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Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, Them NCC, Berg T, Gisslinger B, Pietra D, Chen D, Vladimer GI, Bagienski K, Milanesi C, Casetti IC, Sant'Antonio E, Ferretti V, Elena C, Schischlik F, Cleary C, Six M, Schalling M, Schönegger A, Bock C, Malcovati L, Pascutto C, Superti-Furga G, Cazzola M, Kralovics R. Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med 2013; 369:2379-90. [PMID: 24325356 DOI: 10.1056/nejmoa1311347] [Citation(s) in RCA: 1414] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Approximately 50 to 60% of patients with essential thrombocythemia or primary myelofibrosis carry a mutation in the Janus kinase 2 gene (JAK2), and an additional 5 to 10% have activating mutations in the thrombopoietin receptor gene (MPL). So far, no specific molecular marker has been identified in the remaining 30 to 45% of patients. METHODS We performed whole-exome sequencing to identify somatically acquired mutations in six patients who had primary myelofibrosis without mutations in JAK2 or MPL. Resequencing of CALR, encoding calreticulin, was then performed in cohorts of patients with myeloid neoplasms. RESULTS Somatic insertions or deletions in exon 9 of CALR were detected in all patients who underwent whole-exome sequencing. Resequencing in 1107 samples from patients with myeloproliferative neoplasms showed that CALR mutations were absent in polycythemia vera. In essential thrombocythemia and primary myelofibrosis, CALR mutations and JAK2 and MPL mutations were mutually exclusive. Among patients with essential thrombocythemia or primary myelofibrosis with nonmutated JAK2 or MPL, CALR mutations were detected in 67% of those with essential thrombocythemia and 88% of those with primary myelofibrosis. A total of 36 types of insertions or deletions were identified that all cause a frameshift to the same alternative reading frame and generate a novel C-terminal peptide in the mutant calreticulin. Overexpression of the most frequent CALR deletion caused cytokine-independent growth in vitro owing to the activation of signal transducer and activator of transcription 5 (STAT5) by means of an unknown mechanism. Patients with mutated CALR had a lower risk of thrombosis and longer overall survival than patients with mutated JAK2. CONCLUSIONS Most patients with essential thrombocythemia or primary myelofibrosis that was not associated with a JAK2 or MPL alteration carried a somatic mutation in CALR. The clinical course in these patients was more indolent than that in patients with the JAK2 V617F mutation. (Funded by the MPN Research Foundation and Associazione Italiana per la Ricerca sul Cancro.).
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Affiliation(s)
- Thorsten Klampfl
- From CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (T.K., A.S.H., H.N., J.D.M., N.C.C.T., T.B., D.C., G.I.V., K.B., F.S., C.C., M. Six, A.S., C.B., G.S.-F., R.K.) and the Department of Internal Medicine I, Division of Hematology and Blood Coagulation, Medical University of Vienna (H.G., B.G., M. Schalling, R.K.) - both in Vienna; and the Department of Hematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo (E.R., D.P., C.M., I.C.C., E.S., V.F., C.E., L.M., C.P., M.C.), and the Department of Molecular Medicine, University of Pavia (L.M., M.C.) - both in Pavia, Italy
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Klampfl T, Milosevic JD, Puda A, Schönegger A, Bagienski K, Berg T, Harutyunyan AS, Gisslinger B, Rumi E, Malcovati L, Pietra D, Elena C, Della Porta MG, Pieri L, Guglielmelli P, Bock C, Doubek M, Dvorakova D, Suvajdzic N, Tomin D, Tosic N, Racil Z, Steurer M, Pavlovic S, Vannucchi AM, Cazzola M, Gisslinger H, Kralovics R. Complex patterns of chromosome 11 aberrations in myeloid malignancies target CBL, MLL, DDB1 and LMO2. PLoS One 2013; 8:e77819. [PMID: 24147083 PMCID: PMC3797696 DOI: 10.1371/journal.pone.0077819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
Exome sequencing of primary tumors identifies complex somatic mutation patterns. Assignment of relevance of individual somatic mutations is difficult and poses the next challenge for interpretation of next generation sequencing data. Here we present an approach how exome sequencing in combination with SNP microarray data may identify targets of chromosomal aberrations in myeloid malignancies. The rationale of this approach is that hotspots of chromosomal aberrations might also harbor point mutations in the target genes of deletions, gains or uniparental disomies (UPDs). Chromosome 11 is a frequent target of lesions in myeloid malignancies. Therefore, we studied chromosome 11 in a total of 813 samples from 773 individual patients with different myeloid malignancies by SNP microarrays and complemented the data with exome sequencing in selected cases exhibiting chromosome 11 defects. We found gains, losses and UPDs of chromosome 11 in 52 of the 813 samples (6.4%). Chromosome 11q UPDs frequently associated with mutations of CBL. In one patient the 11qUPD amplified somatic mutations in both CBL and the DNA repair gene DDB1. A duplication within MLL exon 3 was detected in another patient with 11qUPD. We identified several common deleted regions (CDR) on chromosome 11. One of the CDRs associated with de novo acute myeloid leukemia (P=0.013). One patient with a deletion at the LMO2 locus harbored an additional point mutation on the other allele indicating that LMO2 might be a tumor suppressor frequently targeted by 11p deletions. Our chromosome-centered analysis indicates that chromosome 11 contains a number of tumor suppressor genes and that the role of this chromosome in myeloid malignancies is more complex than previously recognized.
