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Verma D, Kapoor S, Kumari S, Sharma D, Singh J, Benjamin M, Bakhshi S, Seth R, Nayak B, Sharma A, Pramanik R, Palanichamy JK, Sivasubbu S, Scaria V, Arora M, Kumar R, Chopra A. Decoding the genetic symphony: Profiling protein-coding and long noncoding RNA expression in T-acute lymphoblastic leukemia for clinical insights. PNAS NEXUS 2024; 3:pgae011. [PMID: 38328782 PMCID: PMC10847906 DOI: 10.1093/pnasnexus/pgae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024]
Abstract
T-acute lymphoblastic leukemia (T-ALL) is a heterogeneous malignancy characterized by the abnormal proliferation of immature T-cell precursors. Despite advances in immunophenotypic classification, understanding the molecular landscape and its impact on patient prognosis remains challenging. In this study, we conducted comprehensive RNA sequencing in a cohort of 35 patients with T-ALL to unravel the intricate transcriptomic profile. Subsequently, we validated the prognostic relevance of 23 targets, encompassing (i) protein-coding genes-BAALC, HHEX, MEF2C, FAT1, LYL1, LMO2, LYN, and TAL1; (ii) epigenetic modifiers-DOT1L, EP300, EML4, RAG1, EZH2, and KDM6A; and (iii) long noncoding RNAs (lncRNAs)-XIST, PCAT18, PCAT14, LINC00202, LINC00461, LINC00648, ST20, MEF2C-AS1, and MALAT1 in an independent cohort of 99 patients with T-ALL. Principal component analysis revealed distinct clusters aligning with immunophenotypic subtypes, providing insights into the molecular heterogeneity of T-ALL. The identified signature genes exhibited associations with clinicopathologic features. Survival analysis uncovered several independent predictors of patient outcomes. Higher expression of MEF2C, BAALC, HHEX, and LYL1 genes emerged as robust indicators of poor overall survival (OS), event-free survival (EFS), and relapse-free survival (RFS). Higher LMO2 expression was correlated with adverse EFS and RFS outcomes. Intriguingly, increased expression of lncRNA ST20 coupled with RAG1 demonstrated a favorable prognostic impact on OS, EFS, and RFS. Conclusively, several hitherto unreported associations of gene expression patterns with clinicopathologic features and prognosis were identified, which may help understand T-ALL's molecular pathogenesis and provide prognostic markers.
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Affiliation(s)
- Deepak Verma
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Shruti Kapoor
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India
| | - Sarita Kumari
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India
| | - Jay Singh
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Mercilena Benjamin
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Baibaswata Nayak
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi-110029, India
| | - Atul Sharma
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Raja Pramanik
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | | | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India
| | - Mohit Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Rajive Kumar
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Anita Chopra
- Laboratory Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi-110029, India
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Lahera A, Vela-Martín L, Fernández-Navarro P, Llamas P, López-Lorenzo JL, Cornago J, Santos J, Fernández-Piqueras J, Villa-Morales M. The JAK3 Q988P mutation reveals oncogenic potential and resistance to ruxolitinib. Mol Carcinog 2024; 63:5-10. [PMID: 37712558 DOI: 10.1002/mc.23632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/08/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) arises from the malignant transformation of T-cell progenitors at various differentiation stages. Given that patients who relapse have a dismal prognosis, there is an urgent need to identify the molecular alterations that are present in such patients and promote leukemogenesis to implement personalized therapies with higher efficacy and fewer adverse effects. In the present manuscript, we identified the JAK3Q988P mutation in a T-ALL patient who did not achieve a durable response after the conventional treatment and whose tumor cells at relapse presented constitutive activation of the JAK/STAT pathway. Although JAK3Q988P has been previously identified in T-ALL patients from different studies, the functional consequences exerted by this mutation remain unexplored. Through the combination of different hematopoietic cellular models, we functionally characterize JAK3Q988P as an oncogenic mutation that contributes to leukemogenesis. Notably, JAK3Q988P not only promotes constitutive activation of the JAK/STAT pathway in the absence of cytokines and growth factors, as is the case for other JAK3 mutations that have been functionally characterized as oncogenic, but also functions independently of JAK1 and IL2RG, resulting in high oncogenic potential as well as resistance to ruxolitinib. Our results indicate that ruxolitinib may not be efficient for future patients bearing the JAK3Q988P mutation who instead may obtain greater benefits from treatments involving other pharmacological inhibitors such as tofacitinib.
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Affiliation(s)
- Antonio Lahera
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Division of Genetics and Genomics, IIS Fundación Jiménez Díaz, Madrid, Spain
| | - Laura Vela-Martín
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Division of Genetics and Genomics, IIS Fundación Jiménez Díaz, Madrid, Spain
| | - Pablo Fernández-Navarro
- Division of Cancer and Environmental Epidemiology, Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
- Division of Epidemiology and Control of Chronic Diseases, Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Pilar Llamas
- Division of Hematology and Hemotherapy, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José L López-Lorenzo
- Division of Hematology and Hemotherapy, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Javier Cornago
- Division of Hematology and Hemotherapy, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Javier Santos
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Division of Genetics and Genomics, IIS Fundación Jiménez Díaz, Madrid, Spain
- Division of Genome Dynamics and Function, Institute for Molecular Biology-IUBM (Universidad Autónoma de Madrid), Madrid, Spain
| | - José Fernández-Piqueras
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Division of Genetics and Genomics, IIS Fundación Jiménez Díaz, Madrid, Spain
- Division of Genome Dynamics and Function, Institute for Molecular Biology-IUBM (Universidad Autónoma de Madrid), Madrid, Spain
| | - María Villa-Morales
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Division of Genetics and Genomics, IIS Fundación Jiménez Díaz, Madrid, Spain
- Division of Genome Dynamics and Function, Institute for Molecular Biology-IUBM (Universidad Autónoma de Madrid), Madrid, Spain
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3
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Paolino J, Dimitrov B, Winger BA, Sandoval-Perez A, Rangarajan AV, Ocasio-Martinez N, Tsai HK, Li Y, Robichaud AL, Khalid D, Hatton C, Gillani R, Polonen P, Dilig A, Gotti G, Kavanagh J, Adhav AA, Gow S, Tsai J, Li YD, Ebert BL, Van Allen EM, Bledsoe J, Kim AS, Tasian SK, Cooper SL, Cooper TM, Hijiya N, Sulis ML, Shukla NN, Magee JA, Mullighan CG, Burke MJ, Luskin MR, Mar BG, Jacobson MP, Harris MH, Stegmaier K, Place AE, Pikman Y. Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res 2023; 29:4613-4626. [PMID: 37725576 PMCID: PMC10872648 DOI: 10.1158/1078-0432.ccr-22-2562] [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: 08/16/2022] [Revised: 05/22/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. EXPERIMENTAL DESIGN We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia. RESULTS Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL. CONCLUSIONS Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Boris Dimitrov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | | | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Julia Kavanagh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Asmani A. Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sean Gow
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jonathan Tsai
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Yen Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jacob Bledsoe
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Sarah K. Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, and Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stacy L. Cooper
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Todd M. Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA
| | - Nobuko Hijiya
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, NY
| | - Maria Luisa Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav N. Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey A. Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, MO
| | | | - Michael J. Burke
- Medical College of Wisconsin, Children’s Hospital of Wisconsin, Milwaukee, WI
| | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
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4
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Walcheck MT, Nukaya M, Ranheim EA, Matkowskyj KA, Ronnekleiv-Kelly S. Pdx1 expression in hematopoietic cells activates Kras-mutation to drive leukemia in KC ( Pdx1-Cre; LSL-KrasG12D/+) mice. Leuk Lymphoma 2023; 64:1112-1122. [PMID: 37081806 PMCID: PMC10503568 DOI: 10.1080/10428194.2023.2202788] [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: 09/02/2022] [Revised: 03/01/2023] [Accepted: 04/09/2023] [Indexed: 04/22/2023]
Abstract
The highly utilized KC model has a reported lethality rate of about 30%, which has been attributed to pancreas cancer. However, a competing cause of lethality in KC mice is due to the activation of mutant-Kras gene (KrasG12D/+) in the multipotent progenitor cells (MPP), and subsequent development of Kras-mutant T-cell acute lymphoblastic leukemia (T-ALL). Overall, 20% (5/25) of KC mice developed T-ALL by 9 months of age. Transplantation of pooled bone marrow from KC mice into CD45 congenic mice caused T-ALL in 100% of recipient mice, confirming that mutant-Kras expression in the hematologic compartment is driving the development of T-ALL in the KC mouse model. These results are an essential consideration for investigators using this model. Further, the lower penetrance of T-ALL in KC mice (versus existing leukemia models) suggests this model could be considered as an alternative research model to evaluate onset and factors that exacerbate the development of T-ALL.
