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Aladily TN, Qiqieh JF, Alshorman A, Alhyari S, Khader M. PAX5 and TDT-Negative B-Acute Lymphoblastic Leukemia with Unusual Genetic Mutations: A Case Report. Avicenna J Med 2022; 12:186-190. [PMID: 36570429 PMCID: PMC9771627 DOI: 10.1055/s-0042-1758387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
B-acute lymphoblastic leukemia (B-ALL) is commonly encountered in clinical practice. Patients present with increased percentage of lymphoblasts in bone marrow and/or peripheral blood. Immunophenotypic study by flow cytometry or immunohistochemistry is essential to establish the diagnosis. Paired box-5 (PAX5) is a B cell lineage protein and terminal deoxynucleotidyl transferase (TDT) is an immature marker, both of which are routinely tested in the pathologic workup of acute leukemia. In this report, we describe a case of B-ALL in a 37-year-old woman in which both PAX5 and TDT were negative. Next-generation sequencing test detected mutations in DNA methyltransferase 3 α and Fms related receptor tyrosine kinase 3 genes, which are frequently mutated in acute myeloid leukemia rather than B-ALL. The constellation of these rare findings in a single case signifies the importance of examining a wide panel of markers when the diagnosis of ALL is suspected.
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Affiliation(s)
- Tariq N. Aladily
- Department of Hematopathology, The University of Jordan, Amman, Jordan,Address for correspondence Tariq N. Aladily, MD Department of Hematopathology, The University of JordanAmman 11814Jordan
| | - Jamil F. Qiqieh
- Department of Hematopathology, The University of Jordan, Amman, Jordan
| | - Alaa Alshorman
- Department of Hematology and Oncology, The University of Jordan, Amman, Jordan
| | - Salem Alhyari
- Department of Hematology and Oncology, The University of Jordan, Amman, Jordan
| | - Majd Khader
- Department of Pathology, King Hussein Cancer Center, Amman, Jordan
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2
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Jia Z, Gu Z. PAX5 alterations in B-cell acute lymphoblastic leukemia. Front Oncol 2022; 12:1023606. [PMID: 36387144 PMCID: PMC9640836 DOI: 10.3389/fonc.2022.1023606] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 12/01/2022] Open
Abstract
PAX5, a master regulator of B cell development and maintenance, is one of the most common targets of genetic alterations in B-cell acute lymphoblastic leukemia (B-ALL). PAX5 alterations consist of copy number variations (whole gene, partial, or intragenic), translocations, and point mutations, with distinct distribution across B-ALL subtypes. The multifaceted functional impacts such as haploinsufficiency and gain-of-function of PAX5 depending on specific variants have been described, thereby the connection between the blockage of B cell development and the malignant transformation of normal B cells has been established. In this review, we provide the recent advances in understanding the function of PAX5 in orchestrating the development of both normal and malignant B cells over the past decade, with a focus on the PAX5 alterations shown as the initiating or driver events in B-ALL. Recent large-scale genomic analyses of B-ALL have identified multiple novel subtypes driven by PAX5 genetic lesions, such as the one defined by a distinct gene expression profile and PAX5 P80R mutation, which is an exemplar leukemia entity driven by a missense mutation. Although altered PAX5 is shared as a driver in B-ALL, disparate disease phenotypes and clinical outcomes among the patients indicate further heterogeneity of the underlying mechanisms and disturbed gene regulation networks along the disease development. In-depth mechanistic studies in human B-ALL and animal models have demonstrated high penetrance of PAX5 variants alone or concomitant with other genetic lesions in driving B-cell malignancy, indicating the altered PAX5 and deregulated genes may serve as potential therapeutic targets in certain B-ALL cases.
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Affiliation(s)
- Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
- *Correspondence: Zhaohui Gu,
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3
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The Pleiotropy of PAX5 Gene Products and Function. Int J Mol Sci 2022; 23:ijms231710095. [PMID: 36077495 PMCID: PMC9456430 DOI: 10.3390/ijms231710095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
PAX5, a member of the Paired Box (PAX) transcription factor family, is an essential factor for B-lineage identity during lymphoid differentiation. Mechanistically, PAX5 controls gene expression profiles, which are pivotal to cellular processes such as viability, proliferation, and differentiation. Given its crucial function in B-cell development, PAX5 aberrant expression also correlates with hallmark cancer processes leading to hematological and other types of cancer lesions. Despite the well-established association of PAX5 in the development, maintenance, and progression of cancer disease, the use of PAX5 as a cancer biomarker or therapeutic target has yet to be implemented. This may be partly due to the assortment of PAX5 expressed products, which layers the complexity of their function and role in various regulatory networks and biological processes. In this review, we provide an overview of the reported data describing PAX5 products, their regulation, and function in cellular processes, cellular biology, and neoplasm.
