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Padmakumar A, Thankamony P, Vasudevan JA, Gopinath P, Chandraprabha VR, Devi ARTV, Anitha GRJ, Sreelatha MM, Padmakumar D, Sreedharan H. Double Philadelphia chromosome: a rare and sole abnormality in pediatric B-acute lymphoblastic leukemia. 3 Biotech 2024; 14:75. [PMID: 38371902 PMCID: PMC10866820 DOI: 10.1007/s13205-024-03935-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/04/2023] [Indexed: 02/20/2024] Open
Abstract
The present study describes a 7-year-old male child who had attended the Pediatric Oncology Clinic of the Regional Cancer Centre, Thiruvananthapuram, Kerala, India, and was pathologically confirmed to have B-Acute Lymphoblastic Leukemia (B-ALL). Conventional cytogenetics analysis at diagnosis showed the presence of a double Philadelphia chromosome and the karyotype of the case was 47, XY, t(9;22)(q34;q11.2), + der(22)t(9;22). FISH, done as a molecular confirmation of the translocation, t(9;22)(q34;q11.2), and this case showed an additional fusion signal that confirms the presence of double Ph. As far as we are aware, this represents the initial and only occurrence of an abnormality report regarding the double Philadelphia chromosome in pediatric B-ALL within India. The double Philadelphia chromosome in B-ALL has a very poor prognosis despite aggressive treatment with chemotherapy. This study reveals the importance of conventional and molecular cytogenetic analysis in risk stratification and prognosis prediction of pediatric B-ALL. The risk stratification based on the conventional and molecular cytogenetic analysis may be taken into consideration for deciding the treatment strategy for each patient.
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Affiliation(s)
- Amritha Padmakumar
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | | | | | - Preethi Gopinath
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Vineetha Radhakrishnan Chandraprabha
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Akhila Raj Thampirajan Vimala Devi
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Geetha Raj John Anitha
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Mahitha Mohanan Sreelatha
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Devipriya Padmakumar
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
| | - Hariharan Sreedharan
- Laboratory of Cytogenetics and Molecular Diagnostics, Division of Cancer Research, Regional Cancer Centre, University of Kerala, Thiruvananthapuram, India
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Zapata-García JA, Riveros-Magaña AR, Ortiz-Lazareno PC, Hernández-Flores G, Jave-Suárez LF, Aguilar-Lemarroy A. Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene. Diagnostics (Basel) 2022; 12:diagnostics12112788. [PMID: 36428851 PMCID: PMC9689318 DOI: 10.3390/diagnostics12112788] [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: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) in children or adults is characterized by structural and numeric aberrations in chromosomes; these anomalies strongly correlate with prognosis and clinical outcome. Therefore, this work aimed to identify the genes present in chromosomal gain regions found more frequently in patients with acute lymphoblastic leukemia (ALL) and ALL-derived cell lines using comparative genomic hybridization (CGH). In addition, validation of the genes found in these regions was performed utilizing RNAseq from JURKAT, CEM, and SUP-B15 cell lines, as well as expression microarrays derived from a MILE study. Chromosomes with common gain zones that were maintained in six or more samples were 14, 17, and 22, in which a total of 22 genes were identified. From them, NT5C3B, CNP, ACLY, and GNB1L maintained overexpression at the mRNA level in the cell lines and in patients with ALL. It is noteworthy that SALL2 showed very high expression in T-ALL, while JUP was highly expressed in B-ALL lineages. Interestingly, the latter correlated with worse survival in patients. This provided evidence that the measurement of these genes has high potential for clinical utility; however, their expressions should first be evaluated with a sensitive test in a more significant number of patients.