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Affiliation(s)
- Morgan T Walcheck
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
| | - Erik A Ranheim
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kristina A Matkowskyj
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sean Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, K3/705 CSC, Madison, WI, USA
- University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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5
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Abolhasani S, Hejazian SS, Karpisheh V, Khodakarami A, Mohammadi H, Gholizadeh Navashenaq J, Hojjat-Farsangi M, Jadidi-Niaragh F. The role of SF3B1 and NOTCH1 in the pathogenesis of leukemia. IUBMB Life 2023; 75:257-278. [PMID: 35848163 DOI: 10.1002/iub.2660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/18/2022] [Indexed: 11/09/2022]
Abstract
The discovery of new genes/pathways improves our knowledge of cancer pathogenesis and presents novel potential therapeutic options. For instance, splicing factor 3b subunit 1 (SF3B1) and NOTCH1 genetic alterations have been identified at a high frequency in hematological malignancies, such as leukemia, and may be related to the prognosis of involved patients because they change the nature of malignancies in different ways like mediating therapeutic resistance; therefore, studying these gene/pathways is essential. This review aims to discuss SF3B1 and NOTCH1 roles in the pathogenesis of various types of leukemia and the therapeutic potential of targeting these genes or their mutations to provide a foundation for leukemia treatment.
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Affiliation(s)
- Shiva Abolhasani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Vahid Karpisheh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Khodakarami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Mohammad Hojjat-Farsangi
- Bioclinicum, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.,The Persian Gulf Marine Biotechnology Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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6
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Sun L, Li X, Tu L, Stucky A, Huang C, Chen X, Cai J, Li SC. RNA-Sequencing Combined With Genome-Wide Allele-Specific Expression Patterning Identifies ZNF44 Variants as a Potential New Driver Gene for Pediatric Neuroblastoma. Cancer Control 2023; 30:10732748231175017. [PMID: 37161925 DOI: 10.1177/10732748231175017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
INTRODUCTION Neuroblastoma (NB) is one of the children's most common solid tumors, accounting for approximately 8% of pediatric malignancies and 15% of childhood cancer deaths. Somatic mutations in several genes, such as ALK, have been associated with NB progression and can facilitate the discovery of novel therapeutic strategies. However, the differential expression of mutated and wild-type alleles on the transcriptome level is poorly studied. METHODS This study analyzed 219 whole-exome sequencing datasets with somatic mutations detected by MuTect from paired normal and tumor samples. RESULTS We prioritized mutations in 8 candidate genes (RIMS4, RUSC2, ALK, MYCN, PTPN11, ALOX12B, ZNF44, and CNGB1) as potential driver mutations. We further confirmed the presence of allele-specific expression of the somatic mutations in NB with integrated analysis of 127 RNA-seq samples (of which 85 also had DNA-seq data available), including MYCN, ALK, and PTPN11. The allele-specific expression of mutations suggests that the same somatic mutation may have different effects on the clinical outcomes of tumors. CONCLUSION Our study suggests 2 novel variants of ZNF44 as a novel candidate driver gene for NB.
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Affiliation(s)
- Lan Sun
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Xiaoqing Li
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Lingli Tu
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andres Stucky
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chuan Huang
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Xuelian Chen
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jin Cai
- Department of Oral and Maxillofacial Surgery, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Shengwen Calvin Li
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Research Institute, Children's Hospital of Orange County (CHOC), Orange, CA, USA
- Department of Neurology, University of California, Irvine School of Medicine, Orange, CA, USA
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7
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Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution. Leukemia 2022; 36:1759-1768. [PMID: 35585141 PMCID: PMC9252914 DOI: 10.1038/s41375-022-01587-0] [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: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia. ![]()
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8
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Kośmider K, Karska K, Kozakiewicz A, Lejman M, Zawitkowska J. Overcoming Steroid Resistance in Pediatric Acute Lymphoblastic Leukemia-The State-of-the-Art Knowledge and Future Prospects. Int J Mol Sci 2022; 23:ijms23073795. [PMID: 35409154 PMCID: PMC8999045 DOI: 10.3390/ijms23073795] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy among children. Despite the enormous progress in ALL therapy, resulting in achieving a 5-year survival rate of up to 90%, the ambitious goal of reaching a 100% survival rate is still being pursued. A typical ALL treatment includes three phases: remission induction and consolidation and maintenance, preceded by a prednisone prephase. Poor prednisone response (PPR) is defined as the presence of ≥1.0 × 109 blasts/L in the peripheral blood on day eight of therapy and results in significantly frequent relapses and worse outcomes. Hence, identifying risk factors of steroid resistance and finding methods of overcoming that resistance may significantly improve patients' outcomes. A mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK-ERK) pathway seems to be a particularly attractive target, as its activation leads to steroid resistance via a phosphorylating Bcl-2-interacting mediator of cell death (BIM), which is crucial in the steroid-induced cell death. Several mutations causing activation of MAPK-ERK were discovered, notably the interleukin-7 receptor (IL-7R) pathway mutations in T-cell ALL and rat sarcoma virus (Ras) pathway mutations in precursor B-cell ALL. MAPK-ERK pathway inhibitors were demonstrated to enhance the results of dexamethasone therapy in preclinical ALL studies. This report summarizes steroids' mechanism of action, resistance to treatment, and prospects of steroids therapy in pediatric ALL.
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Affiliation(s)
- Kamil Kośmider
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland; (K.K.); (A.K.)
| | - Katarzyna Karska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
| | - Agata Kozakiewicz
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland; (K.K.); (A.K.)
