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Capela de Matos RR, Othman M, Ferreira GM, Monteso K, de Souza MT, Rouxinol M, Melo JB, Carreira IM, Abdelhay E, Liehr T, Ribeiro RC, Silva M. Somatic homozygous loss of SH2B3, and a non-Robertsonian translocation t(15;21)(q25.3;q22.1) with NTRK3 rearrangement, in an adolescent with progenitor B-cell acute lymphoblastic leukemia with the iAMP21. Cancer Genet 2021; 262-263:16-22. [PMID: 34974289 DOI: 10.1016/j.cancergen.2021.12.003] [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] [Received: 01/26/2021] [Revised: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) occurs in ∼2% of B-cell acute lymphoblastic leukemia (ALL) and is considered to confer a poor prognosis. The relapse risk is associated with therapy intensity, suggesting that other somatic mutations may influence iAMP21-ALL prognosis. This abnormality is characterized by multiple copies of the RUNX1 gene in chromosome 21 and appears to arise through multiple breakage-fusion bridge cycles and chromothripsis. Rob(15;21) or a ring chromosome 21 have been associated with an increased risk for iAMP21-ALL, suggesting that constitutional genetic abnormalities may also drive leukemogenesis. Here we describe homozygous deletion of the SH2B3 gene, chromothripsis of chromosome 21, and a non-Robertsonian somatic t(15;21)(q25.3;q22.1) with NTRK3 gene rearrangement in an adolescent with iAMP21-B-ALL. Molecular cytogenetic studies detected iAMP21 with aCGH analysis revealing further genomic imbalances. The RT-qPCR analysis detected elevated expression levels of RUNX1 (68-fold) and reduced expression of CDK6 (0.057-fold). Studies with constitutive cells collected from mouth swabs showed that SH2B3 biallelic deletion was a somatic alteration occurring during clonal evolution. The identification of novel secondary genetic changes was valuable to discuss sporadic iAMP21 leukemogenic mechanisms. For the first time, we show a t(15;21)(q25.3;q22.1) with NTRK3 rearrangement in an adolescent with iAMP21-ALL.
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Affiliation(s)
- R R Capela de Matos
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Mak Othman
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - G M Ferreira
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Kca Monteso
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M T de Souza
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M Rouxinol
- Lagoa Federal Hospital, Rio de Janeiro, Brazil
| | - J B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - E Abdelhay
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - T Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - R C Ribeiro
- Departments of Oncology and Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mlm Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil.
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Mishra SR, Rawal L, Othman MAK, Thatai A, Sarkar A, Lal V, Bhattacharya SK. Complex rearrangement in acute myeloid leukemia M2 with RUNX1/RUNX1T1 fusion involving chromosomes 8, 17 and 21. Mol Cytogenet 2021; 14:28. [PMID: 34020686 PMCID: PMC8140419 DOI: 10.1186/s13039-021-00541-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background The translocation t(8;21)(q22;q22) is one of the most frequent chromosomal abnormalities associated with acute myeloid leukemia (AML) sub type M2. About 3–5 % of cases with additional chromosomal abnormalities, including structural and numerical ones, are reported to include a complex translocation t(8;21;N). Case presentation Here we report a chromosome rearrangement observed in a 19 years-old female diagnosed with AML-M2. When subjected to (molecular) cytogenetic analyses a complex three-way translocation involving chromosomes 8, 17 and 21 was detected, forming not a t(8;21;17) as one would expect. Real time-polymerase chain reaction analysis using 6 AML specific markers showed the presence of RUNX1/RUNX1T1 fusion gene transcripts identical to those found in classical translocation t(8;21) coupled with presence of FLT3-ITD mutation identified by fragment analysis. Conclusions The present case highlights importance of complex rearrangements rarely encountered in AML, suggesting that all involved regions harbor critical candidate genes regulating the pathogenesis of AML, leading to novel as well as well-known leukemia associated chromosomal aberrations.
