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Zhang Z, Jing Y, Chen B, Zhang H, Liu T, Dong S, Zhang L, Yan X, Yang S, Chen L, Lin Y, Ru K. The application of targeted RNA sequencing for the analysis of fusion genes, gene mutations, IKZF1 intragenic deletion, and CRLF2 overexpression in acute lymphoblastic leukemia. Int J Lab Hematol 2024; 46:670-677. [PMID: 38553845 DOI: 10.1111/ijlh.14269] [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: 09/07/2023] [Accepted: 03/07/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) is characterized by highly genetic heterogeneity, owing to recurrent fusion genes, gene mutations, intragenic deletion, and gene overexpression, which poses significant challenges in clinical detection. RNA sequencing (RNA-seq) is a powerful tool for detecting multiple genetic abnormalities, especially cryptic gene rearrangements, in a single test. METHODS Sixty samples (B-ALL, n = 49; T-ALL, n = 9; mixed phenotype acute leukemia (MPAL), n = 2) and 20 controls were analyzed by targeted RNA-seq panel of 507 genes developed by our lab. Of these, 16 patients were simultaneously analyzed for gene mutations at the DNA level using a next-generation sequencing panel of 51 genes. Fusion genes, CRLF2 expression, and IKZF1 intragenic deletion were also detected by reverse transcription-polymerase chain reaction (RT-PCR). Karyotype analysis was performed using the R-banding and G-banding technique on bone marrow cells after 24 hours of culture. Partial fusion genes were analyzed using fluorescence in situ hybridization (FISH). RESULTS Compared with the results of Karyotype analysis, FISH, and RT-PCR, the detection rate of fusion genes by targeted RNA-seq increased from 48.3% to 58.3%, and six unexpected fusion genes were discovered, along with one rare isoform of IKZF1 intragenic deletion (IK10). The DNA sequencing analysis of 16 ALL patients revealed that 96.2% (25/26) of gene mutations identified at the DNA level were also detectable at the RNA level, except for one mutation with a low variant allele fraction. The detection of CRLF2 overexpression exhibited complete concordance between RT-PCR and RNA-seq. CONCLUSION The utilization of RNA-seq enables the identification of clinically significant genetic abnormalities that may go undetected through conventional detection methods. Its robust analytical performance might bring great application value for clinical diagnosis, prognosis, and therapy in ALL.
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Affiliation(s)
- Zhenyu Zhang
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yu Jing
- Department of Haematology, The Fifth Medical centre of Chinese PLA General Hospital, Beijing, China
| | - Bin Chen
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Hong Zhang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Tuo Liu
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Shuran Dong
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Lei Zhang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Xiaoyan Yan
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Shaobin Yang
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Long Chen
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Yani Lin
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
| | - Kun Ru
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Sino-US Diagnostics Lab, Tianjin Enterprise Key Laboratory of AI-aided Hematopathology Diagnosis, Tianjin, China
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Moreno-Lorenzana D, Juárez-Velázquez R, Reyes-León A, Martínez-Anaya D, Juárez-Villegas L, Zapata Tarrés M, López Santiago N, Pérez-Vera P. CRLF2 and IKZF1 abnormalities in childhood hematological malignancies other than B-cell Acute Lymphoblastic Leukemia. Leuk Lymphoma 2024:1-11. [PMID: 39034479 DOI: 10.1080/10428194.2024.2378817] [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: 01/17/2024] [Accepted: 07/07/2024] [Indexed: 07/23/2024]
Abstract
Rearrangements and overexpression of CRLF2 are hallmarks of poor outcomes in BCR::ABL1-like B-ALL, and CRLF2 overexpression is a high-risk marker in T-ALL. However, CRLF2 alterations in pediatric hematologic malignancies other than B-ALL have not been reported. In this study, we analyzed the CRLF2 overexpression, rearrangements (P2RY8::CRLF2 and IGH::CRLF2), activation (pSTAT5 and pERK), and the expression of dominant-negative IKZF1 isoforms (Ik6 and Ik8), implied in CRLF2 dysregulation, in 16 pediatric patients (AML, n = 9; T-ALL, n = 3; LBL, n = 2; HL, n = 1; cytopenia, n = 1). A high frequency of CRLF2 rearrangements and overexpression was found in the 16 patients: 28.6% (4/14) showed CRLF2 overexpression, 93.8% (15/16) were positive for CRLF2 total protein (cell-surface and/or cytoplasmic), while 62.5% (10/16) were positive for P2RY8::CRLF2 and 12.6% (2/16) for IGH::CRLF2. In addition, 43.8% (7/16) expressed Ik6 and Ik8 isoforms. However, only a few patients were positive for the surrogate markers pSTAT5 (14.3%; 2/14) and pERK (21.4%; 3/14).