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland;
- Correspondence:
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Integrated genomic analyses identify high-risk factors and actionable targets in T-cell acute lymphoblastic leukemia. BLOOD SCIENCE 2022; 4:16-28. [PMID: 35399540 PMCID: PMC8974951 DOI: 10.1097/bs9.0000000000000102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy often associated with poor outcomes. To identify high-risk factors and potential actionable targets for T-ALL, we perform integrated genomic and transcriptomic analyses on samples from 165 Chinese pediatric and adult T-ALL patients, of whom 85% have outcome information. The genomic mutation landscape of this Chinese cohort is very similar to the Western cohort published previously, except that the rate of NOTCH1 mutations is significant lower in the Chinese T-ALL patients. Among 47 recurrently mutated genes in 7 functional categories, we identify RAS pathway and PTEN mutations as poor survival factors for non-TAL and TAL subtypes, respectively. Mutations in the PI3K pathway are mutually exclusive with mutations in the RAS and NOTCH1 pathways as well as transcription factors. Further analysis demonstrates that approximately 43% of the high-risk patients harbor at least one potential actionable alteration identified in this study, and T-ALLs with RAS pathway mutations are hypersensitive to MEKi in vitro and in vivo. Thus, our integrated genomic analyses not only systematically identify high-risk factors but suggest that these high-risk factors are promising targets for T-ALL therapies.
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van der Zwet JCG, Buijs-Gladdines JGCAM, Cordo' V, Debets DO, Smits WK, Chen Z, Dylus J, Zaman GJR, Altelaar M, Oshima K, Bornhauser B, Bourquin JP, Cools J, Ferrando AA, Vormoor J, Pieters R, Vormoor B, Meijerink JPP. MAPK-ERK is a central pathway in T-cell acute lymphoblastic leukemia that drives steroid resistance. Leukemia 2021; 35:3394-3405. [PMID: 34007050 DOI: 10.1038/s41375-021-01291-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/17/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023]
Abstract
(Patho-)physiological activation of the IL7-receptor (IL7R) signaling contributes to steroid resistance in pediatric T-cell acute lymphoblastic leukemia (T-ALL). Here, we show that activating IL7R pathway mutations and physiological IL7R signaling activate MAPK-ERK signaling, which provokes steroid resistance by phosphorylation of BIM. By mass spectrometry, we demonstrate that phosphorylated BIM is impaired in binding to BCL2, BCLXL and MCL1, shifting the apoptotic balance toward survival. Treatment with MEK inhibitors abolishes this inactivating phosphorylation of BIM and restores its interaction with anti-apoptotic BCL2-protein family members. Importantly, the MEK inhibitor selumetinib synergizes with steroids in both IL7-dependent and IL7-independent steroid resistant pediatric T-ALL PDX samples. Despite the anti-MAPK-ERK activity of ruxolitinib in IL7-induced signaling and JAK1 mutant cells, ruxolitinib only synergizes with steroid treatment in IL7-dependent steroid resistant PDX samples but not in IL7-independent steroid resistant PDX samples. Our study highlights the central role for MAPK-ERK signaling in steroid resistance in T-ALL patients, and demonstrates the broader application of MEK inhibitors over ruxolitinib to resensitize steroid-resistant T-ALL cells. These findings strongly support the enrollment of T-ALL patients in the current phase I/II SeluDex trial (NCT03705507) and contributes to the optimization and stratification of newly designed T-ALL treatment regimens.
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Affiliation(s)
| | | | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center of Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Zhongli Chen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jelle Dylus
- Netherlands Translational Research Center B.V., Oss, the Netherlands
| | - Guido J R Zaman
- Netherlands Translational Research Center B.V., Oss, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center of Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Koichi Oshima
- Institute of Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Beat Bornhauser
- Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jean-Pierre Bourquin
- Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jan Cools
- KU Leuven Center for Human Genetics & VIB Center for Cancer Biology, Leuven, Belgium
| | - Adolfo A Ferrando
- Institute of Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Josef Vormoor
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Newcastle University, Newcastle upon Tyne, UK
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Britta Vormoor
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Keewan E, Matlawska-Wasowska K. The Emerging Role of Suppressors of Cytokine Signaling (SOCS) in the Development and Progression of Leukemia. Cancers (Basel) 2021; 13:4000. [PMID: 34439155 PMCID: PMC8393695 DOI: 10.3390/cancers13164000] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
Cytokines are pleiotropic signaling molecules that execute an essential role in cell-to-cell communication through binding to cell surface receptors. Receptor binding activates intracellular signaling cascades in the target cell that bring about a wide range of cellular responses, including induction of cell proliferation, migration, differentiation, and apoptosis. The Janus kinase and transducers and activators of transcription (JAK/STAT) signaling pathways are activated upon cytokines and growth factors binding with their corresponding receptors. The SOCS family of proteins has emerged as a key regulator of cytokine signaling, and SOCS insufficiency leads to constitutive activation of JAK/STAT signaling and oncogenic transformation. Dysregulation of SOCS expression is linked to various solid tumors with invasive properties. However, the roles of SOCS in hematological malignancies, such as leukemia, are less clear. In this review, we discuss the recent advances pertaining to SOCS dysregulation in leukemia development and progression. We also highlight the roles of specific SOCS in immune cells within the tumor microenvironment and their possible involvement in anti-tumor immunity. Finally, we discuss the epigenetic, genetic, and post-transcriptional modifications of SOCS genes during tumorigenesis, with an emphasis on leukemia.
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Affiliation(s)
- Esra’a Keewan
- Department of Pediatrics, Division of Hematology and Oncology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA;
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ksenia Matlawska-Wasowska
- Department of Pediatrics, Division of Hematology and Oncology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA;
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
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12
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T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness. Genes (Basel) 2021; 12:genes12081118. [PMID: 34440292 PMCID: PMC8394887 DOI: 10.3390/genes12081118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
T-cell acute lymphoblastic leukemias (T-ALL) are immature lymphoid tumors localizing in the bone marrow, mediastinum, central nervous system, and lymphoid organs. They account for 10-15% of pediatric and about 25% of adult acute lymphoblastic leukemia (ALL) cases. It is a widely heterogeneous disease that is caused by the co-occurrence of multiple genetic abnormalities, which are acquired over time, and once accumulated, lead to full-blown leukemia. Recurrently affected genes deregulate pivotal cell processes, such as cycling (CDKN1B, RB1, TP53), signaling transduction (RAS pathway, IL7R/JAK/STAT, PI3K/AKT), epigenetics (PRC2 members, PHF6), and protein translation (RPL10, CNOT3). A remarkable role is played by NOTCH1 and CDKN2A, as they are altered in more than half of the cases. The activation of the NOTCH1 signaling affects thymocyte specification and development, while CDKN2A haploinsufficiency/inactivation, promotes cell cycle progression. Among recurrently involved oncogenes, a major role is exerted by T-cell-specific transcription factors, whose deregulated expression interferes with normal thymocyte development and causes a stage-specific differentiation arrest. Hence, TAL and/or LMO deregulation is typical of T-ALL with a mature phenotype (sCD3 positive) that of TLX1, NKX2-1, or TLX3, of cortical T-ALL (CD1a positive); HOXA and MEF2C are instead over-expressed in subsets of Early T-cell Precursor (ETP; immature phenotype) and early T-ALL. Among immature T-ALL, genomic alterations, that cause BCL11B transcriptional deregulation, identify a specific genetic subgroup. Although comprehensive cytogenetic and molecular studies have shed light on the genetic background of T-ALL, biomarkers are not currently adopted in the diagnostic workup of T-ALL, and only a limited number of studies have assessed their clinical implications. In this review, we will focus on recurrent T-ALL abnormalities that define specific leukemogenic pathways and on oncogenes/oncosuppressors that can serve as diagnostic biomarkers. Moreover, we will discuss how the complex genomic profile of T-ALL can be used to address and test innovative/targeted therapeutic options.
