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Chen C, Wang J, Kang M, Wu P, Zhu L, Fang Y, Xue Y. Identification of a novel MEF2C::SS18L1 fusion in childhood acute B-lymphoblastic leukemia. J Cancer Res Clin Oncol 2024; 150:314. [PMID: 38907739 PMCID: PMC11193691 DOI: 10.1007/s00432-024-05846-8] [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: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
PURPOSE Leukemia-associated fusion genes are closely related to the occurrence, development, diagnosis, and treatment of leukemia. DNA microarrays and second-generation sequencing have discovered multiple B-ALL fusion genes. We identified a novel MEF2C::SS18L1 fusion gene in a child diagnosed with B-ALL. This study investigates the oncogenicity and prognosis of this fusion gene in B-ALL. METHODS A child with B-ALL who has a MEF2C::SS18L1 fusion is reported as a newly discovered case. Compared the breakpoints, structural domains, clinical phenotypes, and differential expression genes of MEF2C::SS18L1 and MEF2D::SS18.Using "ONCOFUSE" software, the carcinogenicity of MEF2C::SS18L1 is predicted. Using whole transcriptome sequencing, we analyze the breakpoints and the secondary structure of the fusion protein. Further, we compared the structures, differentially expressed genes, and clinical phenotypes of MEF2D and MEF2C fusion genes by DESeq, GO functional enrichment, and flow cytometry immunophenotyping analysis. RESULTS Whole transcriptome sequencing identified a MEF2C::SS18L1 fusion transcript in a 3-year-old child with B-ALL. The MADS box, MEF structural domain, HJURP_C structural domain, and TAD I structural domain of MEF2C, and the QPGY structural domain of SS18L1, make up the fusion protein. "Oncofuse" found a 0.99 Bayesian probability that the fusion gene drives cancer. The breakpoint positions, fusion protein secondary structures, differentially expressed genes, and clinical characteristics of this patient were identical to those with MEF2D::SS18 fusion gene. CONCLUSION We identified a novel MEF2C::SS18L1 fusion gene in childhood ALL, which shares similar structural and clinical characteristics with MEF2D::SS18. Further studies with more samples should be conducted in future.
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Affiliation(s)
- Chuqin Chen
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Jiali Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Meiyun Kang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Peng Wu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Liwen Zhu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, 72# Guangzhou Road, Nanjing, 210008, Jiangsu Province, China.
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China.
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Kośmider K, Karska K, Kozakiewicz A, Lejman M, Zawitkowska J. Overcoming Steroid Resistance in Pediatric Acute Lymphoblastic Leukemia-The State-of-the-Art Knowledge and Future Prospects. Int J Mol Sci 2022; 23:ijms23073795. [PMID: 35409154 PMCID: PMC8999045 DOI: 10.3390/ijms23073795] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy among children. Despite the enormous progress in ALL therapy, resulting in achieving a 5-year survival rate of up to 90%, the ambitious goal of reaching a 100% survival rate is still being pursued. A typical ALL treatment includes three phases: remission induction and consolidation and maintenance, preceded by a prednisone prephase. Poor prednisone response (PPR) is defined as the presence of ≥1.0 × 109 blasts/L in the peripheral blood on day eight of therapy and results in significantly frequent relapses and worse outcomes. Hence, identifying risk factors of steroid resistance and finding methods of overcoming that resistance may significantly improve patients' outcomes. A mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK-ERK) pathway seems to be a particularly attractive target, as its activation leads to steroid resistance via a phosphorylating Bcl-2-interacting mediator of cell death (BIM), which is crucial in the steroid-induced cell death. Several mutations causing activation of MAPK-ERK were discovered, notably the interleukin-7 receptor (IL-7R) pathway mutations in T-cell ALL and rat sarcoma virus (Ras) pathway mutations in precursor B-cell ALL. MAPK-ERK pathway inhibitors were demonstrated to enhance the results of dexamethasone therapy in preclinical ALL studies. This report summarizes steroids' mechanism of action, resistance to treatment, and prospects of steroids therapy in pediatric ALL.
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Affiliation(s)
- Kamil Kośmider
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland; (K.K.); (A.K.)
| | - Katarzyna Karska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
| | - Agata Kozakiewicz
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland; (K.K.); (A.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
- Correspondence:
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Genomic Analyses of Pediatric Acute Lymphoblastic Leukemia Ph+ and Ph-Like-Recent Progress in Treatment. Int J Mol Sci 2021; 22:ijms22126411. [PMID: 34203891 PMCID: PMC8232636 DOI: 10.3390/ijms22126411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) with t(9;22)(q34;q11.2) is a very rare malignancy in children. Approximately 3-5% of pediatric ALL patients present with the Philadelphia chromosome. Previously, children with Ph+ had a poor prognosis, and were considered for allogeneic stem cell transplantation (allo-HSCT) in their first remission (CR1). Over the last few years, the treatment of childhood ALL has significantly improved due to standardized research protocols. Hematopoietic stem cell transplantation (HSCT) has been the gold standard therapy in ALL Ph+ patients, but recently first-generation tyrosine kinase inhibitor (TKI)-imatinib became a major milestone in increasing overall survival. Genomic analyses give the opportunity for the investigation of new fusions or mutations, which can be used to establish effective targeted therapies. Alterations of the IKZF1 gene are present in a large proportion of pediatric and adult ALL Ph+ cases. IKZF1 deletions are present in ~15% of patients without BCR-ABL1 rearrangements. In BCR-ABL1-negative cases, IKZF1 deletions have been shown to have an independent prognostic impact, carrying a three-fold increased risk of treatment failure. The prognostic significance of IKZF1 gene aberrations in pediatric ALL Ph+ is still under investigation. More research should focus on targeted therapies and immunotherapy, which is not associated with serious toxicity in the same way as classic chemotherapy, and on the improvement of patient outcomes. In this review, we provide a molecular analysis of childhood ALL with t(9;22)(q34;q11.2), including the Ph-like subtype, and of treatment strategies.
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Cheng Y, Liu N, Yang C, Jiang J, Zhao J, Zhao G, Chen F, Zhao H, Li Y. MicroRNA-383 inhibits proliferation, migration, and invasion in hepatocellular carcinoma cells by targeting PHF8. Mol Genet Genomic Med 2020; 8:e1272. [PMID: 32441881 PMCID: PMC7434733 DOI: 10.1002/mgg3.1272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/20/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022] Open
Abstract
Background To study the effect of microRNA‐383 (miR‐383) on cell proliferation, migration, and invasion of hepatocellular carcinoma (HCC) cells, and explore its mechanism. Methods The expressions of miR‐383 and plant homology domain that refers to protein 8 (PHF8) were detected in tissues and cells by quantitative real‐time polymerase chain reaction (qRT‐PCR) or western blot respectively. The miR‐383 group (transfected miR‐383 mimics), miR‐con group (transfected miR‐con), si‐con group (transfected si‐con), si‐PHF8 group (transfected si‐PHF8), miR‐383 + ctrl group (cotransfected miR‐383 mimics and pcDNA‐3.1), miR‐383 + PHF8 group (cotransfected miR‐383 mimics and pcDNA‐3.1‐PHF8) were transfected into HepG2 cells by liposome method. Cell proliferation, migration and invasion were measured by 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2‐H‐tetrazolium bromide (MTT) or trans‐well assays respectively. The luciferase activity of each group was detected by dual luciferase reporter gene assay. Results Compared with normal adjacent tissues, the expression of miR‐383 was significantly down‐regulated and the expression of PHF8 was significantly up‐regulated (p < .05). Compared with normal hepatocellular cell LO2, the expression of miR‐383 was significantly reduced (p < .05) in HCC cells. Moreover, overexpression of miR‐383 or silencing of PHF8 significantly inhibited the proliferation, migration, and invasion of HCC cells. In addition, PHF8 was targeted by miR‐383 and its restoration rescued the inhibitory effect of miR‐383 on cell proliferation, migration, and invasion of HCC cells. Conclusion miR‐383 could inhibit the proliferation, migration, and invasion of HCC cells by targeting PHF8, which will provide a basis for miR‐383 targeted therapy for HCC.