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Affiliation(s)
- Shiba Ranjan Mishra
- Department of Clinical Cytogenomics, National Reference Laboratory, Dr. Lal Path Labs Ltd., Block E, Sector 18, Rohini, New Delhi, 110085, India
| | - Leena Rawal
- Department of Clinical Cytogenomics, National Reference Laboratory, Dr. Lal Path Labs Ltd., Block E, Sector 18, Rohini, New Delhi, 110085, India
| | - Moneeb A K Othman
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Atul Thatai
- Molecular Diagnostics, National Reference Laboratory, Dr. Lal Path Labs Ltd., New Delhi, India
| | - Aditi Sarkar
- Molecular Diagnostics, National Reference Laboratory, Dr. Lal Path Labs Ltd., New Delhi, India
| | - Vandana Lal
- Department of Clinical Cytogenomics, National Reference Laboratory, Dr. Lal Path Labs Ltd., Block E, Sector 18, Rohini, New Delhi, 110085, India
| | - Saurabh Kumar Bhattacharya
- Department of Clinical Cytogenomics, National Reference Laboratory, Dr. Lal Path Labs Ltd., Block E, Sector 18, Rohini, New Delhi, 110085, India.
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3
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Othman MAK, Đurišić M, Samardzija G, Vujić D, Lakic N, Zecevic Z, Al-Shaheri F, Aroutiounian R, Melo JB, Carreira IM, Meyer B, Liehr T. Complex karyotype with cryptic FUS gene rearrangement and deletion of NR3C1 and VPREB1 genes in childhood B-cell acute lymphoblastic leukemia: A case report. Oncol Lett 2020; 19:2957-2962. [PMID: 32218851 DOI: 10.3892/ol.2020.11387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/02/2019] [Indexed: 12/18/2022] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is a hematopoietic malignancy characterized by overproduction of immature B-lymphoblasts. B-ALL is the most common pediatric tumor and remains the leading cause of mortality in children and adolescents. Molecular and cytogenetic analyses of B-ALL revealed recurrent genetic and structural genomic alterations which are routinely applied for diagnosis, prognosis and choice of treatment regimen. The present case report describes a 4-year-old female diagnosed with B-ALL. GTG-banding at low resolution revealed an abnormal clone with 46,XX,?t(X;19)(q13;q13.3),der(9) besides normal cells. Molecular cytogenetics demonstrated a balanced translocation between chromosomes 16 and 19, and an unbalanced translocation involving chromosomes 5 and 9. A locus-specific probe additionally identified that the FUS gene in 16p11.2 was split and its 5' region was translocated to subband 19q13.33, whereas the 3' region of the FUS gene remained on the derivative chromosome 16. Overall, this complex karyotype included four different chromosomes and five break events. Further analyses, including array-comparative genomic hybridization, additionally revealed biallelic deletion of the tumor suppressor genes CDKN2A/B, and deletion of the NR3C1 and VPREB1 genes. The patient passed away under treatment due to sepsis.
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Affiliation(s)
- Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
| | - Marina Đurišić
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Gordana Samardzija
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Dragana Vujić
- Medical School, University of Belgrade, 11000 Belgrade, Serbia
| | - Nina Lakic
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Zeljko Zecevic
- Mother and Child Health Care Institute of Serbia 'Dr Vukan Cupic', 11070 Belgrade, Serbia
| | - Fawaz Al-Shaheri
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, 0025 Yerevan, Armenia
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO, Center for Research in The Environment, Genetics and Oncobiology, 3000-548 Coimbra, Portugal
| | - Isabel M Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,CIMAGO, Center for Research in The Environment, Genetics and Oncobiology, 3000-548 Coimbra, Portugal
| | | | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D-07747 Jena, Germany
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Thielker J, Weise A, Othman MAK, Carreria IM, Melo JB, Von Eggeling F, Guntinas-Lichius O, Ziegler M, Liehr T. Molecular cytogenetic pilot study on pleomorphic adenomas of salivary glands. Oncol Lett 2019; 19:1125-1130. [PMID: 31966040 PMCID: PMC6955655 DOI: 10.3892/ol.2019.11198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pleomorphic adenomas (PAs) of salivary glands are the most frequent entity of solid parotid tumors. Nonetheless, their genetics is not yet well understood. Thus, the current study characterized 14 PAs using a unique combination of cytogenetic, molecular cytogenetic and/or molecular karyotyping based approaches. The current study applied G-banding based on trypsin treatment and Giemsa-staining in peripheral blood and tumor tissue. Additionally, fluorescence in situ hybridization was performed using whole chromosome painting or centromeric probes. Array-based comparative genomic hybridization was also conducted. In 5 of 14 cases, chromosomal and/or submicroscopic alterations were characterized. Balanced and unbalanced translocations, loss or gain of whole chromosomes and submicroscopic copy number alterations were detected. Furthermore, the first case of a so-called ‘jumping translocation’ in a PA was reported. The genes twist-related protein 1 and distal-less homeobox 5 were also involved in copy number variations in two PAs. In conclusion, approaches utilized in the current study are highly suited to characterize the genetic constitution of PAs.