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13
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Fan WJ, Xu TT, Guo JJ, Li YF, Jiang ZX. [Prognostic analysis of patients with mutations in the JAK/STAT signaling pathway in adult acute lymphoblastic leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:594-597. [PMID: 34455748 PMCID: PMC8408485 DOI: 10.3760/cma.j.issn.0253-2727.2021.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- W J Fan
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - T T Xu
- Department of Blood Transfusion, Henan Provincial People's Hospital, Zhengzhou 450000, China
| | - J J Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y F Li
- Department of Hematology Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Z X Jiang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
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14
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Guo SS, Mi JQ, Wang J. [The role and research progress of NOTCH1 in T-cell acute lymphoblastic leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:165-170. [PMID: 33858050 PMCID: PMC8071660 DOI: 10.3760/cma.j.issn.0253-2727.2021.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- S S Guo
- Department of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - J Q Mi
- Department of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - J Wang
- Department of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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15
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Walker KL, Rinella SP, Hess NJ, Turicek DP, Kabakov SA, Zhu F, Bouchlaka MN, Olson SL, Cho MM, Quamine AE, Feils AS, Gavcovich TB, Rui L, Capitini CM. CXCR4 allows T cell acute lymphoblastic leukemia to escape from JAK1/2 and BCL2 inhibition through CNS infiltration. Leuk Lymphoma 2021; 62:1167-1177. [PMID: 33843403 DOI: 10.1080/10428194.2021.1910684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Targeting the JAK/STAT and BCL2 pathways in patients with relapsed/refractory T cell acute lymphoblastic leukemia (T-ALL) may provide an alternative approach to achieve clinical remissions. Ruxolitinib and venetoclax show a dose-dependent effect on T-ALL individually, but combination treatment reduces survival and proliferation of T-ALL in vitro. Using a xenograft model, the combination treatment fails to improve survival, with death from hind limb paralysis. Despite on-target inhibition by the drugs, histopathology demonstrates increased leukemic infiltration into the central nervous system (CNS) as compared to liver or bone marrow. Liquid chromatography-tandem mass spectroscopy shows that ruxolitinib and venetoclax insufficiently cross into the CNS. The addition of the CXCR4 inhibitor plerixafor with ruxolitinib and venetoclax reduces clinical scores and enhances survival. While combination therapy with ruxolitinib and venetoclax shows promise for treating T-ALL, additional inhibition of the CXCR4-CXCL12 axis may be needed to maximize the possibility of complete remission.
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Affiliation(s)
- Kirsti L Walker
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sean P Rinella
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Nicholas J Hess
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - David P Turicek
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sabrina A Kabakov
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Fen Zhu
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Myriam N Bouchlaka
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sydney L Olson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Monica M Cho
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Aicha E Quamine
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Arika S Feils
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Tara B Gavcovich
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lixin Rui
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Christian M Capitini
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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16
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Borthakur G, Martinelli G, Raffoux E, Chevallier P, Chromik J, Lithio A, Smith CL, Yuen E, Oakley GJ, Benhadji KA, DeAngelo DJ. Phase 1 study to evaluate Crenigacestat (LY3039478) in combination with dexamethasone in patients with T-cell acute lymphoblastic leukemia and lymphoma. Cancer 2020; 127:372-380. [PMID: 33107983 DOI: 10.1002/cncr.33188] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Deregulated Notch signaling is implicated in T-cell acute lymphoblastic leukemia (T-ALL)/T-cell lymphoblastic lymphoma (T-LBL). Crenigacestat (LY3039478) prevents cleavage of Notch proteins and may benefit patients with relapsed/refractory T-ALL/T-LBL. METHODS JJCB was a multicenter, nonrandomized, open-label, dose-escalation, phase 1 study in adult patients with relapsed/refractory T-ALL/T-LBL. Eligible patients received Crenigacestat orally 3 times per week plus dexamethasone at 24 mg twice daily on days 1 to 5 every other week in a 28-day cycle. The starting level of Crenigacestat was 50 mg, and dose escalation was performed with a modified 3+3 scheme for the estimation of dose-limiting toxicity (DLT) at the recommended dose level. RESULTS In total, 36 patients with T-ALL (n = 31 [86.1%]) or T-LBL (n = 5 [13.9%]) were treated with Crenigacestat and dexamethasone. Six patients (16.7%) experienced DLTs: 2 of 12 (16.7%) in the 75-mg cohort (grade 4 gastrointestinal hemorrhage and grade 3 nausea, vomiting, and diarrhea), 1 of 15 (6.7%) in the 100-mg cohort (grade 3 diarrhea), and 3 of 3 (100%) in the 125-mg cohort (grade 3 diarrhea, nausea, and vomiting). The maximum tolerated dosewas 75 mg plus 24 mg of dexamethasone daily on days 1 to 5. Twenty-eight patients (77.8%) experienced 1 or more treatment-emergent adverse events related to the study treatment. The best overall response was a confirmed response, with 1 patient (2.8%) having a duration of response of 10.51 months. Six patients (16.7%) achieved stable disease, and 12 patients (33.3%) experienced progressive disease. The remaining 17 patients (47.2%) were not evaluable. The median event-free survival was 1.18 months (95% confidence interval, 0.76-2.14 months) among all groups. A pharmacodynamic analysis showed decreased plasma amyloid β levels. CONCLUSIONS Crenigacestat demonstrated limited clinical activity at the recommended dose in adult patients with relapsed/refractory T-ALL/T-LBL.