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Affiliation(s)
- Jessica Alejandra Zapata-García
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Alma Rocío Riveros-Magaña
- Centro Universitario del Sur, Universidad de Guadalajara, Ciudad Guzmán C.P. 49000, Mexico
- Hospital General Zona 9, Ciudad Guzmán C.P. 49000, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Georgina Hernández-Flores
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Luis Felipe Jave-Suárez
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Adriana Aguilar-Lemarroy
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
- Correspondence: ; Tel.: +52-331-520-7625
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Abdulaziz ARA, Ali EW. Angiotensin-converting Enzyme Insertion/Deletion Polymorphism (rs4646994) and Susceptibility to Acute Lymphoblastic Leukemia: A Case–control Study. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.9341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Angiotensin-converting enzyme (ACE) stimulates the proliferation of bone marrow hematopoietic progenitors and thought to be involved in pathological neoplastic hematopoiesis and leukemogenesis.
AIM: This study aimed to investigate the association between ACE gene I/D polymorphism and the risk of acute lymphoblastic leukemia (ALL).
MATERIALS AND METHODS: A total of 96 subjects were recruited for the study, 48 patients with ALL, and 48 apparently healthy volunteers as a control group. Genomic DNA was extracted from peripheral leukocytes and ACE I/D polymorphism was analysed using allele-specific polymerase chain reaction.
RESULTS: In both study groups, the ACE D/D polymorphic genotype was the most frequent (52.1% and 54.2%, respectively), followed by the ID genotype (47.9% and 45.8% respectively), while the II genotype was completely absent in both study groups. The distribution of the polymorphic genotypes among the study groups was not significantly different (p = 0. 0.398). The frequency of the D allele was 0.76 in the patients and 0.77 in the control group, while the frequency of I allele was 0.24 in the patients and 0.23 in the control group. No deviation from Hardy–Weinberg equilibrium was observed (χ2 = 4.24, df = 1, p = 0.12).
CONCLUSION: ACE I/D polymorphism is not associated with susceptibility to ALL among the Sudanese population.
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Chen WP, Chiang WF, Chen HM, Chan JS, Hsiao PJ. Preventive Healthcare and Management for Acute Lymphoblastic Leukaemia in Adults: Case Report and Literature Review. Healthcare (Basel) 2021; 9:healthcare9050531. [PMID: 34063253 PMCID: PMC8147493 DOI: 10.3390/healthcare9050531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/14/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023] Open
Abstract
Acute lymphoblastic leukaemia (ALL) is diagnosed by the presence of at least 20% lymphoblasts in the bone marrow. ALL may be aggressive and include the lymph nodes, liver, spleen, central nervous system (CNS), and other organs. Without early recognition and timely treatment, ALL will progress quickly and may have poor prognosis in clinical scenarios. ALL is a rare type of leukaemia in adults but is the most common type in children. Precipitating factors such as environmental radiation or chemical exposure, viral infection, and genetic factors can be associated with ALL. We report a rare case of ALL with symptomatic hypercalcaemia in an adult woman. The patient presented with general weakness, poor appetite, bilateral lower limbs oedema, consciousness disturbance, and lower back pain for 3 weeks. She had a history of cervical cancer and had undergone total hysterectomy, chemotherapy, and radiation therapy. Her serum calcium level was markedly increased, at 14.1 mg/dl at admission. Neck magnetic resonance imaging, abdominal sonography, abdominal computed tomography, and bone marrow examination were performed. Laboratory data, including intact parathyroid hormone (i-PTH), peripheral blood smear, and 25-(OH) D3, were checked. Bone marrow biopsy showed B cell lymphoblastic leukaemia. Chemotherapy was initiated to be administered but was discontinued due to severe sepsis. Finally, the patient died due to septic shock. This was a rare case of B cell ALL in an adult complicated by hypercalcaemic crisis, which could be a life-threatening emergency in clinical practice. Physicians should pay attention to the associated risk factors. Early recognition and appropriate treatment may improve clinical outcomes.
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Affiliation(s)
- Wei-Ping Chen
- Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan;
- Division of Infectious Disease and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Wen-Fang Chiang
- Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan;
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Hung-Ming Chen
- Division of Hematology and Oncology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan;
| | - Jenq-Shyong Chan
- Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan;
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Correspondence: (J.-S.C.); or (P.-J.H.); Tel.: +88-63-479-9595 (P.-J.H.)
| | - Po-Jen Hsiao
- Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan 325, Taiwan;
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Department of Life Sciences, National Central University, Taoyuan 320, Taiwan
- Correspondence: (J.-S.C.); or (P.-J.H.); Tel.: +88-63-479-9595 (P.-J.H.)
