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Lin D, Yang K, Yu L, Huang L, Lai X, Wu L, Xia X, Zhang J, Zheng Q, Yang L. Poor outcome of pediatric B-cell acute lymphoblastic leukemia associated with high level of CRLF2 gene expression in distinct molecular subtypes. Front Oncol 2023; 13:1256054. [PMID: 38023153 PMCID: PMC10661883 DOI: 10.3389/fonc.2023.1256054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Overexpression of the cytokine receptor-like factor 2 (CRLF2) gene is the most common feature in the Philadelphia chromosome (Ph)-like subtype of B-cell acute lymphoblastic leukemia (B-ALL). However, the predictive value of CRLF2 overexpression for the prognosis of pediatric B-ALL patients remain controversial. The molecular mechanisms that upregulate CRLF2 expression level in patients has not been fully elucidated. Methods In this study, the prognostic impact of CRLF2 expression level on molecular types of B-ALL in pediatric patients from Zhujiang Hospital (n = 111) was retrospectively analyzed. Youden index analysis was used to categorize CRLF2 expression into 3 groups, and these categories more precisely described the differences in the prognosis of patients with varying expression levels of CRLF2 in both the Zhujiang Hospital cohort and the TARGET cohort. Results We used the Zhujiang Hospital cohort as a discovery cohort to determine the cutoff value of CRLF2 expression. CRLF2-high patients accounted for approximately 6%. In addition, the percentage of bone marrow blast cells and initial white blood cell count in CRLF2-high patients were higher than those in CRLF2-low patients, and MRD turned negative slower. The results were validated in the TARGET cohort and indicated that CRLF2 overexpression could be subdivided by CRLF2 expression levels into 2 categories: CRLF2-high with a poor survival and CRLF2-medium with a good OS and EFS. Such heterogeneity was attributed to the different molecular mechanisms leading to CLRF2 upregulation, where the CRLF2 overexpression level was high in Ph-like B-ALL and medium in high hyperdiploid B-ALL. Conclusion This study highlights the importance of the molecular mechanisms of the upregulation of CRLF2 expression in predicting the prognosis of pediatric B-ALL patients.
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Affiliation(s)
- Danna Lin
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Keyan Yang
- Laboratory of Molecular Diagnostics, Beijing GoBroad Boren Hospital, Beijing, China
| | - Lihua Yu
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lulu Huang
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaorong Lai
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Li Wu
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiayu Xia
- Laboratory of Molecular Diagnostics, Beijing GoBroad Boren Hospital, Beijing, China
| | - Jingwen Zhang
- Department of Clinical Hematology&Flow Cytometry, Guangzhou KingMed Center for Clinical Lab. Co., Ltd., Guangzhou, China
| | - Qinlong Zheng
- Laboratory of Molecular Diagnostics, Beijing GoBroad Boren Hospital, Beijing, China
| | - Lihua Yang
- Department of Pediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Alghandour R, Sakr DH, Shaaban Y. Philadelphia-like acute lymphoblastic leukemia: the journey from molecular background to the role of bone marrow transplant-review article. Ann Hematol 2023; 102:1287-1300. [PMID: 37129698 PMCID: PMC10181978 DOI: 10.1007/s00277-023-05241-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
Philadelphia chromosome-like (Ph-like) ALL is a recent subtype of acute lymphoblastic leukemia. Although it does not express the BCR-ABL fusion gene, it has a behavior like true BCR/ABL1-positive cases. This subtype harbors different molecular alterations most commonly CRLF2 rearrangements. Most cases of Ph-like ALL are associated with high white blood cell count, high minimal residual disease level after induction therapy, and high relapse rate. Efforts should be encouraged for early recognition of Ph-like ALL to enhance therapeutic strategies. Recently, many trials are investigating the possibility of adding the tyrosine kinase inhibitor (TKI) to chemotherapy to improve clinical outcomes. The role and best timing of allogeneic bone marrow transplant in those cases are still unclear. Precision medicine should be implemented in the treatment of such cases. Here in this review, we summarize the available data on Ph-like ALL.
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Affiliation(s)
- Reham Alghandour
- Medical oncology Unit, Oncology Center Mansoura University, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Doaa H Sakr
- Medical oncology Unit, Oncology Center Mansoura University, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Yasmin Shaaban
- Clinical Hematology Unit, Oncology Center Mansoura University, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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3
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Bogush D, Schramm J, Ding Y, He B, Singh C, Sharma A, Tukaramrao DB, Iyer S, Desai D, Nalesnik G, Hengst J, Bhalodia R, Gowda C, Dovat S. Signaling pathways and regulation of gene expression in hematopoietic cells. Adv Biol Regul 2023; 88:100942. [PMID: 36621151 DOI: 10.1016/j.jbior.2022.100942] [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: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Cellular functions are regulated by signal transduction pathway networks consisting of protein-modifying enzymes that control the activity of many downstream proteins. Protein kinases and phosphatases regulate gene expression by reversible phosphorylation of transcriptional factors, which are their direct substrates. Casein kinase II (CK2) is a serine/threonine kinase that phosphorylates a large number of proteins that have critical roles in cellular proliferation, metabolism and survival. Altered function of CK2 has been associated with malignant transformation, immunological disorders and other types of diseases. Protein phosphatase 1 (PP1) is a serine/threonine phosphatase, which regulates the phosphorylation status of many proteins that are essential for cellular functions. IKAROS is a DNA-binding protein, which functions as a regulator of gene transcription in hematopoietic cells. CK2 directly phosphorylates IKAROS at multiple phosphosites which determines IKAROS activity as a regulator of gene expression. PP1 binds to IKAROS via the PP1-consensus recognition site and dephosphorylates serine/threonine residues that are phosphorylated by CK2. Thus, the interplay between CK2 and PP1 signaling pathways have opposing effects on the phosphorylation status of their mutual substrate - IKAROS. This review summarizes the effects of CK2 and PP1 on IKAROS role in regulation of gene expression and its function as a tumor suppressor in leukemia.
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Affiliation(s)
- Daniel Bogush
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Joseph Schramm
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Yali Ding
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Bing He
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chingakham Singh
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Arati Sharma
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | | | - Soumya Iyer
- University of Chicago, Chicago, IL, 60637, USA
| | - Dhimant Desai
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Gregory Nalesnik
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Jeremy Hengst
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Riya Bhalodia
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chandrika Gowda
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
| | - Sinisa Dovat
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
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Conserva MR, Redavid I, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Parciante E, Coccaro N, Minervini CF, Minervini A, Specchia G, Musto P, Albano F. IKAROS in Acute Leukemia: A Positive Influencer or a Mean Hater? Int J Mol Sci 2023; 24:ijms24043282. [PMID: 36834692 PMCID: PMC9961161 DOI: 10.3390/ijms24043282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
One key process that controls leukemogenesis is the regulation of oncogenic gene expression by transcription factors acting as tumor suppressors. Understanding this intricate mechanism is crucial to elucidating leukemia pathophysiology and discovering new targeted treatments. In this review, we make a brief overview of the physiological role of IKAROS and the molecular pathway that contributes to acute leukemia pathogenesis through IKZF1 gene lesions. IKAROS is a zinc finger transcription factor of the Krüppel family that acts as the main character during hematopoiesis and leukemogenesis. It can activate or repress tumor suppressors or oncogenes, regulating the survival and proliferation of leukemic cells. More than 70% of Ph+ and Ph-like cases of acute lymphoblastic leukemia exhibit IKZF1 gene variants, which are linked to worse treatment outcomes in both childhood and adult B-cell precursor acute lymphoblastic leukemia. In the last few years, much evidence supporting IKAROS involvement in myeloid differentiation has been reported, suggesting that loss of IKZF1 might also be a determinant of oncogenesis in acute myeloid leukemia. Considering the complicated "social" network that IKAROS manages in hematopoietic cells, we aim to focus on its involvement and the numerous alterations of molecular pathways it can support in acute leukemias.