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Affiliation(s)
- Dafné Moreno-Lorenzana
- CONAHCYT-Instituto Nacional de Pediatría, Mexico City, Mexico
- Laboratorio de Genética y Cáncer, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Rocío Juárez-Velázquez
- Laboratorio de Genética y Cáncer, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Adriana Reyes-León
- Laboratorio de Genética y Cáncer, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Daniel Martínez-Anaya
- CONAHCYT-Instituto Nacional de Pediatría, Mexico City, Mexico
- Laboratorio de Genética y Cáncer, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Luis Juárez-Villegas
- Servicio de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Martha Zapata Tarrés
- Coordinación de Investigación, Fundación IMSS, A.C., Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Patricia Pérez-Vera
- Laboratorio de Genética y Cáncer, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City, Mexico
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Gil JV, Miralles A, de las Heras S, Such E, Avetisyan G, Díaz-González Á, Santiago M, Fuentes C, Fernández JM, Lloret P, Navarro I, Montesinos P, Llop M, Barragán E. Comprehensive detection of CRLF2 alterations in acute lymphoblastic leukemia: a rapid and accurate novel approach. Front Mol Biosci 2024; 11:1362081. [PMID: 38370004 PMCID: PMC10869515 DOI: 10.3389/fmolb.2024.1362081] [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: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction: Acute lymphoblastic leukemia (ALL) is a prevalent childhood cancer with high cure rate, but poses a significant medical challenge in adults and relapsed patients. Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL) is a high-risk subtype, with approximately half of cases characterized by CRLF2 overexpression and frequent concomitant IKZF1 deletions. Methods: To address the need for efficient, rapid, and cost-effective detection of CRLF2 alterations, we developed a novel RT-qPCR technique combining SYBR Green and highresolution melting analysis on a single plate. Results: The method successfully identified CRLF2 expression, P2RY8::CRLF2 fusions, and CRLF2 and JAK2 variants, achieving a 100% sensitivity and specificity. Application of this method across 61 samples revealed that 24.59% exhibited CRLF2 overexpression, predominantly driven by IGH::CRLF2 (73.33%). High Resolution Melting analysis unveiled concurrent CRLF2 or JAK2 variants in 8.19% of samples, as well as a dynamic nature of CRLF2 alterations during disease progression. Discussion: Overall, this approach provides an accurate identification of CRLF2 alterations, enabling improved diagnostic and facilitating therapeutic decision-making.
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Affiliation(s)
- José Vicente Gil
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Alberto Miralles
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Sandra de las Heras
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Esperanza Such
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
| | - Gayane Avetisyan
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Álvaro Díaz-González
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Marta Santiago
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
| | - Carolina Fuentes
- Accredited Research Group on Clinical and Translational Cancer Research, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Onco-Hematology Unit, Pediatrics Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - José María Fernández
- Accredited Research Group on Clinical and Translational Cancer Research, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Onco-Hematology Unit, Pediatrics Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Pilar Lloret
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Irene Navarro
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Pau Montesinos
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Hematology Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Marta Llop
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Biology Unit, Clinical Analysis Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
| | - Eva Barragán
- Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Biology Unit, Clinical Analysis Service, Hospital Universitario y Politécnico la Fe, Valencia, Spain
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Huang YH, Wan CL, Dai HP, Xue SL. Targeted therapy and immunotherapy for T cell acute lymphoblastic leukemia/lymphoma. Ann Hematol 2023; 102:2001-2013. [PMID: 37227492 DOI: 10.1007/s00277-023-05286-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
T cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is an aggressive malignancy of progenitor T cells. Despite significant improvements in survival of T-ALL/LBL over the past decades, treatment of relapsed and refractory T-ALL (R/R T-ALL/LBL) remains extremely challenging. The prognosis of R/R T-ALL/LBL patients who are intolerant to intensive chemotherapy remains poor. Therefore, innovative approaches are needed to further improve the survival of R/R T-ALL/LBL patients. With the widespread use of next-generation sequencing in T-ALL/LBL, a range of new therapeutic targets such as NOTCH1 inhibitors, JAK-STAT inhibitors, and tyrosine kinase inhibitors have been identified. These findings led to pre-clinical studies and clinical trials of molecular targeted therapy in T-ALL/LBL. Furthermore, immunotherapies such as CD7 CAR T cell therapy and CD5 CAR T cell therapy have shown profound response rate in R/R T-ALL/LBL. Here, we review the progress of targeted therapies and immunotherapies for T-ALL/LBL, and look at the future directions and challenges for the further use of these therapies in T-ALL/LBL.
