1
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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2
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Thoms JAI, Koch F, Raei A, Subramanian S, Wong JH, Vafaee F, Pimanda J. BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells. Nucleic Acids Res 2024; 52:D1131-D1137. [PMID: 37870453 PMCID: PMC10767868 DOI: 10.1093/nar/gkad918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
The BloodChIP Xtra database (http://bloodchipXtra.vafaeelab.com/) facilitates genome-wide exploration and visualization of transcription factor (TF) occupancy and chromatin configuration in rare primary human hematopoietic stem (HSC-MPP) and progenitor (CMP, GMP, MEP) cells and acute myeloid leukemia (AML) cell lines (KG-1, ME-1, Kasumi1, TSU-1621-MT), along with chromatin accessibility and gene expression data from these and primary patient AMLs. BloodChIP Xtra features significantly more datasets than our earlier database BloodChIP (two primary cell types and two cell lines). Improved methodologies for determining TF occupancy and chromatin accessibility have led to increased availability of data for rare primary cell types across the spectrum of healthy and AML hematopoiesis. However, there is a continuing need for these data to be integrated in an easily accessible manner for gene-based queries and use in downstream applications. Here, we provide a user-friendly database based around genome-wide binding profiles of key hematopoietic TFs and histone marks in healthy stem/progenitor cell types. These are compared with binding profiles and chromatin accessibility derived from primary and cell line AML and integrated with expression data from corresponding cell types. All queries can be exported to construct TF-gene and protein-protein networks and evaluate the association of genes with specific cellular processes.
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Affiliation(s)
- Julie A I Thoms
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Forrest C Koch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Alireza Raei
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Shruthi Subramanian
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, Australia
| | - John E Pimanda
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, Australia
- Haematology Department, Prince of Wales Hospital, Sydney, Australia
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3
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Tan SH, Tan TK, Yokomori R, Liao M, Huang XZ, Yeoh AEJ, Sanda T. TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia. Leukemia 2023; 37:1969-1981. [PMID: 37591943 DOI: 10.1038/s41375-023-01993-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
A hallmark of T-cell acute lymphoblastic leukemia (T-ALL) is the dysregulated expression of oncogenic transcription factors (TFs), including TAL1, NOTCH1 and MYC. Rewiring of the transcriptional program disrupts the tightly controlled spatiotemporal expression of downstream target genes, thereby contributing to leukemogenesis. In this study, we first identify an evolutionarily conserved enhancer element controlling the MYCN oncogene (named enhMYCN) that is aberrantly activated by the TAL1 complex in T-ALL cells. TAL1-positive T-ALL cells are highly dependent on MYCN expression for their maintenance in vitro and in xenograft models. Interestingly, MYCN drives the expression of multiple genes involved in the mevalonate pathway, and T-ALL cells are sensitive to inhibition of HMG-CoA reductase (HMGCR), a rate-limiting enzyme of this pathway. Importantly, MYC and MYCN regulate the same targets and compensate for each other. Thus, MYCN-positive T-ALL cells display a dual dependence on the TAL1-MYCN and NOTCH1-MYC pathways. Together, our results demonstrate that enhMYCN-mediated MYCN expression is required for human T-ALL cells and implicate the TAL1-MYCN-HMGCR axis as a potential therapeutic target in T-ALL.
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Affiliation(s)
- Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Rui Yokomori
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Minghui Liao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Allen Eng Juh Yeoh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Paediatrics, National University of Singapore, Singapore, 119228, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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4
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Lux S, Milsom MD. EVI1-mediated Programming of Normal and Malignant Hematopoiesis. Hemasphere 2023; 7:e959. [PMID: 37810550 PMCID: PMC10553128 DOI: 10.1097/hs9.0000000000000959] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/14/2023] [Indexed: 10/10/2023] Open
Abstract
Ecotropic viral integration site 1 (EVI1), encoded at the MECOM locus, is an oncogenic zinc finger transcription factor with diverse roles in normal and malignant cells, most extensively studied in the context of hematopoiesis. EVI1 interacts with other transcription factors in a context-dependent manner and regulates transcription and chromatin remodeling, thereby influencing the proliferation, differentiation, and survival of cells. Interestingly, it can act both as a transcriptional activator as well as a transcriptional repressor. EVI1 is expressed, and fulfills important functions, during the development of different tissues, including the nervous system and hematopoiesis, demonstrating a rigid spatial and temporal expression pattern. However, EVI1 is regularly overexpressed in a variety of cancer entities, including epithelial cancers such as ovarian and pancreatic cancer, as well as in hematologic malignancies like myeloid leukemias. Importantly, EVI1 overexpression is generally associated with a very poor clinical outcome and therapy-resistance. Thus, EVI1 is an interesting candidate to study to improve the prognosis and treatment of high-risk patients with "EVI1high" hematopoietic malignancies.
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Affiliation(s)
- Susanne Lux
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael D. Milsom
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
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5
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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6
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Li Y, Yang W, Devidas M, Winter SS, Kesserwan C, Yang W, Dunsmore KP, Smith C, Qian M, Zhao X, Zhang R, Gastier-Foster JM, Raetz EA, Carroll WL, Li C, Liu PP, Rabin KR, Sanda T, Mullighan CG, Nichols KE, Evans WE, Pui CH, Hunger SP, Teachey DT, Relling MV, Loh ML, Yang JJ. Germline RUNX1 variation and predisposition to childhood acute lymphoblastic leukemia. J Clin Invest 2021; 131:147898. [PMID: 34166225 PMCID: PMC8409579 DOI: 10.1172/jci147898] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022] Open
Abstract
Genetic alterations in the RUNX1 gene are associated with benign and malignant blood disorders, particularly of megakaryocyte and myeloid lineages. The role of RUNX1 in acute lymphoblastic leukemia (ALL) is less clear, particularly how germline genetic variation influences the predisposition to this type of leukemia. Sequencing 4,836 children with B-ALL and 1,354 cases of T-ALL, we identified 31 and 18 germline RUNX1 variants, respectively. RUNX1 variants in B-ALL consistently showed minimal damaging effects. By contrast, 6 T-ALL-related variants result in drastic loss of RUNX1 activity as a transcription activator in vitro. Ectopic expression of dominant-negative RUNX1 variants in human CD34+ cells repressed differentiation into erythroid, megakaryocytes, and T cells, while promoting myeloid cell development. Chromatin immunoprecipitation sequencing of T-ALL models showed distinctive patterns of RUNX1 binding by variant proteins. Further whole genome sequencing identified JAK3 mutation as the most frequent somatic genomic abnormality in T-ALL with germline RUNX1 variants. Co-introduction of RUNX1 variant and JAK3 mutation in hematopoietic stem and progenitor cells in mice gave rise to T-ALL with early T-cell precursor phenotype. Taken together, these results indicated that RUNX1 is an important predisposition gene for T-ALL and pointed to novel biology of RUNX1-mediated leukemogenesis in the lymphoid lineages.