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Affiliation(s)
- Yan Cheng
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Na Liu
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - CaiFeng Yang
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Jiong Jiang
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Juhui Zhao
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Gang Zhao
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Fenrong Chen
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Hongli Zhao
- Department of Digestive Diseases, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Yang Li
- Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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Ge Z, Gu Y, Zhao G, Li J, Chen B, Han Q, Guo X, Liu J, Li H, Yu MD, Olson J, Steffens S, Payne KJ, Song C, Dovat S. High CRLF2 expression associates with IKZF1 dysfunction in adult acute lymphoblastic leukemia without CRLF2 rearrangement. Oncotarget 2018; 7:49722-49732. [PMID: 27391346 PMCID: PMC5226542 DOI: 10.18632/oncotarget.10437] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/24/2016] [Indexed: 01/09/2023] Open
Abstract
Overexpression of cytokine receptor-like factor 2 (CRLF2) due to chromosomal rearrangement has been observed in acute lymphoblastic leukemia (ALL) and reported to contribute to oncogenesis and unfavorable outcome in ALL. We studied B-ALL and T-ALL patients without CRLF2 rearrangement and observed that CRLF2 is significantly increased in a subset of these patients. Our study shows that high CRLF2expression correlates with high-risk ALL markers, as well as poor survival. We found that the IKZF1-encoded protein, Ikaros, directly binds to the CRLF2 promoter and regulates CRLF2 expression in leukemia cells. CK2 inhibitor, which can increase Ikaros activity, significantly increases Ikaros binding in ALL cells and suppresses CRLF2 expression in an Ikaros-dependent manner. CRLF2 expression is significantly higher in patients with IKZF1 deletion as compared to patients without IKZF1 deletion. Treatment with CK2 inhibitor also results in an increase in IKZF1 binding to the CRLF2 promoter and suppression of CRLF2 expression in primary ALL cells. We further observed that CK2 inhibitor induces increased H3K9me3 histone modifications in the CRLF2 promoter in ALL cell lines and primary cells. Taken together, our results demonstrate that high expression of CRLF2 correlates with high-risk ALL and short survival in patients without CRLF2 rearrangement. Our results are the first to demonstrate that the IKZF1-encoded Ikaros protein directly suppresses CRLF2 expression through enrichment of H3K9me3 in its promoter region. Our data also suggest that high CRLF2 expression works with the IKZF1 deletion to drive oncogenesis of ALL and has significance in an integrated prognostic model for adult high-risk ALL.
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Affiliation(s)
- Zheng Ge
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, China
| | - Yan Gu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Gang Zhao
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, China
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Baoan Chen
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, China
| | - Qi Han
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Xing Guo
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Juan Liu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, 210029, China
| | - Hui Li
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, 17033, USA
| | - Michael D Yu
- Sydney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107 USA
| | - Justin Olson
- University of Wisconsin at Stout, Menomonie, WI, 54751, USA
| | - Sadie Steffens
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, 17033, USA
| | - Kimberly J Payne
- Loma Linda University, Department of Pathology and Human Anatomy, Loma Linda, CA, 92350, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, 17033, USA
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA, 17033, USA
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Ekmekci SS, Ekmekci CG, Kandilci A, Gulec C, Akbiyik M, Emrence Z, Abaci N, Karakas Z, Agaoglu L, Unuvar A, Anak S, Devecioglu O, Ustek D, Grosveld G, Ozbek U. SET Oncogene is Upregulated in Pediatric Acute Lymphoblastic Leukemia. TUMORI JOURNAL 2018; 98:252-6. [DOI: 10.1177/030089161209800212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Aims and background The SET gene is a target of chromosomal translocations in acute leukemia and encodes a widely expressed multifunctional phosphoprotein. It has been shown that SET is upregulated in BCR-ABL1-positive cell lines, patient-derived chronic myeloid leukemia CD34-positive cells, and some solid tumors. Methods and study design We determined the expression level of SET in 59 pediatric acute lymphoblastic leukemia patients who were BCR-ABL-negative using quantitative real-time reverse-transcriptase-polymerase chain reaction. Results We showed that SET expression was significantly upregulated in 96.5% of B-acute lymphoblastic leukemia (28 of 29; 16.6 fold) and 93% of T-acute lymphoblastic leukemia (28 of 30; 47.6 fold) patients. This upregulation was not associated with any clinical features or overall and relapse-free survival. Conclusions Our results showed that SET is significantly overexpressed in pediatric acute lymphoblastic leukemia samples, and an increased level of SET might contribute to leukemic process.
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Affiliation(s)
- Sema Sirma Ekmekci
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
| | - Cumhur G Ekmekci
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
| | - Ayten Kandilci
- Gebze Institute of Technology, Department of Molecular Biology and Genetics, Kocaeli
| | - Cagri Gulec
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Meral Akbiyik
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Zeliha Emrence
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
| | - Neslihan Abaci
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
| | - Zeynep Karakas
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Leyla Agaoglu
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Aysegul Unuvar
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Sema Anak
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Omer Devecioglu
- Istanbul University, Istanbul Medical Faculty, Department of Pediatrics, Istanbul, Turkey
| | - Duran Ustek
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
| | - Gerard Grosveld
- St. Jude Children's Research Hospital, Department of Genetics, Memphis TN, USA
| | - Ugur Ozbek
- Istanbul University, Institute of Experimental Medicine, Department of Genetics, Istanbul
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The histone demethylase PHF8 promotes adult acute lymphoblastic leukemia through interaction with the MEK/ERK signaling pathway. Biochem Biophys Res Commun 2018; 496:981-987. [PMID: 29330049 DOI: 10.1016/j.bbrc.2018.01.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 01/08/2018] [Indexed: 01/21/2023]
Abstract
Adult acute lymphoblastic leukemia (ALL) is a malignant disorder of lymphoid progenitor cells that is associated with a high risk of relapse and poor prognosis. Thus, novel pathogenic mechanisms and therapeutic targets need to be explored. Histone methylation is one of the most significant chromatin post-translational modifications. Here, we show that the histone demethylase PHF8 is highly expressed in a large number of ALL clinical specimens and that PHF8 expression is associated with ALL progression. PHF8 knockdown inhibits proliferation and promotes the apoptosis of ALL cells in vitro as well as attenuates tumor growth in vivo. PHF8 transcriptionally upregulates MEK1, a key molecule in the MEK/ERK pathway, at least partially by directly binding to its promoter, thereby activating the MEK/ERK pathway. In addition, we found that an inhibitor of the MEK/ERK pathway, PD184352, subsequently suppresses PHF8 expression. Thus, PHF8 forms a positive feedback loop with the MEK/ERK pathway, and PHF8 knockdown enhances the lethality of PD184352 in ALL cells. In conclusion, this study identifies oncogenic functions of PHF8 in adult ALL and suggests a novel epigenetic strategy for disease intervention.
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Dinner S, Gurbuxani S, Jain N, Stock W. Acute Lymphoblastic Leukemia in Adults. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00066-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Constitutive Ras signaling and Ink4a/Arf inactivation cooperate during the development of B-ALL in mice. Blood Adv 2017; 1:2361-2374. [PMID: 29296886 DOI: 10.1182/bloodadvances.2017012211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 09/24/2017] [Indexed: 11/20/2022] Open
Abstract
Despite recent advances in treatment, human precursor B-cell acute lymphoblastic leukemia (B-ALL) remains a challenging clinical entity. Recent genome-wide studies have uncovered frequent genetic alterations involving RAS pathway mutations and loss of the INK4A/ARF locus, suggesting their important role in the pathogenesis, relapse, and chemotherapy resistance of B-ALL. To better understand the oncogenic mechanisms by which these alterations might promote B-ALL and to develop an in vivo preclinical model of relapsed B-ALL, we engineered mouse strains with induced somatic KrasG12D pathway activation and/or loss of Ink4a/Arf during early stages of B-cell development. Although constitutive activation of KrasG12D in B cells induced prominent transcriptional changes that resulted in enhanced proliferation, it was not sufficient by itself to induce development of a high-grade leukemia/lymphoma. Instead, in 40% of mice, these engineered mutations promoted development of a clonal low-grade lymphoproliferative disorder resembling human extranodal marginal-zone lymphoma of mucosa-associated lymphoid tissue or lymphoplasmacytic lymphoma. Interestingly, loss of the Ink4a/Arf locus, apart from reducing the number of apoptotic B cells broadly attenuated KrasG12D-induced transcriptional signatures. However, combined Kras activation and Ink4a/Arf inactivation cooperated functionally to induce a fully penetrant, highly aggressive B-ALL phenotype resembling high-risk subtypes of human B-ALL such as BCR-ABL and CRFL2-rearranged. Ninety percent of examined murine B-ALL tumors showed loss of the wild-type Ink4a/Arf locus without acquisition of highly recurrent cooperating events, underscoring the role of Ink4a/Arf in restraining Kras-driven oncogenesis in the lymphoid compartment. These data highlight the importance of functional cooperation between mutated Kras and Ink4a/Arf loss on B-ALL.
