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Shang Z, Lai Y, Cheng H. DPP2/7 is a Potential Predictor of Prognosis and Target in Immunotherapy in Colorectal Cancer: An Integrative Multi-omics Analysis. Comb Chem High Throughput Screen 2024; 27:1642-1660. [PMID: 38454764 DOI: 10.2174/0113862073290831240229060932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) ranks among the leading causes of cancerrelated deaths. OBJECTIVE This study aimed to illuminate the relationship between DPP7 (also known as DPP2) and CRC through a combination of bioinformatics and experimental methodologies. METHODS A multi-dimensional bioinformatic analysis on DPP7 was executed, covering its expression, survival implications, clinical associations, functional roles, immune interactions, and drug sensitivities. Experimental validations involved siRNA-mediated DPP7 knockdown and various cellular assays. RESULTS Data from the Cancer Genome Atlas (TCGA) identified high DPP7 expression in solid CRC tumors, with elevated levels adversely affecting patient prognosis. A shift from the N0 to the N2 stage in CRC was associated with increased DPP7 expression. Functional insights indicated the involvement of DPP7 in cancer progression, particularly in extracellular matrix disassembly. Immunological analyses showed its association with immunosuppressive entities, and in vitro experiments in CRC cell lines underscored its oncogenic attributes. CONCLUSION DPP7 could serve as a CRC prognosis marker, functioning as an oncogene and representing a potential immunotherapeutic target.
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Affiliation(s)
- Zhihao Shang
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Yueyang Lai
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Haibo Cheng
- The First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210046, China
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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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Zhang L, Zhou L, Wang Y, Li C, Liao P, Zhong L, Geng S, Lai P, Du X, Weng J. Deep learning-based transcriptome model predicts survival of T-cell acute lymphoblastic leukemia. Front Oncol 2022; 12:1057153. [DOI: 10.3389/fonc.2022.1057153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Identifying subgroups of T-cell acute lymphoblastic leukemia (T-ALL) with poor survival will significantly influence patient treatment options and improve patient survival expectations. Current efforts to predict T-ALL survival expectations in multiple patient cohorts are lacking. A deep learning (DL)-based model was developed to determine the prognostic staging of T-ALL patients. We used transcriptome sequencing data from TARGET to build a DL-based survival model using 265 T-ALL patients. We found that patients could be divided into two subgroups (K0 and K1) with significant difference (P< 0.0001) in survival rate. The more malignant subgroup was significantly associated with some tumor-related signaling pathways, such as PI3K-Akt, cGMP-PKG and TGF-beta signaling pathway. DL-based model showed good performance in a cohort of patients from our clinical center (P = 0.0248). T-ALL patients survival was successfully predicted using a DL-based model, and we hope to apply it to clinical practice in the future.
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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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Pieters R, de Groot-Kruseman H, Van der Velden V, Fiocco M, van den Berg H, de Bont E, Egeler RM, Hoogerbrugge P, Kaspers G, Van der Schoot E, De Haas V, Van Dongen J. Successful Therapy Reduction and Intensification for Childhood Acute Lymphoblastic Leukemia Based on Minimal Residual Disease Monitoring: Study ALL10 From the Dutch Childhood Oncology Group. J Clin Oncol 2016; 34:2591-601. [PMID: 27269950 DOI: 10.1200/jco.2015.64.6364] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Outcome of childhood acute lymphoblastic leukemia (ALL) improved greatly by intensifying chemotherapy for all patients. Minimal residual disease (MRD) levels during the first months predict outcome and may select patients for therapy reduction or intensification. METHODS Patients 1 to 18 years old with ALL were stratified on the basis of MRD levels after the first and second course of chemotherapy. Thereafter, therapy was substantially reduced in patients with undetectable MRD (standard risk) and intensified in patients with intermediate (medium risk) and high (high risk) levels of MRD. Seven hundred seventy-eight consecutive patients were enrolled. The method of analysis was intention-to-treat. Outcome was compared with historical controls. RESULTS In MRD-based standard-risk patients, the 5-year event-free survival (EFS) rate was 93% (SE 2%), the 5-year survival rate was 99% (SE 1%), and the 5-year cumulative incidence of relapse rate was 6% (SE 2%). The safety upper limit of number of observation years was reached and therapy reduction was declared safe.MRD-based medium-risk patients had a significantly higher 5-year EFS rate (88%, SE 2%) with therapy intensification (including 30 weeks of asparaginase exposure and dexamethasone/vincristine pulses) compared with historical controls (76%, SE 6%). Intensive chemotherapy and stem cell transplantation in MRD-based high-risk patients resulted in a significantly better 5-year EFS rate (78%, SE 8% v 16%, SE 8% in controls). Overall outcome improved significantly (5-year EFS rate 87%, 5-year survival rate 92%, and 5-year cumulative incidence of relapse rate 8%) compared with preceding Dutch Childhood Oncology Group protocols. CONCLUSION Chemotherapy was substantially reduced safely in one-quarter of children with ALL who were selected on the basis of undetectable MRD levels, without jeopardizing the survival rate. Outcomes of patients with intermediate and high levels of MRD improved with therapy intensification.