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Affiliation(s)
- Yizhen Li
- Department of Pharmaceutical Sciences and
| | | | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stuart S. Winter
- Children’s Minnesota Research Institute, Children’s Minnesota, Minneapolis, Minnesota, USA
| | - Chimene Kesserwan
- Center for Cancer Research, Genetics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Kimberly P. Dunsmore
- Children’s Hematology and Oncology, Carilion Clinic and Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | | | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children’s Hospital of Fudan University, Institutes of Biomedical Sciences, Shanghai, China
| | - Xujie Zhao
- Department of Pharmaceutical Sciences and
| | | | | | - Elizabeth A. Raetz
- Division of Pediatric Hematology and Oncology, Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - William L. Carroll
- Division of Pediatric Hematology and Oncology, Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - Chunliang Li
- Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Paul P. Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen R. Rabin
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, and
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | - William E. Evans
- Department of Pharmaceutical Sciences and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stephen P. Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David T. Teachey
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Jun J. Yang
- Department of Pharmaceutical Sciences and
- Department of Oncology, and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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7
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Ottema S, Mulet-Lazaro R, Beverloo HB, Erpelinck C, van Herk S, van der Helm R, Havermans M, Grob T, Valk PJM, Bindels E, Haferlach T, Haferlach C, Smeenk L, Delwel R. Atypical 3q26/MECOM rearrangements genocopy inv(3)/t(3;3) in acute myeloid leukemia. Blood 2020; 136:224-34. [PMID: 32219447 DOI: 10.1182/blood.2019003701] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/11/2020] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) with inv(3)/t(3;3)(q21q26) is a distinct World Health Organization recognized entity, characterized by its aggressive course and poor prognosis. In this subtype of AML, the translocation of a GATA2 enhancer (3q21) to MECOM (3q26) results in overexpression of the MECOM isoform EVI1 and monoallelic expression of GATA2 from the unaffected allele. The full-length MECOM transcript, MDS1-EVI1, is not expressed as the result of the 3q26 rearrangement. Besides the classical inv(3)/t(3;3), a number of other 3q26/MECOM rearrangements with poor treatment response have been reported in AML. Here, we demonstrate, in a group of 33 AML patients with atypical 3q26 rearrangements, MECOM involvement with EVI1 overexpression but no or low MDS1-EVI1 levels. Moreover, the 3q26 translocations in these AML patients often involve superenhancers of genes active in myeloid development (eg, CD164, PROM1, CDK6, or MYC). In >50% of these cases, allele-specific GATA2 expression was observed, either by copy-number loss or by an unexplained allelic imbalance. Altogether, atypical 3q26 recapitulate the main leukemic mechanism of inv(3)/t(3;3) AML, namely EVI1 overexpression driven by enhancer hijacking, absent MDS1-EVI1 expression and potential GATA2 involvement. Therefore, we conclude that both atypical 3q26/MECOM and inv(3)/t(3;3) can be classified as a single entity of 3q26-rearranged AMLs. Routine analyses determining MECOM rearrangements and EVI1 and MDS1-EVI1 expression are required to recognize 3q-rearranged AML cases.
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8
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Czipa E, Schiller M, Nagy T, Kontra L, Steiner L, Koller J, Pálné-Szén O, Barta E. ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. Database (Oxford) 2020; 2020:5700342. [PMID: 31942977 PMCID: PMC6964213 DOI: 10.1093/database/baz141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 01/15/2023]
Abstract
ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein–protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.
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Affiliation(s)
- Erik Czipa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Mátyás Schiller
- Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Levente Kontra
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
| | - László Steiner
- UD-GenoMed Medical Genomic Technologies Research & Development Services Ltd., Nagyerdei krt. 98, Debrecen H-4032, Hungary
| | - Júlia Koller
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Semmelweis University, Institute of Genomic Medicines and Rare Disorders, Üllői út 78/B, Budapest, H-1082, Hungary
| | - Orsolya Pálné-Szén
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Endre Barta
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
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9
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Li S, Chen X, Wang J, Meydan C, Glass JL, Shih AH, Delwel R, Levine RL, Mason CE, Melnick AM. Somatic Mutations Drive Specific, but Reversible, Epigenetic Heterogeneity States in AML. Cancer Discov 2020; 10:1934-1949. [PMID: 32938585 DOI: 10.1158/2159-8290.cd-19-0897] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 07/09/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic allele diversity is linked to inferior prognosis in acute myeloid leukemia (AML). However, the source of epiallele heterogeneity in AML is unknown. Herein we analyzed epiallele diversity in a genetically and clinically annotated AML cohort. Notably, AML driver mutations linked to transcription factors and favorable outcome are associated with epigenetic destabilization in a defined set of susceptible loci. In contrast, AML subtypes linked to inferior prognosis manifest greater abundance and highly stochastic epiallele patterning. We report an epiallele outcome classifier supporting the link between epigenetic diversity and treatment failure. Mouse models with TET2 or IDH2 mutations show that epiallele diversity is especially strongly induced by IDH mutations, precedes transformation to AML, and is enhanced by cooperation between somatic mutations. Furthermore, epiallele complexity was partially reversed by epigenetic therapies in AML driven by TET2/IDH2, suggesting that epigenetic therapy might function in part by reducing population complexity and fitness of AMLs. SIGNIFICANCE: We show for the first time that epigenetic clonality is directly linked to specific mutations and that epigenetic allele diversity precedes and potentially contributes to malignant transformation. Furthermore, epigenetic clonality is reversible with epigenetic therapy agents.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
- The Jackson Laboratory Cancer Center, Bar Harbor, Maine
- The Department of Genetics and Genomic Sciences, The University of Connecticut Health Center, Farmington, Connecticut
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
| | - Xiaowen Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Jacob L Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan H Shih
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center and Oncode Institute, Rotterdam, the Netherlands
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, New York.