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Clinical impacts of copy number variations in B-cell differentiation and cell cycle control genes in pediatric B-cell acute lymphoblastic leukemia: a single centre experience. Radiol Oncol 2021; 56:92-101. [PMID: 34957727 PMCID: PMC8884847 DOI: 10.2478/raon-2021-0050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/05/2021] [Indexed: 01/24/2023] Open
Abstract
Background IKZF1 gene deletions have been identified as a poor prognostic factor in pediatric B-cell acute lymphoblastic leukemia (B-ALL), especially in the presence of co-occurring deletions (IKZF1plus profile). This study aimed to determine the frequency of IKZF1 deletions and deletions in other B-cell differentiation and cell cycle control genes, and their prognostic impact in Slovenian pediatric B-ALL patients. Patients and methods We studied a cohort of 99 patients diagnosed with B-ALL from January 2012 to December 2020 and treated according to the ALL IC-BFM 2009 protocol. Eighty-eight bone marrow or peripheral blood samples were analysed for copy number variations (CNVs) using the SALSA MLPA P335 ALL-IKZF1 probemix. Results At least one CNV was detected in more than 65% of analysed samples. The most frequently altered genes were PAX5 and CDKN2A/B (30.7%, 26.1%, and 25.0%, respectively). Deletions in IKZF1 were present in 18.2% of analysed samples and were associated with an inferior 5-year event-free survival (EFS; 54.8% vs. 85.9%, p = 0.016). The IKZF1plus profile was identified in 12.5% of the analysed samples, and these patients had an inferior 5-year EFS than those with deletions in IKZF1 only and those without deletions (50.8% vs. 75.0% vs. 85.9%, respectively, p = 0.049). Overall survival (OS) was also worse in patients with the IKZF1plus profile than those with deletions in IKZF1 only and those without deletions (5-year OS 76.2% vs. 100% vs. 93.0%, respectively). However, the difference between the groups was not statistically significant. Conclusions Our results are in concordance with the results obtained in larger cooperative clinical trials. Copy number variations analysis using the SALSA MLPA kit is a reliable tool for initial diagnostic approach in children with B-ALL, even in smaller institutions in low- and middle-income countries.
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Wang L, Liang X, Liang M, Li D, Gu J, Huang W, Zhou J. PAX5 haploinsufficiency induces low T cell infiltration in the cancer microenvironment via reduced chemokines. Curr Mol Med 2021; 22:826-834. [PMID: 34872475 DOI: 10.2174/1566524021666211206094046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/10/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
AIMS To investigate the effects of PAXT mutations on tumor immunity. BACKGROUND Loss of function of PAX5 plays a key role in PAX5 mutation tumor. OBJECTIVE PAX5 haploinsufficiency promoting tumorigenesis is related to immune escape, but there was no report about mechanisms of PAX5 mutation inducing tumor immunological escape. METHOD We constructed the PAX5 haplodeletion A20 cell lines using gene-editing technology, built allografted A20 tumor models and evaluated the effect of PAX5 haplodeletion on T cells and chemokines in the tumor microenvironment (TME). RESULT Our results from different methods indicated percentages of CD3+ CD4+ T cells and CD3+ CD8+ T cells in TME of PAX5 haplodeletion clones decreased significantly compared with that of PAX5 wild type control. Several chemokines, such as Ccl2, Ccl4, Cxcl9 and Cxcl10, in TME of PAX5. CONCLUSION Our study showed that PAX5 haploinsufficiency induced low T cell infiltration in TME using decreased chemokines.
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Affiliation(s)
- Lei Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Xue Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Mi Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Dang Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Jia Gu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei. China
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Liang M, Gong D, Wang L, Liang X, Meng J, Huang W, Zhou J. PAX5 haploinsufficiency induced CD8+ T cells dysfunction or exhaustion by high expression of immune inhibitory-related molecules. Cancer Treat Res Commun 2021; 28:100437. [PMID: 34425470 DOI: 10.1016/j.ctarc.2021.100437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/11/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022]
Abstract
PURPOSE PAX5 haploinsufficiency promoting tumorigenesis is related to immune escape. But the mechanisms of PAX5 mutations inducing tumor immune escape have not been clarified. Our aim was to study how PAX5 haploinsufficiency influences effector CD8 + T cells in tumor microenvironment. METHODS We estimated the proportions of 22 immune cell types and the expressions of immune inhibitory-related molecules based on gene expression profiles (GEPs) from children's B- acute lymphoblastic leukemia(B-ALL) with PAX5 mutations by CIBERSORT, an established algorithm. We constructed the PAX5 haplodeletion A20 cell lines, built allografted A20 tumor models and evaluated the effect of PAX5 haplodeletion on immune inhibitory-related molecules in the tumor microenvironment (TME). RESULTS Our results indicated the percentages of T cells in bone marrow of children's B-ALL with PAX5 mutations were not statistically different from that in bone marrow of B-ALL without PAX5 mutations, except for T follicular helper (Tfh) cells. But a variety of up-regulated immune inhibitory-related molecules in bone marrow of children's B- ALL with PAX5 mutations were identified. By different approaches, we found that several immune inhibitory-related molecules of CD8+ T cells in TME of PAX5 haplodeletion clones such as TIM3, NR4A1 and BATF, were increased significantly compared with that of PAX5 wild type control. The IFN-ɤ of CD8+ T cells in TME of PAX5 haplodeletion tumors was decreased significantly compared with that of PAX5 wild type control. CONCLUSION Our study showed that PAX5 haploinsufficiency induced CD8+ T cells dysfunction or exhaustion by high expression of TIM3, NR4A1 and BATF in the CD8+ T cells of TME.