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Affiliation(s)
- Rob Pieters
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada.
| | - Hester de Groot-Kruseman
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Vincent Van der Velden
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Marta Fiocco
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Henk van den Berg
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Evelien de Bont
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - R Maarten Egeler
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Peter Hoogerbrugge
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Gertjan Kaspers
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Ellen Van der Schoot
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Valerie De Haas
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
| | - Jacques Van Dongen
- Rob Pieters, Peter Hoogerbrugge, and Gertjan Kaspers, Princess Máxima Center for Pediatric Oncology, Utrecht; Rob Pieters, Hester de Groot-Kruseman, Marta Fiocco, and Valerie De Haas, Dutch Childhood Oncology Group, The Hague; Vincent Van der Velden and Jacques Van Dongen, University Medical Center Rotterdam, Rotterdam; Marta Fiocco, Leiden University, Leiden; Henk van den Berg, Academic Medical Center; Gertjan Kaspers, Free University Hospital Amsterdam; Ellen Van der Schoot, Sanquin Research, Amsterdam; Evelien de Bont, University of Groningen, Groningen, the Netherlands; and R. Maarten Egeler, The Hospital for Sick Children, Toronto, Canada
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Knoechel B, Bhatt A, Pan L, Pedamallu CS, Severson E, Gutierrez A, Dorfman DM, Kuo FC, Kluk M, Kung AL, Zweidler-McKay P, Meyerson M, Blacklow SC, DeAngelo DJ, Aster JC. Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case. Cold Spring Harb Mol Case Stud 2016; 1:a000539. [PMID: 27148573 PMCID: PMC4850884 DOI: 10.1101/mcs.a000539] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Notch pathway antagonists such as γ-secretase inhibitors (GSIs) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole-exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient's ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-seq documented that GSIs downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSIs was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T-cell type. H3K27ac super-enhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.
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Affiliation(s)
- Birgit Knoechel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ami Bhatt
- Departments of Medicine and Genetics, Stanford University, Stanford, California 95305, USA
| | - Li Pan
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Chandra S Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Eric Severson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Frank C Kuo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michael Kluk
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Patrick Zweidler-McKay
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA;; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Stephen C Blacklow
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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Shen H, Yang P, Liu Q, Tian Y. Nuclear expression and clinical significance of phosphohistidine phosphatase 1 in clear-cell renal cell carcinoma. J Int Med Res 2015; 43:747-57. [PMID: 26537769 DOI: 10.1177/0300060515587576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/25/2015] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To explore expression and clinical relevance of phosphohistidine phosphatase 1 (PHPT1) in clear-cell renal cell carcinoma. METHODS Patients with clear-cell renal cell carcinoma who underwent radical or nephron-sparing nephrectomy were enrolled. Correlations between PHPT1 expression and demographic and clinical characteristics were analysed prospectively. RESULTS In total, 122 patients (78 male/44 female) were included. In normal kidney tissue, PHPT1 expression was observed only in the proximal tubule. High PHPT1 expression levels were associated with larger tumour size, higher Fuhrman nuclear grade and advanced pathological tumour-node-metastasis (pTNM) stage compared with low PHPT1 expression levels. Patients with low PHPT1 expression showed better overall survival and progression-free survival compared with those with high PHPT1 expression. In addition, multivariate analysis showed that nuclear grade and pTNM stage were independent predictors of progression-free survival and overall survival in patients with clear-cell renal cell carcinoma. PHPT1 expression was also an independent predictor of overall survival but not progression-free survival. CONCLUSIONS PHPT1 was expressed in the epithelium of proximal tubuli and nuclei of clear-cell renal cell carcinoma tissue samples. High levels of 14 kDa phosphohistidine phosphatase protein were negatively associated with overall survival and progression-free survival in patients with clear-cell renal cell carcinoma.