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10
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Deniz Ö, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR. Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia. Nat Commun 2020; 11:3506. [PMID: 32665538 DOI: 10.1038/s41467-020-17206-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) is characterised by a series of genetic and epigenetic alterations that result in deregulation of transcriptional networks. One understudied source of transcriptional regulators are transposable elements (TEs), whose aberrant usage could contribute to oncogenic transcriptional circuits. However, the regulatory influence of TEs and their links to AML pathogenesis remain unexplored. Here we identify six endogenous retrovirus (ERV) families with AML-associated enhancer chromatin signatures that are enriched in binding of key regulators of hematopoiesis and AML pathogenesis. Using both locus-specific genetic editing and simultaneous epigenetic silencing of multiple ERVs, we demonstrate that ERV deregulation directly alters the expression of adjacent genes in AML. Strikingly, deletion or epigenetic silencing of an ERV-derived enhancer suppresses cell growth by inducing apoptosis in leukemia cell lines. This work reveals that ERVs are a previously unappreciated source of AML enhancers that may be exploited by cancer cells to help drive tumour heterogeneity and evolution. Transposable elements are a potential source of transcriptional regulators, but how these sequences contribute to oncogenesis remains poorly understood. Here, the authors identify endogenous retroviruses (ERVs) with acute myeloid leukemia (AML)-associated enhancer chromatin signatures, and provide evidence that ERV activation provides an additional layer of gene regulation in AML.
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11
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Ghazi AR, Kong X, Chen ES, Edelstein LC, Shaw CA. Bayesian modelling of high-throughput sequencing assays with malacoda. PLoS Comput Biol 2020; 16:e1007504. [PMID: 32692749 PMCID: PMC7394446 DOI: 10.1371/journal.pcbi.1007504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 07/31/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell's output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. So far, the statistical methods used have been rudimentary, employing transformations on count level data and disregarding experimental and technical structure while failing to quantify uncertainty in the statistical model. We have developed an extensive framework for the analysis of NGS functionalization screens available as an R package called malacoda (available from github.com/andrewGhazi/malacoda). Our software implements a probabilistic, fully Bayesian model of screen data. The model uses the negative binomial distribution with gamma priors to model sequencing counts while accounting for effects from input library preparation and sequencing depth. The method leverages the high-throughput nature of the assay to estimate the priors empirically. External annotations such as ENCODE data or DeepSea predictions can also be incorporated to obtain more informative priors-a transformative capability for data integration. The package also includes quality control and utility functions, including automated barcode counting and visualization methods. To validate our method, we analyzed several datasets using malacoda and alternative MPRA analysis methods. These data include experiments from the literature, simulated assays, and primary MPRA data. We also used luciferase assays to experimentally validate several hits from our primary data, as well as variants for which the various methods disagree and variants detectable only with the aid of external annotations.
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Affiliation(s)
- Andrew R. Ghazi
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xianguo Kong
- Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Ed S. Chen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leonard C. Edelstein
- Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Chad A. Shaw
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
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12
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Martinez-Høyer S, Deng Y, Parker J, Jiang J, Mo A, Docking TR, Gharaee N, Li J, Umlandt P, Fuller M, Jädersten M, Kulasekararaj A, Malcovati L, List AF, Hellström-Lindberg E, Platzbecker U, Karsan A. Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome. Nat Cell Biol 2020; 22:526-533. [PMID: 32251398 DOI: 10.1038/s41556-020-0497-9] [Citation(s) in RCA: 29] [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: 03/26/2019] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the most common structural genomic variant in myelodysplastic syndromes (MDS)1. Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS, but half of the responding patients become resistant2 within 2 years. TP53 mutations are detected in ~20% of LEN-resistant patients3. Here we show that patients who become resistant to LEN harbour recurrent variants of TP53 or RUNX1. LEN upregulated RUNX1 protein and function in a CRBN- and TP53-dependent manner in del(5q) cells, and mutation or downregulation of RUNX1 rendered cells resistant to LEN. LEN induced megakaryocytic differentiation of del(5q) cells followed by cell death that was dependent on calpain activation and CSNK1A1 degradation4,5. We also identified GATA2 as a LEN-responsive gene that is required for LEN-induced megakaryocyte differentiation. Megakaryocytic gene-promoter analyses suggested that LEN-induced degradation of IKZF1 enables a RUNX1-GATA2 complex to drive megakaryocytic differentiation. Overexpression of GATA2 restored LEN sensitivity in the context of RUNX1 or TP53 mutations by enhancing LEN-induced megakaryocytic differentiation. Screening for mutations that block LEN-induced megakaryocytic differentiation should identify patients who are resistant to LEN.
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Affiliation(s)
- Sergio Martinez-Høyer
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Department of Hematology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Yu Deng
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeremy Parker
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jihong Jiang
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela Mo
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Nadia Gharaee
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jenny Li
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Martin Jädersten
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Austin Kulasekararaj
- Department of Haematological Medicine, King's College Hospital and King's College London, London, UK
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alan F List
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University Hospital Leipzig, Leipzig, Germany
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada. .,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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13
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Londero D, Monge J, Hellberg A. A multi-centre study on the performance of the molecular genotyping platform ID RHD XT for resolving serological weak RhD phenotype in routine clinical practice. Vox Sang 2020; 115:241-248. [PMID: 31912520 DOI: 10.1111/vox.12886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/02/2019] [Revised: 10/17/2019] [Accepted: 12/17/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND OBJECTIVES There is concern regarding the lack of prevention of unnecessary transfusion of RhD negative red cells and unnecessary administration of Rh immunoglobulin (RhIG) to pregnant women. In this study, performance of ID RHD XT, a genotyping assay for identification of six RHD allelic variants and human platelet antigens HPA-1a/1b was assessed. MATERIALS AND METHODS Whole blood samples presenting weak, discrepant or inconclusive D phenotype results were genotyped with ID RHD XT and compared to reference molecular tests. Candidacy for RhIG prophylaxis was determined by analysing samples from pregnant women. Hands-on time to complete the procedures was measured. RESULTS Overall, 167 samples were tested (55 donors, 56 patients, 52 pregnant women and four newborns). Agreement between ID RHD XT and the reference method was 100% (51% weak D type 1, 2 or 3; 35·5% weak D Types 1, 2 or 3 not detected; 4% RHD deletion; 1% RHD*Pseudogene; 1% RHD*DIIIa-CE(3-7)-D; and 4% no amplification variant detected for RHD genotype; and 64% HPA-1a/a; 30% HPA-1a/b; and 3% HPA-1b/b for HPA-1 genotype). Call rate was 98·2%. ID RHD XT identified 40% of the pregnant women that would not have required RhIG prophylaxis. Overall hands-on time was 25-45 min to process a batch of 24 samples, and four hours for total assay time. CONCLUSION ID RHD XT yielded reproducible results for RHD typing in serologically weak D phenotype individuals. ID RHD XT was proven useful for the correct management of patients with RhD serological discrepancies and the rational use of RhIG in pregnancy.