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Affiliation(s)
- Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giovanni Martinelli
- Department of Specialized, Diagnostic, and Experimental Medicine, University of Bologna, Bologna, Italy
| | | | - Patrice Chevallier
- Central University Research Hospital (CHRU) De Nantes, Hotel-Dieu, Nantes, France
| | - Jörg Chromik
- University Hospital Frankfurt, Frankfurt am Main, Germany
| | | | | | - Eunice Yuen
- Eli Lilly and Company, Surrey, United Kingdom
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Zhang D, Cheng Y, Fan J, Yao J, Zhao Z, Jiang Y, Li Y, Zuo Z, Tang Y, Guo Y. A Nomogram for the Prediction of Progression and Overall Survival in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 10:1550. [PMID: 32984014 PMCID: PMC7477348 DOI: 10.3389/fonc.2020.01550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/20/2020] [Indexed: 11/25/2022] Open
Abstract
Background: Advances in treatment and supportive care have significantly improved the overall survival (OS) of pediatric patients with acute lymphoblastic leukemia (ALL). However, there is a large number of these patients who continue to relapse after receiving standard treatment. Accurate identification of patients at high risk of relapse and targeted therapy may significantly improve their prognosis. Therefore, the aim of this study was to identify significant prognostic factors for pediatric ALL and establish a novel nomogram for the prediction of survival. Methods: The ALL clinical data of Phases I and II of the Therapeutic Applicable Research to Generate Effective Treatments (TARGET) project were merged and randomly divided into training and validation groups. The LASSO regression model was used to select the specific factors related to the OS of the training group and generate prognostic nomograms according to the selected characteristics. The predictive accuracy of the nomogram for OS was verified using the concordance index of the training and validation groups, the area under the receiver operating characteristic curve for prognostic diagnosis, and the calibration curve. Results: A total of 1,000 children with ALL were included in the TARGET project. Of those, 489 patients had complete follow-up data for further analysis. The data were randomly divided into the training group (n = 345) and the validation group (n = 144). Seven clinical characteristics, namely age at diagnosis, peripheral white blood cells, bone marrow and CNS site of relapse, ETV6/RUNX1 fusion, TCF3/PBX1, and BCR/ABL1 status, were selected to construct the nomogram. The concordance indices of the training and validation groups were 0.809 (95% confidence interval: 0.766–0.852) and 0.826 (95% confidence interval: 0.767–0.885), respectively. The areas under the receiver operating characteristic curve of the 3-year, 5-year, and 10-year OS in the training group were 0.804, 0.848, and 0.885, respectively, while that of the validation group were 0.777, 0.825, and 0.863, respectively. Moreover, the calibration curves demonstrated a favorable consistency between the predicted and actual survival probabilities. Conclusions: Independent predictors of OS in children with ALL included age at diagnosis, white blood cells, bone marrow site of relapse, CNS site of relapse, ETV6/RUNX1 fusion, TCF3/PBX1, and BCR/ABL1 status. The nomograms developed using these high-risk factors can more simply, accurately, and quantitatively predict the survival of children, and improve treatment and prognosis.
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Affiliation(s)
- Dan Zhang
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, China
| | - Yu Cheng
- Sichuan Luzhou Traditional Chinese Medicine Hospital, Luzhou, China
| | - Jia Fan
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, China
| | - Juan Yao
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, China
| | - Zijun Zhao
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, China
| | - Yao Jiang
- Southwest Medical University, Luzhou, China
| | - Yiqin Li
- Southwest Medical University, Luzhou, China
| | - Zhihua Zuo
- Southwest Medical University, Luzhou, China
| | - Yan Tang
- Department of Clinical Laboratory Medicine, Jinniu Maternity and Child Health Hospital of Chengdu, Chengdu, China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, China
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18
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hsa-miR-20b-5p and hsa-miR-363-3p Affect Expression of PTEN and BIM Tumor Suppressor Genes and Modulate Survival of T-ALL Cells In Vitro. Cells 2020; 9:cells9051137. [PMID: 32380791 PMCID: PMC7290785 DOI: 10.3390/cells9051137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis indicated their potential involvement in the regulation of apoptosis. Here, we aimed to test the hypothesis on the pro-tumorigenic roles of these miRNAs in T-ALL cells in vitro. We demonstrate, for the first time, that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster, when upregulated in T-ALL cells in vitro, protect leukemic cells from apoptosis, enhance proliferation, and contribute to growth advantage. We show, using dual luciferase reporter assays, Ago2-RNA immunoprecipitation, RT-qPCR, and Western blots, that the oncogenic effects of these upregulated miRNAs might, at least in part, be mediated by the downregulation of two important tumor suppressor genes, PTEN and BIM, targeted by both miRNAs. Additionally, we demonstrate the cooperative effects of these two miRNAs by simultaneous inhibition of both miRNAs as compared to the inhibition of single miRNAs. We postulate that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster might serve as oncomiRs in T-ALL, by contributing to post-transcriptional repression of key tumor suppressors, PTEN and BIM.
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Adult T-cell acute lymphoblastic leukemias with IL7R pathway mutations are slow-responders who do not benefit from allogeneic stem-cell transplantation. Leukemia 2020; 34:1730-1740. [PMID: 31992840 DOI: 10.1038/s41375-019-0685-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/17/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022]
Abstract
The prognostic value of IL7-receptor pathway (IL7Rp) mutations in T-cell acute lymphoblastic leukemia (T-ALL) remains unclear. We performed a comprehensive study of 200 adult patients with T-ALL included in the GRAALL2003/2005 protocols to address the clinical significance of IL7Rp mutations. Next-generation sequencing of the IL7Rp (IL7R/JAK1/JAK3/STAT5B) revealed that IL7Rp mutations were frequent in adult T-ALL (28%) particularly in immature/early T-cell progenitor (ETP)-ALL. They were associated with mutations of NOTCH-pathway, PHF6, and PRC2 components but not with K/NRAS. IL7Rp mutated (IL7Rpmut) T-ALL were slow-responders, with a high rate of M2/M3 day-8 marrow compared with IL7Rp non-mutated (IL7RpWT) T-ALL (p = 0.002) and minimal residual disease positivity at 6-weeks (MRD1) (p = 0.008) but no difference in MRD2 positivity at 12-weeks. Despite this, no adverse prognosis was evidenced when censored for allogeneic hematopoietic stem cell transplantation (HSCT). In time-dependent analysis, HSCT did not benefit IL7Rpmut patients whereas it was of marked benefit to IL7RpWT cases. IL7Rp-mutations identify a subgroup of slow-responder T-ALLs which benefit from post-induction chemotherapy regimens but not from HSCT. Our data suggest that prior knowledge of the mutation status of IL7Rp may influence HSCT decision and help to guide therapy reduction.
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20
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van der Zwet JCG, Cordo' V, Canté-Barrett K, Meijerink JPP. Multi-omic approaches to improve outcome for T-cell acute lymphoblastic leukemia patients. Adv Biol Regul 2019; 74:100647. [PMID: 31523030 DOI: 10.1016/j.jbior.2019.100647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
In the last decade, tremendous progress in curative treatment has been made for T-ALL patients using high-intensive, risk-adapted multi-agent chemotherapy. Further treatment intensification to improve the cure rate is not feasible as it will increase the number of toxic deaths. Hence, about 20% of pediatric patients relapse and often die due to acquired therapy resistance. Personalized medicine is of utmost importance to further increase cure rates and is achieved by targeting specific initiation, maintenance or resistance mechanisms of the disease. Genomic sequencing has revealed mutations that characterize genetic subtypes of many cancers including T-ALL. However, leukemia may have various activated pathways that are not accompanied by the presence of mutations. Therefore, screening for mutations alone is not sufficient to identify all molecular targets and leukemic dependencies for therapeutic inhibition. We review the extent of the driving type A and the secondary type B genomic mutations in pediatric T-ALL that may be targeted by specific inhibitors. Additionally, we review the need for additional screening methods on the transcriptional and protein levels. An integrated 'multi-omic' screening will identify potential targets and biomarkers to establish significant progress in future individualized treatment of T-ALL patients.