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Affiliation(s)
- Mi Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Duanhao Gong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Lei Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Xue Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jiao Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China.
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
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Nishii R, Baskin-Doerfler R, Yang W, Oak N, Zhao X, Yang W, Hoshitsuki K, Bloom M, Verbist K, Burns M, Li Z, Lin TN, Qian M, Moriyama T, Gastier-Foster JM, Rabin KR, Raetz E, Mullighan C, Pui CH, Yeoh AEJ, Zhang J, Metzger ML, Klco JM, Hunger SP, Newman S, Wu G, Loh ML, Nichols KE, Yang JJ. Molecular basis of ETV6-mediated predisposition to childhood acute lymphoblastic leukemia. Blood 2021; 137:364-373. [PMID: 32693409 PMCID: PMC7819760 DOI: 10.1182/blood.2020006164] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/03/2020] [Indexed: 12/24/2022] Open
Abstract
There is growing evidence supporting an inherited basis for susceptibility to acute lymphoblastic leukemia (ALL) in children. In particular, we and others reported recurrent germline ETV6 variants linked to ALL risk, which collectively represent a novel leukemia predisposition syndrome. To understand the influence of ETV6 variation on ALL pathogenesis, we comprehensively characterized a cohort of 32 childhood leukemia cases arising from this rare syndrome. Of 34 nonsynonymous germline ETV6 variants in ALL, we identified 22 variants with impaired transcription repressor activity, loss of DNA binding, and altered nuclear localization. Missense variants retained dimerization with wild-type ETV6 with potentially dominant-negative effects. Whole-transcriptome and whole-genome sequencing of this cohort of leukemia cases revealed a profound influence of germline ETV6 variants on leukemia transcriptional landscape, with distinct ALL subsets invoking unique patterns of somatic cooperating mutations. 70% of ALL cases with damaging germline ETV6 variants exhibited hyperdiploid karyotype with characteristic recurrent mutations in NRAS, KRAS, and PTPN11. In contrast, the remaining 30% cases had a diploid leukemia genome and an exceedingly high frequency of somatic copy-number loss of PAX5 and ETV6, with a gene expression pattern that strikingly mirrored that of ALL with somatic ETV6-RUNX1 fusion. Two ETV6 germline variants gave rise to both acute myeloid leukemia and ALL, with lineage-specific genetic lesions in the leukemia genomes. ETV6 variants compromise its tumor suppressor activity in vitro with specific molecular targets identified by assay for transposase-accessible chromatin sequencing profiling. ETV6-mediated ALL predisposition exemplifies the intricate interactions between inherited and acquired genomic variations in leukemia pathogenesis.
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Affiliation(s)
| | | | | | - Ninad Oak
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xujie Zhao
- Department of Pharmaceutical Sciences and
| | | | | | - Mackenzie Bloom
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Katherine Verbist
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Melissa Burns
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Zhenhua Li
- Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | | | - Maoxiang Qian
- Department of Pharmaceutical Sciences and
- Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | | | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
- Department of Pathology and
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Karen R Rabin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Elizabeth Raetz
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Charles Mullighan
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Allen Eng-Juh Yeoh
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- VIVA-NUS Center for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Monika L Metzger
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Jeffery M Klco
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Stephen P Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | | | - Gang Wu
- Department of Computational Biology and
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA; and
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences and
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
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8
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Hosein Pour Feizi A, Zeinali S, Toporski J, Sheervalilou R, Mehranfar S. Frequency and Correlation of Common Genes Copy Number Alterations in Childhood Acute Lymphoblastic Leukemia with Prognosis. Asian Pac J Cancer Prev 2020; 21:3493-3500. [PMID: 33369444 PMCID: PMC8046302 DOI: 10.31557/apjcp.2020.21.12.3493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Indexed: 11/25/2022] Open
Abstract
Objective: It was shown by genomic profiling that despite no detectable chromosomal abnormalities a proportion of children with pre-B acute lymphoblastic leukemia harbors copy number alterations (CNA) of genes playing role in B-cell development and function. The aim of the study was to determine the frequency of CNA in pediatric acute lymphoblastic leukemia and correlate these findings with clinical outcome. Methods: DNA extracted from peripheral blood or bone marrow at diagnosis/relapse of fifty newly diagnosed children with precursor B-cell acute lymphoblastic leukemia was analyzed for CNA with multiplex ligation-dependent probe amplification. Results: The analysis revealed 76 CNA in 24 patients most frequently found in PAR1 (17%), CDKN2A/B (15.7%) and PAX5 (14.4%) genes. There were significant CNA co-occurrences between PAX5, CDKN2A/B, BTG1, ETV6, PAR1 or XP22 genes, (p<0.020) and the high-risk group. There was a significant correlation between EBF1, RB1, and IKZF1 alterations and bone marrow relapse. Patients with CNA in screened genes are more likely to succumb to their disease except for those with PAR1 or XP22 genes (p<0.050). Conclusion: The multiplex ligation-dependent probe amplification could be considered as an independent diagnostic tool allowing prompt identification of patients at high risk of treatment failure and, subsequently, a more adequate treatment approach.
