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Batista-Gomes JA, Mello FAR, de Oliveira EHC, de Souza MPC, Wanderley AV, da Costa Pantoja L, dos Santos NPC, Khayat BCM, Khayat AS. Identifying novel genetic alterations in pediatric acute lymphoblastic leukemia based on copy number analysis. Mol Cytogenet 2020; 13:25. [PMID: 32607130 PMCID: PMC7320540 DOI: 10.1186/s13039-020-00491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/08/2020] [Indexed: 11/12/2022] Open
Abstract
Copy number variations (CNVs) analysis may reveal molecular biomarkers and provide information on the pathogenesis of acute lymphoblastic leukemia (ALL). We investigated the gene copy number in childhood ALL by microarray and select three new recurrent CNVs to evaluate by real-time PCR assay: DMBT1, KIAA0125 and PRDM16 were selected due to high frequency of CNVs in ALL samples and based on their potential biological functions in carcinogenesis described in the literature. DBMT1 deletion was associated with patients with chromosomal translocations and is a potential tumor suppressor; KIAA0125 and PRDM16 may act as an oncogene despite having a paradoxical behavior in carcinogenesis. This study reinforces that microarrays/aCGH is it is a powerful tool for detection of genomic aberrations, which may be used in the risk stratification.
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YİĞENOĞLU TN, BAHSİ T, ERDEM H, DUZKALE N, UNCU ULU B, İSKENDER D, KIZIL ÇAKIR M, DAL S, ALTUNTAŞ F. P210 breakpoint is associated with less minimal residual disease compared to p190 breakpoint in acute lymphoblastic leukemia patients with Philadelphia chromosome. JOURNAL OF HEALTH SCIENCES AND MEDICINE 2020. [DOI: 10.32322/jhsm.735979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Handschuh L, Kaźmierczak M, Milewski MC, Góralski M, Łuczak M, Wojtaszewska M, Uszczyńska-Ratajczak B, Lewandowski K, Komarnicki M, Figlerowicz M. Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR. Int J Oncol 2017; 52:656-678. [PMID: 29286103 PMCID: PMC5807040 DOI: 10.3892/ijo.2017.4233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/12/2017] [Indexed: 01/25/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common and severe form of acute leukemia diagnosed in adults. Owing to its heterogeneity, AML is divided into classes associated with different treatment outcomes and specific gene expression profiles. Based on previous studies on AML, in this study, we designed and generated an AML-array containing 900 oligonucleotide probes complementary to human genes implicated in hematopoietic cell differentiation and maturation, proliferation, apoptosis and leukemic transformation. The AML-array was used to hybridize 118 samples from 33 patients with AML of the M1 and M2 subtypes of the French-American-British (FAB) classification and 15 healthy volunteers (HV). Rigorous analysis of the microarray data revealed that 83 genes were differentially expressed between the patients with AML and the HV, including genes not yet discussed in the context of AML pathogenesis. The most overexpressed genes in AML were STMN1, KITLG, CDK6, MCM5, KRAS, CEBPA, MYC, ANGPT1, SRGN, RPLP0, ENO1 and SET, whereas the most underexpressed genes were IFITM1, LTB, FCN1, BIRC3, LYZ, ADD3, S100A9, FCER1G, PTRPE, CD74 and TMSB4X. The overexpression of the CPA3 gene was specific for AML with mutated NPM1 and FLT3. Although the microarray-based method was insufficient to differentiate between any other AML subgroups, quantitative PCR approaches enabled us to identify 3 genes (ANXA3, S100A9 and WT1) whose expression can be used to discriminate between the 2 studied AML FAB subtypes. The expression levels of the ANXA3 and S100A9 genes were increased, whereas those of WT1 were decreased in the AML-M2 compared to the AML-M1 group. We also examined the association between the STMN1, CAT and ABL1 genes, and the FLT3 and NPM1 mutation status. FLT3+/NPM1− AML was associated with the highest expression of STMN1, and ABL1 was upregulated in FLT3+ AML and CAT in FLT3− AML, irrespectively of the NPM1 mutation status. Moreover, our results indicated that CAT and WT1 gene expression levels correlated with the response to therapy. CAT expression was highest in patients who remained longer under complete remission, whereas WT1 expression increased with treatment resistance. On the whole, this study demonstrates that the AML-array can potentially serve as a first-line screening tool, and may be helpful for the diagnosis of AML, whereas the differentiation between AML subgroups can be more successfully performed with PCR-based analysis of a few marker genes.