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Affiliation(s)
- Jovanna Thielker
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Moneeb A K Othman
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Isabel M Carreria
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Ferdinand Von Eggeling
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
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5
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Mitrakos A, Kattamis A, Katsibardi K, Papadhimitriou S, Kitsiou-Tzeli S, Kanavakis E, Tzetis M. High resolution Chromosomal Microarray Analysis (CMA) enhances the genetic profile of pediatric B-cell Acute Lymphoblastic Leukemia patients. Leuk Res 2019; 83:106177. [PMID: 31261022 DOI: 10.1016/j.leukres.2019.106177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/26/2022]
Abstract
Acute Lymphoblastic Leukemia (ALL) is a malignancy of the immature lymphoid cells mainly associated with numerical and structural chromosomal aberrations. The current standard for profiling the diverse genetic background comprises a combination of conventional karyotype and FISH analysis for the most common translocations, albeit with many limitations. Chromosomal Microarray Analysis (CMA) is a high throughput whole genome method that is gradually implemented in routine clinical practice, but not many studies have compared the two methods. Here we aim to investigate the added benefits of utilizing the high resolution 2 x 400 K G3 CGH + SNP CMA platform in routine diagnostics of pediatric ALL. From the 29 bone marrow samples that were analyzed, CMA identified clinically relevant findings in 83%, while detecting chromosomal aberrations in 75% of the patients with normal conventional karyotype. The most common finding was hyperdiploidy (20%), and the most common submicroscopic aberration involved CDKN2A/B genes. The smallest aberration detected was a 9 kb partial NF1 gene duplication. The prognosis of the patients when combining conventional cytogenetics and CMA was either changed or enhanced in 66% of the cases. A rare duplication possibly indicative of a cryptic ABL1-NUP214 fusion gene was found in one patient. We conclude that CMA, when combined with conventional cytogenetic analysis, can significantly enhance the genetic profiling of patients with pediatric ALL in a routine clinical setting.
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Affiliation(s)
- Anastasios Mitrakos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Greece.