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Affiliation(s)
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Kawsar Human Genetics Research Center, Kawsar Genomics Center, Tehran, Iran
| | - Jacek Toporski
- Department of Clinical Sciences, Pediatric Oncology and Hematology, University of Lund, Lund, Sweden
| | | | - Sahar Mehranfar
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.,Social Determinate of Health Research Center, Clinical Research Institute Urmia University of Medical Science, Urmia, Iran
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9
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Komorowski L, Fidyt K, Patkowska E, Firczuk M. Philadelphia Chromosome-Positive Leukemia in the Lymphoid Lineage-Similarities and Differences with the Myeloid Lineage and Specific Vulnerabilities. Int J Mol Sci 2020; 21:E5776. [PMID: 32806528 PMCID: PMC7460962 DOI: 10.3390/ijms21165776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Philadelphia chromosome (Ph) results from a translocation between the breakpoint cluster region (BCR) gene on chromosome 9 and ABL proto-oncogene 1 (ABL1) gene on chromosome 22. The fusion gene, BCR-ABL1, is a constitutively active tyrosine kinase which promotes development of leukemia. Depending on the breakpoint site within the BCR gene, different isoforms of BCR-ABL1 exist, with p210 and p190 being the most prevalent. P210 isoform is the hallmark of chronic myeloid leukemia (CML), while p190 isoform is expressed in majority of Ph-positive B cell acute lymphoblastic leukemia (Ph+ B-ALL) cases. The crucial component of treatment protocols of CML and Ph+ B-ALL patients are tyrosine kinase inhibitors (TKIs), drugs which target both BCR-ABL1 isoforms. While TKIs therapy is successful in great majority of CML patients, Ph+ B-ALL often relapses as a drug-resistant disease. Recently, the high-throughput genomic and proteomic analyses revealed significant differences between CML and Ph+ B-ALL. In this review we summarize recent discoveries related to differential signaling pathways mediated by different BCR-ABL1 isoforms, lineage-specific genetic lesions, and metabolic reprogramming. In particular, we emphasize the features distinguishing Ph+ B-ALL from CML and focus on potential therapeutic approaches exploiting those characteristics, which could improve the treatment of Ph+ B-ALL.
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Affiliation(s)
- Lukasz Komorowski
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Trojdena 2a St, 02-091 Warsaw, Poland
| | - Elżbieta Patkowska
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Indiry Gandhi 14, 02-776 Warsaw, Poland;
| | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 St, 02-097 Warsaw, Poland; (L.K.); (K.F.)
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10
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Lejman M, Włodarczyk M, Zawitkowska J, Kowalczyk JR. Comprehensive chromosomal aberrations in a case of a patient with TCF3-HLF-positive BCP-ALL. BMC Med Genomics 2020; 13:58. [PMID: 32245383 PMCID: PMC7118981 DOI: 10.1186/s12920-020-0709-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/24/2020] [Indexed: 12/16/2022] Open
Abstract
Background The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. The TCF3-HLF fusion gene product acts as a transcriptional factor leading to the dedifferentiation of mature B lymphocytes into an immature state (lymphoid stem cells). This process initiates the formation of pre-leukaemic cells. Due to the rarity of this chromosomal aberration, only a few cases have been described in the literature. The advantage of this work is the presentation of an interesting case of clonal evolution of cancer cells and the cumulative implications (diagnostic and prognostic) of the patient’s genetic alterations. Case presentation This work presents a patient with diagnosed with TCF3-HLF-positive ALL. Moreover, the additional genetic alterations, which play a key role in the pathogenesis of ALL, were detected in this patient: deletion of a fragment from the long arm of chromosome 13 (13q12.2-q21.1) containing the RB1 gene, intragenic deletions within the PAX5 gene and NOTCH1 intragenic duplication. Conclusions A patient with coexistence of chromosomal alterations and the TCF3-HLF fusion has not yet been described. Identifying all these chromosomal aberrations at the time of diagnosis could be sufficient to determine the cumulative effects of the described deletions on the activity of other oncogenes or tumour suppressors, as well as on the clinical course of the disease. On the other hand, complex changes in the patient’s karyotype and clonal evolution of cancer cells call into question the effectiveness of experimental therapy.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, ul. Antoniego Gębali 6, Lublin, Poland.
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology, and Transplantology, Medical University of Lublin, Lublin, Poland
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11
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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12
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Liang X, Gu J, Li T, Zhao L, Fu X, Zhang W, Wang J, Shang Z, Huang W, Zhou J. PAX5 haploinsufficiency induce cancer cell dormancy in Raji cells. Exp Cell Res 2018; 367:30-36. [PMID: 29453973 DOI: 10.1016/j.yexcr.2018.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 12/16/2022]
Abstract
PAX5 mutations have important role in leukemogenesis and leukemia relapse, cancer cell dormancy participates in cancer relapse, but there was no report about PAX5 mutation inducing cancer cell dormancy. we constructed the PAX5 deletion Raji cell lines using gene editing technology, evaluated dormancy biological characteristics of cell lines. Our results showed PAX5 haploinsufficiency restrained the proliferation of Raji cells, induced G0/G1 arrest of Raji cells, reduced chemotherapy sensitivity. The tumor formation rate reduced in PAX5 mutation Raji cells. Our results showed PAX5 insufficiency induced cancer cell dormancy in Raji cell.