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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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6
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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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7
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Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016; 11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL) is still a challenge. Aims: To characterize the presence of additional DNA copy number alterations (CNAs) in children and adults with ALL by whole-genome oligonucleotide array (aCGH) analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults). The NimbleGen CGH 12x135K array (Roche) was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q). CNAs were associated with age, phenotype, genetic subtype and overall survival (OS). In the whole cohort of children, the losses on 14q32.33 (p = 0.019) and 15q13.2 (p = 0.04) were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001) and Xp21.1 (p = 0.029), and the loss of 17p (p = 0.014) were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.
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Affiliation(s)
- Maribel Forero-Castro
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- School of Biological Sciences (GEBIMOL), Pedagogical and Technological University of Colombia (UPTC), Tunja, Colombia
| | - Cristina Robledo
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - María Abáigar
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Ana África Martín
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Maryam Arefi
- Department of Hematology, Clinical University Hospital of Valladolid, Valladolid, Spain
| | - José Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Juan N. Rodríguez
- Department of Hematology, Juan Ramón Jiménez Hospital, Huelva, Spain
| | | | - Susana Riesco
- Department of Pediatric Oncohematology, University Hospital of Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Department of Hematology, Jerez Hospital, Jerez de la Frontera, Cádiz, Spain
| | | | - Isabel Recio
- Department of Hematology, Nuestra Señora de Sonsoles Hospital, Avila, Spain
| | - Jordi Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jorge Labrador
- Department of Hematology, University Hospital of Burgos, Burgos, Spain
| | - José M. Alonso
- Department of Hematology, Rio Carrión Hospital, Palencia, Spain
| | - Carmen Olivier
- Department of Hematology, General Hospital of Segovia, Segovia, Spain
| | - Magdalena Sierra
- Department of Hematology, Virgen de la Concha Hospital, Zamora, Spain
| | - Marta Megido
- Department of Hematology, Bierzo Hospital, León/Ponferrada, Spain
| | | | - Juana Ciudad Pizarro
- Cytometry Service (NUCLEUS Research Support Platform), University of Salamanca (USAL), Salamanca, Spain
| | - Juan Luis García
- Institute of Health Science Studies of Castile and León (IESCYL), Salamanca, Spain
| | - José M. Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jesús M. Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- * E-mail:
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8
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Array-based comparative genomic hybridization detects copy number variations with prognostic relevance in 80% of ALL with normal karyotype or failed chromosome analysis. Leukemia 2015; 30:318-24. [PMID: 26449660 DOI: 10.1038/leu.2015.276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/09/2015] [Accepted: 09/30/2015] [Indexed: 11/08/2022]
Abstract
Pretreatment cytogenetics is an important parameter for risk stratification and therapy approach in acute lymphoblastic leukemia (ALL). However, in up to 30% of cases, chromosome banding analysis (CBA) fails or reveals a normal karyotype. To characterize the subset of ALL with normal karyotype or failed CBA, we performed fluorescence in situ hybridization (FISH) or PCR for BCR-ABL1 and MLL rearrangements as well as array comparative genomic hybridization (aCGH) in 186 adult patients. We further carried out FISH for MYC in cases with Burkitt leukemia phenotype. FISH or PCR revealed one of the respective rearrangements in 22% of patients. In 80% of cases, copy number variations (CNV) were identified by aCGH. In 22% of cases, all CNV were below the resolution of CBA. On the basis of results of FISH, RT-PCR and aCGH, patients were categorized into three groups. The novel subset of patients with submicroscopic CNV only showed an overall survival at 3 years of 84% compared with 64% for patients classified as adverse abnormalities and 77% for cases with other aberrations (P=0.046). Thus, ALL with non-informative CBA can be further classified by FISH and aCGH providing prognostic information, which may be useful for a more individualized therapy.