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Affiliation(s)
- Donatella Londero
- Immunohematology Laboratory, Azienda Sanitaria Universitaria Friuli Centrale (ASU FC), Udine, Italy
| | - Jorge Monge
- Immunohematology Laboratory, Basque Centre for Blood Transfusion & Human Tissues, Galdakao, Spain.,Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Asa Hellberg
- Nordic Reference Laboratory for Genomic Blood Group Typing, Lund University Hospital, Lund, Sweden
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14
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Thoms JAI, Beck D, Pimanda JE. Transcriptional networks in acute myeloid leukemia. Genes Chromosomes Cancer 2019; 58:859-874. [PMID: 31369171 DOI: 10.1002/gcc.22794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 04/04/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease characterized by a diverse range of recurrent molecular aberrations that occur in many different combinations. Components of transcriptional networks are a common target of these aberrations, leading to network-wide changes and deployment of novel or developmentally inappropriate transcriptional programs. Genome-wide techniques are beginning to reveal the full complexity of normal hematopoietic stem cell transcriptional networks and the extent to which they are deregulated in AML, and new understandings of the mechanisms by which AML cells maintain self-renewal and block differentiation are starting to emerge. The hope is that increased understanding of the network architecture in AML will lead to identification of key oncogenic dependencies that are downstream of multiple network aberrations, and that this knowledge will be translated into new therapies that target these dependencies. Here, we review the current state of knowledge of network perturbation in AML with a focus on major mechanisms of transcription factor dysregulation, including mutation, translocation, and transcriptional dysregulation, and discuss how these perturbations propagate across transcriptional networks. We will also review emerging mechanisms of network disruption, and briefly discuss how increased knowledge of network disruption is already being used to develop new therapies.
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Affiliation(s)
- Julie A I Thoms
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Dominik Beck
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - John E Pimanda
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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15
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Ziyad S, Riordan JD, Cavanaugh AM, Su T, Hernandez GE, Hilfenhaus G, Morselli M, Huynh K, Wang K, Chen JN, Dupuy AJ, Iruela-Arispe ML. A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis. Cell Rep 2019; 22:1211-1224. [PMID: 29386109 PMCID: PMC5828030 DOI: 10.1016/j.celrep.2018.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/05/2017] [Accepted: 01/05/2018] [Indexed: 11/19/2022] Open
Abstract
Given its role as the source of definitive hematopoietic cells, we sought to determine whether mutations initiated in the hemogenic endothelium would yield hematopoietic abnormalities or malignancies. Here, we find that endothelium-specific transposon mutagenesis in mice promotes hematopoietic pathologies that are both myeloid and lymphoid in nature. Frequently mutated genes included previously recognized cancer drivers and additional candidates, such as Pi4ka, a lipid kinase whose mutation was found to promote myeloid and erythroid dysfunction. Subsequent validation experiments showed that targeted inactivation of the Pi4ka catalytic domain or reduction in mRNA expression inhibited myeloid and erythroid cell differentiation in vitro and promoted anemia in vivo through a mechanism involving deregulation of AKT, MAPK, SRC, and JAK-STAT signaling. Finally, we provide evidence linking PI4KAP2, previously considered a pseudogene, to human myeloid and erythroid leukemia.
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Affiliation(s)
- Safiyyah Ziyad
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Ann M Cavanaugh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Trent Su
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gloria E Hernandez
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Georg Hilfenhaus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristine Huynh
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Wang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jau-Nian Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - M Luisa Iruela-Arispe
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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16
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Steiner M, Schneider L, Yillah J, Gerlach K, Kuvardina ON, Meyer A, Maring A, Bonig H, Seifried E, Zörnig M, Lausen J. FUSE binding protein 1 (FUBP1) expression is upregulated by T-cell acute lymphocytic leukemia protein 1 (TAL1) and required for efficient erythroid differentiation. PLoS One 2019; 14:e0210515. [PMID: 30653565 PMCID: PMC6336336 DOI: 10.1371/journal.pone.0210515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/23/2018] [Indexed: 11/18/2022] Open
Abstract
During erythropoiesis, haematopoietic stem cells (HSCs) differentiate in successive steps of commitment and specification to mature erythrocytes. This differentiation process is controlled by transcription factors that establish stage- and cell type-specific gene expression. In this study, we demonstrate that FUSE binding protein 1 (FUBP1), a transcriptional regulator important for HSC self-renewal and survival, is regulated by T-cell acute lymphocytic leukaemia 1 (TAL1) in erythroid progenitor cells. TAL1 directly activates the FUBP1 promoter, leading to increased FUBP1 expression during erythroid differentiation. The binding of TAL1 to the FUBP1 promoter is highly dependent on an intact GATA sequence in a combined E-box/GATA motif. We found that FUBP1 expression is required for efficient erythropoiesis, as FUBP1-deficient progenitor cells were limited in their potential of erythroid differentiation. Thus, the finding of an interconnection between GATA1/TAL1 and FUBP1 reveals a molecular mechanism that is part of the switch from progenitor- to erythrocyte-specific gene expression. In summary, we identified a TAL1/FUBP1 transcriptional relationship, whose physiological function in haematopoiesis is connected to proper erythropoiesis.
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Affiliation(s)
- Marlene Steiner
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Jasmin Yillah
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Katharina Gerlach
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Olga N. Kuvardina
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Alisa Maring
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Martin Zörnig
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt/Main, Germany
- * E-mail: (MZ); (JL)
| | - Jörn Lausen
- Institute for Transfusion Medicine and Immunohematology, Goethe-University and German Red Cross Blood Service, Frankfurt am Main, Germany
- * E-mail: (MZ); (JL)
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17
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Jing D, Huang Y, Liu X, Sia KCS, Zhang JC, Tai X, Wang M, Toscan CE, McCalmont H, Evans K, Mayoh C, Poulos RC, Span M, Mi J, Zhang C, Wong JWH, Beck D, Pimanda JE, Lock RB. Lymphocyte-Specific Chromatin Accessibility Pre-determines Glucocorticoid Resistance in Acute Lymphoblastic Leukemia. Cancer Cell 2018; 34:906-921.e8. [PMID: 30537513 DOI: 10.1016/j.ccell.2018.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 10/02/2018] [Accepted: 11/05/2018] [Indexed: 12/24/2022]
Abstract
Glucocorticoids play a critical role in the treatment of lymphoid malignancies. While glucocorticoid efficacy can be largely attributed to lymphocyte-specific apoptosis, its molecular basis remains elusive. Here, we studied genome-wide lymphocyte-specific open chromatin domains (LSOs), and integrated LSOs with glucocorticoid-induced RNA transcription and chromatin modulation using an in vivo patient-derived xenograft model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs critical for glucocorticoid-induced apoptosis. Glucocorticoid receptor cooperated with CTCF at these LSOs to mediate DNA looping, which was inhibited by increased DNA methylation in glucocorticoid-resistant ALL and non-lymphoid cell types. Our study demonstrates that lymphocyte-specific epigenetic modifications pre-determine glucocorticoid resistance in ALL and may account for the lack of glucocorticoid sensitivity in other cell types.