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Affiliation(s)
- Xue Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jia Gu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - TongJuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Lei Zhao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Xing Fu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Wei Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jue Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Zhen Shang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China.
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
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13
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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: 3] [Impact Index Per Article: 0.4] [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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14
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Identification of Significant Pathways Induced by PAX5 Haploinsufficiency Based on Protein-Protein Interaction Networks and Cluster Analysis in Raji Cell Line. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5326370. [PMID: 28316978 PMCID: PMC5339483 DOI: 10.1155/2017/5326370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/02/2022]
Abstract
PAX5 encodes a transcription factor essential for B-cell differentiation, and PAX5 haploinsufficiency is involved in tumorigenesis. There were few studies on how PAX5 haploinsufficiency regulated genes expression to promote tumorigenesis. In this study, we constructed the cell model of PAX5 haploinsufficiency using gene editing technology in Raji cells, detected differentially expressed genes in PAX5 haploinsufficiency Raji cells, and used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in PAX5 haploinsufficiency. The clusters of gene transcription, inflammatory and immune response, and cancer pathways were identified as three important pathways associated with PAX5 haploinsufficiency in Raji cells. These changes hinted that the mechanism of PAX5 haploinsufficiency promoting tumorigenesis may be related to genomic instability, immune tolerance, and tumor pathways.
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15
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Braun M, Pastorczak A, Fendler W, Madzio J, Tomasik B, Taha J, Bielska M, Sedek L, Szczepanski T, Matysiak M, Derwich K, Lejman M, Kowalczyk J, Kazanowska B, Badowska W, Styczynski J, Irga-Jaworska N, Trelinska J, Zalewska-Szewczyk B, Pierlejewski F, Wlodarska I, Młynarski W. Biallelic loss of CDKN2A is associated with poor response to treatment in pediatric acute lymphoblastic leukemia. Leuk Lymphoma 2016; 58:1162-1171. [PMID: 27756164 DOI: 10.1080/10428194.2016.1228925] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The inactivation of tumor suppressor genes located within 9p21 locus (CDKN2A, CDKN2B) occurs in up to 30% of children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but its independent prognostic significance remains controversial. In order to investigate the prognostic impact of deletions and promoter methylation within 9p21, 641 children with newly diagnosed BCP-ALL using methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) were investigated. A total of 169 (26.4%) microdeletions in 9p21 were detected, of which 71 were homozygous. Patients with CDKN2A homozygous deletions were older at diagnosis (p < .001), more frequently steroid resistant (p = .049), had higher WBC count (p < .001), higher MRD at Day 15 (p = .013) and lower relapse-free survival [p = .028, hazard ratio: 2.28 (95% confidence interval: 1.09-4.76)] than patients without these alterations. CDKN2A homozygous deletions coexisted with IKZF1 and PAX5 deletions (p < .001). In conclusion, CDKN2A homozygous deletions, but not promoter methylation, are associated with poor response to treatment and increased relapse risk of pediatric BCP-ALL.
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Affiliation(s)
- Marcin Braun
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland.,b Department of Pathology , Medical University of Lodz , Lodz , Poland.,c Postgraduate School of Molecular Medicine , Medical University of Warsaw , Warsaw , Poland
| | - Agata Pastorczak
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Wojciech Fendler
- d Department of Biostatistics and Translational Medicine , Medical University of Lodz , Lodz , Poland
| | - Joanna Madzio
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland.,c Postgraduate School of Molecular Medicine , Medical University of Warsaw , Warsaw , Poland
| | - Bartlomiej Tomasik
- d Department of Biostatistics and Translational Medicine , Medical University of Lodz , Lodz , Poland
| | - Joanna Taha
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Marta Bielska
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Lukasz Sedek
- e Department of Pediatric Hematology and Oncology , Medical University of Silesia , Zabrze , Poland
| | - Tomasz Szczepanski
- e Department of Pediatric Hematology and Oncology , Medical University of Silesia , Zabrze , Poland
| | - Michal Matysiak
- f Department of Pediatric Hematology and Oncology , Medical University of Warsaw , Warsaw , Poland
| | - Katarzyna Derwich
- g Department of Pediatric Hematology , Oncology and Transplantology, University of Medical Sciences , Poznan , Poland
| | - Monika Lejman
- h Department of Pediatric Hematology and Oncology , Medical University of Lublin , Lublin , Poland
| | - Jerzy Kowalczyk
- h Department of Pediatric Hematology and Oncology , Medical University of Lublin , Lublin , Poland
| | - Bernarda Kazanowska
- i Department of Pediatric Hematology , Oncology and Transplantology, Medical University of Wroclaw , Wroclaw , Poland
| | - Wanda Badowska
- j Department of Pediatric Hematology and Oncology , Olsztyn , Poland
| | - Jan Styczynski
- k Department of Pediatric Hematology and Oncology, Collegium Medicum , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Nina Irga-Jaworska
- l Department of Pediatric Hematology , Gdansk Medical University , Gdansk , Poland
| | - Joanna Trelinska
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Beata Zalewska-Szewczyk
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Filip Pierlejewski
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | | | - Wojciech Młynarski
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
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16
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Zerrouki R, Benhassine T, Bensaada M, Lauzon P, Trabzi A. The complex translocation (9;14;14) involving IGH and CEBPE genes suggests a new subgroup in B-lineage acute lymphoblastic leukemia. Genet Mol Biol 2016; 39:7-13. [PMID: 27007892 PMCID: PMC4807378 DOI: 10.1590/s1415-475738420140368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 06/02/2015] [Indexed: 11/21/2022] Open
Abstract
Many subtypes of acute lymphoblastic leukemia (ALL) are associated with specific chromosomal rearrangements. The complex translocation t(9;14;14), a variant of the translocation (14;14)(q11;q32), is a rare but recurrent chromosomal abnormality involving the immunoglobulin heavy-chain (IGH) and CCAAT enhancer-binding protein (CEBPE) genes in B-lineage ALL (B-ALL) and may represent a new B-ALL subgroup. We report here the case of a 5-year-old girl with B-ALL, positive for CD19, CD38 and HLA-DR. A direct technique and G-banding were used for chromosomal analysis and fluorescentin situ hybridization (FISH) with BAC probes was used to investigate a possible rearrangement of the IGH andCEBPE genes. The karyotype exhibit the chromosomal aberration 46,XX,del(9)(p21),t(14;14)(q11;q32). FISH with dual-color break-apartIGH-specific and CEPBE-specific bacterial artificial chromosome (BAC) probes showed a complex t(9;14;14) associated with a deletion of cyclin-dependent kinase inhibitor 2A (CDKN2A) and paired box gene 5 (PAX5) at 9p21-13 and duplication of the fusion gene IGH-CEBPE.