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Affiliation(s)
- Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Kaźmierczak
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Marek C Milewski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Michał Góralski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Łuczak
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Marzena Wojtaszewska
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Barbara Uszczyńska-Ratajczak
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Mieczysław Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Ebinger S, Özdemir EZ, Ziegenhain C, Tiedt S, Castro Alves C, Grunert M, Dworzak M, Lutz C, Turati VA, Enver T, Horny HP, Sotlar K, Parekh S, Spiekermann K, Hiddemann W, Schepers A, Polzer B, Kirsch S, Hoffmann M, Knapp B, Hasenauer J, Pfeifer H, Panzer-Grümayer R, Enard W, Gires O, Jeremias I. Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia. Cancer Cell 2016; 30:849-862. [PMID: 27916615 PMCID: PMC5156313 DOI: 10.1016/j.ccell.2016.11.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 06/11/2016] [Accepted: 10/31/2016] [Indexed: 01/06/2023]
Abstract
Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche.
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Affiliation(s)
- Sarah Ebinger
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Erbey Ziya Özdemir
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sebastian Tiedt
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Catarina Castro Alves
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Michaela Grunert
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Michael Dworzak
- Children's Cancer Research Institute and St. Anna Kinderspital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Christoph Lutz
- Department of Medicine V, University of Heidelberg, 69120 Heidelberg, Germany
| | | | - Tariq Enver
- University College London Cancer Institute, London WC1E, UK
| | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Karl Sotlar
- Institute of Pathology, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Karsten Spiekermann
- Department of Internal Medicine III, University Hospital Grosshadern, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany
| | - Wolfgang Hiddemann
- Department of Internal Medicine III, University Hospital Grosshadern, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany
| | - Aloys Schepers
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany
| | - Bernhard Polzer
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Stefan Kirsch
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Martin Hoffmann
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, 93053 Regensburg, Germany
| | - Bettina Knapp
- Institute of Computational Biology, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 85764 Neuherberg, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München (TUM), 85748 Munich, Germany
| | - Heike Pfeifer
- Department of Medicine, Hematology and Oncology, Goethe University, 60590 Frankfurt, Germany
| | - Renate Panzer-Grümayer
- Children's Cancer Research Institute and St. Anna Kinderspital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Irmela Jeremias
- Department of Gene Vectors, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), 81377 Munich, Germany; German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University München, 80337 Munich, Germany.
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Aly RM, Ghazy HF. Prognostic significance of MSI2 predicts unfavorable outcome in adult B-acute lymphoblastic leukemia. Int J Lab Hematol 2014; 37:272-8. [PMID: 25090928 DOI: 10.1111/ijlh.12284] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/26/2014] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The Musashi-2 gene (MSI2) is implicated in leukemogenesis, and high MSI2 expression has been associated with decreased survival in acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL), suggesting its use as a new prognostic marker. We aimed to validate the prognostic significance of MSI2 in ALL. METHODS MSI2 expression was measured by real-time polymerase chain reaction in 140 adult B-ALL patients and compared to controls. RESULTS MSI2 expression level in patients was significantly higher when compared to the control group (P = 0.001). High MSI2 expression did not correlate with the clinical characteristics of patients. However, patients with high MSI2 expression had significantly lower incidence of complete remission (CR) (P = 0.03), inferior overall survival (P = 0.018), and shorter disease-free survival (P = 0.001). Multivariate analysis revealed that high MSI2 expression was an independent prognostic factor for adult BCR-ABL1-negative B-ALL patients. CONCLUSION These results confirm the association of MSI2 expression with outcome in adult B-ALL and demonstrate the utility of MSI2 as a clinical prognostic biomarker.
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Affiliation(s)
- R M Aly
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Rabitsch W, Böhm A, Bojic M, Schellongowski P, Wöhrer S, Sliwa T, Keil F, Worel N, Greinix H, Hauswirth A, Kalhs P, Jaeger U, Valent P, Sperr WR. Clofarabine/cyclophosphamide for debulking before stem cell transplantation. Eur J Clin Invest 2014; 44:775-83. [PMID: 24942362 DOI: 10.1111/eci.12294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Allogeneic haematopoietic stem cell transplantation (HSCT) is the only curative rescue therapy for patients (pts) with chemotherapy-refractory acute leukaemia. Disease control prior to HSCT is essential for long-term disease-free survival after HSCT. PATIENTS AND METHODS We have retrospectively analysed the outcome of 20 pts aged 21-64 years with refractory leukaemia (acute myeloid leukaemia, n = 16; acute lymphatic leukaemia, n = 4) who received debulking therapy with clofarabine (10 mg/m², days 1-4) and cyclophosphamide (200 mg/m², days 1-4; ClofCy) prior to HSCT. RESULTS Clofarabine/cyclophosphamide (1-4 cycles) was well tolerated and resulted in a substantial reduction of leukaemic cells in all pts. HSCT was performed in 15 of 20 pts. After HSCT (myeloablative, n = 9; dose-reduced, n = 6), all pts showed engraftment and full donor chimerism (related donors, n = 4 or unrelated donors, n = 11) and all pts achieved complete haematologic remission (CR). The median survival after HSCT is 531 days (range: 48-1462 days), and six pts are still alive after a median of 1245 days. Seven pts died after they had relapsed between days +152 and +1496. One patient died from acute graft-versus-host disease (day +48) and one from systemic fungal infection (day +87). CONCLUSION Clofarabine/cyclophosphamide is a novel effective treatment approach for pts with chemotherapy-refractory acute leukaemia prior to HSCT. Whether this novel debulking protocol leads to improved long-term outcome in pts with refractory leukaemias remains to be determined in forthcoming clinical studies.
