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Wendorff AA, Aidan Quinn S, Alvarez S, Brown JA, Biswas M, Gunning T, Palomero T, Ferrando AA. Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice. Nat Aging 2022; 2:1008-1023. [PMID: 37118089 DOI: 10.1038/s43587-022-00304-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 10/03/2022] [Indexed: 04/30/2023]
Abstract
Aging is characterized by an accumulation of myeloid-biased hematopoietic stem cells (HSCs) with reduced developmental potential. Genotoxic stress and epigenetic alterations have been proposed to mediate age-related HSC loss of regenerative and self-renewal potential. However, the mechanisms underlying these changes remain largely unknown. Genetic inactivation of the plant homeodomain 6 (Phf6) gene, a nucleolar and chromatin-associated factor, antagonizes age-associated HSC decline. Immunophenotyping, single-cell transcriptomic analyses and transplantation assays demonstrated markedly decreased accumulation of immunophenotypically defined HSCs, reduced myeloid bias and increased hematopoietic reconstitution capacity with preservation of lymphoid differentiation potential in Phf6-knockout HSCs from old mice. Moreover, deletion of Phf6 in aged mice rejuvenated immunophenotypic, transcriptional and functional hallmarks of aged HSCs. Long-term HSCs from old Phf6-knockout mice showed epigenetic rewiring and transcriptional programs consistent with decreased genotoxic stress-induced HSC aging. These results identify Phf6 as an important epigenetic regulator of HSC aging.
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Affiliation(s)
- Agnieszka A Wendorff
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Calico Life Sciences, South San Francisco, CA, USA.
| | - S Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Silvia Alvarez
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Mayukh Biswas
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Teresa Palomero
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Regeneron Genetics Center, Tarrytown, NY, USA.
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2
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Wendorff AA, Ferrando AA. Modeling NOTCH1 driven T-cell Acute Lymphoblastic Leukemia in Mice. Bio Protoc 2020; 10:e3620. [PMID: 33659293 DOI: 10.21769/bioprotoc.3620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/13/2019] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that arises from transformation of T-cell primed hematopoietic progenitors. Although T-ALL is a heterogenous and molecularly complex disease, more than 65% of T-ALL patients carry activating mutations in the NOTCH1 gene. The majority of T-ALL-associated NOTCH1 mutations either disrupt the negative regulatory region, allowing signal activation in the absence of ligand binding, or result in truncation of the C-terminal PEST domain involved in the termination of NOTCH1 signaling by proteasomal degradation. To date, retroviral transduction models have relied heavily on the overexpression of aggressively truncated variants of NOTCH1 (such as ICN1 or ΔE-NOTCH1), which result in supraphysiological levels of signaling activity and are rarely found in human T-ALL. The current protocol describes the method for mouse bone marrow isolation, hematopoietic stem and progenitor cell (HSC) enrichment, followed by retroviral transduction with an oncogenic mutant form of the NOTCH1 receptor (NOTCH1-L1601P-ΔP) that closely resembles the gain-of-function mutations most commonly found in patient samples. A hallmark of this forced expression of constitutively active NOTCH1 is a transient wave of extrathymic immature T-cell development, which precedes oncogenic transformation to T-ALL. Furthermore, this approach models leukemic transformation and progression in vivo by allowing for crosstalk between leukemia cells and the microenvironment, an aspect unaccounted for in cell-line based in vitro studies. Thus, the HSC transduction and transplantation model more faithfully recapitulates development of the human disease, providing a highly comprehensive and versatile tool for further in vivo and ex vivo functional studies.