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Affiliation(s)
- Yuan-Hong Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China
| | - Chao-Ling Wan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China
| | - Hai-Ping Dai
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China.
| | - Sheng-Li Xue
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China.
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5
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Palmi C, Bresolin S, Junk S, Fazio G, Silvestri D, Zaliova M, Oikonomou A, Scharov K, Stanulla M, Moericke A, Zimmermann M, Schrappe M, Buldini B, Bhatia S, Borkhardt A, Saitta C, Galbiati M, Bardini M, Lo Nigro L, Conter V, Valsecchi MG, Biondi A, te Kronnie G, Cario G, Cazzaniga G. Definition and Prognostic Value of Ph-like and IKZF1plus Status in Children With Down Syndrome and B-cell Precursor Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e892. [PMID: 37304931 PMCID: PMC10256328 DOI: 10.1097/hs9.0000000000000892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/11/2023] [Indexed: 06/13/2023] Open
Abstract
Children with Down syndrome have an augmented risk for B-cell acute lymphoblastic leukemia (DS-ALL), which is associated with lower survival than in non-DS-ALL. It is known that cytogenetic abnormalities common in childhood ALL are less frequent in DS-ALL, while other genetic aberrancies (ie, CRLF2 overexpression and IKZF1 deletions) are increased. A possible cause for the lower survival of DS-ALL that we herewith evaluated for the first time was the incidence and prognostic value of the Philadelphia-like (Ph-like) profile and the IKZF1plus pattern. These features have been associated with poor outcome in non-DS ALL and therefore introduced in current therapeutic protocols. Forty-six out of 70 DS-ALL patients treated in Italy from 2000 to 2014 displayed Ph-like signature, mostly characterized by CRLF2 (n = 33) and IKZF1 (n = 16) alterations; only 2 cases were positive for ABL-class or PAX5-fusion genes. Moreover, in an Italian and German joint cohort of 134 DS-ALL patients, we observed 18% patients positive for IKZF1plus feature. Ph-like signature and IKZF1 deletion were associated with poor outcome (cumulative incidence of relapse: 27.7 ± 6.8% versus 13 ± 7%; P = 0.04 and 35.2 ± 8.6% versus 17 ± 3.9%; P = 0.007, respectively), which further worsens when IKZF1 deletion was co-occurring with P2RY8::CRLF2, qualifying for the IKZF1plus definition (13/15 patients had an event of relapse or treatment-related death). Notably, ex vivo drug screening revealed sensitivity of IKZF1plus blasts for drugs active against Ph-like ALL such as Birinapant and histone deacetylase inhibitors. We provided data in a large setting of a rare condition (DS-ALL) supporting that these patients, not associated with other high-risk features, need tailored therapeutic strategies.