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Affiliation(s)
- Hongliang Shen
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Peiqian Yang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qingjun Liu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ye Tian
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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Goyal U, Renvoisé B, Chang J, Blackstone C. Spastin-interacting protein NA14/SSNA1 functions in cytokinesis and axon development. PLoS One 2014; 9:e112428. [PMID: 25390646 PMCID: PMC4229207 DOI: 10.1371/journal.pone.0112428] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/15/2014] [Indexed: 01/11/2023] Open
Abstract
Hereditary spastic paraplegias (HSPs) are a genetically diverse group of inherited neurological disorders (SPG1-72) with the cardinal feature of prominent lower-extremity spasticity due to a length-dependent axonopathy of corticospinal motor neurons. The most frequent form of autosomal dominant HSP results from mutations of the SPG4 gene product spastin. This is an ATPase associated with diverse cellular activities (AAA) protein that binds to and severs microtubules. While spastin participates in crucial cellular processes such as cytokinesis, endosomal tubulation, and axon development, its role in HSP pathogenesis remains unclear. Spastin interacts in cells with the NA14 protein, a major target for auto-antibodies in Sjögren's syndrome (nuclear autoantigen 1; SSNA1). Our analysis of endogenous spastin and NA14 proteins in HeLa cells and rat cortical neurons in primary culture revealed a clear distribution of both proteins to centrosomes, with NA14 localizing specifically to centrioles. Stable NA14 knockdown in cell lines dramatically affected cell division, in particular cytokinesis. Furthermore, overexpression of NA14 in neurons significantly increased axon outgrowth and branching, while also enhancing neuronal differentiation. We postulate that NA14 may act as an adaptor protein regulating spastin localization to centrosomes, temporally and spatially regulating the microtubule-severing activity of spastin that is particularly critical during the cell cycle and neuronal development.
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Affiliation(s)
- Uma Goyal
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Benoît Renvoisé
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jaerak Chang
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
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9
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Pui CH, Pei D, Campana D, Cheng C, Sandlund JT, Bowman WP, Hudson MM, Ribeiro RC, Raimondi SC, Jeha S, Howard SC, Bhojwani D, Inaba H, Rubnitz JE, Metzger ML, Gruber TA, Coustan-Smith E, Downing JR, Leung WH, Relling MV, Evans WE. A revised definition for cure of childhood acute lymphoblastic leukemia. Leukemia 2014; 28:2336-43. [PMID: 24781017 PMCID: PMC4214904 DOI: 10.1038/leu.2014.142] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/22/2022]
Abstract
With improved contemporary therapy, we re-assess long-term outcome in patients completing treatment for childhood acute lymphoblastic leukemia to determine when cure can be declared with a high degree of confidence. In 6 successive clinical trials between 1984 and 2007, 1291(84.5%) patients completed all therapy in continuous complete remission. The post-therapy cumulative risk of relapse or development of a second neoplasm and the event-free survival rate and overall survival were analyzed according to the presenting features and the three treatment periods defined by relative outcome. Over the three treatment periods, there has been progressive increase in the rate of event-free survival (65.2% vs. 74.8% vs. 85.1% [P<0.001]) and overall survival (76.5% vs. 81.1% vs. 91.7% [P<0.001]) at 10 years. The most important predictor of outcome after completion of therapy was the type of treatment. In the most recent treatment period, which omitted the use of prophylactic cranial irradiation, the post-treatment cumulative risk of relapse was 6.4%, death in remission 1.5%, and development of a second neoplasm 2.3% at 10 years, with all relapses except one occurring within 4 years off therapy. None of the 106 patients with the t(9;22)/BCR-ABL1, t(1;19)/TCF3-PBX1 or t(4;11)/MLL-AFF1 had relapsed after 2 years from completion of therapy. These findings demonstrate that with contemporary effective therapy that excludes cranial irradiation, approximately 6% of children with acute lymphoblastic leukemia may relapse after completion of treatment, and those who remain in remission at 4 years post-treatment may be considered cured (i.e., less than 1 % chance of relapse).
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Affiliation(s)
- C H Pui
- 1] Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA [2] Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - D Pei
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - D Campana
- Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - C Cheng
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J T Sandlund
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - W P Bowman
- Department of Pediatrics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - M M Hudson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - R C Ribeiro
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S C Raimondi
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Jeha
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S C Howard
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - D Bhojwani
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - H Inaba
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J E Rubnitz
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M L Metzger
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - T A Gruber
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Coustan-Smith
- Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - J R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - W H Leung
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M V Relling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - W E Evans
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
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10
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Laskowska J, Szczepanek J, Styczyński J, Tretyn A. Array comparative genomic hybridization in pediatric acute leukemias. Pediatr Hematol Oncol 2013; 30:677-87. [PMID: 23758127 DOI: 10.3109/08880018.2013.798057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Array comparative genomic hybridization has proven to be a very powerful tool in searching for new biomarkers which can find an application in clinical practise. CGH-array technology is satisfying in almost every possible way. It is highly specific, sensitive, simple, and relatively cheap. Thus, this modern method meets the demands of clinical application. An increasing knowledge about molecular pathways and pathologic genome alterations in acute leukemias enable to define unequivocal diagnosis, prognosis and to predict a response to individual compatible therapy. This review shows a various application of CGH-array in pediatric acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL).
