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IL-15 Prevents the Development of T-ALL from Aberrant Thymocytes with Impaired DNA Repair Functions and Increased NOTCH1 Activation. Cancers (Basel) 2023; 15:cancers15030671. [PMID: 36765626 PMCID: PMC9913776 DOI: 10.3390/cancers15030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
We previously reported that NOD.Scid mice lacking interleukin-15 (IL-15), or IL-15 receptor alpha-chain, develop T-acute lymphoblastic leukemia (T-ALL). To understand the mechanisms by which IL-15 signaling controls T-ALL development, we studied the thymocyte developmental events in IL-15-deficient Scid mice from NOD and C57BL/6 genetic backgrounds. Both kinds of mice develop T-ALL characterized by circulating TCR-negative cells expressing CD4, CD8 or both. Analyses of thymocytes in NOD.Scid.Il15-/- mice prior to T-ALL development revealed discernible changes within the CD4-CD8- double-negative (DN) thymocyte developmental stages and increased frequencies of CD4+CD8+ double-positive cells with a high proportion of TCR-negative CD4+ and CD8+ cells. The DN cells also showed elevated expressions of CXCR4 and CD117, molecules implicated in the expansion of DN thymocytes. T-ALL cell lines and primary leukemic cells from IL-15-deficient NOD.Scid and C57BL/6.Scid mice displayed increased NOTCH1 activation that was inhibited by NOTCH1 inhibitors and blockers of the PI3K/AKT pathway. Primary leukemic cells from NOD.Scid.Il15-/- mice survived and expanded when cultured with MS5 thymic stromal cells expressing Delta-like ligand 4 and supplemented with IL-7 and FLT3 ligand. These findings suggest that IL-15 signaling in the thymus controls T-ALL development from aberrant thymocytes with an impaired DNA repair capacity and increased NOTCH1 activation.
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Laukkanen S, Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher K, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher M, Heckman CA, Lohi O, Langenau DM. Therapeutic targeting of LCK tyrosine kinase and mTOR signaling in T-cell acute lymphoblastic leukemia. Blood 2022; 140:1891-1906. [PMID: 35544598 PMCID: PMC10082361 DOI: 10.1182/blood.2021015106] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Relapse and refractory T-cell acute lymphoblastic leukemia (T-ALL) has a poor prognosis, and new combination therapies are sorely needed. Here, we used an ex vivo high-throughput screening platform to identify drug combinations that kill zebrafish T-ALL and then validated top drug combinations for preclinical efficacy in human disease. This work uncovered potent drug synergies between AKT/mTORC1 (mammalian target of rapamycin complex 1) inhibitors and the general tyrosine kinase inhibitor dasatinib. Importantly, these same drug combinations effectively killed a subset of relapse and dexamethasone-resistant zebrafish T-ALL. Clinical trials are currently underway using the combination of mTORC1 inhibitor temsirolimus and dasatinib in other pediatric cancer indications, leading us to prioritize this therapy for preclinical testing. This combination effectively curbed T-ALL growth in human cell lines and primary human T-ALL and was well tolerated and effective in suppressing leukemia growth in patient-derived xenografts (PDX) grown in mice. Mechanistically, dasatinib inhibited phosphorylation and activation of the lymphocyte-specific protein tyrosine kinase (LCK) to blunt the T-cell receptor (TCR) signaling pathway, and when complexed with mTORC1 inhibition, induced potent T-ALL cell killing through reducing MCL-1 protein expression. In total, our work uncovered unexpected roles for the LCK kinase and its regulation of downstream TCR signaling in suppressing apoptosis and driving continued leukemia growth. Analysis of a wide array of primary human T-ALLs and PDXs grown in mice suggest that combination of temsirolimus and dasatinib treatment will be efficacious for a large fraction of human T-ALLs.