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Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. Blood Adv 2017; 1:1717-1728. [PMID: 29296818 DOI: 10.1182/bloodadvances.2017006023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/07/2017] [Indexed: 11/20/2022] Open
Abstract
The incidence and mortality rates of B-cell acute lymphoblastic leukemia (B-ALL) differ by age and sex. To determine if inherited genetic susceptibility contributes to these differences we performed 2 genome-wide association studies (GWAS) by age, sex, and subtype and subsequent meta-analyses. The GWAS included 446 B-ALL cases, and 3027 healthy unrelated blood and marrow transplant (BMT) donors as controls from the Determining the Influence of Susceptibility Conveying Variants Related to One-Year Mortality after BMT (DISCOVeRY-BMT) study. We identified 1 novel variant, rs189434316, significantly associated with odds of normal cytogenetic B-ALL (odds ratio from meta-analysis [ORmeta] = 3.7; 95% confidence interval [CI], 2.5, 6.2; P value from meta-analysis [Pmeta] = 6.0 × 10-9). The previously reported pediatric B-ALL GWAS variant, rs11980379 (IKZF1), replicated in B-ALL pediatric patients (ORmeta = 2.3; 95% CI, 1.5, 3.7; Pmeta = 1.0 × 10-9), with evidence of heterogeneity (P = .02) between males and females. Sex differences in single-nucleotide polymorphism effect were seen in those >15 years (OR = 1.7; 95% CI, 1.4, 2.2, PMales = 6.38 × 10-6/OR = 1.1; 95% CI, 0.8, 1.5; PFemales = .6) but not ≤15 years (OR = 2.3; 95% CI, 1.4, 3.8; PMales = .0007/OR = 1.9; 95% CI, 1.2, 3.2; PFemales = .007). The latter association replicated in independent pediatric B-ALL cohorts. A previously identified adolescent and young-adult onset ALL-associated variant in GATA3 is associated with B-ALL risk in those >40 years. Our findings provide more evidence of the influence of genetics on B-ALL age of onset and we have shown the first evidence that IKZF1 associations with B-ALL may be sex and age specific.
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11
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Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome. Proc Natl Acad Sci U S A 2017; 114:E4030-E4039. [PMID: 28461505 DOI: 10.1073/pnas.1702489114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Children with Down syndrome (DS) are prone to development of high-risk B-cell precursor ALL (DS-ALL), which differs genetically from most sporadic pediatric ALLs. Increased expression of cytokine receptor-like factor 2 (CRLF2), the receptor to thymic stromal lymphopoietin (TSLP), characterizes about half of DS-ALLs and also a subgroup of sporadic "Philadelphia-like" ALLs. To understand the pathogenesis of relapsed DS-ALL, we performed integrative genomic analysis of 25 matched diagnosis-remission and -relapse DS-ALLs. We found that the CRLF2 rearrangements are early events during DS-ALL evolution and generally stable between diagnoses and relapse. Secondary activating signaling events in the JAK-STAT/RAS pathway were ubiquitous but highly redundant between diagnosis and relapse, suggesting that signaling is essential but that no specific mutations are "relapse driving." We further found that activated JAK2 may be naturally suppressed in 25% of CRLF2pos DS-ALLs by loss-of-function aberrations in USP9X, a deubiquitinase previously shown to stabilize the activated phosphorylated JAK2. Interrogation of large ALL genomic databases extended our findings up to 25% of CRLF2pos, Philadelphia-like ALLs. Pharmacological or genetic inhibition of USP9X, as well as treatment with low-dose ruxolitinib, enhanced the survival of pre-B ALL cells overexpressing mutated JAK2. Thus, somehow counterintuitive, we found that suppression of JAK-STAT "hypersignaling" may be beneficial to leukemic B-cell precursors. This finding and the reduction of JAK mutated clones at relapse suggest that the therapeutic effect of JAK specific inhibitors may be limited. Rather, combined signaling inhibitors or direct targeting of the TSLP receptor may be a useful therapeutic strategy for DS-ALL.
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Bhandari P, Ahmad F, Das BR. Molecular profiling of gene copy number abnormalities in key regulatory genes in high-risk B-lineage acute lymphoblastic leukemia: frequency and their association with clinicopathological findings in Indian patients. Med Oncol 2017; 34:92. [PMID: 28401483 DOI: 10.1007/s12032-017-0940-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/31/2017] [Indexed: 02/06/2023]
Abstract
Genes related to key cellular pathways are frequently altered in B cell ALL and are associated with poor survival especially in high-risk (HR) subgroups. We examined gene copy number abnormalities (CNA) in 101 Indian HR B cell ALL patients and their correlation with clinicopathological features by multiplex ligation-dependent probe amplification. Overall, CNA were detected in 59 (59%) cases, with 26, 10 and 23% of cases harboring 1, 2 or +3 CNA. CNA were more prevalent in BCR-ABL1 (60%), pediatric (64%) and high WCC (WBC count) (63%) patients. Frequent genes deletions included CDNK2A/B (26%), IKZF1 (25%), PAX5 (14%), JAK2 (7%), BTG1 (6%), RB1 (5%), EBF1 (4%), ETV6 (4%), while PAR1 region genes were predominantly duplicated (20%). EBF1 deletions selectively associated with adults, IKZF1 deletions occurred frequently in high WCC and BCR-ABL1 cases, while PAR1 region gains significantly associated with MLL-AF4 cases. IKZF1 haploinsufficiency group was predominant, especially in adults (65%), high WCC (60%) patients and BCR-ABL1-negative (78%) patients. Most cases harbored multiple concurrent CNA, with IKZF1 concomitantly occurring with CDNK2A/B, PAX5 and BTG1, while JAK2 occurred with CDNK2A/B and PAX5. Mutually exclusive CNA included ETV6 and IKZF1/RB1, and EBF1 and JAK2. Our results corroborate with global reports, aggregating molecular markers in Indian HR B-ALL cases. Integration of CNA data from rapid methods like MLPA, onto background of existing gold-standard methods detecting significant chromosomal abnormalities, provides a comprehensive genetic profile in B-ALL.
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Affiliation(s)
- Prerana Bhandari
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India
| | - Firoz Ahmad
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India
| | - Bibhu Ranjan Das
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India.
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13
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BCR-ABL (Ph)-like acute leukemia—Pathogenesis, diagnosis and therapeutic options. Blood Rev 2017; 31:11-16. [DOI: 10.1016/j.blre.2016.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/23/2016] [Accepted: 09/09/2016] [Indexed: 12/31/2022]
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14
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Somasundaram R, Åhsberg J, Okuyama K, Ungerbäck J, Lilljebjörn H, Fioretos T, Strid T, Sigvardsson M. Clonal conversion of B lymphoid leukemia reveals cross-lineage transfer of malignant states. Genes Dev 2016; 30:2486-2499. [PMID: 27913602 PMCID: PMC5159664 DOI: 10.1101/gad.285536.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/31/2016] [Indexed: 11/30/2022]
Abstract
In this study, Somasundaram et al. provide in vitro and in vivo evidence for a leukemic state that can be transferred between lineages even though the alteration in cell identity involves dramatic changes in gene expression and epigenetic state. They show that primary pro-B leukemia cells from mice carrying heterozygous mutations in either or both the Pax5 and Ebf1 genes, commonly mutated in human leukemia, can be converted into T lineage leukemia cells. Even though leukemia is considered to be confined to one specific hematopoietic cell type, cases of acute leukemia of ambiguous lineage and patients relapsing in phenotypically altered disease suggest that a malignant state may be transferred between lineages. Because B-cell leukemia is associated with mutations in transcription factors of importance for stable preservation of lineage identity, we here investigated the potential lineage plasticity of leukemic cells. We report that primary pro-B leukemia cells from mice carrying heterozygous mutations in either or both the Pax5 and Ebf1 genes, commonly mutated in human leukemia, can be converted into T lineage leukemia cells. Even though the conversion process involved global changes in gene expression and lineage-restricted epigenetic reconfiguration, the malignant phenotype of the cells was preserved, enabling them to expand as T lineage leukemia cells in vivo. Furthermore, while the transformed pro-B cells displayed plasticity toward myeloid lineages, the converted cells failed to cause myeloid leukemia after transplantation. These data provide evidence that a malignant phenotype can be transferred between hematopoietic lineages. This has important implications for modern cancer medicine because lineage targeted treatment of leukemia patients can be predicted to provoke the emergence of phenotypically altered subclones, causing clinical relapse.