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Affiliation(s)
- Joanna Laskowska
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University , Torun , Poland
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11
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Abstract
Acute lymphoblastic leukaemia occurs in both children and adults but its incidence peaks between 2 and 5 years of age. Causation is multifactorial and exogenous or endogenous exposures, genetic susceptibility, and chance have roles. Survival in paediatric acute lymphoblastic leukaemia has improved to roughly 90% in trials with risk stratification by biological features of leukaemic cells and response to treatment, treatment modification based on patients' pharmacodynamics and pharmacogenomics, and improved supportive care. However, innovative approaches are needed to further improve survival while reducing adverse effects. Prognosis remains poor in infants and adults. Genome-wide profiling of germline and leukaemic cell DNA has identified novel submicroscopic structural genetic changes and sequence mutations that contribute to leukaemogenesis, define new disease subtypes, affect responsiveness to treatment, and might provide novel prognostic markers and therapeutic targets for personalised medicine.
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Affiliation(s)
- Hiroto Inaba
- Department of Oncology, St Jude Children's Research Hospital and University of Tennessee Health Science Center, Memphis, TN 38105, USA.
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12
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Mullighan CG. Genomic profiling of B-progenitor acute lymphoblastic leukemia. Best Pract Res Clin Haematol 2011; 24:489-503. [PMID: 22127311 DOI: 10.1016/j.beha.2011.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Childhood acute lymphoblastic leukemia (ALL) is comprised of multiple subtypes defined by recurring chromosomal alterations that are important events in leukemogenesis and are widely used in diagnosis and risk stratification, yet fail to fully explain the biology of this disease. In the last 5 years, genome-wide profiling of gene expression, structural DNA alterations and sequence variations has yielded important insights into the nature of submicroscopic genetic alterations that define novel subgroups of acute lymphoblastic leukemia and cooperate with known cytogenetic alterations in leukemogenesis. Importantly, several of these alterations are important determinants of risk of relapse and are potential targets for therapeutic intervention. Here, these advances and future directions in the genomic analysis of ALL are discussed.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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13
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van der Veken LT, Buijs A. Array CGH in human leukemia: from somatics to genetics. Cytogenet Genome Res 2011; 135:260-70. [PMID: 21893961 DOI: 10.1159/000330629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the past decade, array CGH has been applied to study copy number alterations in the genome in human leukemia in relation to prediction of prognosis or responsiveness to therapy. In the first segment of this review, we will focus on the identification of acquired mutations by array CGH, followed by studies on the pathogenesis of leukemia associated with germline genetic variants, phenotypic presentation and response to treatment. In the last section, we will discuss constitutional genomic aberrations causally related to myeloid leukemogenesis.
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Affiliation(s)
- L T van der Veken
- Section of Genome Diagnostics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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14
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Szczepanski T, van der Velden VHJ, Waanders E, Kuiper RP, Van Vlierberghe P, Gruhn B, Eckert C, Panzer-Grümayer R, Basso G, Cavé H, Stadt UZ, Campana D, Schrauder A, Sutton R, van Wering E, Meijerink JPP, van Dongen JJM. Late recurrence of childhood T-cell acute lymphoblastic leukemia frequently represents a second leukemia rather than a relapse: first evidence for genetic predisposition. J Clin Oncol 2011; 29:1643-9. [PMID: 21357790 DOI: 10.1200/jco.2010.30.2877] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Relapse of childhood T-cell acute lymphoblastic leukemia (T-ALL) often occurs during treatment, but in some cases, leukemia re-emerges off therapy. On the basis of previous analyses of T-cell receptor (TCR) gene rearrangement patterns, we hypothesized that some late recurrences of T-ALL might in fact represent second leukemias. PATIENTS AND METHODS In 22 patients with T-ALL who had late relapses (at least 2.5 years from diagnosis), we studied TCR gene rearrangement status at first and second presentation, NOTCH1 gene mutations, and the presence of the SIL-TAL1 gene fusion. We performed genome-wide copy number and homozygosity analysis by using oligonucleotide- and single nucleotide polymorphism (SNP) -based arrays. RESULTS We found evidence of a common clonal origin between diagnosis and relapse in 14 patients (64%). This was based on concordant TCR gene rearrangements (12 patients) or concordant genetic aberrations, as revealed by genome-wide copy number analysis (two patients). In the remaining eight patients (36%), TCR gene rearrangement sequences had completely changed between diagnosis and relapse, and gene copy number analysis showed markedly different patterns of genomic aberrations, suggesting a second T-ALL rather than a resurgence of the original clone. Moreover, NOTCH1 mutation patterns were different at diagnosis and relapse in five of these eight patients. In one patient with a second T-ALL, SNP analysis revealed a germline del(11)(p12;p13), a known recurrent aberration in T-ALL. CONCLUSION More than one third of late T-ALL recurrences are, in fact, second leukemias. Germline genetic abnormalities might contribute to the susceptibility of some patients to develop T-ALL.