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Affiliation(s)
- Saara Laukkanen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alexandra Veloso
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Chuan Yan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Laura Oksa
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric J. Alpert
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Daniel Do
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Noora Hyvärinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Karin McCarthy
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Abhinav Adhikari
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Qiqi Yang
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sara P. Garcia
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Annukka Pello
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sanni Moisio
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Sadiksha Adhikari
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Kayleigh Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Lauren Whelton
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - James R. Allen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Alex H. Jin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Siebe Loontiens
- Cancer Research Institute Ghent and Center for Medical Genetics, Ghent, Belgium
| | - Merja Heinäniemi
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Michelle Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Olli Lohi
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tays Cancer Center, Tampere, Finland
| | - David M. Langenau
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
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3
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Fregona V, Bayet M, Gerby B. Oncogene-Induced Reprogramming in Acute Lymphoblastic Leukemia: Towards Targeted Therapy of Leukemia-Initiating Cells. Cancers (Basel) 2021; 13:cancers13215511. [PMID: 34771671 PMCID: PMC8582707 DOI: 10.3390/cancers13215511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Acute lymphoblastic leukemia is a heterogeneous disease characterized by a diversity of genetic alterations, following a sophisticated and controversial organization. In this review, we present and discuss the concepts exploring the cellular, molecular and functional heterogeneity of leukemic cells. We also review the emerging evidence indicating that cell plasticity and oncogene-induced reprogramming should be considered at the biological and clinical levels as critical mechanisms for identifying and targeting leukemia-initiating cells. Abstract Our understanding of the hierarchical structure of acute leukemia has yet to be fully translated into therapeutic approaches. Indeed, chemotherapy still has to take into account the possibility that leukemia-initiating cells may have a distinct chemosensitivity profile compared to the bulk of the tumor, and therefore are spared by the current treatment, causing the relapse of the disease. Therefore, the identification of the cell-of-origin of leukemia remains a longstanding question and an exciting challenge in cancer research of the last few decades. With a particular focus on acute lymphoblastic leukemia, we present in this review the previous and current concepts exploring the phenotypic, genetic and functional heterogeneity in patients. We also discuss the benefits of using engineered mouse models to explore the early steps of leukemia development and to identify the biological mechanisms driving the emergence of leukemia-initiating cells. Finally, we describe the major prospects for the discovery of new therapeutic strategies that specifically target their aberrant stem cell-like functions.
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Swaminathan S, Hansen AS, Heftdal LD, Dhanasekaran R, Deutzmann A, Fernandez WDM, Liefwalker DF, Horton C, Mosley A, Liebersbach M, Maecker HT, Felsher DW. MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies. Nat Commun 2020; 11:2860. [PMID: 32503978 PMCID: PMC7275060 DOI: 10.1038/s41467-020-16447-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/01/2020] [Indexed: 12/12/2022] Open
Abstract
The MYC oncogene drives T- and B- lymphoid malignancies, including Burkitt's lymphoma (BL) and Acute Lymphoblastic Leukemia (ALL). Here, we demonstrate a systemic reduction in natural killer (NK) cell numbers in SRα-tTA/Tet-O-MYCON mice bearing MYC-driven T-lymphomas. Residual mNK cells in spleens of MYCON T-lymphoma-bearing mice exhibit perturbations in the terminal NK effector differentiation pathway. Lymphoma-intrinsic MYC arrests NK maturation by transcriptionally repressing STAT1/2 and secretion of Type I Interferons (IFNs). Treating T-lymphoma-bearing mice with Type I IFN improves survival by rescuing NK cell maturation. Adoptive transfer of mature NK cells is sufficient to delay both T-lymphoma growth and recurrence post MYC inactivation. In MYC-driven BL patients, low expression of both STAT1 and STAT2 correlates significantly with the absence of activated NK cells and predicts unfavorable clinical outcomes. Our studies thus provide a rationale for developing NK cell-based therapies to effectively treat MYC-driven lymphomas in the future.
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MESH Headings
- Adoptive Transfer
- Animals
- Burkitt Lymphoma/immunology
- Burkitt Lymphoma/mortality
- Cell Line, Tumor/transplantation
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic/immunology
- Humans
- Immunologic Surveillance/genetics
- Interferon Type I/pharmacology
- Interferon Type I/therapeutic use
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/transplantation
- Lymphoma, T-Cell/drug therapy
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Primary Cell Culture
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- STAT1 Transcription Factor/metabolism
- STAT2 Transcription Factor/metabolism
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Signal Transduction/immunology
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Affiliation(s)
- Srividya Swaminathan
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Aida S Hansen
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Line D Heftdal
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Renumathy Dhanasekaran
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Stanford University, Stanford, CA, USA
| | - Anja Deutzmann
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Wadie D M Fernandez
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Daniel F Liefwalker
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Crista Horton
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Adriane Mosley
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Mariola Liebersbach
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Dean W Felsher
- Division of Oncology, Departments of Medicine and Pathology, Stanford University, Stanford, CA, USA.