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Affiliation(s)
- Rajesh Somasundaram
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden
| | - Josefine Åhsberg
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden
| | - Kazuki Okuyama
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden
| | - Jonas Ungerbäck
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden
| | - Henrik Lilljebjörn
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 22184 Lund, Sweden
| | - Thoas Fioretos
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 22184 Lund, Sweden
| | - Tobias Strid
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden
| | - Mikael Sigvardsson
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty of Health Sciences, Linköping University, 58183 Linkoping, Sweden.,Division of Molecular Hematology Lund University, 22184 Lund, Sweden
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Dabaghi M, Rahgozar S, Moshtaghian J, Moafi A, Abedi M, Pourabutaleb E. Overexpression of SORCIN is a Prognostic Biomarker for Multidrug-Resistant Pediatric Acute Lymphoblastic Leukemia and Correlates with Upregulated MDR1/P-gp. Genet Test Mol Biomarkers 2016; 20:516-21. [PMID: 27382961 DOI: 10.1089/gtmb.2016.0031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Multidrug resistance is one of the major causes of treatment failure in pediatric acute lymphoblastic leukemia (ALL), and SORCIN is an intracellular calcium modulator protein. The current study was designed to investigate the in vitro and in vivo relationships between the expression levels of SORCIN: in tumor cell lines and children with ALL; its possible correlation with MDR1/P-glycoprotein (P-gp), a multidrug resistance-related gene; and response to therapy. MATERIALS AND METHODS Childhood T-lymphoblastic leukemia (CCRF-CEM) cell lines resistant to methotrexate (MTX) were developed. Patient studies were performed by including 30 children with ALL at diagnosis, 3 children with bone marrow relapse, and 15 children with no symptoms of cancer. The mRNA expression profiles of SORCIN and MDR1/P-gp was assessed using quantitative polymerase chain reaction (qPCR). Minimal residual disease (MRD) was measured in the patient population, a year following the initial therapy using qPCR. RESULTS Cell line data analyses showed a positive correlation between SORCIN mRNA levels and resistance to MTX. The difference between patient and control groups for SORCIN expression levels was not significant. However, patients with a negative response to therapy showed an increase in SORCIN mRNA levels (up to 6.8-fold) compared with those with negative MRD. In addition, the results demonstrated a significant positive correlation between SORCIN and MDR1/P-gp gene expression levels. CONCLUSION The current study introduces, for the first time, a possible prognostic value of SORCIN in childhood ALL, which may be correlated with MDR1/P-gp gene expression in these patients.
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Affiliation(s)
- Mohammad Dabaghi
- 1 Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
| | - Soheila Rahgozar
- 1 Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
| | - Jamal Moshtaghian
- 1 Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
| | - Alireza Moafi
- 2 Department of Pediatric-Hematology-Oncology, Sayed-ol-Shohada Hospital, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Marjan Abedi
- 1 Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
| | - Elnaz Pourabutaleb
- 1 Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran
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16
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Mikhail FM, Heerema NA, Rao KW, Burnside RD, Cherry AM, Cooley LD. Section E6.1-6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. Genet Med 2016; 18:635-42. [PMID: 27124785 DOI: 10.1038/gim.2016.50] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 12/30/2022] Open
Abstract
DISCLAIMER These American College of Medical Genetics and Genomics standards and guidelines are developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these standards and guidelines. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Cytogenetic analyses of hematological neoplasms are performed to detect and characterize clonal chromosomal abnormalities that have important diagnostic, prognostic, and therapeutic implications. At the time of diagnosis, cytogenetic abnormalities assist in the diagnosis of such disorders and can provide important prognostic information. At the time of relapse, cytogenetic analysis can be used to confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the standards and guidelines applicable to chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. This updated Section E6.1-6.4 has been incorporated into and supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the 2009 Edition (Revised 01/2010), American College of Medical Genetics and Genomics Standards and Guidelines for Clinical Genetics Laboratories.Genet Med 18 6, 635-642.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen W Rao
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Pathology, University of North Carolina, Chapel Hill, North Carolina, USA.,Deceased
| | - Rachel D Burnside
- Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, North Carolina, USA
| | - Athena M Cherry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri Kansas City Medical School, Kansas City, Missouri, USA
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17
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Rational combination therapies targeting survival signaling in aggressive B-cell leukemia/lymphoma. Curr Opin Hematol 2015; 21:297-308. [PMID: 24811162 DOI: 10.1097/moh.0000000000000045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW The identification of oncogenic 'driver' mutations and activated survival pathways in selected aggressive B-cell malignancies directs the development of novel adjunctive therapies using targeted small molecule inhibitors. With a focus on diffuse large B-cell lymphoma 'not otherwise specified', Hodgkin lymphoma and childhood B-cell precursor acute lymphoblastic leukemia, this review will provide an up-to-date account of the current literature on the development of new molecularly targeted treatment modalities for aggressive B-cell malignancies. RECENT FINDINGS Subclassification of B-cell malignancies depending on their particular genetic 'driver' lesions and transcriptional and/or signaling signatures has led to the development of targeted therapeutic approaches using small molecule inhibitors to amend current combination chemotherapy. SUMMARY Treatment outcome with current combination chemotherapy is still poor for subsets of aggressive B-cell malignancies, and demands development of targeted therapeutic approaches. Advanced gene expression profiling and genomic sequencing have revealed a more detailed landscape of recurrent alterations, allowing a better subclassification of B-cell lymphomas and leukemias. Many alterations directly or indirectly lead to activation of survival signaling pathways and expression of key oncoproteins and prosurvival molecules, including Janus kinase-signal transducer and activator of transcription (JAK-STAT), phosphatidylinositol-3 kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR), avian myelocytomatosis viral oncogene homolog (MYC) and B-cell lymphoma 2 (BCLl-2). Small molecule inhibitors targeting these proteins and pathways are currently being tested in clinical trials and preclinically to improve chemotherapeutic regimes and treatment outcomes.
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18
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Stasevich I, Inglott S, Austin N, Chatters S, Chalker J, Addy D, Dryden C, Ancliff P, Ford A, Williams O, Kempski H. PAX5 alterations in genetically unclassified childhood Precursor B-cell acute lymphoblastic leukaemia. Br J Haematol 2015; 171:263-272. [PMID: 26115422 DOI: 10.1111/bjh.13543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/29/2022]
Abstract
Here, we report a high incidence of PAX5 abnormalities observed in 32/68 (47%) of patients with genetically unclassified childhood precursor B-cell acute lymphoblastic leukaemia (pre-B ALL). Various deletions, gains, mutations and rearrangements of PAX5 comprised 45%, 12%, 29% and 14%, respectively, of the abnormalities found. 28% of patients showed more than one abnormality of the gene, implying bi-allelic impairment of PAX5. Novel PAX5-RHOXF2, PAX5-ELK3 and PAX5-CBFA2T2 rearrangements, which lead to aberrant expression of PAX5, were also identified. PAX5 rearrangements demonstrated a complex mechanism of formation including concurrent duplications/deletions of PAX5 and its partner genes. Finally, the splice variant c.1013-2A>G, seen in two patients with loss of one PAX5 allele, was confirmed to be germ-line in one patient and somatic in the other. PAX5 alterations were also found to be clinically associated with a higher white blood cell count (P = 0·015). These findings contribute to the knowledge of PAX5 alterations and their role in the pathogenesis of pre-B ALL.