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Affiliation(s)
| | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Paganelli F, Lonetti A, Anselmi L, Martelli AM, Evangelisti C, Chiarini F. New advances in targeting aberrant signaling pathways in T-cell acute lymphoblastic leukemia. Adv Biol Regul 2019; 74:100649. [PMID: 31523031 DOI: 10.1016/j.jbior.2019.100649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/24/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive disorder characterized by malignant transformation of immature progenitors primed towards T-cell development. Over the past 15 years, advances in the molecular characterization of T-ALL have uncovered oncogenic key drivers and crucial signaling pathways of this disease, opening new chances for the development of novel therapeutic strategies. Currently, T-ALL patients are still treated with aggressive therapies, consisting of high dose multiagent chemotherapy. To minimize and overcome the unfavorable effects of these regimens, it is critical to identify innovative targets and test selective inhibitors of such targets. Major efforts are being made to develop small molecules against deregulated signaling pathways, which sustain T-ALL cell growth, survival, metabolism, and drug-resistance. This review will focus on recent improvements in the understanding of the signaling pathways involved in the pathogenesis of T-ALL and on the challenging opportunities for T-ALL targeted therapies.
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Affiliation(s)
- Francesca Paganelli
- Institute of Molecular Genetics, Luigi Luca Cavalli-Sforza-CNR National Research Council of Italy, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Annalisa Lonetti
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Laura Anselmi
- Department of Biomedical, Metabolic, and Neural Sciences, Section of Morphology, Signal Transduction Unit, University of Modena and Reggio Emilia, Modena, Italy
| | - Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Camilla Evangelisti
- Institute of Molecular Genetics, Luigi Luca Cavalli-Sforza-CNR National Research Council of Italy, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Francesca Chiarini
- Institute of Molecular Genetics, Luigi Luca Cavalli-Sforza-CNR National Research Council of Italy, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.
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22
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Wang Y. Comprehensive long non-coding RNA expression profiling by RNA sequencing reveals potential biomarkers for acute myeloid leukemia risk. Cancer Biomark 2019; 26:93-108. [DOI: 10.3233/cbm-190215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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De Smedt R, Morscio J, Goossens S, Van Vlierberghe P. Targeting steroid resistance in T-cell acute lymphoblastic leukemia. Blood Rev 2019; 38:100591. [PMID: 31353059 DOI: 10.1016/j.blre.2019.100591] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by a variable response to steroids during induction and/or consolidation therapy. Notably, recent work suggested that these differences in glucocorticoid sensitivity might, at least in part, be mediated by hyperactivation of specific oncogenic pathways such as RAS/MEK/ERK, PI3K/AKT and IL7R/JAK/STAT. In this review, we elaborate on putative associations between aberrant signaling, therapy resistance, incidence of relapse and clinical outcome in human T-ALL. Furthermore, we emphasize that this potential association with clinical parameters might also be mediated by the tumor microenvironment as a result of increased sensitivity of leukemic T-cells towards cytokine induced signaling pathway activation. With this in mind, we provide an overview of small molecule inhibitors that might have clinical potential for the treatment of human T-ALL in the near future as a result of their ability to overcome steroid resistance thereby potentially increasing survival rates in this aggressive hematological neoplasm.
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Affiliation(s)
- Renate De Smedt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Julie Morscio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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24
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Martelli AM, Paganelli F, Fazio A, Bazzichetto C, Conciatori F, McCubrey JA. The Key Roles of PTEN in T-Cell Acute Lymphoblastic Leukemia Development, Progression, and Therapeutic Response. Cancers (Basel) 2019; 11:cancers11050629. [PMID: 31064074 PMCID: PMC6562458 DOI: 10.3390/cancers11050629] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/16/2019] [Accepted: 05/04/2019] [Indexed: 02/07/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive blood cancer that comprises 10–15% of pediatric and ~25% of adult ALL cases. Although the curative rates have significantly improved over the past 10 years, especially in pediatric patients, T-ALL remains a challenge from a therapeutic point of view, due to the high number of early relapses that are for the most part resistant to further treatment. Considerable advances in the understanding of the genes, signaling networks, and mechanisms that play crucial roles in the pathobiology of T-ALL have led to the identification of the key drivers of the disease, thereby paving the way for new therapeutic approaches. PTEN is critical to prevent the malignant transformation of T-cells. However, its expression and functions are altered in human T-ALL. PTEN is frequently deleted or mutated, while PTEN protein is often phosphorylated and functionally inactivated by casein kinase 2. Different murine knockout models recapitulating the development of T-ALL have demonstrated that PTEN abnormalities are at the hub of an intricate oncogenic network sustaining and driving leukemia development by activating several signaling cascades associated with drug-resistance and poor outcome. These aspects and their possible therapeutic implications are highlighted in this review.
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Affiliation(s)
- Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Francesca Paganelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Antonietta Fazio
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy.
| | - Chiara Bazzichetto
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - Fabiana Conciatori
- Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - James A McCubrey
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
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25
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Li W, Xu L. Epigenetic Function of TET Family, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Hematologic Malignancies. Oncol Res Treat 2019; 42:309-318. [PMID: 31055566 DOI: 10.1159/000498947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
Abstract
DNA methylation plays significant roles in a variety of biological and pathological processes including mammalian development, genomic imprinting, retrotransposon silencing, and X-chromosome inactivation. Recent discoveries indicated that ten-eleven translocation (TET) family of dioxygenases can convert 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC). The TET family includes three members: TET1, TET2, and TET3. With increasing evidence, more and more biological and pathological processes in which 5-hmC and TET family serve unparalleled biological roles are noticed, for example, DNA demethylation and transcriptional regulation of different target genes, which are involved in many human diseases, especially hematologic malignancies, resembling chronic myelomonocytic leukemia, myelodysplastic syndromes, and so on. In this review, we focus on the diverse functions of TET family and the novel epigenetic marks, 5-mC and 5-hmC, in hematologic malignancies. This review will provide valuable insights into the potential targets of hematologic malignancies. Further understanding of the normal and pathological functions of TET family may provide new methods to develop novel epigenetic therapies for treating hematologic malignancies.