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5
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Development and validation of a multivariate predictive model for rheumatoid arthritis mortality using a machine learning approach. Sci Rep 2017; 7:10189. [PMID: 28860558 PMCID: PMC5579234 DOI: 10.1038/s41598-017-10558-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
We developed and independently validated a rheumatoid arthritis (RA) mortality prediction model using the machine learning method Random Survival Forests (RSF). Two independent cohorts from Madrid (Spain) were used: the Hospital Clínico San Carlos RA Cohort (HCSC-RAC; training; 1,461 patients), and the Hospital Universitario de La Princesa Early Arthritis Register Longitudinal study (PEARL; validation; 280 patients). Demographic and clinical-related variables collected during the first two years after disease diagnosis were used. 148 and 21 patients from HCSC-RAC and PEARL died during a median follow-up time of 4.3 and 5.0 years, respectively. Age at diagnosis, median erythrocyte sedimentation rate, and number of hospital admissions showed the higher predictive capacity. Prediction errors in the training and validation cohorts were 0.187 and 0.233, respectively. A survival tree identified five mortality risk groups using the predicted ensemble mortality. After 1 and 7 years of follow-up, time-dependent specificity and sensitivity in the validation cohort were 0.79–0.80 and 0.43–0.48, respectively, using the cut-off value dividing the two lower risk categories. Calibration curves showed overestimation of the mortality risk in the validation cohort. In conclusion, we were able to develop a clinical prediction model for RA mortality using RSF, providing evidence for further work on external validation.
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6
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Rai AK, Singh A, Saxena A, Seth T, Raina V, Mitra DK. Exonal switch down-regulates the expression of CD5 on blasts of acute T cell leukaemia. Clin Exp Immunol 2017; 190:340-350. [PMID: 28752543 DOI: 10.1111/cei.13019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 11/27/2022] Open
Abstract
To date, CD5 expression and its role in acute T cell lymphoblastic leukaemia (T-ALL) have not been studied closely. We observed a significant reduction in surface expression of CD5 (sCD5) on leukaemic T cells compared to autologous non-leukaemic T cells. In this study, we have shown the molecular mechanism regulating the expression and function of CD5 on leukaemic T cells. A total of 250 patients suffering from leukaemia and lymphoma were immunophenotyped. Final diagnosis was based on their clinical presentation, morphological data and flow cytometry-based immunophenotyping. Thirty-nine patients were found to be of ALL-T origin. Amplification of early region of E1A and E1B transcripts of CD5 was correlated with the levels of surface and intracellular expression of CD5 protein. Functional studies were performed to show the effect of CD5 blocking on interleukin IL-2 production and survival of leukaemic and non-leukaemic cells. Lack of expression of sCD5 on T-ALL blasts was correlated closely with predominant transcription of exon E1B and significant loss of exon E1A of the CD5 gene, which is associated with surface expression of CD5 on lymphocytes. High expression of E1B also correlates with increased expression of cytoplasmic CD5 (cCD5) among leukaemic T cells. Interestingly, we observed a significant increase in the production of IL-2 by non-leukaemic T cells upon CD5 blocking, leading possibly to their increased survival at 48 h. Our study provides understanding of the regulation of CD5 expression on leukaemic T cells, and may help in understanding the molecular mechanism of CD5 down-regulation.