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Affiliation(s)
- Irina Stasevich
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK.,Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
| | - Sarah Inglott
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Nicola Austin
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Steve Chatters
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Jane Chalker
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Dilys Addy
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Carryl Dryden
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Philip Ancliff
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - Anthony Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Owen Williams
- Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
| | - Helena Kempski
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK.,Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
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19
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Kelly BJ, Fitch JR, Hu Y, Corsmeier DJ, Zhong H, Wetzel AN, Nordquist RD, Newsom DL, White P. Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics. Genome Biol 2015; 16:6. [PMID: 25600152 PMCID: PMC4333267 DOI: 10.1186/s13059-014-0577-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/23/2014] [Indexed: 12/18/2022] Open
Abstract
While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter White
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus 43205, OH, USA.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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20
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Rabitsch W, Böhm A, Bojic M, Schellongowski P, Wöhrer S, Sliwa T, Keil F, Worel N, Greinix H, Hauswirth A, Kalhs P, Jaeger U, Valent P, Sperr WR. Clofarabine/cyclophosphamide for debulking before stem cell transplantation. Eur J Clin Invest 2014; 44:775-83. [PMID: 24942362 DOI: 10.1111/eci.12294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Allogeneic haematopoietic stem cell transplantation (HSCT) is the only curative rescue therapy for patients (pts) with chemotherapy-refractory acute leukaemia. Disease control prior to HSCT is essential for long-term disease-free survival after HSCT. PATIENTS AND METHODS We have retrospectively analysed the outcome of 20 pts aged 21-64 years with refractory leukaemia (acute myeloid leukaemia, n = 16; acute lymphatic leukaemia, n = 4) who received debulking therapy with clofarabine (10 mg/m², days 1-4) and cyclophosphamide (200 mg/m², days 1-4; ClofCy) prior to HSCT. RESULTS Clofarabine/cyclophosphamide (1-4 cycles) was well tolerated and resulted in a substantial reduction of leukaemic cells in all pts. HSCT was performed in 15 of 20 pts. After HSCT (myeloablative, n = 9; dose-reduced, n = 6), all pts showed engraftment and full donor chimerism (related donors, n = 4 or unrelated donors, n = 11) and all pts achieved complete haematologic remission (CR). The median survival after HSCT is 531 days (range: 48-1462 days), and six pts are still alive after a median of 1245 days. Seven pts died after they had relapsed between days +152 and +1496. One patient died from acute graft-versus-host disease (day +48) and one from systemic fungal infection (day +87). CONCLUSION Clofarabine/cyclophosphamide is a novel effective treatment approach for pts with chemotherapy-refractory acute leukaemia prior to HSCT. Whether this novel debulking protocol leads to improved long-term outcome in pts with refractory leukaemias remains to be determined in forthcoming clinical studies.
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Affiliation(s)
- Werner Rabitsch
- Bone Marrow Transplantation Unit, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria; Intensive Care Unit, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
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21
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Maino E, Sancetta R, Viero P, Imbergamo S, Scattolin AM, Vespignani M, Bassan R. Current and future management of Ph/BCR-ABL positive ALL. Expert Rev Anticancer Ther 2014; 14:723-40. [PMID: 24611626 DOI: 10.1586/14737140.2014.895669] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Following the introduction of targeted therapy with tyrosine kinase inhibitors (TKI) at the beginning of the past decade, the outcome of patients with Philadelphia-chromosome positive acute lymphoblastic leukemia (Ph+ ALL) has dramatically improved. Presently, the use of refined programs with first/second generation TKI's and chemotherapy together with allogeneic stem cell transplantation allow up to 50% of all patients to be cured. Further progress is expected with the new TKI ponatinib, overcoming resistance caused by T315I point mutation, other targeted therapies, autologous transplantation in molecularly negative patients, therapeutic monoclonal antibodies like inotuzumab ozogamicin and blinatumomab, and chimeric antigen receptor-modified T cells. Ph+ ALL could become curable in the near future even without allogeneic stem cell transplantation, minimizing the risk of therapy-related death and improving greatly the quality of patients' life.
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Affiliation(s)
- Elena Maino
- Hematology/Bone Marrow Transplantation Unit, Ospedale dell'Angelo and Ospedale SS. Giovanni e Paolo, Via Paccagnella 11, 30174 Venezia-Mestre, Italy
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22
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Gibson SE, Luo J, Sathanoori M, Liao J, Surti U, Swerdlow SH. Whole-genome single nucleotide polymorphism array analysis is complementary to classical cytogenetic analysis in the evaluation of lymphoid proliferations. Am J Clin Pathol 2014; 141:247-55. [PMID: 24436273 DOI: 10.1309/ajcprhght28duwla] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. METHODS Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA). RESULTS Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. CONCLUSIONS The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.
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Affiliation(s)
- Sarah E. Gibson
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Malini Sathanoori
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Jun Liao
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Steven H. Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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23
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Yamashita Y, Shimada A, Yamada T, Yamaji K, Hori T, Tsurusawa M, Watanabe A, Kikuta A, Asami K, Saito AM, Horibe K. IKZF1 and CRLF2 gene alterations correlate with poor prognosis in Japanese BCR-ABL1-negative high-risk B-cell precursor acute lymphoblastic leukemia. Pediatr Blood Cancer 2013; 60:1587-92. [PMID: 23804397 DOI: 10.1002/pbc.24571] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 03/25/2013] [Indexed: 11/07/2022]
Abstract
BACKGROUND Genome-wide analysis studies have demonstrated that IKZF1, CRLF2, and JAK2 gene alterations correlate with poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). However, the prognostic significance for these gene alterations has not been clarified in Japanese patients. PROCEDURE A total of 194 patients with BCP-ALL enrolled in the Japanese Children's Cancer & Leukemia Study Group ALL 2004 clinical trial were assessed for the presence of three different gene alterations: IKZF1 deletions, CRLF2 expression and JAK2 mutation. RESULTS IKZF1 deletions and CRLF2-high expression were identified in 22 of 177 (12%) patients and in 15 of 141 (11%) patients, respectively. However, JAK2 R683 mutation was detected only one of 177 patients. The 4-year event-free survival (4y-EFS) was different when comparing patients with or without IKZF1 deletions (68.2% vs. 85.2%; P = 0.04) and was also different when comparing patients with different CRLF2 expression levels (high, 66.7% vs. low, 88.1%; P = 0.03). The differences in 4y-EFS were statistically significant in patients with ALL in the National Cancer Institute (NCI)-high risk group (HR-ALL) (IKZF1 deletions: yes, 58.3% vs. no, 87.0%, P = 0.02; CRLF2 expression: high, 55.6% vs. low, 85.3%, P = 0.04) but not in patients with ALL in the NCI-standard risk group (SR-ALL; IKZF1 deletions: yes, 80.0% vs. no, 84.4%, P = 0.75; CRLF2 expression: high, 83.3% vs. low, 89.2%, P = 0.77). Coexistence of IKZF1 deletions and CRLF2-high expression associated with poor outcomes. CONCLUSIONS IKZF1 deletions and CRLF2-high expression predicted poor outcomes in patients with HR-ALL but not in patients with SR-ALL in our Japanese cohort.