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Affiliation(s)
- Rachid Zerrouki
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et Technologies Houari Boumediene, Alger, Algeria
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et Technologies Houari Boumediene, Alger, Algeria
| | - Mustapha Bensaada
- Laboratoire de Cytogénétique, Clinique de Chirurgie et des Sciences de la Reproduction, Constantine, Algeria
| | - Patricia Lauzon
- Animal Health Unit, University of Calgary, Calgary, Alberta, Canada
| | - Anissa Trabzi
- Hôpital Mustapha Bacha, Service d'Onco-Hématologie, Centre Pierre et Marie-Curie, Alger, Algeria
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17
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Peterson JF, Aggarwal N, Smith CA, Gollin SM, Surti U, Rajkovic A, Swerdlow SH, Yatsenko SA. Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing? Oncotarget 2015; 6:18845-62. [PMID: 26299921 PMCID: PMC4662459 DOI: 10.18632/oncotarget.4586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/21/2015] [Indexed: 12/14/2022] Open
Abstract
Purpose To evaluate the clinical utility, diagnostic yield and rationale of integrating microarray analysis in the clinical diagnosis of hematological malignancies in comparison with classical chromosome karyotyping/fluorescence in situ hybridization (FISH). Methods G-banded chromosome analysis, FISH and microarray studies using customized CGH and CGH+SNP designs were performed on 27 samples from patients with hematological malignancies. A comprehensive comparison of the results obtained by three methods was conducted to evaluate benefits and limitations of these techniques for clinical diagnosis. Results Overall, 89.7% of chromosomal abnormalities identified by karyotyping/FISH studies were also detectable by microarray. Among 183 acquired copy number alterations (CNAs) identified by microarray, 94 were additional findings revealed in 14 cases (52%), and at least 30% of CNAs were in genomic regions of diagnostic/prognostic significance. Approximately 30% of novel alterations detected by microarray were >20 Mb in size. Balanced abnormalities were not detected by microarray; however, of the 19 apparently “balanced” rearrangements, 55% (6/11) of recurrent and 13% (1/8) of non-recurrent translocations had alterations at the breakpoints discovered by microarray. Conclusion Microarray technology enables accurate, cost-effective and time-efficient whole-genome analysis at a resolution significantly higher than that of conventional karyotyping and FISH. Array-CGH showed advantage in identification of cryptic imbalances and detection of clonal aberrations in population of non-dividing cancer cells and samples with poor chromosome morphology. The integration of microarray analysis into the cytogenetic diagnosis of hematologic malignancies has the potential to improve patient management by providing clinicians with additional disease specific and potentially clinically actionable genomic alterations.