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Othman MAK, Melo JB, Carreira IM, Rincic M, Alhourani E, Wilhelm K, Gruhn B, Glaser A, Liehr T. MLLT10 and IL3 rearrangement together with a complex four-way translocation and trisomy 4 in a patient with early T-cell precursor acute lymphoblastic leukemia: A case report. Oncol Rep 2014; 33:625-30. [PMID: 25435396 DOI: 10.3892/or.2014.3624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/13/2014] [Indexed: 11/06/2022] Open
Abstract
Cytogenetic classification of acute lymphoblastic leukemia (ALL) is primarily based on numerical and structural chromosomal abnormalities. In T-cell ALL (T-ALL), chromosomal rearrangements are identified in up to 70% of the patients while the remaining patients show a normal karyotype. In the present study, a 16-year-old male was diagnosed with T-precursor cell ALL and a normal karyotype after standard GTG-banding, was studied retrospectively (>10 years after diagnosis) in frame of a research project by molecular approaches. In addition to molecular cytogenetics, multiplex ligation-dependent probe amplification (MLPA) and high resolution array-comparative genomic hybridization (aCGH) were also applied. Thus, the following yet unrecognized balanced chromosomal aberrations were detected: der(3)t(3;5)(p23;q31.1), der(5)t(3;5)(p23;q35.3), der(5)t(5;10)(q31.1;p12.3) and der(10)t(5;10)(q35.3;p12.3). The oncogene MLLT10 was involved in this rearrangement as was the IL3 gene; in addition, trisomy 4 was present. All of these clonal aberrations were found in 40% of the cells. Even if this complex karyotype would have been identified at the time of diagnosis, most likely no other protocol of anticancer therapy (ALL-BFM 95) would have been applied. Three months after the end of a successful 2-year treatment, the patient suffered from isolated bone marrow relapse and died of sepsis during ALL-REZ-BFM protocol treatment.
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Affiliation(s)
- Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Martina Rincic
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Eyad Alhourani
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Kathleen Wilhelm
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Bernd Gruhn
- Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anita Glaser
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
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10
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Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res 2012; 22:1833-44. [PMID: 22628462 PMCID: PMC3460179 DOI: 10.1101/gr.138511.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/03/2023]
Abstract
Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.
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Affiliation(s)
- Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Dana Battaglia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Bill H. Chang
- Division of Hematology and Oncology, Department of Pediatrics, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - James W. Shirley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Meenakshi Devidas
- COG and Department of Biostatistics, College of Medicine, University of Florida, Gainesville, Florida 32601, USA
| | - Brian J. Druker
- Division of Hematology and Medical Oncology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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Ninomiya S, Tyybäkinoja A, Borze I, Räty R, Saarinen-Pihkala UM, Usvasalo A, Elonen E, Knuutila S. Integrated analysis of gene copy number, copy neutral LOH, and microRNA profiles in adult acute lymphoblastic leukemia. Cytogenet Genome Res 2012; 136:246-55. [PMID: 22456238 DOI: 10.1159/000337297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2012] [Indexed: 01/13/2023] Open
Abstract
We adopted an integrated analysis of gene copy number alterations (CNAs), copy number neutral loss of heterozygosity (CNN LOH), and microRNA (miRNA) profiling in 21 adult acute lymphoblastic leukemia (ALL) patients. This study revealed the most frequent CNAs to be at chromosomes 9p, 7, and 17 and recurrent CNN LOH at 5p, 9p, and Xq. As for the most differentially expressed miRNAs, they included 8 upregulated and 14 downregulated miRNAs, of which miR-148a at 7p15.2, miR-22 at 17p13.3, miR-223 at Xq12, as well as miR-101-2 at 9p24.1 exhibited recurrent CNAs or CNN LOH. miR-101-2 was recurrently downregulated, and although the related CNN LOH was detected only in BCR-ABL1 negative cases (2/14), deletions of miR-101-2 were observed solely in BCR-ABL1 positive cases (4/7). Finally, BCR-ABL1 positive cases, in contrast to negative ones, were characterized by slightly, but still significantly, higher expression levels of miR-29b.
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Affiliation(s)
- S Ninomiya
- Department of Pathology, HUSLAB and University of Helsinki, Finland
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