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Affiliation(s)
- Werner Rabitsch
- Bone Marrow Transplantation Unit, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria; Intensive Care Unit, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
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Li K, Yang M, Sablok G, Fan J, Zhou F. Screening features to improve the class prediction of acute myeloid leukemia and myelodysplastic syndrome. Gene 2013; 512:348-54. [DOI: 10.1016/j.gene.2012.09.123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/29/2012] [Indexed: 02/06/2023]
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Activating CBL mutations are associated with a distinct MDS/MPN phenotype. Ann Hematol 2012; 91:1713-20. [PMID: 23010802 DOI: 10.1007/s00277-012-1521-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/01/2012] [Indexed: 10/28/2022]
Abstract
Activating point mutations in CBL have recently been identified in diverse subtypes of myeloid neoplasms. Because detailed clinical and hematological characteristics of CBL-mutated cases is lacking, we screened 156 BCR-ABL and JAK2 V617F negative patients with myeloproliferative neoplasms (MPN) and overlap syndromes between myelodysplastic syndrome (MDS) and MPN (MPS/MPN) for mutations in exons 8 and 9 of CBL by denaturing high-performance liquid chromatography and direct sequencing. CBL mutations were identified in 16/156 patients (10%), of which five also carried mutations in EZH2 (n = 3) and TET2 (n = 2). Comprehensive clinical and hematological characteristics were available from 13/16 patients (81%). In addition to splenomegaly (77%), striking common hematological features were CML-like left-shifted leukocytosis (85%) with monocytosis (85%), anemia (100%), and thrombocytopenia (62%). Thrombocytosis was not observed in any patient. Relevant bone marrow features (n = 12) included hypercellularity (92%) with marked granulopoiesis (92%), nonclustered microlobulated megakaryocytes (83%), and marrow fibrosis (83%). Nine deaths (progression to secondary acute myeloid leukemia/blast phase, n = 7; cytopenia complications, n = 2) were recorded. Three-year survival rate was 27%, possibly indicating poor prognosis of CBL mutated MDS/MPN patients.
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Iacobucci I, Lonetti A, Candoni A, Sazzini M, Papayannidis C, Formica S, Ottaviani E, Ferrari A, Michelutti A, Simeone E, Astolfi A, Abbenante MC, Parisi S, Cattina F, Malagola M, Russo D, Damiani D, Gherlinzoni F, Gottardi M, Baccarani M, Fanin R, Martinelli G. Profiling of drug-metabolizing enzymes/transporters in CD33+ acute myeloid leukemia patients treated with Gemtuzumab-Ozogamicin and Fludarabine, Cytarabine and Idarubicin. THE PHARMACOGENOMICS JOURNAL 2012; 13:335-41. [DOI: 10.1038/tpj.2012.13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/05/2012] [Accepted: 04/11/2012] [Indexed: 11/09/2022]
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Expression and distribution of PPP2R5C gene in leukemia. J Hematol Oncol 2011; 4:21. [PMID: 21548944 PMCID: PMC3117819 DOI: 10.1186/1756-8722-4-21] [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: 03/22/2011] [Accepted: 05/06/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recently, we clarified at the molecular level novel chromosomal translocation t(14;14)(q11;q32) in a case of Sézary syndrome, which caused a rearrangement from TRAJ7 to the PPP2R5C gene. PPP2R5C is one of the regulatory B subunits of protein phosphatase 2A (PP2A). It plays a crucial role in cell proliferation, differentiation, and transformation. To characterize the expression and distribution of five different transcript variants of the PPP2R5C gene in leukemia, we analyzed the expression level of PPP2R5C in peripheral blood mononuclear cells from 77 patients with de novo leukemia, 26 patients with leukemia in complete remission (CR), and 20 healthy individuals by real-time PCR and identified the different variants of PPP2R5C by RT-PCR. FINDINGS Significantly higher expression of PPP2R5C was found in AML, CML, T-ALL, and B-CLL groups in comparison with healthy controls. High expression of PPP2R5C was detected in the B-ALL group; however, no significant difference was found compared with the healthy group. The expression level of PPP2R5C in the CML-CR group decreased significantly compared with that in the de novo CML group and was not significantly different from the level in the healthy group. By using different primer pairs that covered different exons, five transcript variants of PPP2R5C could be identified. All variants could be detected in healthy samples as well as in all the leukemia samples, and similar frequencies and distributions of PPP2R5C were indicated. CONCLUSIONS Overexpression of PPP2R5C in T-cell malignancy as well as in myeloid leukemia cells might relate to its proliferation and differentiation. Investigation of the effect of target inhibition of this gene might be beneficial to further characterization of molecular mechanisms and targeted therapy in leukemia.
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