| | - Antonis Kattamis
- Hematology-Oncology Unit, First Department of Pediatrics, National and Kapodistrian University of Athens, "Aghia Sofia" Children's Hospital, Athens, Greece
| | - Katerina Katsibardi
- Hematology-Oncology Unit, First Department of Pediatrics, National and Kapodistrian University of Athens, "Aghia Sofia" Children's Hospital, Athens, Greece
| | - Stefanos Papadhimitriou
- Department of Laboratory Hematology, Athens Regional General Hospital "G. Gennimatas", Athens, Greece
| | - Sophia Kitsiou-Tzeli
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Emmanuel Kanavakis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Greece
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6
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Panagopoulos I, Brunetti M, Stoltenberg M, Strandabø RAU, Staurseth J, Andersen K, Kostolomov I, Hveem TS, Lorenz S, Nystad TA, Flægstad T, Micci F, Heim S. Novel GTF2I- PDGFRB and IKZF1- TYW1 fusions in pediatric leukemia with normal karyotype. Exp Hematol Oncol 2019; 8:12. [PMID: 31161074 PMCID: PMC6542082 DOI: 10.1186/s40164-019-0136-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/23/2019] [Indexed: 11/25/2022] Open
Abstract
Background Many cases of acute lymphoblastic leukemia (ALL) carry visible acquired chromosomal changes of pathogenetic, diagnostic, and prognostic importance. Nevertheless, from one-fourth to half of newly diagnosed ALL patients have no visible chromosomal changes detectable by G-banding analysis at diagnosis. The introduction of powerful molecular methodologies has shown that many karyotypically normal ALLs carry clinically important submicroscopic aberrations. Case presentation We used fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH), RNA sequencing, reverse transcription (RT) and genomic polymerase chain reaction (PCR), as well as Sanger sequencing to investigate a case of pediatric ALL with a normal karyotype. FISH with a commercial PDGFRB breakapart probe showed loss of the distal part of the probe suggesting a breakpoint within the PDGFRB locus. aCGH revealed submicroscopic deletions in chromosome bands 5q32q35.3 (about 30 Mb long, starting within PDGFRB and finishing in the CANX locus), 7q34 (within TCRB), 9p13 (PAX5), 10q26.13 (DMBT1), 14q11.2 (TRAC), and 14q32.33 (within the IGH locus). RNA sequencing detected an in-frame GTF2I–PDGFRB and an out-of-frame IKZF1–TYW1 fusion transcript. Both fusion transcripts were verified by RT-PCR together with Sanger sequencing and interphase FISH. The GTF2I–PDGFRB fusion was also verified by genomic PCR and FISH. The corresponding GTF2I–PDGFRB fusion protein would consist of almost the entire GTF2I and that part of PDGFRB which harbors the catalytic domain of the tyrosine kinase. It would therefore seem to lead to abnormal tyrosine kinase activity in a manner similar to what has been seen for other PDGFRB fusion proteins. Conclusions The examined pediatric leukemia is a Ph-like ALL which carries novel GTF2I–PDGFRB and IKZF1–TYW1 fusion genes together with additional submicroscopic deletions. Because hematologic neoplasms with PDGFRB-fusion genes can be treated with tyrosine kinase inhibitors, the detection of such novel fusions may be clinically important. Since the GTF2I–PDGFRB could be detected only after molecular studies of the leukemic cells, further investigations of ALL-cases, perhaps especially but not exclusively with a normal karyotype, are needed in order to determine the frequency of GTF2I–PDGFRB in leukemia, and also to find out which clinical impact the fusion may have.
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Affiliation(s)
- Ioannis Panagopoulos
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Marta Brunetti
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Margrethe Stoltenberg
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Rønnaug A U Strandabø
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Julie Staurseth
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Kristin Andersen
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Ilyá Kostolomov
- 2Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Tarjei S Hveem
- 2Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- 3Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | - Tove Anita Nystad
- 4Department of Pediatrics, Division of Child and Adolescent Health, University Hospital of North-Norway, 9038 Tromsø, Norway
| | - Trond Flægstad
- 4Department of Pediatrics, Division of Child and Adolescent Health, University Hospital of North-Norway, 9038 Tromsø, Norway.,5Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway-UiT, 9037 Tromsø, Norway
| | - Francesca Micci
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Sverre Heim
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway.,6Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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8
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Bellutti F, Tigan AS, Nebenfuehr S, Dolezal M, Zojer M, Grausenburger R, Hartenberger S, Kollmann S, Doma E, Prchal-Murphy M, Uras IZ, Höllein A, Neuberg DS, Ebert BL, Ringler A, Mueller AC, Loizou JI, Hinds PW, Vogl C, Heller G, Kubicek S, Zuber J, Malumbres M, Farlik M, Villunger A, Kollmann K, Sexl V. CDK6 Antagonizes p53-Induced Responses during Tumorigenesis. Cancer Discov 2018; 8:884-897. [PMID: 29899063 DOI: 10.1158/2159-8290.cd-17-0912] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 04/05/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
Abstract
Tumor formation is a multistep process during which cells acquire genetic and epigenetic changes until they reach a fully transformed state. We show that CDK6 contributes to tumor formation by regulating transcriptional responses in a stage-specific manner. In early stages, the CDK6 kinase induces a complex transcriptional program to block p53 in hematopoietic cells. Cells lacking CDK6 kinase function are required to mutate TP53 (encoding p53) to achieve a fully transformed immortalized state. CDK6 binds to the promoters of genes including the p53 antagonists Prmt5, Ppm1d, and Mdm4 The findings are relevant to human patients: Tumors with low levels of CDK6 have mutations in TP53 significantly more often than expected.Significance: CDK6 acts at the interface of p53 and RB by driving cell-cycle progression and antagonizing stress responses. While sensitizing cells to p53-induced cell death, specific inhibition of CDK6 kinase activity may provoke the outgrowth of p53-mutant clones from premalignant cells. Cancer Discov; 8(7); 884-97. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 781.
