluorescence in situ hybridisation (FISH) and molecular genetic analyses revealed a fusion of ETV6 and BAZ2A (at 12q13), generated through a cryptic rearrangement between 12p13 and 12q13, consisting of exons 1 and 2 of ETV6 and a sequence from intron 1 of BAZ2A. This transcript is not expected to produce any chimeric protein, but may encode a truncated form of ETV6, containing the first 54 amino acids (aa), followed by 16 aa from the 3' fusion sequence, reminiscent of ETV6 fusions with MDS2, LOC115548, PER1, and STL. The rearrangement might also modify the regulation of BAZ2A by either activating a cryptic promoter or by coming under the control of the ETV6 promoter. The present case emphasises that 'unproductive' ETV6 rearrangements may play an important pathogenetic role in leukaemia.
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Affiliation(s)
- Ioannis Panagopoulos
- Department of Clinical Genetics, Lund University, University Hospital, Lund, Sweden.
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21
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Garrett RW, Gasiewicz TA. The aryl hydrocarbon receptor agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin alters the circadian rhythms, quiescence, and expression of clock genes in murine hematopoietic stem and progenitor cells. Mol Pharmacol 2006; 69:2076-83. [PMID: 16556773 DOI: 10.1124/mol.105.021006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR) agonist, has been identified as a potent immunohematopoietic toxicant with the ability to alter the number of Lin(-) Sca-1(+) cKit(+) (LSK) bone marrow cells, a population enriched for murine hematopoietic stem cells. The biology of these cells is governed by circadian rhythms and TCDD has been shown to disrupt circadian rhythms of other biological endpoints. We investigated the effect of TCDD on the circadian rhythms of hematopoietic precursors. Female C57BL/6 mice were treated with a single oral dose of 10 mug/kg TCDD. Five days later, bone marrow was harvested every 4 h for 24 h and stained for specific hematopoietic populations using fluorescently labeled antibodies. In addition, cells were placed into semisolid culture to measure different functionally defined populations. Activation of the AhR by TCDD elicited disruptions in the rhythms of LSK cell numbers and phenotypically defined myeloid and erythroid precursors. Simultaneous DNA and RNA staining revealed an abnormal in vivo rhythm of percentage of total number of LSK cells in G(0) phase of the cell cycle, suggesting disruption of stem cell quiescence. Finally, quantitative reverse transcription-polymerase chain reaction revealed that expression of AhR and Arnt mRNA within enriched hematopoietic precursors oscillates with a circadian period. Modest changes in the 24-h expression of mPer1 and mPer2 mRNA and increased AhR repressor mRNA after TCDD exposure suggest a direct effect on the molecular machinery responsible for these rhythms. Together, these data demonstrate that activation of the AhR by TCDD disrupts the circadian rhythms associated with murine hematopoietic precursors.
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Affiliation(s)
- Russell W Garrett
- Department of Environmental Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, 601 Elmwood Avenue, Box EHSC, Rochester, NY 14642, USA
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22
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Zhou W, Wang Y, Liu Y, Peng W, Xiao J, Zhu B, Wang Z. Deoxyribozymes inhibit the expression of period1 gene in vitro. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2005; 48:195-201. [PMID: 16092751 DOI: 10.1007/bf03183612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
To investigate the effect of two deoxyribozymes targeting period1 (per1) mRNA in vitro for exploring a novel gene therapy approach about circadian rhythm diseases, the specific deoxyribozymes targeting per1 were designed and synthesized chemically following MFold analysis according to its mRNA secondary structure. per1 RNA fragments were prepared by in vitro transcription of pcDNA3.1(+)-per1(164:256). The cleavage reactions containing deoxyribozymes and per1 RNA fragments were performed under certain conditions. With the transfection technique mediated by LipofectAMINE, pcDNA3-per1 and DRz164 or DRz256 were introduced into NIH3T3 cells. The effects of deoxyribozymes on per1 were studied by reverse transcript-polymerase chain reaction (RT-PCR) and flow cytometry (FCM). When deoxyribozymes and RNA transcripts were incubated under the adopted conditions at 37 degrees C for 2 h, about 63% of per1(164:256) RNA transcripts were cleaved by DRz164 and about 50.5% by DRz256. After cotransfecting pcDNA3-per1 with DRz164 or DRz256, the expression of per1 mRNA was decreased, as indicated by RT-PCR semi-quantity analysis. FCM analysis showed that Per1 protein was inhibited. Both DRz164 and DRz256 targeting per1 have the specific cleavage activity toward per1 mRNA in vitro and can highly block the expression of per1 gene in cellular milieu.