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Affiliation(s)
- Duohui Jing
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia.
| | - Yizhou Huang
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, UNSW, Sydney, NSW 2052, Australia; Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - Xiaoyun Liu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Keith C S Sia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Julia C Zhang
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Xiaolu Tai
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meng Wang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cara E Toscan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Kathryn Evans
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Rebecca C Poulos
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, UNSW, Sydney, NSW 2052, Australia
| | - Miriam Span
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Jianqing Mi
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Chao Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jason W H Wong
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, UNSW, Sydney, NSW 2052, Australia
| | - Dominik Beck
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, UNSW, Sydney, NSW 2052, Australia; Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, UNSW, Sydney, NSW 2052, Australia; Department of Haematology, Prince of Wales Hospital, Sydney, NSW 2210, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia.
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18
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Chiu SK, Saw J, Huang Y, Sonderegger SE, Wong NC, Powell DR, Beck D, Pimanda JE, Tremblay CS, Curtis DJ. A novel role for Lyl1 in primitive erythropoiesis. Development 2018; 145:dev.162990. [PMID: 30185409 DOI: 10.1242/dev.162990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 01/04/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Stem cell leukemia (Scl or Tal1) and lymphoblastic leukemia 1 (Lyl1) encode highly related members of the basic helix-loop-helix family of transcription factors that are co-expressed in the erythroid lineage. Previous studies have suggested that Scl is essential for primitive erythropoiesis. However, analysis of single-cell RNA-seq data of early embryos showed that primitive erythroid cells express both Scl and Lyl1 Therefore, to determine whether Lyl1 can function in primitive erythropoiesis, we crossed conditional Scl knockout mice with mice expressing a Cre recombinase under the control of the Epo receptor, active in erythroid progenitors. Embryos with 20% expression of Scl from E9.5 survived to adulthood. However, mice with reduced expression of Scl and absence of Lyl1 (double knockout; DKO) died at E10.5 because of progressive loss of erythropoiesis. Gene expression profiling of DKO yolk sacs revealed loss of Gata1 and many of the known target genes of the SCL-GATA1 complex. ChIP-seq analyses in a human erythroleukemia cell line showed that LYL1 exclusively bound a small subset of SCL targets including GATA1. Together, these data show for the first time that Lyl1 can maintain primitive erythropoiesis.
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Affiliation(s)
- Sung K Chiu
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Jesslyn Saw
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Yizhou Huang
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - Stefan E Sonderegger
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Nicholas C Wong
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia.,Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - Dominic Beck
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.,Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Cedric S Tremblay
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia .,Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
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19
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Molano A, Apraiz I, España P, Azkarate M, Vesga MÁ, Rubia M, Piedrabuena M, Puente F, Veldhuisen B, Schoot E, Tejedor D, López M. Performance evaluation study of ID RHD XT, a new genotyping assay for the detection of high‐prevalence RhD negative and weak D types. Vox Sang 2018; 113:694-700. [DOI: 10.1111/vox.12701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/27/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Araitz Molano
- R&D Area Progenika Biopharma A Grifols Company Derio Spain
| | - Izaskun Apraiz
- R&D Area Progenika Biopharma A Grifols Company Derio Spain
| | | | - Maria Azkarate
- Centro Vasco de Transfusiones y Tejidos Humanos Galdakao Spain
| | | | | | | | | | | | - Ellen Schoot
- Sanquin Blood Supply Research Amsterdam the Netherlands
| | - Diego Tejedor
- R&D Area Progenika Biopharma A Grifols Company Derio Spain
| | - Mónica López
- R&D Area Progenika Biopharma A Grifols Company Derio Spain
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20
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Navarro-Montero O, Ayllon V, Lamolda M, López-Onieva L, Montes R, Bueno C, Ng E, Guerrero-Carreno X, Romero T, Romero-Moya D, Stanley E, Elefanty A, Ramos-Mejia V, Menendez P, Real PJ. RUNX1c Regulates Hematopoietic Differentiation of Human Pluripotent Stem Cells Possibly in Cooperation with Proinflammatory Signaling. Stem Cells 2017; 35:2253-2266. [PMID: 28869683 DOI: 10.1002/stem.2700] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 09/16/2016] [Revised: 07/19/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023]
Abstract
Runt-related transcription factor 1 (Runx1) is a master hematopoietic transcription factor essential for hematopoietic stem cell (HSC) emergence. Runx1-deficient mice die during early embryogenesis due to the inability to establish definitive hematopoiesis. Here, we have used human pluripotent stem cells (hPSCs) as model to study the role of RUNX1 in human embryonic hematopoiesis. Although the three RUNX1 isoforms a, b, and c were induced in CD45+ hematopoietic cells, RUNX1c was the only isoform induced in hematoendothelial progenitors (HEPs)/hemogenic endothelium. Constitutive expression of RUNX1c in human embryonic stem cells enhanced the appearance of HEPs, including hemogenic (CD43+) HEPs and promoted subsequent differentiation into blood cells. Conversely, specific deletion of RUNX1c dramatically reduced the generation of hematopoietic cells from HEPs, indicating that RUNX1c is a master regulator of human hematopoietic development. Gene expression profiling of HEPs revealed a RUNX1c-induced proinflammatory molecular signature, supporting previous studies demonstrating proinflammatory signaling as a regulator of HSC emergence. Collectively, RUNX1c orchestrates hematopoietic specification of hPSCs, possibly in cooperation with proinflammatory signaling. Stem Cells 2017;35:2253-2266.