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Affiliation(s)
- Wei Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Linping Xu
- Department of Research and Foreign Affairs, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China,
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26
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Luo M, Zhang Q, Xia M, Hu F, Ma Z, Chen Z, Guo AY. Differential Co-expression and Regulatory Network Analysis Uncover the Relapse Factor and Mechanism of T Cell Acute Leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:184-194. [PMID: 30195757 PMCID: PMC6023839 DOI: 10.1016/j.omtn.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/02/2018] [Accepted: 05/04/2018] [Indexed: 01/17/2023]
Abstract
The pediatric T cell acute lymphoblastic leukemia (T-ALL) still remains a cancer with worst prognosis for high recurrence. Massive studies were conducted for the leukemia relapse based on diagnosis and relapse paired samples. However, the initially diagnostic samples may contain the relapse information and mechanism, which were rarely studied. In this study, we collected mRNA and microRNA (miRNA) data from initially diagnosed pediatric T-ALL samples with their relapse or remission status after treatment. Integrated differential co-expression and miRNA-transcription factor (TF)-gene regulatory network analyses were used to reveal the possible relapse mechanisms for pediatric T-ALL. We detected miR-1246/1248 and NOTCH2 served as key nodes in the relapse network, and they combined with TF WT1/SOX4/REL to form regulatory modules that influence the progress of T-ALL. A regulatory loop miR-429-MYCN-MFHAS1 was found potentially associated with the remission of T-ALL. Furthermore, we proved miR-1246/1248 combined with NOTCH2 could promote cell proliferation in the T-ALL cell line by experiments. Meanwhile, analysis based on the miRNA-drug relationships demonstrated that drugs 5-fluorouracil, ascorbate, and trastuzumab targeting miR-1246 could serve as potential supplements for the standard therapy. In conclusion, our findings revealed the potential molecular mechanisms of T-ALL relapse by the combination of co-expression and regulatory network, and they provide preliminary clues for precise treatment of T-ALL patients.
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Affiliation(s)
- Mei Luo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengxuan Xia
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Feifei Hu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaowu Ma
- Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Zehua Chen
- Joint Laboratory for the Research of Pharmaceutics-Huazhong University of Science and Technology and Infinitus, Wuhan, China
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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27
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Gianfelici V, Messina M, Paoloni F, Peragine N, Lauretti A, Fedullo AL, Di Giacomo F, Vignetti M, Vitale A, Guarini A, Chiaretti S, Foà R. IL7R overexpression in adult acute lymphoblastic leukemia is associated to JAK/STAT pathway mutations and identifies patients who could benefit from targeted therapies. Leuk Lymphoma 2018; 60:829-832. [PMID: 30188230 DOI: 10.1080/10428194.2018.1499906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Valentina Gianfelici
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Monica Messina
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | | | - Nadia Peragine
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Alessia Lauretti
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Anna Lucia Fedullo
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Filomena Di Giacomo
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Marco Vignetti
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy.,b GIMEMA Data Center, GIMEMA , Rome , Italy
| | - Antonella Vitale
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Anna Guarini
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Sabina Chiaretti
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Robin Foà
- a Hematology, Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
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28
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Biological Aspects of mTOR in Leukemia. Int J Mol Sci 2018; 19:ijms19082396. [PMID: 30110936 PMCID: PMC6121663 DOI: 10.3390/ijms19082396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is a central processor of intra- and extracellular signals, regulating many fundamental cellular processes such as metabolism, growth, proliferation, and survival. Strong evidences have indicated that mTOR dysregulation is deeply implicated in leukemogenesis. This has led to growing interest in the development of modulators of its activity for leukemia treatment. This review intends to provide an outline of the principal biological and molecular functions of mTOR. We summarize the current understanding of how mTOR interacts with microRNAs, with components of cell metabolism, and with controllers of apoptotic machinery. Lastly, from a clinical/translational perspective, we recapitulate the therapeutic results in leukemia, obtained by using mTOR inhibitors as single agents and in combination with other compounds.
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29
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Therapeutic Targeting of mTOR in T-Cell Acute Lymphoblastic Leukemia: An Update. Int J Mol Sci 2018; 19:ijms19071878. [PMID: 29949919 PMCID: PMC6073309 DOI: 10.3390/ijms19071878] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive blood malignancy that arises from the clonal expansion of transformed T-cell precursors. Although T-ALL prognosis has significantly improved due to the development of intensive chemotherapeutic protocols, primary drug-resistant and relapsed patients still display a dismal outcome. In addition, lifelong irreversible late effects from conventional therapy are a growing problem for leukemia survivors. Therefore, novel targeted therapies are required to improve the prognosis of high-risk patients. The mechanistic target of rapamycin (mTOR) is the kinase subunit of two structurally and functionally distinct multiprotein complexes, which are referred to as mTOR complex 1 (mTORC1) and mTORC2. These two complexes regulate a variety of physiological cellular processes including protein, lipid, and nucleotide synthesis, as well as autophagy in response to external cues. However, mTOR activity is frequently deregulated in cancer, where it plays a key oncogenetic role driving tumor cell proliferation, survival, metabolic transformation, and metastatic potential. Promising preclinical studies using mTOR inhibitors have demonstrated efficacy in many human cancer types, including T-ALL. Here, we highlight our current knowledge of mTOR signaling and inhibitors in T-ALL, with an emphasis on emerging evidence of the superior efficacy of combinations consisting of mTOR inhibitors and either traditional or targeted therapeutics.
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30
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Montaño A, Forero-Castro M, Marchena-Mendoza D, Benito R, Hernández-Rivas JM. New Challenges in Targeting Signaling Pathways in Acute Lymphoblastic Leukemia by NGS Approaches: An Update. Cancers (Basel) 2018; 10:cancers10040110. [PMID: 29642462 PMCID: PMC5923365 DOI: 10.3390/cancers10040110] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/18/2022] Open
Abstract
The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures. We reviewed the molecular basis of pathways including transcriptional regulation, lymphoid differentiation and development, TP53 and the cell cycle, RAS signaling, JAK/STAT, NOTCH, PI3K/AKT/mTOR, Wnt/β-catenin signaling, chromatin structure modifiers, and epigenetic regulators. The implementation of NGS strategies has enabled important mutated genes in each pathway, their associations with the genetic subtypes of ALL, and their outcomes, which will be described further. We also discuss classic and new cryptic DNA rearrangements in ALL identified by mRNA-seq strategies. Novel cooperative abnormalities in ALL could be key prognostic and/or predictive biomarkers for selecting the best frontline treatment and for developing therapies after the first relapse or refractory disease.
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Affiliation(s)
- Adrián Montaño
- IBSAL, IBMCC, Universidad de Salamanca-CSIC, Cancer Research Center, 37007 Salamanca, Spain.
| | - Maribel Forero-Castro
- Escuela de Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150001, Colombia.
| | - Darnel Marchena-Mendoza
- IBSAL, IBMCC, Universidad de Salamanca-CSIC, Cancer Research Center, 37007 Salamanca, Spain.
- Escuela de Ciencias Biológicas, Grupo de investigación en Ciencias Biomédicas (GICBUPTC), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150001, Colombia.
| | - Rocío Benito
- IBSAL, IBMCC, Universidad de Salamanca-CSIC, Cancer Research Center, 37007 Salamanca, Spain.