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Affiliation(s)
- Maria Rosa Conserva
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Luisa Anelli
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Elisa Parciante
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Angela Minervini
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
| | - Francesco Albano
- Hematology Section, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
- Correspondence:
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5
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High occurrence of CRLF2 abnormalities in Mexican children with B-cell acute lymphoblastic leukemia. Cytokine 2022; 155:155896. [DOI: 10.1016/j.cyto.2022.155896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/31/2022]
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6
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Maciel ALT, Wolch K, Emerenciano M, Mansur MB. CRLF2 overexpression defines an immature-like subgroup which is rescued through restoration of the PRC2 function in T-cell precursor acute lymphoblastic leukaemia. Genes Chromosomes Cancer 2022; 61:437-442. [PMID: 35253299 DOI: 10.1002/gcc.23036] [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: 10/20/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/09/2022] Open
Abstract
CRLF2 overexpression has been described as a biomarker of poor prognosis in T-cell acute lymphoblastic leukaemia (T-ALL). In the present study, we aimed to unravel the genomic profile underlying CRLF2 overexpression (CRLF2-high) by analysing RNA-seq, WES and SNP-array data from 264 T-ALL patients and five cell lines deposited on the TARGET initiative, Cancer Cell Line Encyclopedia and Gene Expression Omnibus. These data allowed us to delineate the genomic landscape of CRLF2-high in T-ALL, which was associated with PTEN, JAK3, PHF6, EZH2 and RUNX1 mutations. We also observed an enrichment of CRLF2-high in early T-precursor (ETP)-ALL (23.08% vs 4.02%, P = 7.579e-06 ) and a very similar gene upregulation profile between these two entities. The inhibition of BET (iBET) proteins is a strategy previously demonstrated to reverse the gene upregulation pattern of ETP cells through restoration of polycomb repressive complex 2 (PRC2) activity. While CRLF2 expression was rescued by using this strategy in LOUCY (untreated vs iBET P = 0.0095, DMSO vs iBET P = 0.0286), a classical ETP-ALL cell line, PRC2 loss was not sufficient to promote CRLF2 upregulation in JURKAT, a more mature T-ALL cell line. Considering the role of IKZF1 in CRLF2 regulation and in recruitment of PCR2, we evaluated IKZF1 status according to CRLF2-expression subgroups. We identified that IKZF1 transcripts with intron retention were upregulated in the CRLF2-high subgroup. Here, we delineated the gene expression profile of CRLF2-high T-ALL samples and unravelled the crucial role of PRC2 in CRLF2 regulation in ETP-ALL.
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Affiliation(s)
- Ana L T Maciel
- Acute Leukaemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, RJ, Brazil
| | - Karolyne Wolch
- Acute Leukaemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, RJ, Brazil
| | - Mariana Emerenciano
- Acute Leukaemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, RJ, Brazil
| | - Marcela B Mansur
- Acute Leukaemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, RJ, Brazil.,Department of Paediatrics, Children's Hospital, John Radcliffe Hospital and MRC Weatherall Institute of Molecular Medicine - WIMM, University of Oxford, Oxford, UK
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7
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Lejman M, Chałupnik A, Chilimoniuk Z, Dobosz M. Genetic Biomarkers and Their Clinical Implications in B-Cell Acute Lymphoblastic Leukemia in Children. Int J Mol Sci 2022; 23:ijms23052755. [PMID: 35269896 PMCID: PMC8911213 DOI: 10.3390/ijms23052755] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a heterogeneous group of hematologic malignancies characterized by abnormal proliferation of immature lymphoid cells. It is the most commonly diagnosed childhood cancer with an almost 80% cure rate. Despite favorable survival rates in the pediatric population, a significant number of patients develop resistance to therapy, resulting in poor prognosis. ALL is a heterogeneous disease at the genetic level, but the intensive development of sequencing in the last decade has made it possible to broaden the study of genomic changes. New technologies allow us to detect molecular changes such as point mutations or to characterize epigenetic or proteomic profiles. This process made it possible to identify new subtypes of this disease characterized by constellations of genetic alterations, including chromosome changes, sequence mutations, and DNA copy number alterations. These genetic abnormalities are used as diagnostic, prognostic and predictive biomarkers that play an important role in earlier disease detection, more accurate risk stratification, and treatment. Identification of new ALL biomarkers, and thus a greater understanding of their molecular basis, will lead to better monitoring of the course of the disease. In this article, we provide an overview of the latest information on genomic alterations found in childhood ALL and discuss their impact on patients' clinical outcomes.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
| | - Aleksandra Chałupnik
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Zuzanna Chilimoniuk
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Maciej Dobosz
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
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8
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Xia R, Cheng Y, Han X, Wei Y, Wei X. Ikaros Proteins in Tumor: Current Perspectives and New Developments. Front Mol Biosci 2021; 8:788440. [PMID: 34950704 PMCID: PMC8689071 DOI: 10.3389/fmolb.2021.788440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023] Open
Abstract
Ikaros is a zinc finger transcription factor (TF) of the Krüppel family member, which significantly regulates normal lymphopoiesis and tumorigenesis. Ikaros can directly initiate or suppress tumor suppressors or oncogenes, consequently regulating the survival and proliferation of cancer cells. Over recent decades, a series of studies have been devoted to exploring and clarifying the relationship between Ikaros and associated tumors. Therapeutic strategies targeting Ikaros have shown promising therapeutic effects in both pre-clinical and clinical trials. Nevertheless, the increasingly prominent problem of drug resistance targeted to Ikaros and its analog is gradually appearing in our field of vision. This article reviews the role of Ikaros in tumorigenesis, the mechanism of drug resistance, the progress of targeting Ikaros in both pre-clinical and clinical trials, and the potential use of associated therapy in cancer therapy.