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Affiliation(s)
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, USA.,Department of Pediatrics, Columbia University Medical Center, New York, USA.,Department of Systems Biology, Columbia University, New York, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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3
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Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Pérez-Durán P, Álvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortés JR, Cooke AJ, Wendorff AA, Cordó V, Meijerink JP, Rabadan R, Ferrando AA. GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia. Cancer Discov 2019; 9:1774-1791. [PMID: 31519704 DOI: 10.1158/2159-8290.cd-19-0471] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/15/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022]
Abstract
Long-range enhancers govern the temporal and spatial control of gene expression; however, the mechanisms that regulate enhancer activity during normal and malignant development remain poorly understood. Here, we demonstrate a role for aberrant chromatin accessibility in the regulation of MYC expression in T-cell lymphoblastic leukemia (T-ALL). Central to this process, the NOTCH1-MYC enhancer (N-Me), a long-range T cell-specific MYC enhancer, shows dynamic changes in chromatin accessibility during T-cell specification and maturation and an aberrant high degree of chromatin accessibility in mouse and human T-ALL cells. Mechanistically, we demonstrate that GATA3-driven nucleosome eviction dynamically modulates N-Me enhancer activity and is strictly required for NOTCH1-induced T-ALL initiation and maintenance. These results directly implicate aberrant regulation of chromatin accessibility at oncogenic enhancers as a mechanism of leukemic transformation. SIGNIFICANCE: MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. Here, we show a major role for GATA3-mediated enhancer nucleosome eviction as a driver of MYC expression and leukemic transformation. These results support the role of aberrant chromatin accessibility and consequent oncogenic MYC enhancer activation in NOTCH1-induced T-ALL.This article is highlighted in the In This Issue feature, p. 1631.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Alexander Y Yang
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
| | | | - S Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Pablo Pérez-Durán
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Silvia Álvarez
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Francesca Gianni
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Devya Gurung
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Pedro P Rocha
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, La Jolla, California.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Clara Reglero
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Jose R Cortés
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Anisha J Cooke
- Institute for Cancer Genetics, Columbia University, New York, New York
| | | | - Valentina Cordó
- Department of Pediatric Oncology/Hematology, Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jules P Meijerink
- Department of Pediatric Oncology/Hematology, Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Raúl Rabadan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey.,Department of Biomedical Informatics, Columbia University, New York, New York
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York. .,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey.,Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Pathology, Columbia University Medical Center, New York, New York
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4
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Wendorff AA, Quinn SA, Rashkovan M, Madubata CJ, Ambesi-Impiombato A, Litzow MR, Tallman MS, Paietta E, Paganin M, Basso G, Gastier-Foster JM, Loh ML, Rabadan R, Van Vlierberghe P, Ferrando AA. Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL. Cancer Discov 2018; 9:436-451. [PMID: 30567843 DOI: 10.1158/2159-8290.cd-18-1005] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 11/16/2022]
Abstract
The plant homeodomain 6 gene (PHF6) is frequently mutated in human T-cell acute lymphoblastic leukemia (T-ALL); however, its specific functional role in leukemia development remains to be established. Here, we show that loss of PHF6 is an early mutational event in leukemia transformation. Mechanistically, genetic inactivation of Phf6 in the hematopoietic system enhances hematopoietic stem cell (HSC) long-term self-renewal and hematopoietic recovery after chemotherapy by rendering Phf6 knockout HSCs more quiescent and less prone to stress-induced activation. Consistent with a leukemia-initiating tumor suppressor role, inactivation of Phf6 in hematopoietic progenitors lowers the threshold for the development of NOTCH1-induced T-ALL. Moreover, loss of Phf6 in leukemia lymphoblasts activates a leukemia stem cell transcriptional program and drives enhanced T-ALL leukemia-initiating cell activity. These results implicate Phf6 in the control of HSC homeostasis and long-term self-renewal and support a role for PHF6 loss as a driver of leukemia-initiating cell activity in T-ALL. SIGNIFICANCE: Phf6 controls HSC homeostasis, leukemia initiation, and T-ALL leukemia-initiating cell self-renewal. These results substantiate a role for PHF6 mutations as early events and drivers of leukemia stem cell activity in the pathogenesis of T-ALL.This article is highlighted in the In This Issue feature, p. 305.