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Affiliation(s)
- Yuka Yamashita
- National Hospital Organization Nagoya Medical Center Clinical Research Center, Nagoya, Japan
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24
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Clappier E, Auclerc MF, Rapion J, Bakkus M, Caye A, Khemiri A, Giroux C, Hernandez L, Kabongo E, Savola S, Leblanc T, Yakouben K, Plat G, Costa V, Ferster A, Girard S, Fenneteau O, Cayuela JM, Sigaux F, Dastugue N, Suciu S, Benoit Y, Bertrand Y, Soulier J, Cavé H. An intragenic ERG deletion is a marker of an oncogenic subtype of B-cell precursor acute lymphoblastic leukemia with a favorable outcome despite frequent IKZF1 deletions. Leukemia 2013; 28:70-7. [PMID: 24064621 DOI: 10.1038/leu.2013.277] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/13/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022]
Abstract
Oncogenic subtypes in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) are used for risk stratification. However, a significant number of BCP-ALL patients are still genetically unassigned. Using array-comparative genomic hybridization in a selected BCP-ALL cohort, we characterized a recurrent V(D)J-mediated intragenic deletion of the ERG gene (ERG(del)). A breakpoint-specific PCR assay was designed and used to screen an independent non-selected cohort of 897 children aged 1-17 years treated for BCP-ALL in the EORTC-CLG 58951 trial. ERG(del) was found in 29/897 patients (3.2%) and was mutually exclusive of known classifying genetic lesions, suggesting that it characterized a distinct leukemia entity. ERG(del) was associated with higher age (median 7.0 vs. 4.0 years, P=0.004), aberrant CD2 expression (43.5% vs. 3.7%, P<0.001) and frequent IKZF1 Δ4-7 deletions (37.9% vs. 5.3%, P<0.001). However, ERG(del) patients had a very good outcome, with an 8-year event-free survival (8-y EFS) and an 8-year overall survival of 86.4% and 95.6%, respectively, suggesting that the IKZF1 deletion had no impact on prognosis in this genetic subtype. Accordingly, within patients with an IKZF1 Δ4-7 deletion, those with ERG(del) had a better outcome (8-y EFS: 85.7% vs. 51.3%; hazard ratio: 0.16; 95% confidence interval: 0.02-1.20; P=0.04). These findings have implications for further stratification including IKZF1 status.
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Affiliation(s)
- E Clappier
- 1] U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France [2] Department of Genetics, Robert Debré Hospital, APHP, Paris, France [3] Hematology University Institute, University Paris-Diderot, Paris, France
| | - M F Auclerc
- 1] U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France [2] Department of Pediatric Hematology, St-Louis Hospital, APHP, Paris, France
| | - J Rapion
- EORTC Headquarters, Brussels, Belgium
| | - M Bakkus
- Molecular Hematology Laboratory, UZ Brussels, Brussels, Belgium
| | - A Caye
- Department of Genetics, Robert Debré Hospital, APHP, Paris, France
| | - A Khemiri
- Department of Genetics, Robert Debré Hospital, APHP, Paris, France
| | - C Giroux
- Department of Genetics, Robert Debré Hospital, APHP, Paris, France
| | - L Hernandez
- U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France
| | - E Kabongo
- Molecular Hematology Laboratory, UZ Brussels, Brussels, Belgium
| | - S Savola
- MRC-Holland, Amsterdam, The Netherlands
| | - T Leblanc
- Department of Pediatric Hematology, St-Louis Hospital, APHP, Paris, France
| | - K Yakouben
- Department of Pediatric Hematology, Robert-Debré Hospital, APHP, Paris, France
| | - G Plat
- Department of Pediatric Onco-Hematology, University Hospital Purpan, Toulouse, France
| | - V Costa
- Department of Pediatrics, Portuguese Oncology Institute, Porto, Portugal
| | - A Ferster
- Department of Pediatric Onco-Hematology, Children's University Hospital Reine Fabiola, Brussels, Belgium
| | - S Girard
- Hematology Laboratory, IHOP, Lyon, France
| | - O Fenneteau
- Hematology Laboratory, Robert Debré Hospital, APHP, Paris, France
| | - J M Cayuela
- 1] U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France [2] Hematology University Institute, University Paris-Diderot, Paris, France
| | - F Sigaux
- 1] U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France [2] Hematology University Institute, University Paris-Diderot, Paris, France
| | - N Dastugue
- Hematology Laboratory, University Hospital Purpan, Toulouse, France
| | - S Suciu
- EORTC Headquarters, Brussels, Belgium
| | - Y Benoit
- Department of Pediatric Hematology-Oncology, Ghent University Hospital, Ghent, Belgium
| | - Y Bertrand
- Department of Pediatric Hematology, IHOP and Claude Bernard University, Lyon, France
| | - J Soulier
- 1] U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Paris, France [2] Hematology University Institute, University Paris-Diderot, Paris, France
| | - H Cavé
- 1] Department of Genetics, Robert Debré Hospital, APHP, Paris, France [2] Hematology University Institute, University Paris-Diderot, Paris, France
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25
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Asai D, Imamura T, Suenobu SI, Saito A, Hasegawa D, Deguchi T, Hashii Y, Matsumoto K, Kawasaki H, Hori H, Iguchi A, Kosaka Y, Kato K, Horibe K, Yumura-Yagi K, Hara J, Oda M. IKZF1 deletion is associated with a poor outcome in pediatric B-cell precursor acute lymphoblastic leukemia in Japan. Cancer Med 2013; 2:412-9. [PMID: 23930217 PMCID: PMC3699852 DOI: 10.1002/cam4.87] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/13/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022] Open
Abstract
Genetic alterations of Ikaros family zinc finger protein 1 (IKZF1), point mutations in Janus kinase 2 (JAK2), and overexpression of cytokine receptor-like factor 2 (CRLF2) were recently reported to be associated with poor outcomes in pediatric B-cell precursor (BCP)-ALL. Herein, we conducted genetic analyses of IKZF1 deletion, point mutation of JAK2 exon 16, 17, and 21, CRLF2 expression, the presence of P2RY8-CRLF2 fusion and F232C mutation in CRLF2 in 202 pediatric BCP-ALL patients newly diagnosed and registered in Japan Childhood Leukemia Study ALL02 protocol to find out if alterations in these genes are determinants of poor outcome. All patients showed good response to initial prednisolone (PSL) treatment. Ph+, infantile, and Down syndrome–associated ALL were excluded. Deletion of IKZF1 occurred in 19/202 patients (9.4%) and CRLF2 overexpression occurred in 16/107 (15.0%), which are similar to previous reports. Patients with IKZF1 deletion had reduced event-free survival (EFS) and overall survival (OS) compared to those in patients without IKZF1 deletion (5-year EFS, 62.7% vs. 88.8%, 5-year OS, 71.8% vs. 90.2%). Our data also showed significantly inferior 5-year EFS (48.6% vs. 84.7%, log rank P = 0.0003) and 5-year OS (62.3% vs. 85.4%, log rank P = 0.009) in NCI-HR patients (n = 97). JAK2 mutations and P2RY8-CRLF2 fusion were rarely detected. IKZF1 deletion was identified as adverse prognostic factor even in pediatric BCP-ALL in NCI-HR showing good response to PSL.
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Affiliation(s)
- Daisuke Asai
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
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26
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Impact of IKZF1 deletions and PAX5 amplifications in pediatric B-cell precursor ALL treated according to NOPHO protocols. Leukemia 2013; 27:1936-9. [PMID: 23538749 DOI: 10.1038/leu.2013.92] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Loh ML, Mullighan CG. Advances in the genetics of high-risk childhood B-progenitor acute lymphoblastic leukemia and juvenile myelomonocytic leukemia: implications for therapy. Clin Cancer Res 2012; 18:2754-67. [PMID: 22589484 DOI: 10.1158/1078-0432.ccr-11-1936] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hematologic malignancies of childhood comprise the most common childhood cancers. These neoplasms derive from the pathologic clonal expansion of an abnormal cancer-initiating cell and span a diverse spectrum of phenotypes, including acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), and myelodysplastic syndromes (MDS). Expansion of immature lymphoid or myeloid blasts with suppression of normal hematopoiesis is the hallmark of ALL and AML, whereas MPN is associated with proliferation of 1 or more lineages that retain the ability to differentiate, and MDS is characterized by abnormal hematopoiesis and cytopenias. The outcomes for children with the most common childhood cancer, B-progenitor ALL (B-ALL), in general, is quite favorable, in contrast to children affected by myeloid malignancies. The advent of highly sensitive genomic technologies reveals the remarkable genetic complexity of multiple subsets of high-risk B-progenitor ALL, in contrast to a somewhat simpler model of myeloid neoplasms, although a number of recently discovered alterations displayed by both types of malignancies may lead to common therapeutic approaches. This review outlines recent advances in our understanding of the genetic underpinnings of high-risk B-ALL and juvenile myelomonocytic leukemia, an overlap MPN/MDS found exclusively in children, and we also discuss novel therapeutic approaches that are currently being tested in clinical trials. Recent insights into the clonal heterogeneity of leukemic samples and the implications for diagnostic and therapeutic approaches are also discussed.
