151
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Hamey FK, Nestorowa S, Wilson NK, Göttgens B. Advancing haematopoietic stem and progenitor cell biology through single-cell profiling. FEBS Lett 2016; 590:4052-4067. [PMID: 27259698 DOI: 10.1002/1873-3468.12231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022]
Abstract
Haematopoietic stem and progenitor cells (HSPCs) sit at the top of the haematopoietic hierarchy, and their fate choices need to be carefully controlled to ensure balanced production of all mature blood cell types. As cell fate decisions are made at the level of the individual cells, recent technological advances in measuring gene and protein expression in increasingly large numbers of single cells have been rapidly adopted to study both normal and pathological HSPC function. In this review we emphasise the importance of combining the correct computational models with single-cell experimental techniques, and illustrate how such integrated approaches have been used to resolve heterogeneities in populations, reconstruct lineage differentiation, identify regulatory relationships and link molecular profiling to cellular function.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Sonia Nestorowa
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
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152
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Dasgupta T, Antony J, Braithwaite AW, Horsfield JA. HDAC8 Inhibition Blocks SMC3 Deacetylation and Delays Cell Cycle Progression without Affecting Cohesin-dependent Transcription in MCF7 Cancer Cells. J Biol Chem 2016; 291:12761-12770. [PMID: 27072133 PMCID: PMC4933439 DOI: 10.1074/jbc.m115.704627] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/11/2016] [Indexed: 12/19/2022] Open
Abstract
Cohesin, a multi-subunit protein complex involved in chromosome organization, is frequently mutated or aberrantly expressed in cancer. Multiple functions of cohesin, including cell division and gene expression, highlight its potential as a novel therapeutic target. The SMC3 subunit of cohesin is acetylated (ac) during S phase to establish cohesion between replicated chromosomes. Following anaphase, ac-SMC3 is deacetylated by HDAC8. Reversal of SMC3 acetylation is imperative for recycling cohesin so that it can be reloaded in interphase for both non-mitotic and mitotic functions. We blocked deacetylation of ac-SMC3 using an HDAC8-specific inhibitor PCI-34051 in MCF7 breast cancer cells, and examined the effects on transcription of cohesin-dependent genes that respond to estrogen. HDAC8 inhibition led to accumulation of ac-SMC3 as expected, but surprisingly, had no influence on the transcription of estrogen-responsive genes that are altered by siRNA targeting of RAD21 or SMC3. Knockdown of RAD21 altered estrogen receptor α (ER) recruitment at SOX4 and IL20, and affected transcription of these genes, while HDAC8 inhibition did not. Rather, inhibition of HDAC8 delayed cell cycle progression, suppressed proliferation and induced apoptosis in a concentration-dependent manner. We conclude that HDAC8 inhibition does not change the estrogen-specific transcriptional role of cohesin in MCF7 cells, but instead, compromises cell cycle progression and cell survival. Our results argue that candidate inhibitors of cohesin function may differ in their effects depending on the cellular genotype and should be thoroughly tested for predicted effects on cohesin's mechanistic roles.
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Affiliation(s)
- Tanushree Dasgupta
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and
| | - Jisha Antony
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and
| | - Antony W Braithwaite
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Julia A Horsfield
- From the Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, and; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.
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154
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Duployez N, Marceau-Renaut A, Boissel N, Petit A, Bucci M, Geffroy S, Lapillonne H, Renneville A, Ragu C, Figeac M, Celli-Lebras K, Lacombe C, Micol JB, Abdel-Wahab O, Cornillet P, Ifrah N, Dombret H, Leverger G, Jourdan E, Preudhomme C. Comprehensive mutational profiling of core binding factor acute myeloid leukemia. Blood 2016; 127:2451-9. [PMID: 26980726 PMCID: PMC5457131 DOI: 10.1182/blood-2015-12-688705] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
Acute myeloid leukemia (AML) with t(8;21) or inv(16) have been recognized as unique entities within AML and are usually reported together as core binding factor AML (CBF-AML). However, there is considerable clinical and biological heterogeneity within this group of diseases, and relapse incidence reaches up to 40%. Moreover, translocations involving CBFs are not sufficient to induce AML on its own and the full spectrum of mutations coexisting with CBF translocations has not been elucidated. To address these issues, we performed extensive mutational analysis by high-throughput sequencing in 215 patients with CBF-AML enrolled in the Phase 3 Trial of Systematic Versus Response-adapted Timed-Sequential Induction in Patients With Core Binding Factor Acute Myeloid Leukemia and Treating Patients with Childhood Acute Myeloid Leukemia with Interleukin-2 trials (age, 1-60 years). Mutations in genes activating tyrosine kinase signaling (including KIT, N/KRAS, and FLT3) were frequent in both subtypes of CBF-AML. In contrast, mutations in genes that regulate chromatin conformation or encode members of the cohesin complex were observed with high frequencies in t(8;21) AML (42% and 18%, respectively), whereas they were nearly absent in inv(16) AML. High KIT mutant allele ratios defined a group of t(8;21) AML patients with poor prognosis, whereas high N/KRAS mutant allele ratios were associated with the lack of KIT or FLT3 mutations and a favorable outcome. In addition, mutations in epigenetic modifying or cohesin genes were associated with a poor prognosis in patients with tyrosine kinase pathway mutations, suggesting synergic cooperation between these events. These data suggest that diverse cooperating mutations may influence CBF-AML pathophysiology as well as clinical behavior and point to potential unique pathogenesis of t(8;21) vs inv(16) AML.