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Affiliation(s)
| | - S Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, New York.,Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Chioma J Madubata
- Department of Systems Biology, Columbia University, New York, New York
| | | | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Martin S Tallman
- Department of Hematologic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisabeth Paietta
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Maddalena Paganin
- Onco-Hematology Division, Department, Salute della Donna e del Bambino (SDB), University of Padua, Padua, Italy
| | - Giuseppe Basso
- Onco-Hematology Division, Department, Salute della Donna e del Bambino (SDB), University of Padua, Padua, Italy.,Italian Institute for Genomic Medicine (HMG), Turin, Italy
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pathology, Ohio State University School of Medicine, Columbus, Ohio.,Department of Pediatrics, Ohio State University School of Medicine, Columbus, Ohio.,Children's Oncology Group, Arcadia, California
| | - Mignon L Loh
- Department of Pediatrics, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, New York.,Department of Biomedical Informatics, Columbia University, New York, New York
| | - Pieter Van Vlierberghe
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York. .,Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Systems Biology, Columbia University, New York, New York.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
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5
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Herranz D, Ambesi-Impiombato A, Sudderth J, Sánchez-Martín M, Belver L, Tosello V, Xu L, Wendorff AA, Castillo M, Haydu JE, Márquez J, Matés JM, Kung AL, Rayport S, Cordon-Cardo C, DeBerardinis RJ, Ferrando AA. Metabolic reprogramming induces resistance to anti-NOTCH1 therapies in T cell acute lymphoblastic leukemia. Nat Med 2015; 21:1182-9. [PMID: 26390244 PMCID: PMC4598309 DOI: 10.1038/nm.3955] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/27/2015] [Indexed: 12/14/2022]
Abstract
Activating mutations in NOTCH1 are common in T-cell acute lymphoblastic leukemia (TALL). Here we identify glutaminolysis as a critical pathway for leukemia cell growth downstream of NOTCH1 and a key determinant of clinical response to anti-NOTCH1 therapies. Mechanistically, inhibition of NOTCH1 signaling in T-ALL induces a metabolic shutdown with prominent inhibition of glutaminolysis and triggers autophagy as a salvage pathway supporting leukemia cell metabolism. Consequently, both inhibition of glutaminolysis and inhibition of autophagy strongly and synergistically enhance the antileukemic effects of anti-NOTCH1 therapies. Moreover, we demonstrate that Pten loss induces increased glycolysis and consequently rescues leukemic cell metabolism abrogating the antileukemic effects of NOTCH1 inhibition. Overall, these results identify glutaminolysis as a major node in cancer metabolism controlled by NOTCH1 and as therapeutic target for the treatment of T-ALL.
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Affiliation(s)
- Daniel Herranz
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | | | - Jessica Sudderth
- Children's Medical Center Research Institute, University of Texas-Southwestern Medical Center, Dallas, Texas, USA
| | | | - Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Valeria Tosello
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Luyao Xu
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | | | - Mireia Castillo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - J Erika Haydu
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Javier Márquez
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, Campus de Teatinos, University of Málaga-Instituto de Investigación Biomédica de Málaga, Málaga, Spain
| | - José M Matés
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, Campus de Teatinos, University of Málaga-Instituto de Investigación Biomédica de Málaga, Málaga, Spain
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Stephen Rayport
- Department of Psychiatry, Columbia University Medical Center, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas-Southwestern Medical Center, Dallas, Texas, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Pathology, Columbia University Medical Center, New York, New York, USA
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6