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31
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Shen Y, Liu Q, Lou S, Luo Y, Sun H, Zeng H, Deng J. Decreased expression of the augmenter of liver regeneration results in growth inhibition and increased chemosensitivity of acute T lymphoblastic leukemia cells. Oncol Rep 2017; 38:3130-3136. [PMID: 29048676 DOI: 10.3892/or.2017.5984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/17/2017] [Indexed: 11/06/2022] Open
Abstract
Augmenter of liver regeneration (ALR) plays crucial roles in cell survival and growth. Previous studies have demonstrated that ALR exerts a protective effect on toxic agent‑induced cell death in acute T lymphoblastic leukemia cells and ALR knockdown can sensitize cancer cells to radiation. However, the biological functions of ALR against drug resistance in T-cell acute lymphoblastic leukemia are mostly unknown. In the present study, we investigated the effect of small interfering RNA (siRNA)-induced ALR silencing on cell proliferation and sensitivity to vincristine (VCR) of Jurkat cells. We found that ALR siRNA effectively decreased the ALR expression, then inhibited cell growth and increased sensitivity to VCR in Jurkat cells. Flow cytometry assay revealed that the downregulation of ALR expression promoted cell apoptosis and regulated cell cycle distribution. Following incubation with VCR, apoptosis-related proteins, such as pro-PARP, pro-caspase 8, pro-caspase 3 and Bcl-2 were downregulated in the siRNA/ALR group. Pretreatment with siRNA/ALR in combination with VCR resulted in prolonged G2/M arrest, accompanied by downregulation of cdc25c and cdc2 expression and dissociation of cyclin B1. In conclusion, the results of this study demonstrated that targeted inhibition of the ALR expression in Jurkat cells triggered cell growth inhibition and sensitized cells to VCR via promoting apoptosis and regulating the cell cycle.
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Affiliation(s)
- Yan Shen
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Qi Liu
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Shifeng Lou
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Yun Luo
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Hang Sun
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Hanqing Zeng
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
| | - Jianchuan Deng
- Department of Hematology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, P.R. China
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32
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Kumar A, Kankainen M, Parsons A, Kallioniemi O, Mattila P, Heckman CA. The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia. BMC Genomics 2017; 18:629. [PMID: 28818039 PMCID: PMC5561555 DOI: 10.1186/s12864-017-4039-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022] Open
Abstract
Background RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient samples. Here, we applied two commonly used RNA-seq library preparation protocols to samples from acute leukemia patients to understand how poly-A-tailed mRNA selection (PA) and ribo-depletion (RD) based RNA-seq library preparation protocols affect gene fusion detection, variant calling, and gene expression profiling. Results Overall, the protocols produced similar results with consistent outcomes. Nevertheless, the PA protocol was more efficient in quantifying expression of leukemia marker genes and showed better performance in the expression-based classification of leukemia. Independent qRT-PCR experiments verified that the PA protocol better represented total RNA compared to the RD protocol. In contrast, the RD protocol detected a higher number of non-coding RNA features and had better alignment efficiency. The RD protocol also recovered more known fusion-gene events, although variability was seen in fusion gene predictions. Conclusion The overall findings provide a framework for the use of RNA-seq in a precision medicine setting with limited number of samples and suggest that selection of the library preparation protocol should be based on the objectives of the analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4039-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashwini Kumar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Alun Parsons
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland.,Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland.,Finnish Red Cross Blood Service, Kivihaantie 7, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, P.O. Box 20, Tukholmankatu 8, FI-00014, Helsinki, Finland.
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33
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Marincevic-Zuniga Y, Dahlberg J, Nilsson S, Raine A, Nystedt S, Lindqvist CM, Berglund EC, Abrahamsson J, Cavelier L, Forestier E, Heyman M, Lönnerholm G, Nordlund J, Syvänen AC. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles. J Hematol Oncol 2017; 10:148. [PMID: 28806978 PMCID: PMC5557398 DOI: 10.1186/s13045-017-0515-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. RESULTS We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. CONCLUSION Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.
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Affiliation(s)
- Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Dahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nilsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nystedt
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carl Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lucia Cavelier
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Mats Heyman
- Karolinska Institutet, Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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34
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Tesio M, Trinquand A, Ballerini P, Hypolite G, Lhermitte L, Petit A, Ifrah N, Baruchel A, Dombret H, Macintyre E, Asnafi V. Age-related clinical and biological features of PTEN abnormalities in T-cell acute lymphoblastic leukaemia. Leukemia 2017; 31:2594-2600. [DOI: 10.1038/leu.2017.157] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 04/03/2017] [Accepted: 05/15/2017] [Indexed: 01/07/2023]
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35
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Hof J, Kox C, Groeneveld-Krentz S, Bandapalli OR, Karawajew L, Schedel K, Kunz JB, Eckert C, Ludwig WD, Ratei R, Rhein P, Henze G, Muckenthaler MU, Kulozik AE, von Stackelberg A, Kirschner-Schwabe R. NOTCH1 mutation, TP53 alteration and myeloid antigen expression predict outcome heterogeneity in children with first relapse of T-cell acute lymphoblastic leukemia. Haematologica 2017; 102:e249-e252. [PMID: 28360149 DOI: 10.3324/haematol.2016.157792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jana Hof
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin.,German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinne Kox
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Stefanie Groeneveld-Krentz
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Obul R Bandapalli
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Leonid Karawajew
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Katharina Schedel
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Cornelia Eckert
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin.,German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolf-Dieter Ludwig
- HELIOS Medical Clinic Berlin-Buch, Clinic for Hematology, Oncology, Tumor Immunology and Palliative Care, Berlin
| | - Richard Ratei
- HELIOS Medical Clinic Berlin-Buch, Clinic for Hematology, Oncology, Tumor Immunology and Palliative Care, Berlin
| | - Peter Rhein
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Günter Henze
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Arend von Stackelberg
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin
| | - Renate Kirschner-Schwabe
- Department of Pediatrics, Division of Oncology and Hematology, Charité - University Medical Center Berlin .,German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), Heidelberg, Germany
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36
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Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE. Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia. Blood Cancer J 2017; 7:e523. [PMID: 28157215 PMCID: PMC5386337 DOI: 10.1038/bcj.2017.3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
In the search for genes that define critical steps of relapse in pediatric T-cell acute lymphoblastic leukemia (T-ALL) and can serve as prognostic markers, we performed targeted sequencing of 313 leukemia-related genes in 214 patients: 67 samples collected at the time of relapse and 147 at initial diagnosis. As relapse-specific genetic events, we identified activating mutations in NT5C2 (P=0.0001, Fisher's exact test), inactivation of TP53 (P=0.0007, Fisher's exact test) and duplication of chr17:q11.2-24.3 (P=0.0068, Fisher's exact test) in 32/67 of T-ALL relapse samples. Alterations of TP53 were frequently homozygous events, which significantly correlated with higher rates of copy number alterations in other genes compared with wild-type TP53 (P=0.0004, Mann–Whitney's test). We subsequently focused on mutations with prognostic impact and identified genes governing DNA integrity (TP53, n=8; USP7, n=4; MSH6, n=4), having key roles in the RAS signaling pathway (KRAS, NRAS, n=8), as well as IL7R (n=4) and CNOT3 (n=4) to be exclusively mutated in fatal relapses. These markers recognize 24/49 patients with a second event. In 17 of these patients with mostly refractory relapse and dire need for efficient treatment, we identified candidate targets for personalized therapy with p53 reactivating compounds, MEK inhibitors or JAK/STAT-inhibitors that may be incorporated in future treatment strategies.
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Affiliation(s)
- P Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - J B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - J Hof
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - M Zimmermann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - T Rausch
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - O R Bandapalli
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - E Orlova
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - G Scapinello
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,University of Padua, Padua, Italy
| | - J C Sagi
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - M Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - M Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - G Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - R Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - C Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - V Benes
- European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - J O Korbel
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - M U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - A E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
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