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Affiliation(s)
- Tomasz Szczepanski
- Erasmus Medical Center, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
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15
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Shao L, Kang SHL, Li J, Hixson P, Taylor J, Yatsenko SA, Shaw CA, Milosavljevic A, Chang CC, Cheung SW, Patel A. Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics. J Mol Diagn 2010; 12:670-9. [PMID: 20724749 DOI: 10.2353/jmoldx.2010.090192] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Application of array comparative genomic hybridization (aCGH) has allowed an unprecedented high-resolution analysis of cancer genomes. We developed a custom genome-wide oligonucleotide microarray interrogating 493 genes involved in hematological disorders. We analyzed 55 patients with hematological neoplasms by using this microarray. In 33 patients with apparent normal conventional cytogenetic analysis, aneuploidy or isochromosomes were detected in 12% (4 of 33) of the patients by aCGH. The chromosomal changes included trisomy of chromosomes 10, 14, and 15, tetrasomy 11, and isochromosome 17q. In 17 patients with chronic lymphocytic leukemia who were initially investigated by using a panel of standard fluorescence in situ hybridization probes, additional copy number changes that were not interrogated by the fluorescence in situ hybridization (FISH) panel were detected in 47% (8 of 17) of the patients by aCGH. Important copy number changes included gain on 2p16 involving REL and BCL11A genes, rearrangements of chromosomes 8 and 15, and trisomy of chromosomes 19 and 22. In five patients with known abnormal karyotypes, aCGH identified the origin of two marker chromosomes and detected microdeletions at five breakpoints involved in three apparent balanced translocations. Our results suggest that a subset of potentially significant genomic alterations is missed by the currently available cytogenetic techniques. This pilot study clearly demonstrates high sensitivity of oligonucleotide aCGH for potential use in diagnosis and follow-up in patients with hematological neoplasms.
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Affiliation(s)
- Lina Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77021-2039, USA
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16
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Staal FJT, van Dongen JJM, Langerak AW. Novel insights into the development of T-cell acute lymphoblastic leukemia. Curr Hematol Malig Rep 2010; 2:176-82. [PMID: 20425367 DOI: 10.1007/s11899-007-0024-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) results from malignant transformation of immature cells of the T-cell lineage. T-ALL is a heterogeneous disease both clinically and genetically. It is generally accepted that T-ALL cells are the malignant counterpart of normally developing T cells in the thymus (thymocytes). Recent data using genome-wide gene expression profiling and assessment of the rearrangement status of the T-cell receptor loci confirm this notion. T-ALL cells differ from normal thymocytes in the overexpression of oncogenes that arise either from chromosomal translocations or via other mechanisms. In addition, signaling pathways that control the very first stages of thymocyte development (of note, the Notch and Wnt pathways) are involved in development of T-ALL in mice and humans when constitutively expressed. In particular, the activating mutations in the Notch pathways are believed to occur in a large proportion of human T-ALL. These findings on genetic events open up new therapeutic possibilities.
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Affiliation(s)
- Frank J T Staal
- Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, Rotterdam, The Netherlands.
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17
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Array comparative genomic hybridization analysis of adult acute leukemia patients. ACTA ACUST UNITED AC 2010; 197:122-9. [PMID: 20193845 DOI: 10.1016/j.cancergencyto.2009.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 12/27/2022]
Abstract
We have performed a retrospective array-based comparative hybridization (array-CGH) study on 41 acute leukemia samples [n=17 acute lymphoblastic leukemia (ALL) patients only at diagnosis, n=3 ALL patients both at diagnosis and relapse; n=20 acute myeloid leukemia (AML) patients only at diagnosis and n=1 AML patient both at diagnosis and relapse] using an Agilent 44K array. In addition to previously detected cytogenetic aberrations, we observed cryptic aberrations in 95% of ALL and 90.5% of AML cases. ALL-specific recurrent abnormalities were RB1 (n=3), PAX5 (n=4), and CDKN2B (n=3) deletions; AML-specific recurrent abnormalities were HOXA9 and HOXA10 (n=2) deletions and NOTCH1 duplication (n=2). Recurrent duplication of the ELK1 oncogene was observed in both ALL (n=2) and AML (n=3) cases. Our results demonstrate that oligo-array CGH (oaCGH) is an effective method for defining copy number alterations and identification of novel recurring unbalanced abnormalities. At least for now, however, the use of oaCGH for routine diagnosis still has some restrictions.