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Affiliation(s)
- Chiara Palmi
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Silvia Bresolin
- Women’s and Children’s Health Department, Hematology-Oncology Clinic and Laboratory, University-Hospital of Padua, Italy
- Istituto di Ricerca Pediatrica-Città della Speranza, Padua, Italy
| | - Stefanie Junk
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Grazia Fazio
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Daniela Silvestri
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marketa Zaliova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Katerina Scharov
- Department of Paediatric Oncology, Haematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Düsseldorf, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Anja Moericke
- Pediatrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Martin Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Pediatrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Barbara Buldini
- Women’s and Children’s Health Department, Hematology-Oncology Clinic and Laboratory, University-Hospital of Padua, Italy
- Istituto di Ricerca Pediatrica-Città della Speranza, Padua, Italy
| | - Sanil Bhatia
- Department of Paediatric Oncology, Haematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Haematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Medical Faculty, Düsseldorf, Germany
| | - Claudia Saitta
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marta Galbiati
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Michela Bardini
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Luca Lo Nigro
- Center of Pediatric Hematology and Oncology, Azienda Policlinico-San Marco, Catania, Italy
| | - Valentino Conter
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Maria Grazia Valsecchi
- Statistics, University of Milan Bicocca, Monza, Italy
- Biostatistics and Clinical Epidemiology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Andrea Biondi
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milan Bicocca, Italy
| | - Geertruy te Kronnie
- Women’s and Children’s Health Department, Hematology-Oncology Clinic and Laboratory, University-Hospital of Padua, Italy
| | - Gunnar Cario
- Pediatrics, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Giovanni Cazzaniga
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Medical Genetics, School of Medicine and Surgery, University of Milan Bicocca, Monza, Italy
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Abstract
Thymic stromal lymphopoietin (TSLP) is a pleiotropic cytokine that acts on multiple cell lineages, including dendritic cells, T cells, B cells, neutrophils, mast cells, eosinophils and innate lymphoid cells, affecting their maturation, survival and recruitment. It is best known for its role in promoting type 2 immune responses such as in allergic diseases and, in 2021, a monoclonal antibody targeting TSLP was approved for the treatment of severe asthma. However, it is now clear that TSLP has many other important roles in a variety of settings. Indeed, several genetic variants for TSLP are linked to disease severity, and chromosomal alterations in TSLP are common in certain cancers, indicating important roles of TSLP in disease. In this Review, we discuss recent advances in TSLP biology, highlighting how it regulates the tissue environment not only in allergic disease but also in infectious diseases, inflammatory diseases and cancer. Encouragingly, therapies targeting the TSLP pathway are being actively pursued for several diseases.
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Affiliation(s)
- Risa Ebina-Shibuya
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Warren J Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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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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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: 3] [Impact Index Per Article: 1.5] [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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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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10
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Wee Y, Liu Y, Zhao M. Identification of consistent post-translational regulatory triplets related to oncogenic and tumour suppressive modulators in childhood acute lymphoblastic leukemia. PeerJ 2021; 9:e11803. [PMID: 34316412 PMCID: PMC8286060 DOI: 10.7717/peerj.11803] [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: 10/01/2019] [Accepted: 06/26/2021] [Indexed: 11/24/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is the most common type of childhood cancer. It can be caused by mutations that turn on oncogenes or turn off tumour suppressor genes. For instance, changes in certain genes including Rb and p53 are common in ALL cells. Oncogenes and TSGs may serve as a modulator gene to regulate the gene expression level via their respective target genes. To investigate the regulatory relationship between oncogenes, tumour suppressor genes and transcription factors at the post translational level in childhood ALL, we performed an integrative network analysis on the gene regulation in the post-translational level for childhood ALL based on many publicly available cancer gene expression data including TARGET and GEO database. Methods We collected 259 childhood ALL-related genes from the latest online leukemia database, Leukemia Gene Literature Database. These 259 genes were selected from a comprehensive systematic literature with experimental evidences. The identified and curated genes were also associated with patient survival cases and we incorporated this pediatric ALL-related gene list into our analysis. We extracted the known human TFs from the TRRUST database. Among 259 childhood ALL-related genes, 101 unique regulators were mapped to the list of oncogene and tumour suppressor genes (TSGs) from the ONGene and the TSGene databases, and these included 74 TSGs, 62 oncogenes and 46 TF genes. Results The resulted regulation was presented as a hierarchical regulatory network with transcription factors (TFs) as intermediate regulators connecting the top modulators (oncogene and TSGs) to the common target genes. Cross-validation was applied to the results from the TARGET dataset by identifying the consistent regulatory motifs based on three independent ALL expression datasets. A three-layer regulatory network of consistent positive modulators in childhood ALL was constructed in which 74 modulators (40 oncogenes, 34 TSGs) are considered as the most important regulators. The middle layer and the bottom layer contain 34 TFs and 176 target genes, respectively. Oncogenes mostly participated in positive regulation of gene expression and the transcription process of RNA II polymerase, while TSGs were mainly involved in the negative regulation of gene expression. In addition, the oncogene-specific targets were enriched with regulators of the MAPK cascade while tumour suppressor-specific targets were associated with cell death. Conclusion The results revealed that oncogenes and TSGs possess a different functional regulatory pattern with regard to not only their biological functions but also their specific target genes in childhood ALL cancer progression. Taken together, our findings could contribute to a better understanding of the important regulatory mechanisms and this method could be used to analyse the targeted genes at the post-translational level in childhood ALL through integrative network analysis.