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Affiliation(s)
- Thorsten Klampfl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jelena D. Milosevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ana Puda
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Schönegger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Klaudia Bagienski
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tiina Berg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ashot S. Harutyunyan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gisslinger
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Elisa Rumi
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luca Malcovati
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Daniela Pietra
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Chiara Elena
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Matteo Giovanni Della Porta
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Lisa Pieri
- Section of Hematology, University of Florence, Florence, Italy
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael Doubek
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Dana Dvorakova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Nada Suvajdzic
- Clinic of Hematology, Clinical Center of Serbia, University of Belgrade, School of Medicine, Belgrade, Serbia
| | - Dragica Tomin
- Clinic of Hematology, Clinical Center of Serbia, University of Belgrade, School of Medicine, Belgrade, Serbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Zdenek Racil
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Michael Steurer
- Division of Hematology and Oncology, Innsbruck University Hospital, Innsbruck, Austria
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Mario Cazzola
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Heinz Gisslinger
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Rumi E, Milosevic JD, Casetti I, Dambruoso I, Pietra D, Boveri E, Boni M, Bernasconi P, Passamonti F, Kralovics R, Cazzola M. Efficacy of Ruxolitinib in Chronic Eosinophilic Leukemia Associated With a PCM1-JAK2 Fusion Gene. J Clin Oncol 2013; 31:e269-71. [DOI: 10.1200/jco.2012.46.4370] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Elisa Rumi
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Jelena D. Milosevic
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ilaria Casetti
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Irene Dambruoso
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Daniela Pietra
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Emanuela Boveri
- Institute of Anatomic Pathology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Marina Boni
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Paolo Bernasconi
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo; and University of Pavia, Pavia, Italy
| | | | - Robert Kralovics
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Mario Cazzola
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo; and University of Pavia, Pavia, Italy
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Milosevic JD, Kralovics R. Genetic and epigenetic alterations of myeloproliferative disorders. Int J Hematol 2012; 97:183-97. [PMID: 23233154 DOI: 10.1007/s12185-012-1235-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 11/27/2012] [Accepted: 11/27/2012] [Indexed: 01/07/2023]
Abstract
The classical BCR-ABL negative myeloproliferative neoplasms (MPN) polycythemia vera, essential thrombocythemia, and primary myelofibrosis are clonal hematopoietic disorders characterized by excessive production of terminally differentiated myeloid cells. In MPN patients, the disease can progress to secondary myelofibrosis or acute myeloid leukemia. Clonal hematopoiesis, disease phenotype, and progression are caused by somatically acquired genetic lesions of genes involved in cytokine signaling, RNA splicing, as well as epigenetic regulation. This review provides an overview of point mutations and cytogenetic lesions associated with MPN and addresses the role of these somatic lesions in MPN disease progression.
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Affiliation(s)
- Jelena D Milosevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
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Milosevic JD, Puda A, Malcovati L, Berg T, Hofbauer M, Stukalov A, Klampfl T, Harutyunyan AS, Gisslinger H, Gisslinger B, Burjanivova T, Rumi E, Pietra D, Elena C, Vannucchi AM, Doubek M, Dvorakova D, Robesova B, Wieser R, Koller E, Suvajdzic N, Tomin D, Tosic N, Colinge J, Racil Z, Steurer M, Pavlovic S, Cazzola M, Kralovics R. Clinical significance of genetic aberrations in secondary acute myeloid leukemia. Am J Hematol 2012; 87:1010-6. [PMID: 22887079 DOI: 10.1002/ajh.23309] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 07/02/2012] [Indexed: 12/30/2022]
Abstract
The study aimed to identify genetic lesions associated with secondary acute myeloid leukemia (sAML) in comparison with AML arising de novo (dnAML) and assess their impact on patients' overall survival (OS). High-resolution genotyping and loss of heterozygosity mapping was performed on DNA samples from 86 sAML and 117 dnAML patients, using Affymetrix Genome-Wide Human SNP 6.0 arrays. Genes TP53, RUNX1, CBL, IDH1/2, NRAS, NPM1, and FLT3 were analyzed for mutations in all patients. We identified 36 recurrent cytogenetic aberrations (more than five events). Mutations in TP53, 9pUPD, and del7q (targeting CUX1 locus) were significantly associated with sAML, while NPM1 and FLT3 mutations associated with dnAML. Patients with sAML carrying TP53 mutations demonstrated lower 1-year OS rate than those with wild-type TP53 (14.3% ± 9.4% vs. 35.4% ± 7.2%; P = 0.002), while complex karyotype, del7q (CUX1) and del7p (IKZF1) showed no significant effect on OS. Multivariate analysis confirmed that mutant TP53 was the only independent adverse prognostic factor for OS in sAML (hazard ratio 2.67; 95% CI: 1.33-5.37; P = 0.006). Patients with dnAML and complex karyotype carried sAML-associated defects (TP53 defects in 54.5%, deletions targeting FOXP1 and ETV6 loci in 45.4% of the cases). We identified several co-occurring lesions associated with either sAML or dnAML diagnosis. Our data suggest that distinct genetic lesions drive leukemogenesis in sAML. High karyotype complexity of sAML patients does not influence OS. Somatic mutations in TP53 are the only independent adverse prognostic factor in sAML. Patients with dnAML and complex karyotype show genetic features associated with sAML and myeloproliferative neoplasms.