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18
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Pieters R, Carroll WL. Biology and Treatment of Acute Lymphoblastic Leukemia. Hematol Oncol Clin North Am 2010; 24:1-18. [DOI: 10.1016/j.hoc.2009.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Molecular classification of T-cell lymphomas. Crit Rev Oncol Hematol 2009; 72:125-43. [DOI: 10.1016/j.critrevonc.2009.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 01/04/2009] [Accepted: 01/09/2009] [Indexed: 11/19/2022] Open
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20
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High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat Methods 2009; 6:837-42. [PMID: 19820713 DOI: 10.1038/nmeth.1391] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 09/16/2009] [Indexed: 01/13/2023]
Abstract
Balanced chromosomal rearrangements can cause disease, but techniques for their rapid and accurate identification are missing. Here we demonstrate that chromatin conformation capture on chip (4C) technology can be used to screen large genomic regions for balanced and complex inversions and translocations at high resolution. The 4C technique can be used to detect breakpoints also in repetitive DNA sequences as it uniquely relies on capturing genomic fragments across the breakpoint. Using 4C, we uncovered LMO3 as a potentially leukemogenic translocation partner of TRB@. We developed multiplex 4C to simultaneously screen for translocation partners of multiple selected loci. We identified unsuspected translocations and complex rearrangements. Furthermore, using 4C we detected translocations even in small subpopulations of cells. This strategy opens avenues for the rapid fine-mapping of cytogenetically identified translocations and inversions, and the efficient screening for balanced rearrangements near candidate loci, even when rearrangements exist only in subpopulations of cells.
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22
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High-resolution genomic profiling of childhood T-ALL reveals frequent copy-number alterations affecting the TGF-beta and PI3K-AKT pathways and deletions at 6q15-16.1 as a genomic marker for unfavorable early treatment response. Blood 2009; 114:1053-62. [PMID: 19406988 DOI: 10.1182/blood-2008-10-186536] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Precursor T-cell acute lymphoblastic leukemia (T-ALL) in children represents a clinical challenge, because relapses are usually fatal. It is thus necessary to identify high-risk patients as early as possible to effectively individualize treatment. We aimed to define novel molecular risk markers in T-ALL and performed array-based comparative genomic hybridization (array-CGH) and expression analyses in 73 patients. We show that DNA copy-number changes are common in T-ALL and affect 70 of 73 (96%) patients. Notably, genomic imbalances predicted to down-regulate the TGF-beta or up-regulate the PI3K-AKT pathways are identified in 25 of 73 (34%) and 21 of 73 (29%) patients, suggesting that these pathways play key roles in T-ALL leukemogenesis. Furthermore, we identified a deletion at 6q15-16.1 in 9 of 73 (12%) of the patients, which predicts poor early treatment response. This deletion includes the CASP8AP2 gene, whose expression is shown to be down-regulated. The interaction of CASP8AP2 with CASP8 plays a crucial role in apoptotic regulation, suggesting a functional link between the clinical effect of the deletion and the molecular mode of action. The data presented here implicate the TGF-beta and PI3K-AKT pathways in T-ALL leukemogenesis and identify a subgroup of patients with CASP8AP2 deletions and poor early treatment response.
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23
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Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions. Leukemia 2009; 23:1209-18. [DOI: 10.1038/leu.2009.18] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
A key goal in cancer research is to identify the total complement of genetic and epigenetic alterations that contribute to tumorigenesis. We are currently witnessing the rapid evolution and convergence of multiple genome-wide platforms that are making this goal a reality. Leading this effort are studies of the molecular lesions that underlie pediatric acute lymphoblastic leukemia (ALL). The recent application of microarray-based analyses of DNA copy number abnormalities (CNAs) in pediatric ALL, complemented by transcriptional profiling, resequencing and epigenetic approaches, has identified a high frequency of common genetic alterations in both B-progenitor and T-lineage ALL. These approaches have identified abnormalities in key pathways, including lymphoid differentiation, cell cycle regulation, tumor suppression, and drug responsiveness. Moreover, the nature and frequency of CNAs differ markedly among ALL genetic subtypes. In this article, we review the key findings from the published data on genome-wide analyses of ALL and highlight some of the technical aspects of data generation and analysis that must be carefully controlled to obtain optimal results.
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25
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Mikulasovich M, LeBlanc A, Scalise A, Manwani D, Keyzner A, Najfeld V. Duplication and triplication of der(21)t(8;21)(q22;q22) in acute myeloid leukemia. ACTA ACUST UNITED AC 2009; 188:83-7. [PMID: 19100510 DOI: 10.1016/j.cancergencyto.2008.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 10/08/2008] [Indexed: 01/18/2023]
Abstract
We report on two patients with complicons resulting in duplication der(21)t(8;21)(q22;q22), triplication in the form of isochromosome of der(21)t(8;21), and four copies of ETO-AML1 fusion. Duplication of der(21) was present at diagnosis as a minor cell population in one patient, while the presence of isoderivative (21)t(8;21) characterized the relapse cells of the second patient. Due to the rarity of these cases, literature search of other reported cases of complicons may be taken as evidence that duplication and triplication of ETO-AML1 may be a poor prognostic indicator, regardless of whether it is present at diagnosis or relapse.