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Affiliation(s)
- Oscar Navarro-Montero
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Veronica Ayllon
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Mar Lamolda
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Granada, Spain
| | - Lourdes López-Onieva
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Rosa Montes
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Elizabeth Ng
- Blood Cell Development and Disease Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Xiomara Guerrero-Carreno
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Tamara Romero
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Damià Romero-Moya
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ed Stanley
- Stem Cell Technology Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Andrew Elefanty
- Blood Cell Development and Disease Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Verónica Ramos-Mejia
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain.,Instituciò Catalana de Reserca i EstudisAvançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Pedro J Real
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Granada, Spain
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21
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Simon L, Lavallée VP, Bordeleau ME, Krosl J, Baccelli I, Boucher G, Lehnertz B, Chagraoui J, MacRae T, Ruel R, Chantigny Y, Lemieux S, Marinier A, Hébert J, Sauvageau G. Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity. Clin Cancer Res 2017; 23:6969-6981. [DOI: 10.1158/1078-0432.ccr-17-1259] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 11/16/2022]
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22
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Kong X, Simon LM, Holinstat M, Shaw CA, Bray PF, Edelstein LC. Identification of a functional genetic variant driving racially dimorphic platelet gene expression of the thrombin receptor regulator, PCTP. Thromb Haemost 2017; 117:962-970. [PMID: 28251237 DOI: 10.1160/th16-09-0692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 09/09/2016] [Accepted: 02/12/2017] [Indexed: 01/08/2023]
Abstract
Platelet activation in response to stimulation of the Protease Activated Receptor 4 (PAR4) receptor differs by race. One factor that contributes to this difference is the expression level of Phosphatidylcholine Transfer Protein (PCTP), a regulator of platelet PAR4 function. We have conducted an expression Quantitative Trait Locus (eQTL) analysis that identifies single nucleotide polymorphisms (SNPs) linked to the expression level of platelet genes. This analysis revealed 26 SNPs associated with the expression level of PCTP at genome-wide significance (p < 5×10-8). Using annotation from ENCODE and other public data we prioritised one of these SNPs, rs2912553, for functional testing. The allelic frequency of rs2912553 is racially-dimorphic, in concordance with the racially differential expression of PCTP. Reporter gene assays confirmed that the single nucleotide change caused by rs2912553 altered the transcriptional potency of the surrounding genomic locus. Electromobility shift assays, luciferase assays, and overexpression studies indicated a role for the megakaryocytic transcription factor GATA1. In summary, we have integrated multi-omic data to identify and functionalise an eQTL. This, along with the previously described relationship between PCTP and PAR4 function, allows us to characterise a genotype-phenotype relationship through the mechanism of gene expression.
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Affiliation(s)
| | | | | | | | | | - Leonard C Edelstein
- Leonard C. Edelstein, Department of Medicine Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Suite 394, Philadelphia, PA 19107, USA, Tel.: +1 215 955 1797, Fax: +1 215 955 9170,
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23
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Unnikrishnan A, Guan YF, Huang Y, Beck D, Thoms JAI, Peirs S, Knezevic K, Ma S, de Walle IV, de Jong I, Ali Z, Zhong L, Raftery MJ, Taghon T, Larsson J, MacKenzie KL, Van Vlierberghe P, Wong JWH, Pimanda JE. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network. Nucleic Acids Res 2016; 44:10644-10661. [PMID: 27604872 PMCID: PMC5159545 DOI: 10.1093/nar/gkw804] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.
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MESH Headings
- Base Sequence
- Binding Sites
- Cell Line, Tumor
- Consensus Sequence
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Humans
- Ikaros Transcription Factor/physiology
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Prognosis
- Proportional Hazards Models
- Protein Binding
- Proteome
- Proteomics
- Proto-Oncogene Proteins c-ets/physiology
- Repressor Proteins/physiology
- Transcription, Genetic
- Transcriptional Regulator ERG/physiology
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Ashwin Unnikrishnan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yi F Guan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yizhou Huang
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Dominik Beck
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Center for Medical Genetics, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Julie A I Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Sofie Peirs
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Kathy Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Shiyong Ma
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Inge V de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Ineke de Jong
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Zara Ali
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Pieter Van Vlierberghe
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Jason W H Wong
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - John E Pimanda
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Department of Haematology, Prince of Wales Hospital, Sydney, 2031, Australia
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24
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Zhang Q, Ding N, Zhang L, Zhao X, Yang Y, Qu H, Fang X. Biological Databases for Hematology Research. Genomics Proteomics Bioinformatics 2016; 14:333-337. [PMID: 27965103 PMCID: PMC5200935 DOI: 10.1016/j.gpb.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 09/29/2016] [Accepted: 10/13/2016] [Indexed: 01/14/2023]
Abstract
With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been generated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research.
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Affiliation(s)
- Qian Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuetong Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yadong Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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25
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Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res 2016; 45:D658-D662. [PMID: 27789702 PMCID: PMC5210658 DOI: 10.1093/nar/gkw983] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/23/2016] [Accepted: 10/15/2016] [Indexed: 12/31/2022] Open
Abstract
Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies.
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Affiliation(s)
- Shenglin Mei
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.,Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qian Qin
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.,Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qiu Wu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China.,Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hanfei Sun
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Rongbin Zheng
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muyuan Zhu
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiaxin Wu
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaohui Shi
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Len Taing
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Tao Liu
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Clifford A Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - X Shirley Liu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China .,Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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26
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Kauts ML, Vink CS, Dzierzak E. Hematopoietic (stem) cell development - how divergent are the roads taken? FEBS Lett 2016; 590:3975-3986. [PMID: 27543859 PMCID: PMC5125883 DOI: 10.1002/1873-3468.12372] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 12/29/2022]
Abstract
The development of the hematopoietic system during early embryonic stages occurs in spatially and temporally distinct waves. Hematopoietic stem cells (HSC), the most potent and self‐renewing cells of this system, are produced in the final ‘definitive’ wave of hematopoietic cell generation. In contrast to HSCs in the adult, which differentiate via intermediate progenitor populations to produce functional blood cells, the generation of hematopoietic cells in the embryo prior to HSC generation occurs in the early waves by producing blood cells without intermediate progenitors (such as the ‘primitive’ hematopoietic cells). The lineage relationship between the early hematopoietic cells and the cells giving rise to HSCs, the genetic networks controlling their emergence, and the precise temporal determination of HSC fate remain topics of intense research and debate. This Review article discusses the current knowledge on the step‐wise embryonic establishment of the adult hematopoietic system, examines the roles of pivotal intrinsic regulators in this process, and raises questions concerning the temporal onset of HSC fate determination.
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Affiliation(s)
- Mari-Liis Kauts
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK.,Department of Cell Biology, Erasmus MC Stem Cell Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Chris S Vink
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK.,Department of Cell Biology, Erasmus MC Stem Cell Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elaine Dzierzak
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK.,Department of Cell Biology, Erasmus MC Stem Cell Institute, Erasmus Medical Center, Rotterdam, The Netherlands
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27
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Abstract
Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html.
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28
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Lichtenberg J, Heuston EF, Mishra T, Keller CA, Hardison RC, Bodine DM. SBR-Blood: systems biology repository for hematopoietic cells. Nucleic Acids Res 2015; 44:D925-31. [PMID: 26590403 PMCID: PMC4702891 DOI: 10.1093/nar/gkv1263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022] Open
Abstract
Extensive research into hematopoiesis (the development of blood cells) over several decades has generated large sets of expression and epigenetic profiles in multiple human and mouse blood cell types. However, there is no single location to analyze how gene regulatory processes lead to different mature blood cells. We have developed a new database framework called hematopoietic Systems Biology Repository (SBR-Blood), available online at http://sbrblood.nhgri.nih.gov, which allows user-initiated analyses for cell type correlations or gene-specific behavior during differentiation using publicly available datasets for array- and sequencing-based platforms from mouse hematopoietic cells. SBR-Blood organizes information by both cell identity and by hematopoietic lineage. The validity and usability of SBR-Blood has been established through the reproduction of workflows relevant to expression data, DNA methylation, histone modifications and transcription factor occupancy profiles.