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Affiliation(s)
- Ruolan Xia
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuejiao Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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9
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Maciel ALT, Barbosa TDC, Blunck CB, Wolch K, Machado ADAL, da Costa ES, Bergier LL, Schramm MT, Ikoma-Coltutato MRV, Lins MM, Aguiar TF, Mansur MB, Emerenciano M. IKZF1 deletions associate with CRLF2 overexpression leading to a poor prognosis in B-cell precursor acute lymphoblastic leukaemia. Transl Oncol 2021; 15:101291. [PMID: 34826720 PMCID: PMC8633010 DOI: 10.1016/j.tranon.2021.101291] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 11/20/2022] Open
Abstract
CRLF2 overexpression associates with IKZF1 deletions that lead to a dominant-negative effect and with IKZF1 plus. Paediatric patients with a high load expression of IK4 isoform presented higher CRLF2 transcript levels. CRLF2 overexpression and IKZF1 deletions conferred poorer prognosis both to paediatric patients treated with RELLA05 protocol as well as to adult patients.
Cytokine Receptor-Like Factor 2 (CRLF2) overexpression occurs in 5-15% of B-cell precursor acute lymphoblastic leukaemia (B-ALL). In ∼50% of these cases, the mechanisms underlying this dysregulation are unknown. IKAROS Family Zinc Finger 1 (IKZF1) is a possible candidate to play a role in this dysregulation since it binds to the CRLF2 promoter region and suppresses its expression. We hypothesised that IKZF1 loss of function, caused by deletions or its short isoforms expression, could be associated with CRLF2 overexpression in B-ALL. A total of 131 paediatric and adult patients and 7 B-ALL cell lines were analysed to investigate the presence of IKZF1 deletions and its splicing isoforms expression levels, the presence of CRLF2 rearrangements or mutations, CRLF2 expression and JAK2 mutations. Overall survival analyses were performed according to the CRLF2 and IKZF1 subgroups. Our analyses showed that 25.2% of patients exhibited CRLF2 overexpression (CRLF2-high). CRLF2-high was associated with the presence of IKZF1 deletions (IKZF1del, p = 0.001), particularly with those resulting in dominant-negative isoforms (p = 0.006). Moreover, CRLF2 expression was higher in paediatric samples with high loads of the short isoform IK4 (p = 0.011). It was also associated with the occurrence of the IKZF1 plus subgroup (p = 0.004). Furthermore, patients with CRLF2-high/IKZF1del had a poorer prognosis in the RELLA05 protocol (p = 0.067, 36.1 months, 95%CI 0.0-85.9) and adult cohort (p = 0.094, 29.7 months, 95%CI 11.8–47.5). In this study, we show that IKZF1 status is associated with CRLF2-high and dismal outcomes in B-ALL patients regardless of age.
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Affiliation(s)
- Ana Luiza Tardem Maciel
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil
| | - Thayana da Conceição Barbosa
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil
| | - Caroline Barbieri Blunck
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil
| | - Karolyne Wolch
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil
| | - Amanda de Albuquerque Lopes Machado
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil
| | - Elaine Sobral da Costa
- Department of Paediatrics, Instituto de Puericultura e Pediatria Martagão Gesteira, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Márcia Trindade Schramm
- Onco-Haematology Section, Prontobaby Hospital da Criança Ltda, Rio de Janeiro, Brazil; Haematology Unit, Hospital do Câncer I, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Brazil
| | | | - Mecneide Mendes Lins
- Paediatric Oncology Unit, Instituto de Medicina Integral Prof Fernando Figueira, Recife, PE, Brazil
| | - Thais Ferraz Aguiar
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil; Onco-Haematology Section, Instituto Estadual de Hematologia Arthur Siqueira Cavalcanti, Rio de Janeiro, Brazil
| | - Marcela Braga Mansur
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil; Department of Paediatrics, Children's Hospital, John Radcliffe Hospital and MRC Weatherall Institute of Molecular Medicine - WIMM, University of Oxford, Oxford, UK.
| | - Mariana Emerenciano
- Acute Leukemia RioSearch Group, Division of Clinical Research and Technological Development, Research Centre, Instituto Nacional de Câncer - INCA, Rua André Cavalcanti, 37, Rio de Janeiro, RJ, 20231050, Brazil.
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Lymphoid blast transformation in an MPN with BCR-JAK2 treated with ruxolitinib: putative mechanisms of resistance. Blood Adv 2021; 5:3492-3496. [PMID: 34505882 DOI: 10.1182/bloodadvances.2020004174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
The basis for acquired resistance to JAK inhibition in patients with JAK2-driven hematologic malignancies is not well understood. We report a patient with a myeloproliferative neoplasm (MPN) with a BCR activator of RhoGEF and GTPase (BCR)-JAK2 fusion with initial hematologic response to ruxolitinib who rapidly developed B-lymphoid blast transformation. We analyzed pre-ruxolitinib and blast transformation samples using genome sequencing, DNA mate-pair sequencing (MPseq), RNA sequencing (RNA-seq), and chromosomal microarray to characterize possible mechanisms of resistance. No resistance mutations in the BCR-JAK2 fusion gene or transcript were identified, and fusion transcript expression levels remained stable. However, at the time of blast transformation, MPseq detected a new IKZF1 copy-number loss, which is predicted to result in loss of normal IKZF1 protein translation. RNA-seq revealed significant upregulation of genes negatively regulated by IKZF1, including IL7R and CRLF2. Disease progression was also characterized by adaptation to an activated B-cell receptor (BCR)-like signaling phenotype, with marked upregulation of genes such as CD79A, CD79B, IGLL1, VPREB1, BLNK, ZAP70, RAG1, and RAG2. In summary, IKZF1 deletion and a switch from cytokine dependence to activated BCR-like signaling phenotype represent putative mechanisms of ruxolitinib resistance in this case, recapitulating preclinical data on resistance to JAK inhibition in CRLF2-rearranged Philadelphia chromosome-like acute lymphoblastic leukemia.
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11
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Yeung C, Qu X, Sala-Torra O, Woolston D, Radich J, Fang M. Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing. Cancer Med 2021; 10:5629-5642. [PMID: 34288525 PMCID: PMC8366081 DOI: 10.1002/cam4.4101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/03/2022] Open
Abstract
Background Comprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B‐acute lymphoblastic leukemia (B‐ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next‐generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B‐ALL. Methods We performed RNA NGS and CGAT on 28 B‐ALL samples and, in four patients, compared fixed cell pellets to paired cryo‐preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis. Results Among the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT‐qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well‐known drug resistance implications. Conclusions We conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.