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Affiliation(s)
- Florian Bellutti
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Anca-Sarmiza Tigan
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Sofie Nebenfuehr
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Marlies Dolezal
- Platform Bioinformatics and Biostatistics, University of Veterinary Medicine, Vienna, Austria
| | - Markus Zojer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Reinhard Grausenburger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Svenja Hartenberger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Sebastian Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Eszter Doma
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Michaela Prchal-Murphy
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Iris Z Uras
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | | | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Benjamin L Ebert
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Anna Ringler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andre C Mueller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philip W Hinds
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, and Tufts Cancer Center, Boston, Massachusetts
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | | | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria.
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9
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Liehr T, Othman MAK, Rittscher K. Multicolor Karyotyping and Fluorescence In Situ Hybridization-Banding (MCB/mBAND). Methods Mol Biol 2017; 1541:181-187. [PMID: 27910024 DOI: 10.1007/978-1-4939-6703-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multicolor fluorescence in situ hybridization (mFISH) approaches are routine applications in tumor as well as clinical cytogenetics nowadays. The first approach when thinking about mFISH is multicolor karyotyping using human whole chromosome paints as probes; this can be achieved by narrow-band filter-based multiplex-FISH (M-FISH) or interferometer/spectroscopy-based spectral karyotyping (SKY). Besides, various FISH-based banding approaches were reported in the literature, including multicolor banding (MCB/mBAND) the latter being evaluated by narrow-band filters, and using specific software. Here, we describe the combined application of multicolor karyotyping and MCB/mBAND for the characterization of simple and complex acquired chromosomal changes in cancer cytogenetics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany.
| | - Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
| | - Katharina Rittscher
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
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10
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Carrasco Salas P, Fernández L, Vela M, Bueno D, González B, Valentín J, Lapunzina P, Pérez-Martínez A. The role of CDKN2A/B deletions in pediatric acute lymphoblastic leukemia. Pediatr Hematol Oncol 2016; 33:415-422. [PMID: 27960642 DOI: 10.1080/08880018.2016.1251518] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CDKN2A/B genes in the 9p21 chromosomal region are frequently involved in human cancer, including pediatric acute lymphoblastic leukemia (ALL). These genes encode 3 proteins that belong to the RB1 and TP53 pathways and act as tumor suppressors by regulating the G1/S checkpoint of the cell cycle. The prognostic value of deletions in the CDKN2A/B locus in ALL is controversial in part due to the limitations of the methodologies used. Further studies with advanced technologies are needed for elucidation. Future studies would also highlight whether CDK4/CDK6 selective inhibitors might be useful therapies for children with these genetic aberrations.