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Affiliation(s)
- Jens Lichtenberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elisabeth F Heuston
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tejaswini Mishra
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - David M Bodine
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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29
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Bagger FO, Sasivarevic D, Sohi SH, Laursen LG, Pundhir S, Sønderby CK, Winther O, Rapin N, Porse BT. BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. Nucleic Acids Res 2015; 44:D917-24. [PMID: 26507857 PMCID: PMC4702803 DOI: 10.1093/nar/gkv1101] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/11/2015] [Indexed: 01/01/2023] Open
Abstract
Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space.
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Affiliation(s)
- Frederik Otzen Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark
| | | | - Sina Hadi Sohi
- DTU Compute, Technical University of Denmark, Lyngby, Denmark
| | - Linea Gøricke Laursen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Casper Kaae Sønderby
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark
| | - Ole Winther
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark DTU Compute, Technical University of Denmark, Lyngby, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Denmark
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30
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Mundade R, Ozer HG, Wei H, Prabhu L, Lu T. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. Cell Cycle 2015; 13:2847-52. [PMID: 25486472 PMCID: PMC4614920 DOI: 10.4161/15384101.2014.949201] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP with second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay. This review addresses the important applications of ChIP-seq with an emphasis on its role in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation that are governed by specific transcription factors, and the identification of epigenetic marks. Furthermore, we also describe the ChIP-seq data analysis workflow and a perspective for the exciting potential advancement of ChIP-seq technology in the future.
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Affiliation(s)
- Rasika Mundade
- a Department of Pharmacology and Toxicology ; Indiana University School of Medicine ; Indianapolis , IN USA
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31
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Nabbi A, Almami A, Thakur S, Suzuki K, Boland D, Bismar TA, Riabowol K. ING3 protein expression profiling in normal human tissues suggest its role in cellular growth and self-renewal. Eur J Cell Biol 2015; 94:214-22. [PMID: 25819753 DOI: 10.1016/j.ejcb.2015.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 01/17/2015] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 12/17/2022] Open
Abstract
Members of the INhibitor of Growth (ING) family of proteins act as readers of the epigenetic code through specific recognition of the trimethylated form of lysine 4 of histone H3 (H3K4Me3) by their plant homeodomains. The founding member of the family, ING1, was initially identified as a tumor suppressor with altered regulation in a variety of cancer types. While alterations in ING1 and ING4 levels have been reported in a variety of cancer types, little is known regarding ING3 protein levels in normal or transformed cells due to a lack of reliable immunological tools. In this study we present the characterization of a new monoclonal antibody we have developed against ING3 that specifically recognizes human and mouse ING3. The antibody works in western blots, immunofluorescence, immunoprecipitation and immunohistochemistry. Using this antibody we show that ING3 is most highly expressed in small intestine, bone marrow and epidermis, tissues in which cells undergo rapid proliferation and renewal. Consistent with this observation, we show that ING3 is expressed at significantly higher levels in proliferating versus quiescent epithelial cells. These data suggest that ING3 levels may serve as a surrogate for growth rate, and suggest possible roles for ING3 in growth and self renewal and related diseases such as cancer.
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Affiliation(s)
- Arash Nabbi
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Amal Almami
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Satbir Thakur
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Keiko Suzuki
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Donna Boland
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tarek A Bismar
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Karl Riabowol
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Oncology, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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Solaimani Kartalaei P, Yamada-Inagawa T, Vink CS, de Pater E, van der Linden R, Marks-Bluth J, van der Sloot A, van den Hout M, Yokomizo T, van Schaick-Solernó ML, Delwel R, Pimanda JE, van IJcken WFJ, Dzierzak E. Whole-transcriptome analysis of endothelial to hematopoietic stem cell transition reveals a requirement for Gpr56 in HSC generation. ACTA ACUST UNITED AC 2014; 212:93-106. [PMID: 25547674 PMCID: PMC4291529 DOI: 10.1084/jem.20140767] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Using highly sensitive RNAseq to examine the whole transcriptome of enriched aortic hematopoietic stem cells and endothelial cells, the authors find G-protein–coupled receptor, Gpr56, is required to generate the first HSCs during endothelial to hematopoietic cell transition. Hematopoietic stem cells (HSCs) are generated via a natural transdifferentiation process known as endothelial to hematopoietic cell transition (EHT). Because of small numbers of embryonal arterial cells undergoing EHT and the paucity of markers to enrich for hemogenic endothelial cells (ECs [HECs]), the genetic program driving HSC emergence is largely unknown. Here, we use a highly sensitive RNAseq method to examine the whole transcriptome of small numbers of enriched aortic HSCs, HECs, and ECs. Gpr56, a G-coupled protein receptor, is one of the most highly up-regulated of the 530 differentially expressed genes. Also, highly up-regulated are hematopoietic transcription factors, including the “heptad” complex of factors. We show that Gpr56 (mouse and human) is a target of the heptad complex and is required for hematopoietic cluster formation during EHT. Our results identify the processes and regulators involved in EHT and reveal the surprising requirement for Gpr56 in generating the first HSCs.
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Affiliation(s)
- Parham Solaimani Kartalaei
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Tomoko Yamada-Inagawa
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Chris S Vink
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Emma de Pater
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Reinier van der Linden
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Jonathon Marks-Bluth
- Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Anthon van der Sloot
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Mirjam van den Hout
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Tomomasa Yokomizo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
| | - M Lucila van Schaick-Solernó
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Ruud Delwel
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - John E Pimanda
- Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Wilfred F J van IJcken
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Elaine Dzierzak
- Erasmus MC Stem Cell Institute, Department of Cell Biology, Center for Biomics, and Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
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Jing D, Bhadri VA, Beck D, Thoms JA, Yakob NA, Wong JW, Knezevic K, Pimanda JE, Lock RB. Opposing regulation of BIM and BCL2 controls glucocorticoid-induced apoptosis of pediatric acute lymphoblastic leukemia cells. Blood 2015; 125:273-83. [PMID: 25336632 DOI: 10.1182/blood-2014-05-576470] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). The proapoptotic BIM protein is an important mediator of glucocorticoid-induced apoptosis in normal and malignant lymphocytes, whereas the antiapoptotic BCL2 confers resistance. The signaling pathways regulating BIM and BCL2 expression in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenografts (PDXs) inherently sensitive or resistant to glucocorticoids were exposed to dexamethasone in vivo. Microarray analysis showed that KLF13 and MYB gene expression changes were significantly greater in dexamethasone-sensitive than -resistant PDXs. Chromatin immunoprecipitation (ChIP) analysis detected glucocorticoid receptor (GR) binding at the KLF13 promoter to trigger KLF13 expression only in sensitive PDXs. Next, KLF13 bound to the MYB promoter, deactivating MYB expression only in sensitive PDXs. Sustained MYB expression in resistant PDXs resulted in maintenance of BCL2 expression and inhibition of apoptosis. ChIP sequencing analysis revealed a novel GR binding site in a BIM intronic region (IGR) that was engaged only in dexamethasone-sensitive PDXs. The absence of GR binding at the BIM IGR was associated with BIM silencing and dexamethasone resistance. This study has identified novel mechanisms of opposing BCL2 and BIM gene regulation that control glucocorticoid-induced apoptosis in pediatric ALL cells in vivo.