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Affiliation(s)
- Cecilia Yeung
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Xiaoyu Qu
- Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Olga Sala-Torra
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - David Woolston
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Jerry Radich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
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12
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Moreno Lorenzana D, Juárez Velázquez MDR, Reyes León A, Martínez Anaya D, Hernández Monterde A, Salas Labadía C, Navarrete Meneses MDP, Zapata Tarrés M, Juárez Villegas L, Jarquín Ramírez B, Cárdenas Cardós R, Herrera Almanza M, Paredes Aguilera R, Pérez Vera P. CRLF2 and IKZF1 abnormalities in Mexican children with acute lymphoblastic leukemia and recurrent gene fusions: exploring surrogate markers of signaling pathways. J Pathol Clin Res 2021; 7:410-421. [PMID: 33890726 PMCID: PMC8185361 DOI: 10.1002/cjp2.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 11/29/2022]
Abstract
The gene fusions BCR-ABL1, TCF3-PBX1, and ETV6-RUNX1 are recurrent in B-cell acute lymphoblastic leukemia (B-ALL) and are found with low frequency in coexistence with CRLF2 (cytokine receptor-like factor 2) rearrangements and overexpression. There is limited information regarding the CRLF2 abnormalities and dominant-negative IKZF1 isoforms associated with surrogate markers of Jak2, ABL, and Ras signaling pathways. To assess this, we evaluated 24 Mexican children with B-ALL positive for recurrent gene fusions at diagnosis. We found CRLF2 rearrangements and/or overexpression, dominant-negative IKZF1 isoforms, and surrogate phosphorylated markers of signaling pathways coexisting with recurrent gene fusions. All the BCR-ABL1 patients expressed CRLF2 and were positive for pCrkl (ABL); most of them were also positive for pStat5 (Jak2/Stat5) and negative for pErk (Ras). TCF3-PBX1 patients with CRLF2 abnormalities were positive for pStat5, most of them were also positive for pCrkl, and two patients were also positive for pErk. One patient with ETV6-RUNX1 and intracellular CRLF2 protein expressed pCrkl. In some cases, the activated signaling pathways were reverted in vitro by specific inhibitors. We further analyzed a TCF3-PBX1 patient at relapse, identifying a clone with the recurrent gene fusion, P2RY8-CRLF2, rearrangement, and phosphorylation of the three surrogate markers that we studied. These results agree with the previous reports regarding resistance to treatment observed in patients with recurrent gene fusions and coexisting CRLF2 gene abnormalities. A marker phosphorylation signature was identified in BCR-ABL1 and TCF3-PBX1 patients. To obtain useful information for the assessment of treatment in B-ALL patients with recurrent gene fusions, we suggest that they should be evaluated at diagnosis for CRLF2 gene abnormalities and dominant-negative IKZF1 isoforms, in addition to the analyses of activation and inhibition of signaling pathways.
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Affiliation(s)
- Dafné Moreno Lorenzana
- Laboratorio de Genética y CáncerInstituto Nacional de PediatríaMexico CityMexico
- Cátedra CONACYT‐Instituto Nacional de PediatríaMexico CityMexico
| | | | - Adriana Reyes León
- Laboratorio de Genética y CáncerInstituto Nacional de PediatríaMexico CityMexico
| | - Daniel Martínez Anaya
- Laboratorio de Genética y CáncerInstituto Nacional de PediatríaMexico CityMexico
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | | | | | | | | | - Luis Juárez Villegas
- Servicio de Hemato‐OncologíaHospital Infantil de México Federico GómezMexico CityMexico
| | | | | | - Martha Herrera Almanza
- Laboratorio de Genética y CáncerInstituto Nacional de PediatríaMexico CityMexico
- Becaria de la Dirección General de Calidad y Educación en SaludSecretaría de Salud MéxicoMexico CityMexico
| | | | - Patricia Pérez Vera
- Laboratorio de Genética y CáncerInstituto Nacional de PediatríaMexico CityMexico
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13
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Virk H, Rana S, Sharma P, Bose PL, Yadav DD, Sachdeva MUS, Varma N, Trehan A, Lad D, Khadwal AR, Malhotra P, Sreedharanunni S. Hematological characteristics, cytogenetic features, and post-induction measurable residual disease in thymic stromal lymphopoietin receptor (TSLPR) overexpressed B-cell acute lymphoblastic leukemia in an Indian cohort. Ann Hematol 2021; 100:2031-2041. [PMID: 34159401 DOI: 10.1007/s00277-021-04574-0] [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: 04/09/2021] [Accepted: 06/08/2021] [Indexed: 11/24/2022]
Abstract
The overexpression of cytokine receptor-like factor-2 (CRLF2) identified by anti-thymic stromal lymphopoietin receptor/TSLPR flow cytometry (FCM) has been reported as a screening tool for the identification of BCR-ABL1-like B-cell acute lymphoblastic leukemia/B-ALL with CRLF2 re-arrangement. TSLPR expression was studied prospectively in consecutive 478 B-ALLs (≤ 12 years (n = 244); 13-25 years (n = 129); > 25 years (n = 105)) and correlated with various hematological parameters and end-of-induction measurable residual disease (day 29; MRD ≥ 0.01% by 10-color FCM). TSLPR positivity in ≥ 10% leukemic cells was detected in 14.6% (n = 70) of B-ALLs. CRLF2 re-arrangement was detected in eight cases (11.4%) including P2RY8-CRLF2 (n = 6), and IgH-CRLF2 (n = 2) with a median TSLPR positivity of 48.8% and 99% leukemic cells, respectively. Recurrent gene fusions/RGF (BCR-ABL1 (17.1%); ETV6-RUNX1 (4.2%), TCF3-PBX1 (1.4%)), other BCR-ABL1-like chimeric gene fusions/CGFs (PDGFRB-rearrangement (2.9%), IgH-EPOR (1.4%)), CRLF2 extra-copies/hyperdiploidy (17.1%), and IgH translocation without a known partner (10%) were also detected in TSLPR-positive patients. CD20 positivity (52.9% vs 38.5%; p = 0.02) as well as iAMP21 (4.3% vs 0.5%; p = 0.004) was significantly more frequent in TSLPR-positive cases. TSLPR-positive patients did not show a significantly higher MRD, compared to TSLPR-negative cases (37% vs 33%). Increasing the threshold cut-off (from ≥ 10 to > 50% or > 74%) increased the specificity to 88% and 100% respectively in identifying CRLF2 translocation. TSLPR expression is not exclusive for CRLF2 translocations and can be seen with various other RGFs, necessitating their testing before its application in diagnostic algorithms. In patients with high TSLPR positivity (> 50%), the testing may be restricted to CRLF2 aberrancies, while patients with 10-50% TSLPR positivity need to be tested for both CRLF2- and non-CRLF2 BCR-ABL1-like CGFs.
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Affiliation(s)
- Harpreet Virk
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Sonia Rana
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Praveen Sharma
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Parveen Lata Bose
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Diksha Dev Yadav
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Neelam Varma
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012
| | - Amita Trehan
- Pediatric Hematology/Oncology Unit, Department of Pediatric Medicine, Advanced Pediatric Center, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepesh Lad
- Adult Clinical Hematology Unit, Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Rani Khadwal
- Adult Clinical Hematology Unit, Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Adult Clinical Hematology Unit, Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sreejesh Sreedharanunni
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 160012.