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Affiliation(s)
- YongKiat Wee
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Yining Liu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Min Zhao
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
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11
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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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12
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Féral K, Jaud M, Philippe C, Di Bella D, Pyronnet S, Rouault-Pierre K, Mazzolini L, Touriol C. ER Stress and Unfolded Protein Response in Leukemia: Friend, Foe, or Both? Biomolecules 2021; 11:biom11020199. [PMID: 33573353 PMCID: PMC7911881 DOI: 10.3390/biom11020199] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
The unfolded protein response (UPR) is an evolutionarily conserved adaptive signaling pathway triggered by a stress of the endoplasmic reticulum (ER) lumen compartment, which is initiated by the accumulation of unfolded proteins. This response, mediated by three sensors-Inositol Requiring Enzyme 1 (IRE1), Activating Transcription Factor 6 (ATF6), and Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK)—allows restoring protein homeostasis and maintaining cell survival. UPR represents a major cytoprotective signaling network for cancer cells, which frequently experience disturbed proteostasis owing to their rapid proliferation in an usually unfavorable microenvironment. Increased basal UPR also participates in the resistance of tumor cells against chemotherapy. UPR activation also occurs during hematopoiesis, and growing evidence supports the critical cytoprotective role played by ER stress in the emergence and proliferation of leukemic cells. In case of severe or prolonged stress, pro-survival UPR may however evolve into a cell death program called terminal UPR. Interestingly, a large number of studies have revealed that the induction of proapoptotic UPR can also strongly contribute to the sensitization of leukemic cells to chemotherapy. Here, we review the current knowledge on the consequences of the deregulation of UPR signaling in leukemias and their implications for the treatment of these diseases.
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Affiliation(s)
- Kelly Féral
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Manon Jaud
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (K.R.-P.)
| | - Laurent Mazzolini
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
- Correspondence: (L.M.); (C.T.)
| | - Christian Touriol
- Inserm UMR1037-Cancer Research Center of Toulouse, 2 avenue Hubert Curien, Oncopole entrée C, CS 53717, 31037 Toulouse, France; (K.F.); (M.J.); (S.P.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France
- Correspondence: (L.M.); (C.T.)
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13
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Wang M, Wen J, Guo Y, Shen Y, An X, Hu Y, Xiao J. Clinical characterization and prognosis of T cell acute lymphoblastic leukemia with high CRLF2 gene expression in children. PLoS One 2019; 14:e0224652. [PMID: 31830053 PMCID: PMC6907766 DOI: 10.1371/journal.pone.0224652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 10/20/2019] [Indexed: 01/11/2023] Open
Abstract
It has been reported that overexpression of the CRLF2 gene is associated with poor outcomes in pediatric B cell acute lymphoblastic leukemia (B-ALL), but the incidence rates, clinical characteristics and outcomes of CRLF2 gene overexpression in pediatric T cell ALL (T-ALL) have not been systematically analyzed. In this study, CRLF2 mRNA expression levels and clinical and laboratory parameters in 63 pediatric T-ALL patients were detected at the Children's Hospital of Chongqing Medical University and Children’s Hospital of Xianyang between February 2015 and June 2018. The patients were treated according to the modified St. Jude TXV ALL protocol, and early treatment responses (bone marrow smear and MRD level) and prognoses in the enrolled patients were assessed. CRLF2 overexpression was detected in 21/63 (33.33%) patients. Statistical differences were not found for clinical or laboratory parameters (including sex, age, initial WBC count, incidence mediastinal involvement, abnormal karyotype and fusion genes) between patients with high CRLF2 expression and patients with low expression of CRLF2 (P>0.05). One patient died of tumor lysis syndrome and renal failure, and the treatment response was monitored on day 19 (TP1) of remission in 62 patients. One patient quit treatment because of family decisions, and 61 patients underwent treatment response evaluation on day 46 (TP2) of remission. Significant differences were not found between patients with high CRLF2 expression and patients with low CRLF2 expression in terms of the treatment responses at TP1 or TP2 (P>0.05). Following October 2018, 12 patients among the 61 evaluable patients relapsed (relapse rate: 19.67%), 3 patients died from chemotherapy, and the treatment-related mortality (TRM) rate was 4.92%. Secondary tumors occurred in 1 patient. The 3-year prospective EFS rate was 54.1±11.2% and 77.7±6.6% for the 61 evaluable patients and 58 patients without TRM. Patients with low CRLF2 expression had longer EFS durations than patients with high CRLF2 expression (61 evaluable patients: 35.91± 2.38 months vs 23.43± 2.57 months; 58 patients without TRM: 37.86± 2.08 months vs 24.55±2.43 months, P<0.05). CRLF2 expression levels were also monitored in 13 patients at TP1 and TP2, and the MRD level did not vary with the CRLF2 expression level. Our data suggest that clinical features, laboratory findings and treatment responses in the pediatric T-ALL population do not vary based on the overexpression of CRLF2 but that CRLF2 overexpression can contribute to a high risk of relapse in pediatric T-ALL. Thus, CRLF2 expression levels should not be used as biomarkers for monitoring MRD.