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Wendorff AA, Chen J, Li Y, Hitzler J. Abstract 1488: Role of niche requirements in transient leukemia of Down syndrome. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background. Children with Down syndrome (DS; constitutional trisomy 21) display an estimated 150-fold increased incidence of acute myeloid leukemia (AML/AMkL). Leukemic blasts are detectable in the peripheral blood of approximately 10% of newborns with DS. This pre-leukemic disorder, known as Transient Leukemia (TL) or Transient Myeloproliferative Disorder (TMD), predominantly undergoes spontaneous resolution, although 20% of cases go on to develop AML later in life. Available data suggest that TL is a disorder of fetal hematopoiesis, triggered by somatic mutations of the hematopoietic transcription factor GATA1. We hypothesize that the transition from fetal to post-natal hematopoiesis results in the elimination of TL blasts in the majority of cases, and that progression events acquired during the first three years of life account for the transformation of Down syndrome TL to AML. Methods and Results. During embryonic development, the fetal liver (FL) constitutes the primary site of hematopoiesis. Data from our xenotransplant model suggest that the post-natal bone marrow (BM) environment provides insufficient or inappropriate cues for the survival, proliferation and dissemination of TL blasts. To identify the unique combination of signals provided by the FL but not the post-natal BM, we reconstructed both hematopoietic niches in vitro by culturing primary human TL cells on murine stromal cell lines derived from either FL (Aft024) or adult BM (MS-5). We found that TL cells underwent a striking >80-fold expansion in total cell number when cultured on FL-derived stromal cells for 2 weeks. In contrast, BM-derived MS-5 stromal cells supported only a moderate 8-fold expansion of TL cells, simultaneously allowing for progressive induction of apoptosis, and inducing increased myeloid differentiation. The superior ability of fetal-derived stromal cells compared to those derived from bone marrow to support TL cells was confirmed under hypoxic culture conditions, in keeping with their fetal origin. Comparative gene expression analysis successfully identified both soluble and membrane-bound components of the fetal hematopoietic niche (modeled by Aft024), such as BMPs and mediators of cell adhesion, as candidate regulators of TL cell growth. Conclusions. We have developed an ex vivo culture system which allows the expansion of primary DS-TL blast cells. We demonstrate that survival/proliferative signals are preferentially provided by the fetal liver vs. adult bone marrow environment, consistent with a fetal origin of TL blasts. Our current focus is on the identification and functional validation of signaling pathways that are essential for TL blast survival and whose interruption in this pre-leukemic disorder may lead to prevention of subsequent AML in children with Down syndrome.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1488. doi:1538-7445.AM2012-1488
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Affiliation(s)
- Agnieszka A. Wendorff
- 1Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jian Chen
- 1Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Yue Li
- 1Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Johann Hitzler
- 2Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute; Department of Pediatrics, Division of Hematology/Oncology, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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Wendorff AA, Koch U, Wunderlich FT, Wirth S, Dubey C, Brüning JC, MacDonald HR, Radtke F. Hes1 is a critical but context-dependent mediator of canonical Notch signaling in lymphocyte development and transformation. Immunity 2010; 33:671-84. [PMID: 21093323 DOI: 10.1016/j.immuni.2010.11.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 08/19/2010] [Accepted: 09/17/2010] [Indexed: 01/03/2023]
Abstract
Although canonical Notch signaling regulates multiple hematopoietic lineage decisions including T cell and marginal zone B cell fate specification, the downstream molecular mediators of Notch function are largely unknown. We showed here that conditional inactivation of Hes1, a well-characterized Notch target gene, in adult murine bone marrow (BM) cells severely impaired T cell development without affecting other Notch-dependent hematopoietic lineages such as marginal zone B cells. Competitive mixed BM chimeras, intrathymic transfer experiments, and in vitro culture of BM progenitors on Delta-like-expressing stromal cells further demonstrated that Hes1 is required for T cell lineage commitment, but dispensable for Notch-dependent thymocyte maturation through and beyond the beta selection checkpoint. Furthermore, our data strongly suggest that Hes1 is essential for the development and maintenance of Notch-induced T cell acute lymphoblastic leukemia. Collectively, our studies identify Hes1 as a critical but context-dependent mediator of canonical Notch signaling in the hematopoietic system.
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Affiliation(s)
- Agnieszka A Wendorff
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Station 19, 1015 Lausanne, Switzerland
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