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14
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Gu M, Jia Y, Xu M, Feng J, Tian Z, Ma X, Wang M, Wang J, Xu Y, Rao Q, Hao L, Mi Y, Yang W. Effects of different aberrations in the CRLF2 gene on the biological characteristics and drug sensitivities of Nalm6 cells. Int J Lab Hematol 2020; 43:441-449. [PMID: 33615710 DOI: 10.1111/ijlh.13419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 11/29/2022]
Abstract
INTRODUCTION To investigate the effects and mechanism of action of upregulated CRLF2 expression resulting from different aberrations in the CRLF2 gene (CRLF2, CRLF2 + IK6, P2RY8-CRLF2 and CRLF2 F232C) in the B cell ALL cell line Nalm6. METHODS Cell proliferation was measured using cell counting kit-8. Transcriptome sequencing technology (RNA-seq) was used to compare changes in gene expression resulting from different aberrations in CRLF2. High-throughput drug sensitivity testing was used to determine the drug sensitivity of cells. RESULTS All four aberrations in CRLF2 upregulated CRLF2 expression and promoted the proliferation of Nalm6 cells. The RNA-seq results showed the upregulation of genes in the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway and the downregulation of genes in the cell cycle pathway in the CRLF2 F232C-overexpressing cells. Western blotting showed that the expression of p-STAT5 protein was significantly higher in the CRLF2 F232C-overexpressing cells. Cells with aberrations in CRLF2 were more resistant to cyclophosphamide and drugs commonly used during treatment than cells in the vector group. The half-maximal inhibitory concentration (IC50 or GI50 ) of dexamethasone was significantly higher in the CRLF2 F232C-overexpressing cell line. CONCLUSIONS The overexpression of CRLF2, CRLF2 + IK6, P2RY8-CRLF2 and CRLF2 F232C promotes the proliferation of Nalm6 cells, activates the JAK/STAT signalling pathway and leads to a reduction in sensitivity towards various chemotherapeutic drugs.
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Affiliation(s)
- Min Gu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yannan Jia
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Meizhen Xu
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Juan Feng
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zheng Tian
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaotong Ma
- State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases, Tianjin, China
| | - Min Wang
- State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases, Tianjin, China
| | - Jianxiang Wang
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases, Tianjin, China
| | - Yingxi Xu
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qing Rao
- State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases, Tianjin, China
| | - Liangchun Hao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yingchang Mi
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases, Tianjin, China
| | - Wei Yang
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, China
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15
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The Current Genomic and Molecular Landscape of Philadelphia-like Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21062193. [PMID: 32235787 PMCID: PMC7139642 DOI: 10.3390/ijms21062193] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 01/03/2023] Open
Abstract
Philadelphia (Ph)-like acute lymphoblastic leukemia (ALL) is a high-risk B-cell Acute Lymphoblastic Leukemia (B-ALL) characterized by a gene expression profile similar to Ph-positive B-ALL but lacking the BCR-ABL1 translocation. The molecular pathogenesis of Ph-like B-ALL is heterogenous and involves aberrant genomics, receptor overexpression, kinase fusions, and mutations leading to kinase signaling activation, leukemogenic cellular proliferation, and differentiation blockade. Testing for the Ph-like signature, once only a research technique, is now available to the clinical oncologist. The plethora of data pointing to poor outcomes for this ALL subset has triggered investigations into the role of targeted therapies, predominantly involving tyrosine kinase inhibitors that are showing promising results.
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16
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Regulation of Small GTPase Rab20 by Ikaros in B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21051718. [PMID: 32138279 PMCID: PMC7084408 DOI: 10.3390/ijms21051718] [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: 01/25/2020] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Ikaros is a DNA-binding protein that regulates gene expression and functions as a tumor suppressor in B-cell acute lymphoblastic leukemia (B-ALL). The full cohort of Ikaros target genes have yet to be identified. Here, we demonstrate that Ikaros directly regulates expression of the small GTPase, Rab20. Using ChIP-seq and qChIP we assessed Ikaros binding and the epigenetic signature at the RAB20 promoter. Expression of Ikaros, CK2, and RAB20 was determined by qRT-PCR. Overexpression of Ikaros was achieved by retroviral transduction, whereas shRNA was used to knockdown Ikaros and CK2. Regulation of transcription from the RAB20 promoter was analyzed by luciferase reporter assay. The results showed that Ikaros binds the RAB20 promoter in B-ALL. Gain-of-function and loss-of-function experiments demonstrated that Ikaros represses RAB20 transcription via chromatin remodeling. Phosphorylation by CK2 kinase reduces Ikaros’ affinity toward the RAB20 promoter and abolishes its ability to repress RAB20 transcription. Dephosphorylation by PP1 phosphatase enhances both Ikaros’ DNA-binding affinity toward the RAB20 promoter and RAB20 repression. In conclusion, the results demonstrated opposing effects of CK2 and PP1 on expression of Rab20 via control of Ikaros’ activity as a transcriptional regulator. A novel regulatory signaling network in B-cell leukemia that involves CK2, PP1, Ikaros, and Rab20 is identified.
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17
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Transcriptional Regulation of Genes by Ikaros Tumor Suppressor in Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21041377. [PMID: 32085659 PMCID: PMC7073093 DOI: 10.3390/ijms21041377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/27/2022] Open
Abstract
Regulation of oncogenic gene expression by transcription factors that function as tumor suppressors is one of the major mechanisms that regulate leukemogenesis. Understanding this complex process is essential for explaining the pathogenesis of leukemia as well as developing targeted therapies. Here, we provide an overview of the role of Ikaros tumor suppressor and its role in regulation of gene transcription in acute leukemia. Ikaros (IKZF1) is a DNA-binding protein that functions as a master regulator of hematopoiesis and the immune system, as well as a tumor suppressor in acute lymphoblastic leukemia (ALL). Genetic alteration or functional inactivation of Ikaros results in the development of high-risk leukemia. Ikaros binds to the specific consensus binding motif at upstream regulatory elements of its target genes, recruits chromatin-remodeling complexes and activates or represses transcription via chromatin remodeling. Over the last twenty years, a large number of Ikaros target genes have been identified, and the role of Ikaros in the regulation of their expression provided insight into the mechanisms of Ikaros tumor suppressor function in leukemia. Here we summarize the role of Ikaros in the regulation of the expression of the genes whose function is critical for cellular proliferation, development, and progression of acute lymphoblastic leukemia.
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18
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Gowda C, Song C, Ding Y, Iyer S, Dhanyamraju PK, McGrath M, Bamme Y, Soliman M, Kane S, Payne JL, Dovat S. Cellular signaling and epigenetic regulation of gene expression in leukemia. Adv Biol Regul 2019; 75:100665. [PMID: 31623972 PMCID: PMC7239353 DOI: 10.1016/j.jbior.2019.100665] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
Alterations in normal regulation of gene expression is one of the key features of hematopoietic malignancies. In order to gain insight into the mechanisms that regulate gene expression in these diseases, we dissected the role of the Ikaros protein in leukemia. Ikaros is a DNA-binding, zinc finger protein that functions as a transcriptional regulator and a tumor suppressor in leukemia. The use of ChIP-seq, RNA-seq, and ATAC-seq—coupled with functional experiments—revealed that Ikaros regulates both the global epigenomic landscape and epigenetic signature at promoter regions of its target genes. Casein kinase II (CK2), an oncogenic kinase that is overexpressed in leukemia, directly phosphorylates Ikaros at multiple, evolutionarily-conserved residues. Phosphorylation of Ikaros impairs the protein's ability to regulate both the transcription of its target genes and global epigenetic landscape in leukemia. Treatment of leukemia cells with a specific inhibitor of CK2 restores Ikaros function, resulting in cytotoxicity of leukemia cells. Here, we review the mechanisms through which the CK2-Ikaros signaling axis regulates the global epigenomic landscape and expression of genes that control cellular proliferation in leukemia.