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Affiliation(s)
- Wei Zhou
- Biomedical Engineering Department, School of West China Basic and Forensic Science, Sichuan University, Chengdu 610041, China
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23
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Abstract
Alterations of the ets family transcription factor ETV6 (TEL) and the RUNT domain transcription factor RUNX1 (AML1) play pivotal roles in the leukemogenesis of various types of leukemia. While only three fusion partners of RUNX1 namely ETO, ETV6 and MTG16 have been described so far, there is a plethora of ETV6 fusion partners with about 20 partners described so far. Apart from forming fusion genes there are other genetic alterations of ETV6 including deletions, point mutations and possible alterations at the promoter level that might contribute to the malignant phenotype. This review will focus on ETV6 and on the different mechanisms that are used by this gene to cause leukemia.
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Affiliation(s)
- Stefan K Bohlander
- Department of Medicine III, University Hospital Grosshadern, Marchioninistr. 15, D-81377 Munich, Germany.
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24
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Vieira L, Marques B, Cavaleiro C, Ambrósio AP, Jorge M, Neto A, Costa JM, Júnior EC, Boavida MG. Molecular cytogenetic characterization of rearrangements involving 12p in leukemia. CANCER GENETICS AND CYTOGENETICS 2005; 157:134-9. [PMID: 15721634 DOI: 10.1016/j.cancergencyto.2004.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Accepted: 07/27/2004] [Indexed: 10/25/2022]
Abstract
Translocations involving the short arm of chromosome 12 are frequent events among patients with various hematologic malignancies. In approximately half of these patients, fluorescence in situ hybridization (FISH) analysis has shown that the breakpoints are clustered within the ETS-variant gene 6 (ETV6) at 12p13, leading to its fusion with a variety of partner genes on different chromosomes. The remaining patients have breakpoints centromeric or telomeric to ETV6 or, less frequently, interstitial 12p13 deletions that invariably involve this gene. In most cases reported, 12p translocations were found to be associated with other structural and/or numerical abnormalities as part of a complex karyotype. Initially using conventional cytogenetic analysis, we characterized the chromosomal breakpoints of three leukemia patients (two with B-acute lymphoblastic leukemia and one with myelodysplastic/myeloproliferative disorder) presenting a t(5;12)(q13;p13), t(12;15)(p13;q22), and dic(9;12)(p11;p11), respectively, as the only structural abnormalities in the karyotype. These rearrangements were further investigated using FISH and molecular studies. Two cases revealed cryptic three-way translocations that had gone undetected in the conventional cytogenetic analyses. One of the cases presented an ETV6 rearrangement with an unsuspected fusion, with the CBFA2 gene at 21q22. In the other two, small and large 12p deletions that included ETV6 were found. This report illustrates the chromosomal and molecular heterogeneity of rearrangements underlying 12p chromosome translocations in leukemia.
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Affiliation(s)
- L Vieira
- Centro de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisboa, Portugal.
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25
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van der Burg M, Poulsen TS, Hunger SP, Beverloo HB, Smit EME, Vang-Nielsen K, Langerak AW, van Dongen JJM. Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia. Leukemia 2004; 18:895-908. [PMID: 15042105 DOI: 10.1038/sj.leu.2403340] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 02/03/2004] [Indexed: 11/08/2022]
Abstract
Chromosome aberrations are frequently observed in precursor-B-acute lymphoblastic leukemias (ALL) and T-cell acute lymphoblastic leukemias (T-ALL). These translocations can form leukemia-specific chimeric fusion proteins or they can deregulate expression of an (onco)gene, resulting in aberrant expression or overexpression. Detection of chromosome aberrations is an important tool for risk classification. We developed rapid and sensitive split-signal fluorescent in situ hybridization (FISH) assays for six of the most frequent chromosome aberrations in precursor-B-ALL and T-ALL. The split-signal FISH approach uses two differentially labeled probes, located in one gene at opposite sites of the breakpoint region. Probe sets were developed for the genes TCF3 (E2A) at 19p13, MLL at 11q23, ETV6 at 12p13, BCR at 22q11, SIL-TAL1 at 1q32 and TLX3 (HOX11L2) at 5q35. In normal karyotypes, two colocalized green/red signals are visible, but a translocation results in a split of one of the colocalized signals. Split-signal FISH has three main advantages over the classical fusion-signal FISH approach, which uses two labeled probes located in two genes. First, the detection of a chromosome aberration is independent of the involved partner gene. Second, split-signal FISH allows the identification of the partner gene or chromosome region if metaphase spreads are present, and finally it reduces false-positivity.