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Affiliation(s)
- Mingmin Wang
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R. China.,Chongqing Key Laboratory of Pediatrics, Chongqing, P.R. China
| | - Jinquan Wen
- Department of Hematology, Children's Hospital of Xianyang, Xi'an, P.R. China
| | - Yuxia Guo
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R. China.,China International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, P.R. China
| | - Yali Shen
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Chongqing Key Laboratory of Pediatrics, Chongqing, P.R. China.,China International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, P.R. China
| | - Xizhou An
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R. China
| | - Yanni Hu
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R. China.,China International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, P.R. China
| | - Jianwen Xiao
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R. China.,Chongqing Key Laboratory of Pediatrics, Chongqing, P.R. China
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14
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The effect of co-occurring lesions on leukaemogenesis and drug response in T-ALL and ETP-ALL. Br J Cancer 2019; 122:455-464. [PMID: 31792348 PMCID: PMC7028932 DOI: 10.1038/s41416-019-0647-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 01/27/2023] Open
Abstract
Despite advances in the management of acute lymphoblastic leukaemia (ALL), current regimens fail to significantly transform outcomes for patients with high-risk subtypes. Advances in genomic analyses have identified novel lesions including mutations in genes that encode chromatin modifiers and those that influence cytokine and kinase signalling, rendering many of these alterations potentially targetable by tyrosine kinase and epigenetic inhibitors currently in clinical use. Although specific genomic lesions, gene expression patterns, and immunophenotypic profiles have been associated with specific clinical outcomes in some cancers, the application of precision medicine approaches based on these data has been slow. This approach is complicated by the reality that patients often harbour multiple mutations, and in many cases, the precise functional significance and interaction of these mutations in driving leukaemia and drug responsiveness/resistance remains unknown. Given that signalling pathways driving leukaemic pathogenesis could plausibly result from the co-existence of specific lesions and the resultant perturbation of protein interactions, the use of combined therapeutics that target multiple aberrant pathways, according to an individual’s mutational profile, might improve outcomes and lower a patient’s risk of relapse. Here we outline the genomic alterations that occur in T cell ALL (T-ALL) and early T cell precursor (ETP)-ALL and review studies highlighting the possible effects of co-occurring lesions on leukaemogenesis and drug response.
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15
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Tomar AK, Agarwal R, Kundu B. Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients. Interdiscip Sci 2019; 11:668-678. [PMID: 30972690 DOI: 10.1007/s12539-019-00325-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/21/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients' mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathogenesis and aggression. For analysis, 3361 most variable genes, including 276 transcription factors (out of 16,807 genes) were sorted based on the coefficient of variance. Silhouette width analysis classified 207 ALL patients into 6 subtypes and heat map analysis suggests a need of large and multicenter dataset for non-overlapping subtype classification. Overall, 265 GO terms and 32 KEGG pathways were enriched. The lists were dominated by cancer-associated entries and highlight crucial genes and pathways that can be targeted for designing more specific ALL therapeutics. Differential gene expression analysis identified upregulation of two important genes, JCHAIN and CRLF2 in dead patients' cohort suggesting their possible involvement in different clinical outcomes in ALL patients undergoing the same treatment.