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Affiliation(s)
- Chandrika Gowda
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yali Ding
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mary McGrath
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yevgeniya Bamme
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mario Soliman
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Shriya Kane
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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Frisch A, Ofran Y. How I diagnose and manage Philadelphia chromosome-like acute lymphoblastic leukemia. Haematologica 2019; 104:2135-2143. [PMID: 31582548 PMCID: PMC6821607 DOI: 10.3324/haematol.2018.207506] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/03/2019] [Indexed: 01/31/2023] Open
Abstract
Advances in our understanding of mechanisms of leukemogenesis and driver mutations in acute lymphoblastic leukemia (ALL) lead to a more precise and informative sub-classification, mainly of B-cell ALL. In parallel, in recent years, novel agents have been approved for the therapy of B-cell ALL, and many others are in active clinical research. Among the newly recognized disease subtypes, Philadelphia-chromosome-like ALL is the most heterogeneous and thus, diagnostically challenging. Given that this subtype of B-cell ALL is associated with a poorer prognosis, improvement of available therapeutic approaches and protocols is a burning issue. Herein, we summarize, in a clinically relevant manner, up-to-date information regarding diagnostic strategies developed for the identification of patients with Philadelphia-chromosome-like ALL. Common therapeutic dilemmas, presented as several case scenarios, are also discussed. It is currently acceptable that patients with B-cell ALL, treated with an aim of cure, irrespective of their age, be evaluated for a Philadelphia-chromosome-like signature as early as possible. Following Philadelphia-chromosome-like recognition, a higher risk of resistance or relapse must be realized and treatment should be modified based on the patient’s specific genetic driver and clinical features. However, while active targeted therapeutic options are limited, there is much more to do than just prescribe a matched inhibitor to the identified mutated driver genes. In this review, we present a comprehensive evidence-based approach to the diagnosis and management of Philadelphia-chromosome-like ALL at different time-points during the disease course.
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Affiliation(s)
- Avraham Frisch
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa
| | - Yishai Ofran
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa .,Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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20
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Han Q, Ma J, Gu Y, Song H, Kapadia M, Kawasawa YI, Dovat S, Song C, Ge Z. RAG1 high expression associated with IKZF1 dysfunction in adult B-cell acute lymphoblastic leukemia. J Cancer 2019; 10:3842-3850. [PMID: 31333801 PMCID: PMC6636280 DOI: 10.7150/jca.33989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
The recombination mediated by recombination activating gene (RAG) is not only the dominant mutational process but also the predominant driver of oncogenic genomic rearrangement in acute lymphoblastic leukemia (ALL). It is further responsible for leukemic clonal evolution. In this study, significant RAG1 increase is observed in the subsets of B-ALL patients, and high expression of RAG1 is observed to be correlated with high proliferation markers. IKZF1-encoded protein, IKAROS, directly binds to the RAG1 promoter and regulates RAG1 expression in leukemic cells. CK2 inhibitor by increasing IKAROS activity significantly suppresses RAG1 expression in ALL in an IKAROS-dependent manner. Patients with IKZF1 deletion have significantly higher expression of RAG1 compared to that without IKZF1 deletion. CK2 inhibitor treatment also results in an increase in IKZF1 binding to the RAG1 promoter and suppression of RAG1 expression in primary ALL cells. Taken together, these results demonstrate that RAG1 high expression is associated with high proliferation markers in B-ALL. Our data for the first time proved that RAG1 expression is directly suppressed by IKAROS. Our results also reveal drive oncogenesis of B-ALL is driven by high expression of RAG1 with IKAROS dysfunction together, which have significance in an integrated prognostic model for adult ALL.
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Affiliation(s)
- Qi Han
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University,Nanjing 210009, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China
| | - Jinlong Ma
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University,Nanjing 210009, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China
| | - Yan Gu
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University,Nanjing 210009, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China
| | - Huihui Song
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University,Nanjing 210009, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China
| | - Malika Kapadia
- Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA17033, USA
| | - Yuka Imamura Kawasawa
- International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China.,Genome Sciences and Bioinformatics Core Facility, Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA17033, USA
| | - Sinisa Dovat
- International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China.,Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA17033, USA
| | - Chunhua Song
- International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China.,Department of Pediatrics, Pennsylvania State University Medical College, Hershey, PA17033, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University,Nanjing 210009, China.,International Cooperative Leukemia Group and International Cooperative Laboratory of Hematology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210009, China
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21
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Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia 2019; 33:2720-2731. [PMID: 31073152 PMCID: PMC6842075 DOI: 10.1038/s41375-019-0474-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Ikaros encodes a transcription factor that functions as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells resulted in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic, global, epigenomic and gene expression analyses to determine the mechanisms of Ikaros tumor suppressor activity. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effects of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Our results establish that Ikaros’ tumor suppressor function occurs via global regulation of the enhancer and super-enhancer landscape and through pioneering activity. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.