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Affiliation(s)
- A K Rai
- Cellular Immunology Division, Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences (AIIMS), New Delhi, India.,Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - A Singh
- Cellular Immunology Division, Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - A Saxena
- Cellular Immunology Division, Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - T Seth
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - V Raina
- Department of Medical Oncology, BRAIRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - D K Mitra
- Cellular Immunology Division, Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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7
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Gerby B, Veiga DFT, Krosl J, Nourreddine S, Ouellette J, Haman A, Lavoie G, Fares I, Tremblay M, Litalien V, Ottoni E, Kosic M, Geoffrion D, Ryan J, Maddox PS, Chagraoui J, Marinier A, Hébert J, Sauvageau G, Kwok BH, Roux PP, Hoang T. High-throughput screening in niche-based assay identifies compounds to target preleukemic stem cells. J Clin Invest 2016; 126:4569-4584. [PMID: 27797342 DOI: 10.1172/jci86489] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/22/2016] [Indexed: 12/15/2022] Open
Abstract
Current chemotherapies for T cell acute lymphoblastic leukemia (T-ALL) efficiently reduce tumor mass. Nonetheless, disease relapse attributed to survival of preleukemic stem cells (pre-LSCs) is associated with poor prognosis. Herein, we provide direct evidence that pre-LSCs are much less chemosensitive to existing chemotherapy drugs than leukemic blasts because of a distinctive lower proliferative state. Improving therapies for T-ALL requires the development of strategies to target pre-LSCs that are absolutely dependent on their microenvironment. Therefore, we designed a robust protocol for high-throughput screening of compounds that target primary pre-LSCs maintained in a niche-like environment, on stromal cells that were engineered for optimal NOTCH1 activation. The multiparametric readout takes into account the intrinsic complexity of primary cells in order to specifically monitor pre-LSCs, which were induced here by the SCL/TAL1 and LMO1 oncogenes. We screened a targeted library of compounds and determined that the estrogen derivative 2-methoxyestradiol (2-ME2) disrupted both cell-autonomous and non-cell-autonomous pathways. Specifically, 2-ME2 abrogated pre-LSC viability and self-renewal activity in vivo by inhibiting translation of MYC, a downstream effector of NOTCH1, and preventing SCL/TAL1 activity. In contrast, normal hematopoietic stem/progenitor cells remained functional. These results illustrate how recapitulating tissue-like properties of primary cells in high-throughput screening is a promising avenue for innovation in cancer chemotherapy.
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8
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DNA methylation of CiRIG-I gene notably relates to the resistance against GCRV and negatively-regulates mRNA expression in grass carp, Ctenopharyngodon idella. Immunobiology 2016; 221:23-30. [DOI: 10.1016/j.imbio.2015.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/29/2015] [Accepted: 08/11/2015] [Indexed: 11/19/2022]
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9
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Ruffalo M, Husseinzadeh H, Makishima H, Przychodzen B, Ashkar M, Koyutürk M, Maciejewski JP, LaFramboise T. Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J Biomed Inform 2015; 58:104-113. [PMID: 26453823 DOI: 10.1016/j.jbi.2015.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/14/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
PURPOSE To date the standard nosology and prognostic schemes for myeloid neoplasms have been based on morphologic and cytogenetic criteria. We sought to test the hypothesis that a comprehensive, unbiased analysis of somatic mutations may allow for an improved classification of these diseases to predict outcome (overall survival). EXPERIMENTAL DESIGN We performed whole-exome sequencing (WES) of 274 myeloid neoplasms, including myelodysplastic syndrome (MDS, N=75), myelodysplastic/myeloproliferative neoplasia (MDS/MPN, N=33), and acute myeloid leukemia (AML, N=22), augmenting the resulting mutational data with public WES results from AML (N=144). We fit random survival forests (RSFs) to the patient survival and clinical/cytogenetic data, with and without gene mutation information, to build prognostic classifiers. A targeted sequencing assay was used to sequence predictor genes in an independent cohort of 507 patients, whose accompanying data were used to evaluate performance of the risk classifiers. RESULTS We show that gene mutations modify the impact of standard clinical variables on patient outcome, and therefore their incorporation hones the accuracy of prediction. The mutation-based classification scheme robustly predicted patient outcome in the validation set (log rank P=6.77 × 10(-21); poor prognosis vs. good prognosis categories HR 10.4, 95% CI 3.21-33.6). The RSF-based approach also compares favorably with recently-published efforts to incorporate mutational information for MDS prognosis. CONCLUSION The results presented here support the inclusion of mutational information in prognostic classification of myeloid malignancies. Our classification scheme is implemented in a publicly available web-based tool (http://myeloid-risk. CASE edu/).
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Affiliation(s)
- Matthew Ruffalo
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA
| | - Holleh Husseinzadeh
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohamed Ashkar
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, OH, USA.
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10
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Abstract
PURPOSE OF REVIEW Recent genome sequencing studies have identified a broad spectrum of gene mutations in T-cell acute lymphoblastic leukemia (T-ALL). The purpose of this review is to outline the latest advances in our understanding of how these mutations contribute to the formation of T-ALL. RECENT FINDINGS Aberrant expression of transcription factors that control hematopoiesis can induce an aberrant stem cell-like program in T-cell progenitors, allowing the emergence of an ancestral or preleukemic stem cell (pre-LSC). In contrast, gain-of-function mutations of genes involved in signaling pathways regulating T-cell development, such as NOTCH1, interleukin-7, KIT and FLT3, are insufficient per se to initiate T-ALL but promote pre-LSC growth independent of the thymic niche. Loss-of-function mutations of epigenetic regulators, such as DNMT3A, have been identified in T-ALL, but their role in leukemogenesis remains to be defined. SUMMARY Relapse is associated with clonal evolution from a population of pre-LSCs that acquire the whole set of malignant mutations leading to a full-blown T-ALL. Understanding the genetic events that underpin the pre-LSC will be crucial for reducing the risk of relapse.