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MESH Headings
- Adolescent
- Adult
- Alleles
- Cell Cycle Proteins/genetics
- Child
- Child, Preschool
- Chromatin/genetics
- Chromatin/ultrastructure
- Chromosomal Proteins, Non-Histone/genetics
- Chromosome Inversion
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factors/genetics
- DNA Mutational Analysis
- DNA, Neoplasm/genetics
- Female
- Genetic Association Studies
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Leukemia, Myeloid, Acute/genetics
- Male
- Middle Aged
- Mutation
- Oncogene Proteins, Fusion/genetics
- Prognosis
- RUNX1 Translocation Partner 1 Protein
- Translocation, Genetic
- Young Adult
- Cohesins
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Affiliation(s)
- Nicolas Duployez
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Alice Marceau-Renaut
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Nicolas Boissel
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Maxime Bucci
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
| | - Sandrine Geffroy
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | | | - Aline Renneville
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
| | - Christine Ragu
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Lille University, Lille, France
| | - Karine Celli-Lebras
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Jean-Baptiste Micol
- Department of Hematology, Gustave Roussy Institute, INSERM UMR 1170, Villejuif, France; Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | - Norbert Ifrah
- Department of Hematology, CHU Angers, Angers, France; and
| | - Hervé Dombret
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Guy Leverger
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Eric Jourdan
- Department of Hematology, CHU Nîmes, Nîmes, France
| | - Claude Preudhomme
- Biology and Pathology Center, Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France; Cancer Research Institute, INSERM Unité Mixte de Recherche (UMR)-S 1172, Lille, France
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155
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Galeev R, Baudet A, Kumar P, Rundberg Nilsson A, Nilsson B, Soneji S, Törngren T, Borg Å, Kvist A, Larsson J. Genome-wide RNAi Screen Identifies Cohesin Genes as Modifiers of Renewal and Differentiation in Human HSCs. Cell Rep 2016; 14:2988-3000. [PMID: 26997282 DOI: 10.1016/j.celrep.2016.02.082] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022] Open
Abstract
To gain insights into the regulatory mechanisms of hematopoietic stem cells (HSCs), we employed a genome-wide RNAi screen in human cord-blood derived cells and identified candidate genes whose knockdown maintained the HSC phenotype during culture. A striking finding was the identification of members of the cohesin complex (STAG2, RAD21, STAG1, and SMC3) among the top 20 genes from the screen. Upon individual validation of these cohesin genes, we found that their knockdown led to an immediate expansion of cells with an HSC phenotype in vitro. A similar expansion was observed in vivo following transplantation to immunodeficient mice. Transcriptome analysis of cohesin-deficient CD34(+) cells showed an upregulation of HSC-specific genes, demonstrating an immediate shift toward a more stem-cell-like gene expression signature upon cohesin deficiency. Our findings implicate cohesin as a major regulator of HSCs and illustrate the power of global RNAi screens to identify modifiers of cell fate.
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Affiliation(s)
- Roman Galeev
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Aurélie Baudet
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Praveen Kumar
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | | | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Lund University, 221 84 Lund, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Therese Törngren
- Division of Oncology and Pathology, Lund University, 223 63 Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Lund University, 223 63 Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology, Lund University, 223 63 Lund, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden.
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156
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Corces MR, Corces VG. The three-dimensional cancer genome. Curr Opin Genet Dev 2016; 36:1-7. [PMID: 26855137 PMCID: PMC4880523 DOI: 10.1016/j.gde.2016.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
The past decade of cancer research has ushered in a comprehensive understanding of the way that the sequence of the genome can be co-opted during the process of tumorigenesis. However, only recently has the epigenome, and in particular the three-dimensional topology of chromatin, been implicated in cancer progression. Here we review recent findings of how the cancer genome is regulated and dysregulated to effect changes in 3D genome topology. We discuss the impact of the spatial organization of the genome on the frequency of tumorigenic chromosomal translocations and the effects of disruption of the proteins responsible for the establishment of chromatin loops. Alteration of the three-dimensional cancer genome is a rapidly emerging hallmark of multiple cancer subtypes.
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Affiliation(s)
- M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA.
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157
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Grimwade D, Ivey A, Huntly BJP. Molecular landscape of acute myeloid leukemia in younger adults and its clinical relevance. Blood 2016; 127:29-41. [PMID: 26660431 PMCID: PMC4705608 DOI: 10.1182/blood-2015-07-604496] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 08/04/2015] [Indexed: 01/13/2023] Open
Abstract
Recent major advances in understanding the molecular basis of acute myeloid leukemia (AML) provide a double-edged sword. Although defining the topology and key features of the molecular landscape are fundamental to development of novel treatment approaches and provide opportunities for greater individualization of therapy, confirmation of the genetic complexity presents a huge challenge to successful translation into routine clinical practice. It is now clear that many genes are recurrently mutated in AML; moreover, individual leukemias harbor multiple mutations and are potentially composed of subclones with differing mutational composition, rendering each patient's AML genetically unique. In order to make sense of the overwhelming mutational data and capitalize on this clinically, it is important to identify (1) critical AML-defining molecular abnormalities that distinguish biological disease entities; (2) mutations, typically arising in subclones, that may influence prognosis but are unlikely to be ideal therapeutic targets; (3) mutations associated with preleukemic clones; and (4) mutations that have been robustly shown to confer independent prognostic information or are therapeutically relevant. The reward of identifying AML-defining molecular lesions present in all leukemic populations (including subclones) has been exemplified by acute promyelocytic leukemia, where successful targeting of the underlying PML-RARα oncoprotein has eliminated the need for chemotherapy for disease cure. Despite the molecular heterogeneity and recognizing that treatment options for other forms of AML are limited, this review will consider the scope for using novel molecular information to improve diagnosis, identify subsets of patients eligible for targeted therapies, refine outcome prediction, and track treatment response.
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Affiliation(s)
- David Grimwade
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Adam Ivey
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrookes Hospital, University of Cambridge, and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
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