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Affiliation(s)
- Jess F Peterson
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nidhi Aggarwal
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Clayton A Smith
- Department of Medicine, Division of Hematology, University of Colorado, Denver, CO
| | - Susanne M Gollin
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Urvashi Surti
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aleksandar Rajkovic
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven H Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Svetlana A Yatsenko
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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18
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Othman MAK, Melo JB, Carreira IM, Rincic M, Glaser A, Grygalewicz B, Gruhn B, Wilhelm K, Rittscher K, Meyer B, Silva MLM, de Jesus Marques Salles T, Liehr T. High rates of submicroscopic aberrations in karyotypically normal acute lymphoblastic leukemia. Mol Cytogenet 2015; 8:45. [PMID: 26136832 PMCID: PMC4486437 DOI: 10.1186/s13039-015-0153-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/20/2015] [Indexed: 11/16/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is not a single uniform disease. It consists of several subgroups with different cytogenetic and molecular genetic aberrations, clinical presentations and outcomes. Banding cytogenetics plays a pivotal role in the detection of recurrent chromosomal rearrangements and is the starting point of genetic analysis in ALL, still. Nowadays, molecular (cyto)genetic tools provide substantially to identify previously non-detectable, so-called cryptic chromosomal aberrations in ALL. However, ALL according to banding cytogenetics with normal karyotype - in short cytogenetically normal ALL (CN-ALL) - represent up to ~50 % of all new diagnosed ALL cases. The overall goal of this study was to identify and characterize the rate of cryptic alterations in CN-ALL and to rule out if one single routine approach may be sufficient to detect most of the cryptic alterations present. Results Sixty-one ALL patients with CN-ALL were introduced in this study. All of them underwent high resolution fluorescence in situ hybridization (FISH) analysis. Also DNA could be extracted from 34 ALL samples. These DNA-samples were studied using a commercially available MLPA (multiplex ligation-dependent probe amplification) probe set directed against 37 loci in hematological malignancies and/or array-comparative genomic hybridization (aCGH). Chromosomal aberrations were detected in 21 of 61 samples (~34 %) applying FISH approaches: structural abnormalities were present in 15 cases and even numerical ones were identified in 6 cases. Applying molecular approaches copy number alterations (CNAs) were detected in 27/34 samples. Overall, 126 CNAs were identified and only 34 of them were detectable by MLPA (~27 %). Loss of CNs was identified in ~80 % while gain of CNs was present in ~20 % of the 126 CNAs. A maximum of 13 aberrations was detected per case; however, only one aberration per case was found in 8 of all in detail studied 34 cases. Of special interest among the detected CNAs are the following new findings: del(15)(q26.1q26.1) including CHD2 gene was found in 20 % of the studied ALL cases, dup(18)(q21.2q21.2) with the DCC gene was present in 9 % of the cases, and the CDK6 gene in 7q21.2 was deleted in 12 % of the here in detail studied ALL cases. Conclusions In conclusion, high resolution molecular cytogenetic tools and molecular approaches like MLPA and aCGH need to be combined in a cost-efficient way, to identify disease and progression causing alterations in ALL, as majority of them are cryptic in banding cytogenetic analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0153-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO, Centro de Investigação em Meio Ambiente, Genéticae Oncobiologia, Coimbra, Portugal
| | - Isabel M Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO, Centro de Investigação em Meio Ambiente, Genéticae Oncobiologia, Coimbra, Portugal
| | - Martina Rincic
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany ; Croatian Institute of Brain Research, Zagreb, Croatia
| | - Anita Glaser
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Beata Grygalewicz
- Cytogenetic Laboratory, Maria Sklodowska-Curie Memorial Cancer Centre and Institute, Warsaw, Poland
| | - Bernd Gruhn
- Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Kathleen Wilhelm
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany ; Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Katharina Rittscher
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | | | - Maria Luiza Macedo Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, National Cancer Institute, Rio de Janeiro, RJ Brazil ; Post Graduation Program in Oncology, National Cancer Institute (INCA), Rio de Janeiro, RJ Brazil
| | - Terezinha de Jesus Marques Salles
- Pediatric Oncohematology Center, Hospital Oswaldo Cruz/ Pos Graduation Course of the Faculty of Medical Sciences, University of Pernambuco, Recife, PE Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
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19
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Barbosa TC, Terra-Granado E, Quezado Magalhães IM, Neves GR, Gadelha A, Guedes Filho GE, Souza MS, Melaragno R, Emerenciano M, Pombo-de-Oliveira MS. Frequency of copy number abnormalities in common genes associated with B-cell precursor acute lymphoblastic leukemia cytogenetic subtypes in Brazilian children. Cancer Genet 2015; 208:492-501. [PMID: 26277549 DOI: 10.1016/j.cancergen.2015.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/08/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
Abstract
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of patients with B-cell precursor acute lymphoblastic leukemia (BCP-ALL). We investigated submicroscopic alterations in a series of 274 Brazilian children with BCP-ALL by multiplex ligation-dependent probe amplification and evaluated their correlation with clinical and laboratory features. The relevance of overlapping CNA abnormalities was also explored. Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than 2 years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A, and CDKN2B, whereas the pseudoautosomal region 1 (PAR1) had deletions that were found more frequently in infants (P <0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups showed more deletions than other subgroups that occurred simultaneously, specifically ETV6 deletions (P <0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. The results corroborate with previous genome-wide studies and aggregate new markers for risk stratification of BCP-ALL in Brazil.
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Affiliation(s)
- Thayana Conceição Barbosa
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Eugenia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
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20
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The role of Pax5 in leukemia: diagnosis and prognosis significance. Med Oncol 2014; 32:360. [PMID: 25428382 DOI: 10.1007/s12032-014-0360-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/12/2014] [Indexed: 12/12/2022]
Abstract
Pax5 transcription factor, also known as B-cell specific activator protein (BSAP), plays a dual role in the hematopoietic system. Pax5 expression is essential in B-cell precursors for normal differentiation and maturation of B-cells. On the other hand, it inhibits the differentiation and progress toward other lineages. The expression of this factor is involved in several aspects of B-cell differentiation, including commitment, immunoglobulin gene rearrangement, BCR signal transduction and B-cell survival, so that the deletion or inactivating mutations of Pax5 cause cell arrest in Pro-B-cell stage. In recent years, point mutations, deletions and various rearrangements in Pax5 gene have been reported in several types of human cancers. However, no clear relationship has been found between these aberrations and disease prognosis. Specific expression of Pax5 in B-cells can raise it as a marker for the diagnosis and differentiation of B-cell leukemias and lymphomas as well as account for remission or relapse. Extensive studies on Pax5 along with other genes and immunomarkers are necessary for decisive results in this regard.