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Affiliation(s)
- Michael Mikulasovich
- Tumor Cytogenetics Laboratory, The Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 1002, USA
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26
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Array-Based Comparative Genomic Hybridization as a Tool for Analyzing the Leukemia Genome. Methods Mol Biol 2009; 538:151-77. [DOI: 10.1007/978-1-59745-418-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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27
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Zhang XQ, Sundh UB, Jansson L, Zetterqvist Ö, Ek P. Immunohistochemical localization of phosphohistidine phosphatase PHPT1 in mouse and human tissues. Ups J Med Sci 2009; 114:65-72. [PMID: 19396692 PMCID: PMC2852761 DOI: 10.1080/03009730802642337] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein histidine phosphorylation accounts for about 6% of the total protein phosphorylation in eukaryotic cells; still details concerning histidine phosphorylation and dephosphorylation are limited. A mammalian 14-kDa phosphohistidine phosphatase, also denominated PHPT1, was found 6 years ago that provided a new tool in the study of phosphohistidine phosphorylation. The localization of PHPT1 mRNA by Northern blot analysis revealed high expression in heart and skeletal muscle. The main object of the present study was to determine the PHPT1 expression on protein level in mouse tissues in order to get further information on the physiological role of the enzyme. Tissue samples from adult mice and 14.5-day-old mouse embryos were processed for immunostaining using a PHPT1-specific polyclonal antibody. The same antibody was also provided to the Swedish human protein atlas project (HPR) (http://www.proteinatlas.org/index.php). The results from both studies were essentially consistent with the previously reported expression of mRNA of a few human tissues. In addition, several other tissues, including testis, displayed a high protein expression. A salient result of the present investigation was the ubiquitous expression of the PHPT1 protein and its high expression in continuously dividing epithelial cells.
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Affiliation(s)
- Xiau-Qun Zhang
- 1Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | | | - Leif Jansson
- 3Department of Medical Cellbiology, Uppsala UniversityUppsalaSweden
| | - Örjan Zetterqvist
- 1Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
| | - Pia Ek
- 1Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
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Puces à ADN (CGH-array) : application pour le diagnostic de déséquilibres cytogénétiques cryptiques. ACTA ACUST UNITED AC 2008; 56:368-74. [DOI: 10.1016/j.patbio.2008.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/16/2008] [Indexed: 01/05/2023]
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29
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Van Vlierberghe P, Pieters R, Beverloo HB, Meijerink JPP. Molecular-genetic insights in paediatric T-cell acute lymphoblastic leukaemia. Br J Haematol 2008; 143:153-68. [PMID: 18691165 DOI: 10.1111/j.1365-2141.2008.07314.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Paediatric T-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive malignancy of thymocytes that accounts for about 15% of ALL cases and for which treatment outcome remains inferior compared to B-lineage acute leukaemias. In T-ALL, leukemic transformation of maturating thymocytes is caused by a multistep pathogenesis involving numerous genetic abnormalities that drive normal T-cells into uncontrolled cell growth and clonal expansion. This review provides an overview of the current knowledge on onco- and tumor suppressor genes in T-ALL and suggests a classification of these genetic defects into type A and type B abnormalities. Type A abnormalities may delineate distinct molecular-cytogenetic T-ALL subgroups, whereas type B abnormalities are found in all major T-ALL subgroups and synergize with these type A mutations during T-cell pathogenesis.
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Affiliation(s)
- Pieter Van Vlierberghe
- Department of Paediatric Oncology/Haematology, Erasmus MC/Sophia Children's Hospital, Rotterdam, The Netherlands
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Aster JC, Pear WS, Blacklow SC. Notch signaling in leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2008; 3:587-613. [PMID: 18039126 DOI: 10.1146/annurev.pathmechdis.3.121806.154300] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent discoveries indicate that gain-of-function mutations in the Notch1 receptor are very common in human T cell acute lymphoblastic leukemia/lymphoma. This review discusses what these mutations have taught us about normal and pathophysiologic Notch1 signaling, and how these insights may lead to new targeted therapies for patients with this aggressive form of cancer.