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Affiliation(s)
- Mignon L Loh
- Department of Pediatrics and the Helen Diller Comprehensive Cancer Center, Benioff Children's Hospital, University of California, San Francisco, San Francisco, California, USA
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28
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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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29
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Simons A, Sikkema-Raddatz B, de Leeuw N, Konrad NC, Hastings RJ, Schoumans J. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat 2012; 33:941-8. [PMID: 22488943 DOI: 10.1002/humu.22057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 02/03/2012] [Indexed: 11/10/2022]
Abstract
Over the last three decades, cytogenetic analysis of malignancies has become an integral part of disease evaluation and prediction of prognosis or responsiveness to therapy. In most diagnostic laboratories, conventional karyotyping, in conjunction with targeted fluorescence in situ hybridization analysis, is routinely performed to detect recurrent aberrations with prognostic implications. However, the genetic complexity of cancer cells requires a sensitive genome-wide analysis, enabling the detection of small genomic changes in a mixed cell population, as well as of regions of homozygosity. The advent of comprehensive high-resolution genomic tools, such as molecular karyotyping using comparative genomic hybridization or single-nucleotide polymorphism microarrays, has overcome many of the limitations of traditional cytogenetic techniques and has been used to study complex genomic lesions in, for example, leukemia. The clinical impact of the genomic copy-number and copy-neutral alterations identified by microarray technologies is growing rapidly and genome-wide array analysis is evolving into a diagnostic tool, to better identify high-risk patients and predict patients' outcomes from their genomic profiles. Here, we review the added clinical value of an array-based genome-wide screen in leukemia, and discuss the technical challenges and an interpretation workflow in applying arrays in the acquired cytogenetic diagnostic setting.
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Affiliation(s)
- Annet Simons
- Laboratory of Tumor Genetics, Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
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30
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Tasian SK, Loh ML. Understanding the biology of CRLF2-overexpressing acute lymphoblastic leukemia. Crit Rev Oncog 2012; 16:13-24. [PMID: 22150304 DOI: 10.1615/critrevoncog.v16.i1-2.30] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent genomic analyses of childhood and adult B-precursor acute lymphoblastic leukemia (ALL) samples have identified novel genetic alterations in essential lymphoid development and signal transduction pathways, providing insight into the pathogenesis of high-risk ALL associated with treatment failure. Particular advances have been made in unraveling the genetics of ALL associated with overexpression of the cytokine receptor-like factor 2 gene (CRLF2), which is frequently accompanied by simultaneous activating mutations in genes encoding Ikaros (IKZF1), Janus kinase 1 (JAK1) and Janus kinase 2 (JAK2), and/or the IL-7 receptor alpha chain (IL7RA). Children and adults with high-risk CRLF2-overexpressing ALL have high rates of relapse and dismal overall survival. Various groups have thus attempted to characterize the biochemical consequences of these genetic lesions via preclinical models with the goal of identifying targets for new therapies. These studies provide early data suggesting the promise of signal transduction inhibitors (STIs) of the JAK/STAT and PI3K pathways for CRLF2-overexpressing ALL. Additional research efforts continue to elucidate these aberrant signaling networks to provide rationale for bringing STIs into the clinic for these high-risk patients. This review highlights the current knowledge of the incidence, prognostic significance, and biology of CRLF2-overexpressing ALL and future directions for development of targeted therapies.
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Affiliation(s)
- Sarah K Tasian
- Department of Pediatrics, Division of Pediatric Hemotology-Oncology, University of California San Francisco, San Francisco, CA 94143, USA
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31
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Chen B, Wang YY, Shen Y, Zhang WN, He HY, Zhu YM, Chen HM, Gu CH, Fan X, Chen JM, Cao Q, Yang G, Jiang CL, Weng XQ, Zhang XX, Xiong SM, Shen ZX, Jiang H, Gu LJ, Chen Z, Mi JQ, Chen SJ. Newly diagnosed acute lymphoblastic leukemia in China (I): abnormal genetic patterns in 1346 childhood and adult cases and their comparison with the reports from Western countries. Leukemia 2012; 26:1608-16. [PMID: 22382891 DOI: 10.1038/leu.2012.26] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It has been generally acknowledged that the diagnosis, treatment and prognosis evaluation of leukemia largely rely on an adequate identification of genetic abnormalities. A systemic analysis of genetic aberrations was performed in a cohort of 1346 patients with newly diagnosed acute lymphoblastic leukemia (ALL) in China. The pediatric patients had higher incidence of hyperdiploidy and t(12;21) (p13;q22)/ETV6-RUNX1 than adults (P<0.0001); in contrast, the occurrence of Ph and Ik6 variant of IKZF1 gene was much more frequent in adult patients (all P<0.0001). In B-ALL, the existence of Ik6 and that of BCR-ABL were statistically correlated (P<0.0001). In comparison with Western cohorts, the incidence of t(9;22) (q34;q11)/BCR-ABL (14.60%) in B-ALL and HOX11 expression in T-ALL (25.24%) seemed to be much higher in our group, while the incidence of t(12;21) (p13;q22)/ETV6-RUNX1 (15.34%) seemed to be lower in Chinese pediatric patients. The occurrence of hyperdiploidy was much lower either in pediatric (10.61% vs 20-38%) or adult patients (2.36% vs 6.77-12%) in our study than in Western reports. In addition, the frequencies of HOX11L2 in adult patients were much higher in our cohort than in Western countries (20.69% vs 4-11%). In general, it seems that Chinese ALL patients bear more adverse prognostic factors than their Western counterparts do.
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Affiliation(s)
- B Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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32
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Tang JY, Chang CC, Lin PC, Chang JG. Isocitrate dehydrogenase mutation hot spots in acute lymphoblastic leukemia and oral cancer. Kaohsiung J Med Sci 2012; 28:138-44. [PMID: 22385606 DOI: 10.1016/j.kjms.2011.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/31/2011] [Indexed: 10/14/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) encodes a nicotinamide adenine dinucleotide phosphate+-dependent enzyme for oxidative decarboxylation of isocitrate and has an essential role in the tricarboxylic acid cycle. Mutations of IDH1 and IDH2 have been identified in patients with glioma, leukemia, and other cancers. However, the incidence of IDH mutations in acute myeloid leukemia in Taiwan is much lower than that reported in Western countries. The reason for the difference is unknown and its clinical implications remain unclear. Acute lymphoblastic leukemia (ALL) is a heterogenous hematopoietic malignancy. Oral squamous cell carcinoma (OSCC) results from chronic carcinogen exposures and is highly prevalent in trucking workers, especially in southern Taiwan. Subtypes of both diseases require specific treatments, and molecular markers for developing tailored treatments are limited. High-resolution melting (HRM) analysis is now a widely used methodology for rapid, accurate, and low-cost mutation scanning. In this study, 90 adults with OSC and 31 children with ALL were scanned by HRM analysis for IDH1 and IDH2 mutation hot spots. In ALL, the allele frequency was 3.23% in both IDH1 and IDH2. In OSCC, the allele frequency was 2.22% in IDH2. A synonymous mutation over pG313 (c.939A > G) of IDH2 was found in both pediatric ALL and adult OSCC. Therefore, we concluded that mutations of IDH are uncommon in ALL and OSCC and are apparently not a major consideration when selecting treatment modalities.