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Affiliation(s)
- Jelena D Milosevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Bento C, Maia TM, Milosevic JD, Carreira IM, Kralovics R, Ribeiro ML. β Thalassemia major due to acquired uniparental disomy in a previously healthy adolescent. Haematologica 2012; 98:e4-6. [PMID: 22875618 DOI: 10.3324/haematol.2012.064097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Celeste Bento
- Serviço de Hematologia, CHC. Centro Hospitalar e Universitário de Coimbra, Portugal. .
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Puda A, Milosevic JD, Berg T, Klampfl T, Harutyunyan AS, Gisslinger B, Rumi E, Pietra D, Malcovati L, Elena C, Doubek M, Steurer M, Tosic N, Pavlovic S, Guglielmelli P, Pieri L, Vannucchi AM, Gisslinger H, Cazzola M, Kralovics R. Frequent deletions of JARID2 in leukemic transformation of chronic myeloid malignancies. Am J Hematol 2012; 87:245-50. [PMID: 22190018 DOI: 10.1002/ajh.22257] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 11/15/2011] [Indexed: 11/06/2022]
Abstract
Chronic myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS) have an inherent tendency to progress to acute myeloid leukemia (AML). Using high-resolution SNP microarrays, we studied a total of 517 MPN and MDS patients in different disease stages, including 77 AML cases with previous history of MPN (N = 46) or MDS (N = 31). Frequent chromosomal deletions of variable sizes were detected, allowing the mapping of putative tumor suppressor genes involved in the leukemic transformation process. We detected frequent deletions on the short arm of chromosome 6 (del6p). The common deleted region on 6p mapped to a 1.1-Mb region and contained only the JARID2 gene--member of the polycomb repressive complex 2 (PRC2). When we compared the frequency of del6p between chronic and leukemic phase, we observed a strong association of del6p with leukemic transformation (P = 0.0033). Subsequently, analysis of deletion profiles of other PRC2 members revealed frequent losses of genes such as EZH2, AEBP2, and SUZ12; however, the deletions targeting these genes were large. We also identified two patients with homozygous losses of JARID2 and AEBP2. We observed frequent codeletion of AEBP2 and ETV6, and similarly, SUZ12 and NF1. Using next generation exome sequencing of 40 patients, we identified only one somatic mutation in the PRC2 complex member SUZ12. As the frequency of point mutations in PRC2 members was found to be low, deletions were the main type of lesions targeting PRC2 complex members. Our study suggests an essential role of the PRC2 complex in the leukemic transformation of chronic myeloid disorders.
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Affiliation(s)
- Ana Puda
- Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Jovanovic ZS, Milosevic JD, Radovic SR. Antioxidative enzymes in the response of buckwheat (Fagopyrum esculentum moench) to ultraviolet B radiation. J Agric Food Chem 2006; 54:9472-8. [PMID: 17147435 DOI: 10.1021/jf061324v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The behavior of the enzymatic antioxidant defense system was studied in buckwheat leaves and seedlings subjected to short-term enhanced UV-B radiation. The effects of UV-B action were monitored immediately after irradiation as well as after recovery. The applied dose induced an increase in lipid peroxidation and total flavonoid content, a decrease in chlorophyll content, and a change in enzymatic digestibility of extracted DNA. The activity of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase, and soluble peroxidase, as well as the isoelectric focusing (IEF) pattern of peroxidase isoforms, was analyzed. In treated as well as recovered seedlings, soluble and ascorbate peroxidase activities were increased. The activity of SOD was not altered, whereas CAT activity was decreased. In contrast to seedlings, only CAT activity was increased in treated and recovered leaves.
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Affiliation(s)
- Zivko S Jovanovic
- Faculty of Biology, University of Belgrade, Studentski trg 3/II, 11000 Belgrade, Serbia and Montenegro.
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