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Landscape of driver mutations and their clinical impacts in pediatric B-cell precursor acute lymphoblastic leukemia. Blood Adv 2021; 4:5165-5173. [PMID: 33095873 DOI: 10.1182/bloodadvances.2019001307] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 09/01/2020] [Indexed: 12/21/2022] Open
Abstract
Recent genetic studies using high-throughput sequencing have disclosed genetic alterations in B-cell precursor acute lymphoblastic leukemia (B-ALL). However, their effects on clinical outcomes have not been fully investigated. To address this, we comprehensively examined genetic alterations and their prognostic impact in a large series of pediatric B-ALL cases. We performed targeted capture sequencing in a total of 1003 pediatric patients with B-ALL from 2 Japanese cohorts. Transcriptome sequencing (n = 116) and/or array-based gene expression analysis (n = 120) were also performed in 203 (84%) of 243 patients who were not categorized into any disease subgroup by panel sequencing or routine reverse transcription polymerase chain reaction analysis for major fusions in B-ALL. Our panel sequencing identified novel recurrent mutations in 2 genes (CCND3 and CIC), and both had positive correlations with ETV6-RUNX1 and hypodiploid ALL, respectively. In addition, positive correlations were also newly reported between TCF3-PBX1 ALL with PHF6 mutations. In multivariate Cox proportional hazards regression models for overall survival, TP53 mutation/deletion, hypodiploid, and MEF2D fusions were selected in both cohorts. For TP53 mutations, the negative effect on overall survival was confirmed in an independent external cohort (n = 466). TP53 mutation was frequently found in IGH-DUX4 (5 of 57 [9%]) ALL, with 4 cases having 17p LOH and negatively affecting overall survival therein, whereas TP53 mutation was not associated with poor outcomes among NCI (National Cancer Institute) standard risk (SR) patients. A conventional treatment approach might be enough, and further treatment intensification might not be necessary, for patients with TP53 mutations if they are categorized into NCI SR.
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Vázquez-Reyes A, Bobadilla-Morales L, Barba-Barba C, Macías-Salcedo G, Serafín-Saucedo G, Velázquez-Rivera ME, Almodóvar-Cuevas MC, Márquez-Mora A, Pimentel-Gutiérrez HJ, Ortega-de-la-Torre C, Cruz-Osorio RM, Nava-Gervasio S, Rivera-Vargas J, Sánchez-Zubieta F, Corona-Rivera JR, Corona-Rivera A. Aneuploidy identification in pre-B acute lymphoblastic leukemia patients at diagnosis by Multiplex Ligation-dependent Probe Amplification (MLPA). Leuk Res 2017. [PMID: 28624713 DOI: 10.1016/j.leukres.2017.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Three-quarters of the patients with acute lymphoblastic leukemia (ALL), show numerical or structural chromosomal alterations, which are important factors in leukemogenesis. The use of Multiplex Ligation-dependent Probes Amplification (MLPA) has been mainly limited for searching copy number alterations of genes, suggesting that MLPA could detect numerical alterations in cancer. However, the use of MLPA in pediatrics to analyze subtelomeric sequences for aneuploidy detection has not been considered in previous studies. The aim of this study was to identify aneuploidy for the first time using MLPA and correlate the results with karyotype and DNA-index (DI), from preB ALL patients. Forty-two bone marrow samples were analyzed by cytogenetics and flow cytometry to determine the DI. The chromosomal gains and/or losses were detected by the SALSA MLPA P036 Subtelomere Mix 1 probemix®. The chromosomal number matched in 36 out of 42 samples between MLPA and karyotype (R2=0.7829, p=3.7×10-10), 18/42 between MLPA and DI (R2=0.1556, p=0.023), and 20/42 between karyotype and DI (R2=0.1509, p=0.015). MLPA results correlated with karyotype and DI. The use of MLPA led us to identify a gained marker chromosome. Our results indicate that MLPA could be a useful and fast alternative tool for aneuploidy identification in pediatric leukemia.
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Affiliation(s)
- A Vázquez-Reyes
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - L Bobadilla-Morales
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - C Barba-Barba
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - G Macías-Salcedo
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - G Serafín-Saucedo
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - M E Velázquez-Rivera
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - M C Almodóvar-Cuevas
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - A Márquez-Mora
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - H J Pimentel-Gutiérrez
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - C Ortega-de-la-Torre
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - R M Cruz-Osorio
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - S Nava-Gervasio
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - J Rivera-Vargas
- Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - F Sánchez-Zubieta
- Servicio de Hematología y Oncología Pediátrica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - J R Corona-Rivera
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - A Corona-Rivera
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico.
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Paulsson K, Johansson B. High hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2009; 48:637-60. [PMID: 19415723 DOI: 10.1002/gcc.20671] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High hyperdiploidy (51-67 chromosomes) is the most common cytogenetic abnormality pattern in childhood B-cell precursor acute lymphoblastic leukemia (ALL), occurring in 25-30% of such cases. High hyperdiploid ALL is characterized cytogenetically by a nonrandom gain of chromosomes X, 4, 6, 10, 14, 17, 18, and 21 and clinically by a favorable prognosis. Despite the high frequency of this karyotypic subgroup, many questions remain regarding the epidemiology, etiology, presence of other genetic changes, the time and cell of origin, and the formation and pathogenetic consequences of high hyperdiploidy. However, during the last few years, several studies have addressed some of these important issues, and these, as well as previous reports on high hyperdiploid childhood ALL, are reviewed herein.