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Affiliation(s)
- Yali Ding
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chunhua Song
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital Southeast University, Institute of Hematology Southeast University, 210009, Nanjing, China
| | - Chandrika Gowda
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Glenn Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Mark E Reeves
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Dhimant Desai
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suming Huang
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kimberly J Payne
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Sinisa Dovat
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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22
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Zia S, Shahid R. Mutagenic players in ALL progression and their associated signaling pathways. Cancer Genet 2019; 233-234:7-20. [DOI: 10.1016/j.cancergen.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/10/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
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23
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Chen H, Wang XJ, Liu S, Yuan FF, Ai H, Chen L, Mi RH, Xiong YY, Li MJ, Fan RH, Yin QS, Wei XD. [The expression of CRLF2 in adult Ph negative acute B lymphocytic leukemia and its prognostic significance]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2019; 39:822-827. [PMID: 30369203 PMCID: PMC7348285 DOI: 10.3760/cma.j.issn.0253-2727.2018.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
目的 检测CRLF2蛋白在初诊成人非Ph阳性急性B淋巴细胞白血病(B-ALL)中的表达情况,探讨CRLF2蛋白的表达与患者临床特征、疗效及预后的关系。 方法 收集郑州大学附属肿瘤医院血液科2016年4月1日至2017年12月31日收治的103例初治成人B-ALL患者骨髓标本,应用流式细胞术CD45/SSC设门检测原始细胞CRLF2表达率,将CRLF2表达率≥20%定义为高表达组,<20%定义为低表达组,比较两组患者的临床特征及预后差异。 结果 CRLF2高表达组中位总生存(OS)、无病生存(DFS)时间分别为9.0和4.25个月,CRLF2低表达组分别为15.5和10.25个月,差异有统计学意义(P值分别为0.007、0.000)。CRLF2高表达组18个月OS率、DFS率分别为38.6%和25.1%,CRLF2低表达组分别为57.8%和42.3%,差异有统计学意义(P值分别为0.047、0.016)。多因素分析显示CRLF2高表达是影响患者OS(HR=2.991,95%CI 1.429~6.261,P=0.004)和DFS(HR=2.374,95%CI 1.146~4.960,P=0.041)的独立危险因素。 结论 合并CRLF2高表达的成人初治B-ALL患者预后不良。
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Affiliation(s)
- H Chen
- Department of Hematology, the Affiliated Cancer Hospital of Zhengzhou University; Henan Cancer Hospital, Zhengzhou 450008, China
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24
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Maciel ALT, Poubel CP, Noronha EP, Pombo-de-Oliveira MS, Mansur MB, Emerenciano M. CRLF2 expression associates with ICN1 stabilization in T-cell acute lymphoblastic leukemia. Genes Chromosomes Cancer 2018; 58:396-401. [PMID: 30578688 DOI: 10.1002/gcc.22723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 01/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematopoietic malignancy with few molecular alterations showing a consensual prognostic value. CRLF2 overexpression was recently identified in high-risk T-ALL patients. For these cases, no genomic abnormality was found to be associated with CRLF2 overexpression. IKZF1 has been recently shown to be a direct transcriptional regulator of CRLF2 expression. Moreover, it is known that NOTCH1 antagonizes IKZF1 in T-ALL. In light of these pieces of evidence, we reasoned that IKZF1 binding perturbation and CRLF2 upregulation could be associated in T-ALL. We evaluated two independent series of pediatric T-ALL cases (PHOP, n = 57 and TARGET, n = 264) for the presence of common T-ALL molecular abnormalities, such as NOTCH1/FBXW7 mutations. We also assessed CRLF2 and IKZF1 gene expression. CRLF2 overexpression was observed in 14% (PHOP) and 16% (TARGET) of T-ALL patients. No correlation was found between mRNA expression of CRLF2 and IKZF1 in both cohorts. Interestingly, we show that patients with mutations affecting NOTCH1-PEST domain and/or FBXW7 had higher CRLF2 expression (P = .04). In summary, we demonstrate for the first time that only mutations resulting in ICN1 (intracellular domain of NOTCH1) stabilization are associated with CRLF2 overexpression.
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Affiliation(s)
- Ana Luiza Tardem Maciel
- Molecular Cancer Study Group, Division of Clinical Research, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caroline Pires Poubel
- Molecular Cancer Study Group, Division of Clinical Research, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elda Pereira Noronha
- Paediatric Haematology-Oncology Program - PHOP, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program - PHOP, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcela Braga Mansur
- Molecular Cancer Study Group, Division of Clinical Research, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Emerenciano
- Molecular Cancer Study Group, Division of Clinical Research, Research Centre, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Rio de Janeiro, Brazil
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25
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Chiaretti S, Messina M, Grammatico S, Piciocchi A, Fedullo AL, Di Giacomo F, Peragine N, Gianfelici V, Lauretti A, Bareja R, Martelli MP, Vignetti M, Apicella V, Vitale A, Li LS, Salek C, Elemento O, Inghirami G, Weinstock DM, Guarini A, Foà R. Rapid identification of BCR/ABL1-like acute lymphoblastic leukaemia patients using a predictive statistical model based on quantitative real time-polymerase chain reaction: clinical, prognostic and therapeutic implications. Br J Haematol 2018; 181:642-652. [PMID: 29675955 DOI: 10.1111/bjh.15251] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/01/2018] [Indexed: 01/07/2023]
Abstract
BCR/ABL1-like acute lymphoblastic leukaemia (ALL) is a subgroup of B-lineage acute lymphoblastic leukaemia that occurs within cases without recurrent molecular rearrangements. Gene expression profiling (GEP) can identify these cases but it is expensive and not widely available. Using GEP, we identified 10 genes specifically overexpressed by BCR/ABL1-like ALL cases and used their expression values - assessed by quantitative real time-polymerase chain reaction (Q-RT-PCR) in 26 BCR/ABL1-like and 26 non-BCR/ABL1-like cases to build a statistical "BCR/ABL1-like predictor", for the identification of BCR/ABL1-like cases. By screening 142 B-lineage ALL patients with the "BCR/ABL1-like predictor", we identified 28/142 BCR/ABL1-like patients (19·7%). Overall, BCR/ABL1-like cases were enriched in JAK/STAT mutations (P < 0·001), IKZF1 deletions (P < 0·001) and rearrangements involving cytokine receptors and tyrosine kinases (P = 0·001), thus corroborating the validity of the prediction. Clinically, the BCR/ABL1-like cases identified by the BCR/ABL1-like predictor achieved a lower rate of complete remission (P = 0·014) and a worse event-free survival (P = 0·0009) compared to non-BCR/ABL1-like ALL. Consistently, primary cells from BCR/ABL1-like cases responded in vitro to ponatinib. We propose a simple tool based on Q-RT-PCR and a statistical model that is capable of easily, quickly and reliably identifying BCR/ABL1-like ALL cases at diagnosis.
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Affiliation(s)
- Sabina Chiaretti
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Monica Messina
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Sara Grammatico
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | | | - Anna L Fedullo
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Filomena Di Giacomo
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nadia Peragine
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Valentina Gianfelici
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Alessia Lauretti
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Rohan Bareja
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Maria P Martelli
- Institute of Haematology, Centro Ricerche Onco-Ematologiche (CREO), University of Perugia, Perugia, Italy
| | - Marco Vignetti
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Valerio Apicella
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Antonella Vitale
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
| | - Loretta S Li
- Department of Paediatric Haematology/Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyril Salek
- Institute of Haematology and Blood Transfusion, Prague, Czech Republic
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anna Guarini
- Department of Molecular Medicine, "Sapienza" University, Rome, Italy
| | - Robin Foà
- Haematology, Department of Cellular Biotechnologies and Haematology, "Sapienza" University, Rome, Italy
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26
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Buontempo F, McCubrey JA, Orsini E, Ruzzene M, Cappellini A, Lonetti A, Evangelisti C, Chiarini F, Evangelisti C, Barata JT, Martelli AM. Therapeutic targeting of CK2 in acute and chronic leukemias. Leukemia 2017; 32:1-10. [PMID: 28951560 PMCID: PMC5770594 DOI: 10.1038/leu.2017.301] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 12/22/2022]
Abstract
CK2 is a ubiquitously expressed, constitutively active Ser/Thr protein kinase, which is considered the most pleiotropic protein kinase in the human kinome. Such a pleiotropy explains the involvement of CK2 in many cellular events. However, its predominant roles are stimulation of cell growth and prevention of apoptosis. High levels of CK2 messenger RNA and protein are associated with CK2 pathological functions in human cancers. Over the last decade, basic and translational studies have provided evidence of CK2 as a pivotal molecule driving the growth of different blood malignancies. CK2 overexpression has been demonstrated in nearly all the types of hematological cancers, including acute and chronic leukemias, where CK2 is a key regulator of signaling networks critical for cell proliferation, survival and drug resistance. The findings that emerged from these studies suggest that CK2 could be a valuable therapeutic target in leukemias and supported the initiation of clinical trials using CK2 antagonists. In this review, we summarize the recent advances on the understanding of the signaling pathways involved in CK2 inhibition-mediated effects with a particular emphasis on the combinatorial use of CK2 inhibitors as novel therapeutic strategies for treating both acute and chronic leukemia patients.