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Affiliation(s)
- P Carrasco Salas
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain
| | - L Fernández
- b Clinical Research Program , Cancer Research National Centre , Madrid , Spain
| | - M Vela
- c Innate Immune Research Group, IdiPAZ , Madrid , Spain
| | - D Bueno
- d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
| | - B González
- d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
| | - J Valentín
- c Innate Immune Research Group, IdiPAZ , Madrid , Spain
| | - P Lapunzina
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain
| | - A Pérez-Martínez
- a Laboratory of Molecular Pediatric Hemato-Oncology , Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz , Madrid , Spain.,c Innate Immune Research Group, IdiPAZ , Madrid , Spain.,d Department of Pediatric Hemato-Oncology and Stem Cell Transplantation , Hospital Infantil Universitario La Paz , Madrid , Spain
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11
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Ivanov Öfverholm I, Tran AN, Olsson L, Zachariadis V, Heyman M, Rudd E, Syk Lundberg E, Nordenskjöld M, Johansson B, Nordgren A, Barbany G. Detailed gene dose analysis reveals recurrent focal gene deletions in pediatric B-cell precursor acute lymphoblastic leukemia. Leuk Lymphoma 2016; 57:2161-70. [DOI: 10.3109/10428194.2015.1136740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Zhang L, Liu XM, Guo Y, Yang WY, Zhang JY, Liu F, Liu TF, Wang SC, Chen XJ, Ruan M, Qi BQ, Chang LX, Zou Y, Chen YM, Zhu XF. [Detection of copy number variations in pediatric ETV6/RUNX1-positive acute lymphoblastic leukemia with multiplex ligation-dependent probe amplification]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:34-38. [PMID: 26781410 PMCID: PMC7390102 DOI: 10.7499/j.issn.1008-8830.2016.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To investigate the application of multiplex ligation-dependent probe amplification (MLPA) in the detection of copy number variations (CNVs) in pediatric ETV6/RUNX1-positive acute lymphoblastic leukemia (ALL), to compare this method with conventional karyotype analysis and fluorescence in situ hybridization (FISH), and to evaluate the value of MLPA. METHODS The clinical data of 95 children with ETV6/RUNX1-positive ALL who were treated from January 2006 to November 2012 were analyzed retrospectively, including clinical features, results of karyotype analysis, and results of FISH. CNVs were detected with MLPA. RESULTS CNVs were detected in 73 (77%), and the median number of CNVs was 1 (range 0-6). The CNVs of EBF1, CDKN2A/2B, PAX5, ETV6, RB1, and BTG1 were detected in more than 10% of all the patients. The changes in the chromosome segments carrying the genes with CNVs detected by MLPA were not detected by conventional karyotype analysis. The coincidence rate between the CNVs in ETV6 gene detected by FISH and those detected by MLPA was 66%. CONCLUSIONS MLPA is an efficient and convenient method to detect CNVs in children with ETV6/RUNX1-positive ALL.
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Affiliation(s)
- Li Zhang
- Department of Pediatrics, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
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13
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Zhang L, Liu XM, Guo Y, Yang WY, Zhang JY, Liu F, Liu TF, Wang SC, Chen XJ, Ruan M, Qi BQ, Chang LX, Zou Y, Chen YM, Zhu XF. [Detection of copy number variations in pediatric ETV6/RUNX1-positive acute lymphoblastic leukemia with multiplex ligation-dependent probe amplification]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:34-8. [PMID: 26781410 PMCID: PMC7390102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/18/2015] [Indexed: 11/12/2023]
Abstract
OBJECTIVE To investigate the application of multiplex ligation-dependent probe amplification (MLPA) in the detection of copy number variations (CNVs) in pediatric ETV6/RUNX1-positive acute lymphoblastic leukemia (ALL), to compare this method with conventional karyotype analysis and fluorescence in situ hybridization (FISH), and to evaluate the value of MLPA. METHODS The clinical data of 95 children with ETV6/RUNX1-positive ALL who were treated from January 2006 to November 2012 were analyzed retrospectively, including clinical features, results of karyotype analysis, and results of FISH. CNVs were detected with MLPA. RESULTS CNVs were detected in 73 (77%), and the median number of CNVs was 1 (range 0-6). The CNVs of EBF1, CDKN2A/2B, PAX5, ETV6, RB1, and BTG1 were detected in more than 10% of all the patients. The changes in the chromosome segments carrying the genes with CNVs detected by MLPA were not detected by conventional karyotype analysis. The coincidence rate between the CNVs in ETV6 gene detected by FISH and those detected by MLPA was 66%. CONCLUSIONS MLPA is an efficient and convenient method to detect CNVs in children with ETV6/RUNX1-positive ALL.
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Affiliation(s)
- Li Zhang
- Department of Pediatrics, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
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