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Affiliation(s)
- Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Mansour MR, Duke V, Foroni L, Patel B, Allen CG, Ancliff PJ, Gale RE, Linch DC. Notch-1 mutations are secondary events in some patients with T-cell acute lymphoblastic leukemia. Clin Cancer Res 2008; 13:6964-9. [PMID: 18056171 DOI: 10.1158/1078-0432.ccr-07-1474] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Activating Notch-1 mutations are frequent in T-cell acute lymphoblastic leukemia (T-ALL), occurring in >50% of patients. In murine models of T-ALL, Notch-1 activation can both directly initiate leukemia and cooperate secondarily to other primary events. Whether acquisition of Notch-1 mutations is an early initiating event or a secondary event in the pathogenesis of human T-ALL is unclear. EXPERIMENTAL DESIGN We used denaturing high-performance liquid chromatography, sequencing, and fragment analysis to analyze Notch-1 mutational status and mutant level in 62 patients at presentation as well as 16 matched presentation-relapse samples. RESULTS We detected Notch-1 mutations in 47 patients (76%). Seven of these were low-level mutations (quantified at < or =10%), despite high blast counts, suggesting that they were acquired as a secondary event in a subclone. Of 16 matched presentation-relapse samples studied, 7 were wild-type at both presentation and relapse. Five of nine mutant-positive patients at presentation relapsed with the same mutation(s) at the same high level. Four patients had evidence of a change in mutant at relapse. One lost a PEST mutation and became wild-type. Two others lost mutations at relapse but acquired different mutations, despite unchanged T-cell receptor rearrangements, suggesting that the latter event predated the acquisition of the Notch-1 mutation. One relapsed with a secondary T-cell leukemia and different Notch mutation. CONCLUSIONS These results suggest that Notch-1 mutations can sometimes be acquired as secondary events in leukemogenesis and must be used cautiously as solitary minimal residual disease markers.
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Affiliation(s)
- Marc R Mansour
- Department of Haematology, University College London, UK.
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Abstract
Acute lymphoblastic leukemia (ALL), the most common type of cancer in children, is a heterogeneous disease in which many genetic lesions result in the development of multiple biologic subtypes. Today, with intensive multiagent chemotherapy, most children who have ALL are cured. The many national or institutional ALL therapy protocols in use tend to stratify patients in a multitude of different ways to tailor treatment to the rate of relapse. This article discusses the factors used in risk stratification and the treatment of pediatric ALL.
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Affiliation(s)
- Rob Pieters
- Department of Pediatric Oncology and Hematology, Erasmus MC-Sophia Children's Hospital, Dr Molewaterplein 60, Rotterdam, The Netherlands.
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Brazma D, Grace C, Howard J, Melo JV, Holyoke T, Apperley JF, Nacheva EP. Genomic profile of chronic myelogenous leukemia: Imbalances associated with disease progression. Genes Chromosomes Cancer 2007; 46:1039-50. [PMID: 17696194 DOI: 10.1002/gcc.20487] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The expression of the chimeric BCR/ABL1 fusion gene resulting from t(9;22)(q34;q11) in chronic myelogenous leukemia (CML) is necessary for malignant transformation, but not sufficient to maintain disease progression. The appearance of various chromosomal and molecular alterations in the accelerated and terminal phase of CML is well documented, but evidence for causal relationship is largely lacking. We carried out a genome wide screening at a resolution of 1 Mb of 54 samples at different stages of CML together with 12 CML cell lines and found that disease progression is accompanied by a spectrum of recurrent genome imbalances. Among the most frequent are losses at 1p36, 5q21, 9p21, and 9q34 and gains at 1q, 8q24, 9q34, 16p, and 22q11, all of which were located with higher precision within the genome than previously possible. These genome imbalances are unique to CML cases with clinically manifested or suspected accelerated/blast stage alike, but not seen in chronic phase samples. Previously unrecognized cryptic imbalances occurring within the Ph-chromosome were also detected, although further scrutiny is required to pin-point gene involvement and seek association with disease features. Importantly, some of these imbalances were seen in the CD34(+) cells but not in the whole BM samples of patients in accelerated phase. Taken together, these findings highlight the potential of screening CD34(+) cells for genome wide imbalances associated with disease progression. Finally, the numerous single copy number variations recorded, many unique to this cohort of patients, raise the possible association of genome polymorphism and CML.
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Affiliation(s)
- D Brazma
- Royal Free and UCL Medical School, Academic Haematology, Molecular Cytogenetics, Rowland Hill Street, Hampstead, and Hammersmith Hospital, London NW3 2PF, UK
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Roy M, Pear WS, Aster JC. The multifaceted role of Notch in cancer. Curr Opin Genet Dev 2006; 17:52-9. [PMID: 17178457 DOI: 10.1016/j.gde.2006.12.001] [Citation(s) in RCA: 233] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 12/11/2006] [Indexed: 12/11/2022]
Abstract
The diverse roles that Notch signals play during the development and maintenance of normal tissues are recapitulated in different forms of cancer. Depending on the tumor type, Notch can variously promote or limit tumor growth through either cell autonomous or cell non-autonomous effects on differentiation, cellular metabolism, cell cycle progression, angiogenesis, and possibly self-renewal and immune function. Of particular interest, recent findings indicate that a high fraction of T-cell acute lymphoblastic leukemias and lymphomas have activating mutations in the Notch 1 receptor, and that Notch signaling might have a role in the maintenance of normal and malignant stem cells.
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Affiliation(s)
- Monideepa Roy
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
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