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Affiliation(s)
- Anil Kumar Tomar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Rahul Agarwal
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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16
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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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17
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Rhee ES, Kim H, Kang SH, Yoo JW, Koh KN, Im HJ, Seo JJ. Outcome and Prognostic Factors in Pediatric Precursor T-Cell Acute Lymphoblastic Leukemia: A Single-Center Experience. CLINICAL PEDIATRIC HEMATOLOGY-ONCOLOGY 2018. [DOI: 10.15264/cpho.2018.25.2.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Eun Sang Rhee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Hyery Kim
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Sung-Han Kang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jae Won Yoo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Kyung-Nam Koh
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Ho Joon Im
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jong Jin Seo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
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18
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Sarno J, Savino AM, Buracchi C, Palmi C, Pinto S, Bugarin C, Jager A, Bresolin S, Barber RC, Silvestri D, Israeli S, Dyer MJ, Cazzaniga G, Nolan GP, Biondi A, Davis KL, Gaipa G. SRC/ABL inhibition disrupts CRLF2-driven signaling to induce cell death in B-cell acute lymphoblastic leukemia. Oncotarget 2018; 9:22872-22885. [PMID: 29796158 PMCID: PMC5955419 DOI: 10.18632/oncotarget.25089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/19/2018] [Indexed: 01/31/2023] Open
Abstract
Children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) overexpressing the CRLF2 gene (hiCRLF2) have poor prognosis. CRLF2 protein overexpression leads to activated JAK/STAT signaling and trials are underway using JAK inhibitors to overcome treatment failure. Pre-clinical studies indicated limited efficacy of single JAK inhibitors, thus additional pathways must be targeted in hiCRLF2 cells. To identify additional activated networks, we used single-cell mass cytometry to examine 15 BCP-ALL primary patient samples. We uncovered a coordinated signaling network downstream of CRLF2 characterized by co-activation of JAK/STAT, PI3K, and CREB pathways. This CRLF2-driven network could be more effectively disrupted by SRC/ABL inhibition than single-agent JAK or PI3K inhibition, and this could be demonstrated even in primary minimal residual disease (MRD) cells. Our study suggests SCR/ABL inhibition as effective in disrupting the cooperative functional networks present in hiCRLF2 BCP-ALL patients, supporting further investigation of this strategy in pre-clinical studies.
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Affiliation(s)
- Jolanda Sarno
- Department of Pediatrics, Bass Center for Childhood Cancer and Blood Disorders, Stanford University, Stanford, CA, USA
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | | | - Chiara Buracchi
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Chiara Palmi
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Stefania Pinto
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Cristina Bugarin
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Astraea Jager
- Department of Pediatrics, Bass Center for Childhood Cancer and Blood Disorders, Stanford University, Stanford, CA, USA
| | - Silvia Bresolin
- Laboratory of Onco-Hematology, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Ruth C. Barber
- Leicester Drug Discovery & Diagnostic Centre, University of Leicester, Leicester, United Kingdom
| | - Daniela Silvestri
- Biostatistics and Clinic Epidemiology Center, University of Milano Bicocca, Monza, Italy
| | - Shai Israeli
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Martin J.S. Dyer
- Ernest and Helen Scott Haematological Research Institute, University of Leicester, Leicester, United Kingdom
| | - Giovanni Cazzaniga
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Garry P. Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Andrea Biondi
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
- Department of Pediatrics, ASST-Monza, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Kara L. Davis
- Department of Pediatrics, Bass Center for Childhood Cancer and Blood Disorders, Stanford University, Stanford, CA, USA
| | - Giuseppe Gaipa
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
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TFDP3 confers chemoresistance in minimal residual disease within childhood T-cell acute lymphoblastic leukemia. Oncotarget 2018; 8:1405-1415. [PMID: 27902457 PMCID: PMC5352064 DOI: 10.18632/oncotarget.13630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023] Open
Abstract
Acquired drug resistance in childhood T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem. In this study, a novel gene therapy target for childhood T-ALL to overcome chemoresistance was discovered: TFDP3 increased in the minimal residual disease (MRD) positive childhood T-ALL patients. Then, we established a preclinical model of resistance to induction therapy to examine the functional relevance of TFDP3 to chemoresistance in MRD derived from Jurkat/E6-1. Jurkat xenografts in NOD/SCID mice were exposed to a four drug combination (VXLD) of vincristine (VCR), dexamethasone (DEX), L-asparaginase (L-asp) and daunorubicin (DNR). During the 4-week VXLD treatment, the level of TFDP3 increased 4-fold. High expression of TFDP3 was identified in the re-emerging lines (Jurkat/MRD) with increased chemoresistance, which is correlated with partially promoter demethylation of TFDP3. Downregulation of TFDP3 by RNA interference reversed chemoresistance in Jurkat/MRD accompanied by reinstated E2F1 activity that coincided with increased levels of p53, p73, and associated proapoptotic target genes. Importantly, TFDP3 silencing in vivo induced apparent benefit to overcome chemoresistance in combination with VXLD treatment. Collectively, TFDP3 confers chemoresistance in MRD within childhood T-ALL, indicating that TFDP3 is a potential gene therapy target for residual cancer.