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21
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Koh KN, Lee JO, Seo EJ, Lee SW, Suh JK, Im HJ, Seo JJ. Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses. J Korean Med Sci 2014; 29:926-33. [PMID: 25045224 PMCID: PMC4101780 DOI: 10.3346/jkms.2014.29.7.926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/16/2014] [Indexed: 11/20/2022] Open
Abstract
The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.
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Affiliation(s)
- Kyung-Nam Koh
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Ok Lee
- Genome Research Center, Asan Medical Center, Seoul, Korea
| | - Eul Ju Seo
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seong Wook Lee
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Kyung Suh
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho Joon Im
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jong Jin Seo
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
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22
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Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics. ACTA ACUST UNITED AC 2013; 21:189-206. [PMID: 23111197 DOI: 10.1097/pdm.0b013e3182595516] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The increasing knowledge about genetic alterations and molecular biomarkers in cancer initiation and progression opens new possibilities for the treatment of various types of cancer. This requires the inclusion of sensitive, and preferably multiplex, methods for the detection of molecular genetic alterations in the toolbox of classic pathology. Multiplex ligation-dependent probe amplification (MLPA) is a multiplex polymerase chain reaction-based method that can detect changes in the gene copy number status, DNA methylation, and point mutations simultaneously. MLPA probes recognize target sequences of only 50 to 100 nucleotides in length. This makes it possible to use MLPA even on highly fragmented DNA, and allows the detection of small deletions encompassing only a single exon. MLPA is a reliable, cost-effective, and robust method that can be performed using a standard thermocycler and capillary electrophoresis equipment, generating results within 24 hours with a short hands-on working time. Up to 50 different genomic locations can be tested in a single reaction, which can be sufficient to detect those genetic alterations that are of diagnostic and prognostic significance in a certain tumor entity. In the last years, MLPA has been used successfully in tumor diagnostics and in cancer research. This review gives an overview on the collected experience of MLPA applications on tumor DNA, about the advantages but also potential pitfalls and limitations of this technique.
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23
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Shang Z, Zhao Y, Zhou K, Xu Y, Huang W. PAX5 alteration-associated gene-expression signatures in B-cell acute lymphoblastic leukemia. Int J Hematol 2013; 97:599-603. [PMID: 23529845 DOI: 10.1007/s12185-013-1309-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/18/2013] [Accepted: 03/08/2013] [Indexed: 11/26/2022]
Abstract
The paired box domain gene 5 (PAX5) is frequently altered in both childhood and adult B-cell acute lymphoblastic leukemia, and takes part in leukemogenesis. We analyzed data from the database of Gene Expression Omnibus (accession number: GSE11877) using bioinformatical and statistical methods. The results showed that cases of PAX5 alteration can cluster using unsupervised clustering algorithms, and one gene, zinc and ring finger 1 (ZNRF1), was characterized and validated by quantitative RT-PCR. ZNRF1 may be associated with leukemogenesis of ALL with PAX5 alteration.
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Affiliation(s)
- Zhen Shang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Da Dao, Wuhan 430030, People's Republic of China
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24
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Tijchon E, Havinga J, van Leeuwen FN, Scheijen B. B-lineage transcription factors and cooperating gene lesions required for leukemia development. Leukemia 2012; 27:541-52. [PMID: 23047478 DOI: 10.1038/leu.2012.293] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Differentiation of hematopoietic stem cells into B lymphocytes requires the concerted action of specific transcription factors, such as RUNX1, IKZF1, E2A, EBF1 and PAX5. As key determinants of normal B-cell development, B-lineage transcription factors are frequently deregulated in hematological malignancies, such as B-cell precursor acute lymphoblastic leukemia (BCP-ALL), and affected by either chromosomal translocations, gene deletions or point mutations. However, genetic aberrations in this developmental pathway are generally insufficient to induce BCP-ALL, and often complemented by genetic defects in cytokine receptors and tyrosine kinases (IL-7Rα, CRLF2, JAK2 and c-ABL1), transcriptional cofactors (TBL1XR1, CBP and BTG1), as well as the regulatory pathways that mediate cell-cycle control (pRB and INK4A/B). Here we provide a detailed overview of the genetic pathways that interact with these B-lineage specification factors, and describe how mutations affecting these master regulators together with cooperating lesions drive leukemia development.
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Affiliation(s)
- E Tijchon
- Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
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25
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Krentz S, Hof J, Mendioroz A, Vaggopoulou R, Dörge P, Lottaz C, Engelmann JC, Groeneveld TWL, Körner G, Seeger K, Hagemeier C, Henze G, Eckert C, von Stackelberg A, Kirschner-Schwabe R. Prognostic value of genetic alterations in children with first bone marrow relapse of childhood B-cell precursor acute lymphoblastic leukemia. Leukemia 2012; 27:295-304. [DOI: 10.1038/leu.2012.155] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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