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Affiliation(s)
- F Buontempo
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - J A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - E Orsini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - M Ruzzene
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - A Cappellini
- Department of Human, Social and Health Sciences, University of Cassino, Cassino, Italy
| | - A Lonetti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - C Evangelisti
- Institute of Molecular Genetics, National Research Council, Bologna, Italy.,Cell and Molecular Biology Laboratory, Rizzoli Orthopedic Institute, Bologna, Italy
| | - F Chiarini
- Institute of Molecular Genetics, National Research Council, Bologna, Italy.,Cell and Molecular Biology Laboratory, Rizzoli Orthopedic Institute, Bologna, Italy
| | - C Evangelisti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - J T Barata
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - A M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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27
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Gowda C, Soliman M, Kapadia M, Ding Y, Payne K, Dovat S. Casein Kinase II (CK2), Glycogen Synthase Kinase-3 (GSK-3) and Ikaros mediated regulation of leukemia. Adv Biol Regul 2017. [PMID: 28623166 DOI: 10.1016/j.jbior.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Signaling networks that regulate cellular proliferation often involve complex interactions between several signaling pathways. In this manuscript we review the crosstalk between the Casein Kinase II (CK2) and Glycogen Synthase Kinase-3 (GSK-3) pathways that plays a critical role in the regulation of cellular proliferation in leukemia. Both CK2 and GSK-3 are potential targets for anti-leukemia treatment. Previously published data suggest that CK2 and GSK-3 act synergistically to promote the phosphatidylinositol-3 kinase (PI3K) pathway via phosphorylation of PTEN. More recent data demonstrate another mechanism through which CK2 promotes the PI3K pathway - via transcriptional regulation of PI3K pathway genes by the newly-discovered CK2-Ikaros axis. Together, these data suggest that the CK2 and GSK-3 pathways regulate AKT/PI3K signaling in leukemia via two complementary mechanisms: a) direct phosphorylation of PTEN and b) transcriptional regulation of PI3K-promoting genes. Functional interactions between CK2, Ikaros and GSK3 define a novel signaling network that regulates proliferation of leukemia cells. This regulatory network involves both direct posttranslational modifications (by CK and GSK-3) and transcriptional regulation (via CK2-mediated phosphorylation of Ikaros). This information provides a basis for the development of targeted therapy for leukemia.
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Affiliation(s)
- Chandrika Gowda
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Mario Soliman
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Malika Kapadia
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Yali Ding
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Kimberly Payne
- Department of Anatomy, Loma Linda University, Loma Linda, CA, USA.
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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28
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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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29
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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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30
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Prognostic significance of IKZF1 deletion in adult B cell acute lymphoblastic leukemia: a meta-analysis. Ann Hematol 2016; 96:215-225. [PMID: 27815723 DOI: 10.1007/s00277-016-2869-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/22/2016] [Indexed: 02/05/2023]
Abstract
The IKAROS family zinc finger 1 (IKZF1) gene is frequently altered in adults with B cell acute lymphoblastic leukemia (ALL). Although many studies have indicated that IKZF1 alterations might be associated with poor outcomes in adults with ALL, the results remain controversial. A previous meta-analysis demonstrated the negative prognostic significance of IKZF1 deletion in ALL. However, most of the included studies (14 out of 15) were conducted in pediatric patients with ALL, and age was identified as a significant source of heterogeneity. Thus, performing the present meta-analysis provides valuable information to further elucidate the prognostic value of IKZF1 deletion in adults with ALL. Eight studies were identified that had been published prior to August 1, 2016. The studies included a total of 1008 patients. Hazard ratios (HRs) with 95% confidence intervals (CIs) of overall survival (OS) and disease-free survival (DFS)/relapse-free survival (RFS)/progression-free survival (PFS)/event-free survival (EFS) were pooled to estimate the prognostic power of IKZF1 deletion. Pooled HRs suggested that IKZF1 deletion had a negative impact on both OS (HR = 1.40, 95% CI 1.13-1.73) and DFS/RFS/PFS/EFS (HR = 1.67, 95% CI 1.28-2.17) in the overall population. Subgroup analyses indicated that IKZF1 deletion could independently predict unfavorable OS (HR = 1.60, 95% CI 1.25-2.06) and DFS/RFS/PFS/EFS (HR = 1.67, 95% CI 1.28-2.17) in BCR-ABL1-negative but not in BCR-ABL1-positive B cell ALL patients. Our meta-analysis suggests that IKZF1 deletion is a poor prognostic factor for adults with B cell ALL and may be more valuable in BCR-ABL1-negative B cell ALL patients.
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31
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Gowda C, Song C, Kapadia M, Payne JL, Hu T, Ding Y, Dovat S. Regulation of cellular proliferation in acute lymphoblastic leukemia by Casein Kinase II (CK2) and Ikaros. Adv Biol Regul 2016; 63:71-80. [PMID: 27666503 DOI: 10.1016/j.jbior.2016.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 12/23/2022]
Abstract
The IKZF1 gene encodes the Ikaros protein, a zinc finger transcriptional factor that acts as a master regulator of hematopoiesis and a tumor suppressor in leukemia. Impaired activity of Ikaros is associated with the development of high-risk acute lymphoblastic leukemia (ALL) with a poor prognosis. The molecular mechanisms that regulate Ikaros' function as a tumor suppressor and regulator of cellular proliferation are not well understood. We demonstrated that Ikaros is a substrate for Casein Kinase II (CK2), an oncogenic kinase that is overexpressed in ALL. Phosphorylation of Ikaros by CK2 impairs Ikaros' DNA-binding ability, as well as Ikaros' ability to regulate gene expression and function as a tumor suppressor in leukemia. Targeting CK2 with specific inhibitors restores Ikaros' function as a transcriptional regulator and tumor suppressor resulting in a therapeutic, anti-leukemia effect in a preclinical model of ALL. Here, we review the genes and pathways that are regulated by Ikaros and the molecular mechanisms through which Ikaros and CK2 regulate cellular proliferation in leukemia.
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Affiliation(s)
- Chandrika Gowda
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Malika Kapadia
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jonathon L Payne
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA; Loma Linda University, Loma Linda, CA, USA
| | - Tommy Hu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yali Ding
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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