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Schmäh J, Fedders B, Panzer-Grümayer R, Fischer S, Zimmermann M, Dagdan E, Bens S, Schewe D, Moericke A, Alten J, Bleckmann K, Siebert R, Schrappe M, Stanulla M, Cario G. Molecular characterization of acute lymphoblastic leukemia with high CRLF2 gene expression in childhood. Pediatr Blood Cancer 2017; 64. [PMID: 28371317 DOI: 10.1002/pbc.26539] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 01/06/2023]
Abstract
BACKGROUND A high-level expression of the CRLF2 gene is frequent in precursor B-cell acute lymphoblastic leukemia (pB-ALL) and can be caused by different genetic aberrations. The presence of the most frequent alteration, the P2RY8/CRLF2 fusion, was shown to be associated with a high relapse incidence in children treated according to ALL-Berlin-Frankfurt-Münster (BFM) protocols, which is poorly understood. Moreover, the frequency of other alterations has not been systematically analyzed yet. PROCEDURE CRLF2 mRNA expression and potential genetic aberrations causing a CRLF2 high expression were prospectively assessed in 1,105 patients treated according to the Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP)-BFM ALL 2009 protocol. Additionally, we determined copy number alterations in selected B-cell differentiation genes for all CRLF2 high-expressing pB-ALL cases, as well as JAK2 and CRLF2 mutations. RESULTS A CRLF2 high expression was detected in 26/178 (15%) T-cell acute lymphoblastic leukemia (T-ALL) cases, 21 of them (81%) had been stratified as high-risk patients by treatment response. In pB-ALL, a CRLF2 high expression was determined in 91/927 (10%) cases; the P2RY8/CRLF2 rearrangement in 44/91 (48%) of them, supernumerary copies of CRLF2 in 18/91 (20%), and, notably, the IGH/CRLF2 translocation was detected in 16/91 (18%). Remarkably, 7 of 16 (44%) patients with IGH/CRLF2 translocation had already relapsed. P2RY8/CRLF2- and IGH/CRLF2-positive samples (70 and 94%, respectively) were characterized by a high frequency of additional deletions in B-cell differentiation genes such as IKZF1 or PAX5. CONCLUSION Our data suggest that this high frequency of genetic aberrations in the context of a high CRLF2 expression could contribute to the high risk of relapse in P2RY8/CRLF2- and IGH/CRLF2-positive ALL.
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Affiliation(s)
- Juliane Schmäh
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Birthe Fedders
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - Susanna Fischer
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Elif Dagdan
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Susanne Bens
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Medical Center Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Denis Schewe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anja Moericke
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Kirsten Bleckmann
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Medical Center Schleswig-Holstein, Kiel, Germany.,Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
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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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Savino AM, Izraeli S. Interleukin-7 signaling as a therapeutic target in acute lymphoblastic leukemia. Expert Rev Hematol 2017; 10:183-185. [PMID: 28162019 DOI: 10.1080/17474086.2017.1292121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Angela Maria Savino
- a Safra Children's Hospital, Sheba Medical Center, Tel Hashomer , Ramat Gan , Israel
| | - Shai Izraeli
- b Sackler Faculty of Medicine , Tel Aviv University , Ramat Aviv , Israel
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