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11
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Affiliation(s)
- Steven Goossens
- VIB Inflammation Research Center, Ghent University, Ghent, Belgium
- Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Mammalian Functional Genetics Laboratory, Division of Blood Cancers, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
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12
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Yui MA, Rothenberg EV. Developmental gene networks: a triathlon on the course to T cell identity. Nat Rev Immunol 2014; 14:529-45. [PMID: 25060579 PMCID: PMC4153685 DOI: 10.1038/nri3702] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells acquire their ultimate identities by activating combinations of transcription factors that initiate and sustain expression of the appropriate cell type-specific genes. T cell development depends on the progression of progenitor cells through three major phases, each of which is associated with distinct transcription factor ensembles that control the recruitment of these cells to the thymus, their proliferation, lineage commitment and responsiveness to T cell receptor signals, all before the allocation of cells to particular effector programmes. All three phases are essential for proper T cell development, as are the mechanisms that determine the boundaries between each phase. Cells that fail to shut off one set of regulators before the next gene network phase is activated are predisposed to leukaemic transformation.
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Affiliation(s)
- Mary A Yui
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Ellen V Rothenberg
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
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13
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Gerby B, Hoang T. Modelling acute leukemias in mice: clonal evolution and the emergence of leukemic stem cells. BMC Proc 2013; 7 Suppl 2:K1. [PMID: 24764466 PMCID: PMC3624666 DOI: 10.1186/1753-6561-7-s2-k1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Bastien Gerby
- Institute of Research in Immunology and Cancer, University of Montréal, Montréal, Québec, Canada H3C 3J7 ; Molecular Biology Program, University of Montréal, Montréal, Québec, Canada H3C 3J7
| | - Trang Hoang
- Institute of Research in Immunology and Cancer, University of Montréal, Montréal, Québec, Canada H3C 3J7 ; Molecular Biology Program, University of Montréal, Montréal, Québec, Canada H3C 3J7 ; Departments of Medicine, University of Montréal, Montréal, Québec, Canada H3C 3J7 ; Department of Pharmacology. University of Montréal, Montréal, Québec, Canada H3C 3J7 ; Department of Biochemistry, University of Montréal, Montréal, Québec, Canada H3C 3J7
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Clinical and molecular characterization of early T-cell precursor leukemia: a high-risk subgroup in adult T-ALL with a high frequency of FLT3 mutations. Blood Cancer J 2012; 2:e55. [PMID: 22829239 PMCID: PMC3270253 DOI: 10.1038/bcj.2011.49] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 11/18/2011] [Accepted: 11/25/2011] [Indexed: 12/22/2022] Open
Abstract
A subgroup of pediatric acute T-lymphoblastic leukemia (T-ALL) was characterized by a gene expression profile comparable to that of early T-cell precursors (ETPs) with a highly unfavorable outcome. We have investigated clinical and molecular characteristics of the ETP-ALL subgroup in adult T-ALL. As ETP-ALL represents a subgroup of early T-ALL we particularly focused on this cohort and identified 178 adult patients enrolled in the German Acute Lymphoblastic Leukemia Multicenter studies (05/93–07/03). Of these, 32% (57/178) were classified as ETP-ALL based on their characteristic immunophenotype. The outcome of adults with ETP-ALL was poor with an overall survival of only 35% at 10 years, comparable to the inferior outcome of early T-ALL with 38%. The molecular characterization of adult ETP-ALL revealed distinct alterations with overexpression of stem cell-related genes (BAALC, IGFBP7, MN1, WT1). Interestingly, we found a low rate of NOTCH1 mutations and no FBXW7 mutations in adult ETP-ALL. In contrast, FLT3 mutations, rare in the overall cohort of T-ALL, were very frequent and nearly exclusively found in ETP-ALL characterized by a specific immunophenotype. These molecular characteristics provide biologic insights and implications with respect to innovative treatment strategies (for example, tyrosine kinase inhibitors) for this high-risk subgroup of adult ETP-ALL.
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