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Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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Blandin AT, Mühlematter D, Bougeon S, Gogniat C, Porter S, Beyer V, Parlier V, Beckmann JS, van Melle G, Jotterand M. Automated four-color interphase fluorescence in situ hybridization approach for the simultaneous detection of specific aneuploidies of diagnostic and prognostic significance in high hyperdiploid acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2008; 186:69-77. [PMID: 18940469 DOI: 10.1016/j.cancergencyto.2008.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/12/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
In high hyperdiploid acute lymphoblastic leukemia (ALL), the concurrence of specific trisomies confers a more favorable outcome than hyperdiploidy alone. Interphase fluorescence in situ hybridization (FISH) complements conventional cytogenetics (CC) through its sensitivity and ability to detect chromosome aberrations in nondividing cells. To overcome the limits of manual I-FISH, we developed an automated four-color I-FISH approach and assessed its ability to detect concurrent aneuploidies in ALL. I-FISH was performed using centromeric probes for chromosomes 4, 6, 10, and 17. Parameters established for nucleus selection and signal detection were evaluated. Cutoff values were determined. Combinations of aneuploidies were considered relevant when each aneuploidy was individually significant. Results obtained in 10 patient samples were compared with those obtained with CC. Various combinations of aneuploidies were identified. All clones detected by CC were observed also by I-FISH, and I-FISH revealed numerous additional abnormal clones in all patients, ranging from < or =1% to 31.6% of cells analyzed. We conclude that four-color automated I-FISH permits the identification of concurrent aneuploidies of potential prognostic significance. Large numbers of cells can be analyzed rapidly. The large number of nuclei scored revealed a high level of chromosome variability both at diagnosis and relapse, the prognostic significance of which is of considerable clinical interest and merits further evaluation.
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Affiliation(s)
- Anna Talamo Blandin
- Cancer Cytogenetics Unit, Medical Genetics Service, University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
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Choi YW, Bae SM, Kim YW, Lee HN, Kim YW, Park TC, Ro DY, Shin JC, Shin SJ, Seo JS, Ahn WS. Gene expression profiles in squamous cell cervical carcinoma using array-based comparative genomic hybridization analysis. Int J Gynecol Cancer 2007; 17:687-96. [PMID: 17504382 DOI: 10.1111/j.1525-1438.2007.00834.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Our aim was to identify novel genomic regions of interest and provide highly dynamic range information on correlation between squamous cell cervical carcinoma and its related gene expression patterns by a genome-wide array-based comparative genomic hybridization (array-CGH). We analyzed 15 cases of cervical cancer from KangNam St Mary's Hospital of the Catholic University of Korea. Microdissection assay was performed to obtain DNA samples from paraffin-embedded cervical tissues of cancer as well as of the adjacent normal tissues. The bacterial artificial chromosome (BAC) array used in this study consisted of 1440 human BACs and the space among the clones was 2.08 Mb. All the 15 cases of cervical cancer showed the differential changes of the cervical cancer-associated genetic alterations. The analysis limit of average gains and losses was 53%. A significant positive correlation was found in 8q24.3, 1p36.32, 3q27.1, 7p21.1, 11q13.1, and 3p14.2 changes through the cervical carcinogenesis. The regions of high level of gain were 1p36.33-1p36.32, 8q24.3, 16p13.3, 1p36.33, 3q27.1, and 7p21.1. And the regions of homozygous loss were 2q12.1, 22q11.21, 3p14.2, 6q24.3, 7p15.2, and 11q25. In the high level of gain regions, GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA, and RPS6KA4 were significantly correlated with cervical cancer. The genes encoded by frequently lost clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B, and NR3C2. Therefore, array-CGH analyses showed that specific genomic alterations were maintained in cervical cancer that were critical to the malignant phenotype and may give a chance to find out possible target genes present in the gained or lost clones.
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Affiliation(s)
- Y-W Choi
- Department of Anesthesiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Forestier E, Schmiegelow K. The incidence peaks of the childhood acute leukemias reflect specific cytogenetic aberrations. J Pediatr Hematol Oncol 2006; 28:486-95. [PMID: 16912588 DOI: 10.1097/01.mph.0000212972.90877.28] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The correlation between age and karyotype was studied in 1425, 0 to 14.9 years old children who were diagnosed with acute lymphoblastic leukemia (ALL) or acute myeloblastic leukemia. Almost 80% of the non-Down B-cell precursor ALL cases in the 2 to 7 years frequency peak group who had aberrant cytogenetic results had either a high-hyperdiploid clone (51 to 61 chromosomes) or a translocation t(12;21)(p13;q22). Among B-cell precursor ALL cases, high white blood cell counts correlated with earlier age at diagnosis (rS=-0.23; P<0.001) being most evident for 11q23/MLL-aberrations, translocation t(12;21)(p13;q22), and high-hyperdiploidy. Among acute myeloblastic leukemia patients, frequency peaks were found for those with MLL/11q23 rearrangements (peak: first year), Down syndrome (peak: second to third year), or cytogenetic abnormalities other than translocations t(8;21), t(15;17), and inv(16)/t(16;16) (peak: first to third year). The epidemiology of the cytogenetic subsets of acute leukemias questions whether age as a disease-related prognostic parameter has any relevance in childhood leukemia clinical research beyond being a surrogate marker for more important, truly biologic features such as cytogenetic aberrations and white cell count at diagnosis. Further research is needed to explore whether the 2 to 7 years age incidence peak in childhood ALL harbor yet unidentified cytogenetic subsets with the same natural history as the high-hyperdiploid and t(12;21)-positive leukemias.
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Affiliation(s)
- Erik Forestier
- Department of Clinical Sciences, Pediatrics, University of Umeå, Sweden, and Pediatric Clinic II, The University Hospital Rigshospitalet, Copenhagen, Denmark
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