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Tursky ML, Beck D, Thoms JAI, Huang Y, Kumari A, Unnikrishnan A, Knezevic K, Evans K, Richards LA, Lee E, Morris J, Goldberg L, Izraeli S, Wong JWH, Olivier J, Lock RB, MacKenzie KL, Pimanda JE. Overexpression of ERG in cord blood progenitors promotes expansion and recapitulates molecular signatures of high ERG leukemias. Leukemia 2014; 29:819-27. [PMID: 25306899 DOI: 10.1038/leu.2014.299] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/04/2014] [Accepted: 10/03/2014] [Indexed: 02/07/2023]
Abstract
High expression of the ETS family transcription factor ERG is associated with poor clinical outcome in acute myeloid leukemia (AML) and acute T-cell lymphoblastic leukemia (T-ALL). In murine models, high ERG expression induces both T-ALL and AML. However, no study to date has defined the effect of high ERG expression on primary human hematopoietic cells. In the present study, human CD34+ cells were transduced with retroviral vectors to elevate ERG gene expression to levels detected in high ERG AML. RNA sequencing was performed on purified populations of transduced cells to define the effects of high ERG on gene expression in human CD34+ cells. Integration of the genome-wide expression data with other data sets revealed that high ERG drives an expression signature that shares features of normal hematopoietic stem cells, high ERG AMLs, early T-cell precursor-ALLs and leukemic stem cell signatures associated with poor clinical outcome. Functional assays linked this gene expression profile to enhanced progenitor cell expansion. These results support a model whereby a stem cell gene expression network driven by high ERG in human cells enhances the expansion of the progenitor pool, providing opportunity for the acquisition and propagation of mutations and the development of leukemia.
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Affiliation(s)
- M L Tursky
- 1] Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia [2] Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - D Beck
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - J A I Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - Y Huang
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - A Kumari
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - A Unnikrishnan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - K Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - K Evans
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - L A Richards
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - E Lee
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - J Morris
- Department of Obstetrics and Gynaecology, Royal North Shore Hospital, University of Sydney, Sydney, Australia
| | - L Goldberg
- 1] Cancer Research Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel [2] Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | - S Izraeli
- 1] Cancer Research Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel [2] Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
| | - J W H Wong
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - J Olivier
- School of Mathematics and Statistics, UNSW, Sydney, Australia
| | - R B Lock
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - K L MacKenzie
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - J E Pimanda
- 1] Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, Australia [2] Department of Haematology, Prince of Wales Hospital, Sydney, Australia
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Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FSL, Hannah R, Diamanti E, Lombard P, Wilson NK, Gottgens B. CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. Nucleic Acids Res 2014; 43:D1117-23. [PMID: 25270877 PMCID: PMC4384009 DOI: 10.1093/nar/gku895] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
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Affiliation(s)
- Manuel Sánchez-Castillo
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - David Ruau
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Adam C Wilkinson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Felicia S L Ng
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Patrick Lombard
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Berthold Gottgens
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
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Abstract
Transcription factors (TFs) play a key role in determining the gene expression profiles of stem/progenitor cells, and defining their potential to differentiate into mature cell lineages. TF interactions within gene-regulatory networks are vital to these processes, and dysregulation of these networks by TF overexpression, deletion or abnormal gene fusions have been shown to cause malignancy. While investigation of these processes remains a challenge, advances in genome-wide technologies and growing interactions between laboratory and computational science are starting to produce increasingly accurate network models. The haematopoietic system provides an attractive experimental system to elucidate gene regulatory mechanisms, and allows experimental investigation of both normal and dysregulated networks. In this review we examine the principles of TF-controlled gene regulatory networks and the key experimental techniques used to investigate them. We look in detail at examples of how these approaches can be used to dissect out the regulatory mechanisms controlling normal haematopoiesis, as well as the dysregulated networks associated with haematological malignancies.
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Affiliation(s)
- Jonathan I Sive
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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DeVilbiss AW, Sanalkumar R, Johnson KD, Keles S, Bresnick EH. Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points. Exp Hematol 2014; 42:618-29. [PMID: 24816274 DOI: 10.1016/j.exphem.2014.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/04/2014] [Indexed: 12/12/2022]
Abstract
Hematopoiesis is an exquisitely regulated process in which stem cells in the developing embryo and the adult generate progenitor cells that give rise to all blood lineages. Master regulatory transcription factors control hematopoiesis by integrating signals from the microenvironment and dynamically establishing and maintaining genetic networks. One of the most rudimentary aspects of cell type-specific transcription factor function, how they occupy a highly restricted cohort of cis-elements in chromatin, remains poorly understood. Transformative technologic advances involving the coupling of next-generation DNA sequencing technology with the chromatin immunoprecipitation assay (ChIP-seq) have enabled genome-wide mapping of factor occupancy patterns. However, formidable problems remain; notably, ChIP-seq analysis yields hundreds to thousands of chromatin sites occupied by a given transcription factor, and only a fraction of the sites appear to be endowed with critical, non-redundant function. It has become en vogue to map transcription factor occupancy patterns genome-wide, while using powerful statistical tools to establish correlations to inform biology and mechanisms. With the advent of revolutionary genome editing technologies, one can now reach beyond correlations to conduct definitive hypothesis testing. This review focuses on key discoveries that have emerged during the path from single loci to genome-wide analyses, specifically in the context of hematopoietic transcriptional mechanisms.
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Affiliation(s)
- Andrew W DeVilbiss
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Rajendran Sanalkumar
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Kirby D Johnson
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA
| | - Sunduz Keles
- University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H Bresnick
- Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA; University of Wisconsin-Madison Blood Research Program, Madison, Wisconsin, USA.
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Fernández-Suárez XM, Rigden DJ, Galperin MY. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. Nucleic Acids Res 2013; 42:D1-6. [PMID: 24316579 PMCID: PMC3965027 DOI: 10.1093/nar/gkt1282] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI’s MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).
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Affiliation(s)
- Xosé M Fernández-Suárez
- Life Technologies, Inchinnan Business Park, Paisley PA4 9RF, UK, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK and National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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