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Affiliation(s)
- Jen-Yang Tang
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan
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Rusiniak ME, Kunnev D, Freeland A, Cady GK, Pruitt SC. Mcm2 deficiency results in short deletions allowing high resolution identification of genes contributing to lymphoblastic lymphoma. Oncogene 2011; 31:4034-44. [PMID: 22158038 PMCID: PMC3309111 DOI: 10.1038/onc.2011.566] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mini-chromosome maintenance (Mcm) proteins are part of the replication licensing complex that is loaded onto chromatin during the G1-phase of the cell cycle and required for initiation of DNA replication in the subsequent S-phase. Mcm proteins are typically loaded in excess of the number of locations that are utilized during S-phase. Nonetheless, partial depletion of Mcm proteins leads to cancers and stem cell deficiencies. Mcm2 deficient mice, on a 129Sv genetic background, display a high rate of thymic lymphoblastic lymphoma. Here array comparative genomic hybridization (aCGH) is utilized to characterize the genetic damage accruing in these tumors. The predominant events are deletions averaging less than 0.5 Mb, considerably shorter than observed in prior studies using alternative mouse lymphoma models or human tumors. Such deletions facilitate identification of specific genes and pathways responsible for the tumors. Mutations in many genes that have been implicated in human lymphomas are recapitulated in this mouse model. These features, and the fact that the mutation underlying the accelerated genetic damage does not target a specific gene or pathway a priori, are valuable features of this mouse model for identification of tumor suppressor genes. Genes affected in all tumors include Pten, Tcfe2a, Mbd3 and Setd1b. Notch1 and additional genes are affected in subsets of tumors. The high frequency of relatively short deletions is consistent with elevated recombination between nearby stalled replication forks in Mcm2 deficient mice.
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Affiliation(s)
- M E Rusiniak
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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The Fat1 cadherin is overexpressed and an independent prognostic factor for survival in paired diagnosis–relapse samples of precursor B-cell acute lymphoblastic leukemia. Leukemia 2011; 26:918-26. [DOI: 10.1038/leu.2011.319] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Lundin C, Hjorth L, Behrendtz M, Nordgren A, Palmqvist L, Andersen MK, Biloglav A, Forestier E, Paulsson K, Johansson B. High frequency of BTG1 deletions in acute lymphoblastic leukemia in children with down syndrome. Genes Chromosomes Cancer 2011; 51:196-206. [PMID: 22072402 DOI: 10.1002/gcc.20944] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/28/2011] [Indexed: 02/02/2023] Open
Abstract
Previous cytogenetic studies of myeloid and acute lymphoblastic leukemias in children with Down syndrome (ML-DS and DS-ALL) have revealed significant differences in abnormality patterns between such cases and acute leukemias in general. Also, certain molecular genetic aberrations characterize DS-related leukemias, such as GATA1 mutations in ML-DS and deregulation of the CRLF2 gene in DS-ALL. Whether microdeletions/microduplications also vary between DS and non-DS cases is presently unclear. To address this issue, we performed single nucleotide polymorphism array analyses of eight pediatric ML-DS and 17 B-cell precursor DS-ALL. In the ML-DS cases, a total of 29 imbalances (20 gains and nine losses) and two partial uniparental isodisomies (pUPDs) were detected. None of the 11 small (defined as <10 Mb) imbalances were recurrent, nor were the pUPDs, whereas of the 18 large aberrations, three were recurrent-dup(1q), +8 and +21. In contrast, several frequent changes were identified in the DS-ALL cases, which harbored 82 imbalances (30 gains and 52 losses) and four pUPDs. Of the 40 large changes, 28 were gains and 12 losses, with +X, dup(Xq), dup(1q), del(7p), dup(8q), del(9p), dup(9p), del(12p), dup(17q), and +21 being recurrent. Of the 40 microdeletions identified, several targeted specific genes, with the following being repeatedly deleted: BTG1 and CDKN2A/B (29% of cases), ETV6, IKZF1, PAX5 and SERP2 (18%), and BTLA, INPP4B, P2RY8, and RB1 (12%). Loss of the SERP2 and INPP4B genes, encoding the stress-associated endoplasmic reticulum protein family member 2 and the inositol polyphosphate 4-phosphatase-II, respectively, has previously never been implicated in leukemia. Although deletions of the other genes have been associated with ALL, the high frequency of BTG1 loss is a novel finding. Such deletions may characterize a clinical subgroup of DS-ALL, comprising mainly boys with a high median age. In conclusion, ML-DS and DS-ALL are genetically distinct, with mainly gains in ML-DS and deletions in DS-ALL. Furthermore, DS-ALL is characterized by several recurrent gene deletions, with BTG1 loss being particularly frequent.
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Affiliation(s)
- Catarina Lundin
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Sweden.
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36
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Mutations in the transmembrane and juxtamembrane domains enhance IL27R transforming activity. Biochem J 2011; 438:155-64. [PMID: 21631431 DOI: 10.1042/bj20110351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cytokines and their receptors regulate haemopoiesis by controlling cellular growth, survival and differentiation. Thus it is not surprising that mutations of cytokine receptors contribute to the formation of haemopoietic disorders, including cancer. We recently identified transforming properties of IL27R, the ligand-binding component of the receptor for interleukin-27. Although wild-type IL27R exhibits transforming properties in haemopoietic cells, in the present study we set out to determine if the transforming activity of IL27R could be enhanced by mutation. We identified three mutations of IL27R that enhance its transforming activity. One of these mutations is a phenylalanine to cysteine mutation at residue 523 (F523C) in the transmembrane domain of the receptor. The two other mutations identified involve deletions of amino acids in the cytoplasmic juxtamembrane region of the receptor. Expression of each of these mutant IL27R proteins led to rapid cytokine-independent transformation in haemopoietic cells. Moreover, the rate of transformation induced by these mutants was significantly greater than that induced by wild-type IL27R. Expression of these IL27R mutants also induced enhanced activation of JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling compared with wild-type. An activating deletion mutation of IL27R enhanced homodimerization of the receptor by a mechanism that may involve disulfide bonding. These transforming IL27R mutants displayed equal or greater transforming activity than bona fide haemopoietic oncogenes such as BCR-ABL (breakpoint cluster region-Abelson murine leukaemia viral oncogene homologue) and JAK2-V617F. Since IL27R is expressed on haemopoietic stem cells, lymphoid cells and myeloid cells, including acute myeloid leukaemia blast cells, mutation of this receptor has the potential to contribute to a variety of haemopoietic neoplasms.
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37
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Simons A, Stevens-Kroef M, Idrissi-Zaynoun NE, van Gessel S, Weghuis DO, van den Berg E, Waanders E, Hoogerbrugge P, Kuiper R, van Kessel AG. Microarray-based genomic profiling as a diagnostic tool in acute lymphoblastic leukemia. Genes Chromosomes Cancer 2011; 50:969-81. [DOI: 10.1002/gcc.20919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 07/14/2011] [Indexed: 01/12/2023] Open
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Mullighan CG, Willman CL. Advances in the Biology of Acute Lymphoblastic Leukemia-From Genomics to the Clinic. J Adolesc Young Adult Oncol 2011; 1:77-86. [PMID: 23610732 DOI: 10.1089/jayao.2011.0012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite impressive advances in cure rates for childhood acute lymphoblastic leukemia (ALL), ALL remains the leading cause of disease-related death in young people and new therapeutic approaches directed against rational therapeutic targets are urgently required to improve treatment outcomes. This is particularly true for ALL in older children, adolescents, and adults, in whom treatment outcomes are markedly inferior to those of young children. A major goal of current leukemia research is to use comprehensive genomic analysis of the leukemic cell genome, transcriptome, and epigenome to identify critical new genomic alterations that drive leukemogenesis and influence responsiveness to therapy. Genomic analyses in childhood ALL have been remarkably informative and have identified a number of new structural genetic alterations that play important roles in the establishment of the leukemic clone and determine risk of relapse. Notably, many high-risk ALL cases harbor loss-of-function and dominant mutations of genes that encode transcriptional regulators of lymphoid development coupled with mutations that result in activation of cytokine receptor and kinase signaling pathways. These advances have resulted in new diagnostic approaches and therapeutic trials in ALL. This review will discuss these advances and outline challenges for future studies, including the potential role of genome-wide sequencing approaches and the need for detailed studies of the genetics of ALL in the adolescent and young adult population.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital , Memphis, Tennessee
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de Leeuw N, Hehir-Kwa JY, Simons A, Geurts van Kessel A, Smeets DF, Faas BHW, Pfundt R. SNP Array Analysis in Constitutional and Cancer Genome Diagnostics – Copy Number Variants, Genotyping and Quality Control. Cytogenet Genome Res 2011; 135:212-21. [PMID: 21934286 DOI: 10.1159/000331273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N de Leeuw
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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