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Affiliation(s)
- M van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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26
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Rawat VPS, Cusan M, Deshpande A, Hiddemann W, Quintanilla-Martinez L, Humphries RK, Bohlander SK, Feuring-Buske M, Buske C. Ectopic expression of the homeobox gene Cdx2 is the transforming event in a mouse model of t(12;13)(p13;q12) acute myeloid leukemia. Proc Natl Acad Sci U S A 2004; 101:817-22. [PMID: 14718672 PMCID: PMC321764 DOI: 10.1073/pnas.0305555101] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Creation of fusion genes by balanced chromosomal translocations is one of the hallmarks of acute myeloid leukemia (AML) and is considered one of the key leukemogenic events in this disease. In t(12;13)(p13;q12) AML, ectopic expression of the homeobox gene CDX2 was detected in addition to expression of the ETV6-CDX2 fusion gene, generated by the chromosomal translocation. Here we show in a murine model of t(12;13)(p13;q12) AML that myeloid leukemogenesis is induced by the ectopic expression of CDX2 and not by the ETV6-CDX2 chimeric gene. Mice transplanted with bone marrow cells retrovirally engineered to express Cdx2 rapidly succumbed to fatal and transplantable AML. The transforming capacity of Cdx2 depended on an intact homeodomain and the N-terminal transactivation domain. Transplantation of bone marrow cells expressing ETV6-CDX2 failed to induce leukemia. Furthermore, coexpression of ETV6-CDX2 and Cdx2 in bone marrow cells did not accelerate the course of disease in transplanted mice compared to Cdx2 alone. These data demonstrate that activation of a protooncogene by a balanced chromosomal translocation can be the pivotal leukemogenic event in AML, characterized by the expression of a leukemia-specific fusion gene. Furthermore, these findings link protooncogene activation to myeloid leukemogenesis, an oncogenic mechanism so far associated mainly with lymphoid leukemias and lymphomas.
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MESH Headings
- Animals
- Bone Marrow Transplantation
- CDX2 Transcription Factor
- Cell Transformation, Neoplastic/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Disease Models, Animal
- Gene Expression
- Genes, Homeobox
- Homeodomain Proteins/genetics
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Transgenic
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/genetics
- Oncogene Proteins, Fusion/genetics
- Trans-Activators
- Translocation, Genetic
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Affiliation(s)
- Vijay P S Rawat
- GSF-Clinical Cooperative Group Leukemia and Department of Medicine III, Grosshadern, Ludwig Maximilians University, 81377 Munich, Germany
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27
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Tosi S, Hughes J, Scherer SW, Nakabayashi K, Harbott J, Haas OA, Cazzaniga G, Biondi A, Kempski H, Kearney L. Heterogeneity of the 7q36 breakpoints in the t(7;12) involving ETV6 in infant leukemia. Genes Chromosomes Cancer 2003; 38:191-200. [PMID: 12939747 DOI: 10.1002/gcc.10258] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The t(7;12)(q36;p13) is a recurrent chromosome abnormality in infant leukemia. In these cases, the involvement of ETV6, with disruption of the gene consistently at its 5' end, has been reported by several groups. A fusion transcript between ETV6 and HLXB9 has been detected in some, but not all, reported cases of t(7;12). We report here a study based on fluorescence in situ hybridization (FISH) mapping of the translocation breakpoints in seven patients and detailed molecular studies using Southern blotting on two of these patients. The FISH studies have shown a cluster of breakpoints within a cosmid contig proximal to the HLXB9 gene. Southern blotting analysis enabled us to define two distinct breakpoints within the area covered by the cosmid contig in two patients. The analysis of an unusual case of t(7;12)(q22;p13) [full karyotype: 46,XX,der(7)t(7;12)(q22;p13)del(7)(q22q36)] also revealed a break in 7q36, although in a region proximal to the overlapping cosmids. 5' RACE PCR in one patient has shown a rearrangement involving the ETV6 allele not involved in the t(7;12), suggesting that no functional ETV6 allele might be present in this case. These data show some heterogeneity in the distribution of breakpoints in 7q36, indicating that the generation of a fusion gene might not be the mechanism responsible for leukemogenesis in the t(7;12), at least in some cases.
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MESH Headings
- Base Sequence
- Chromosome Breakage/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 7/genetics
- DNA-Binding Proteins/genetics
- Female
- Genetic Heterogeneity
- Humans
- In Situ Hybridization, Fluorescence
- Infant
- Leukemia/genetics
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myelomonocytic, Acute/genetics
- Male
- Molecular Sequence Data
- Myelodysplastic Syndromes/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Proto-Oncogene Proteins c-ets
- Repressor Proteins/genetics
- Translocation, Genetic/genetics
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Sabrina Tosi
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom.
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