1
|
Bercier P, de Thé H. History of Developing Acute Promyelocytic Leukemia Treatment and Role of Promyelocytic Leukemia Bodies. Cancers (Basel) 2024; 16:1351. [PMID: 38611029 PMCID: PMC11011038 DOI: 10.3390/cancers16071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The story of acute promyelocytic leukemia (APL) discovery, physiopathology, and treatment is a unique journey, transforming the most aggressive form of leukemia to the most curable. It followed an empirical route fueled by clinical breakthroughs driving major advances in biochemistry and cell biology, including the discovery of PML nuclear bodies (PML NBs) and their central role in APL physiopathology. Beyond APL, PML NBs have emerged as key players in a wide variety of biological functions, including tumor-suppression and SUMO-initiated protein degradation, underscoring their broad importance. The APL story is an example of how clinical observations led to the incremental development of the first targeted leukemia therapy. The understanding of APL pathogenesis and the basis for cure now opens new insights in the treatment of other diseases, especially other acute myeloid leukemias.
Collapse
Affiliation(s)
- Pierre Bercier
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75231 Paris, France;
- GenCellDis, Inserm U944, CNRS UMR7212, Université Paris Cité, 75010 Paris, France
| | - Hugues de Thé
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75231 Paris, France;
- GenCellDis, Inserm U944, CNRS UMR7212, Université Paris Cité, 75010 Paris, France
- Hematology Laboratory, Hôpital St Louis, AP/HP, 75010 Paris, France
| |
Collapse
|
2
|
Liu X, Zhang L, Yang Y, Yin W, Liu Y, Luo C, Zhang R, Long Z, Jiang Y, Wang B. CD71-mediated liposomal arsenic-nickel complex combined with all-trans retinoic acid for the efficacy of acute promyelocytic leukemia. Asian J Pharm Sci 2023; 18:100826. [PMID: 37583710 PMCID: PMC10423880 DOI: 10.1016/j.ajps.2023.100826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/09/2023] [Accepted: 06/09/2023] [Indexed: 08/17/2023] Open
Abstract
Clinically, arsenic trioxide (ATO) was applied to the treatment of acute promyelocytic leukemia (APL) as a reliable and effective frontline drug. However, the administration regimen of AsⅢ was limited due to its fast clearance, short therapeutic window and toxicity as well. Based on CD71 overexpressed on APL cells, in present study, a transferrin (Tf)-modified liposome (LP) was established firstly to encapsulate AsⅢ in arsenic-nickel complex by nickel acetate gradient method. The AsⅢ-loaded liposomes (AsLP) exhibited the feature of acid-sensitive release in vitro. Tf-modified AsLP (Tf-AsLP) were specifically taken up by APL cells and the acidic intracellular environment triggered liposome to release AsⅢ which stimulated reactive oxygen species level and caspase-3 activity. Tf-AsLP prolonged half-life of AsⅢ in blood circulation, lowered systemic toxicity, and promoted apoptosis and induced cell differentiation at lesion site in vivo. Considering that ATO combined with RA is usually applied as the first choice in clinic for APL treatment to improve the therapeutic effect, accordingly, a Tf-modified RA liposome (Tf-RALP) was designed to reduce the severe side effects of free RA and assist Tf-AsLP for better efficacy. As expected, the tumor inhibition rate of Tf-AsLP was improved significantly with the combination of Tf-RALP on subcutaneous tumor model. Furthermore, APL orthotopic NOD/SCID mice model was established by 60CO irradiation and HL-60 cells intravenously injection. The effect of co-administration (Tf-AsLP + Tf-RALP) was also confirmed to conspicuous decrease the number of leukemia cells in the circulatory system and prolong the survival time of APL mice by promoting the APL cells' apoptosis and differentiation in peripheral blood and bone marrow. Collectively, Tf-modified acid-sensitive AsLP could greatly reduce the systemic toxicity of free drug. Moreover, Tf-AsLP combined with Tf-RALP could achieve better efficacy. Thus, transferrin-modified AsⅢ liposome would be a novel clinical strategy to improve patient compliance, with promising translation prospects.
Collapse
Affiliation(s)
- Xiao Liu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Lili Zhang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yueying Yang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Weiwei Yin
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Yunhu Liu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Chunyi Luo
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Ruizhe Zhang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Zhiguo Long
- Department of Hematology, Shanghai Pudong Hospital, Fudan University, Shanghai 201399, China
| | - Yanyan Jiang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201023, China
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
3
|
Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
Collapse
Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
| |
Collapse
|
4
|
Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia. Nat Commun 2023; 14:724. [PMID: 36759620 PMCID: PMC9911410 DOI: 10.1038/s41467-023-36262-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
The PML::RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML::RARA binding on gene expression and regulation in an inducible PML::RARA cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML::RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a computational machine learning implementation called Regulatory Element Behavior Extraction Learning to deconvolute the complex, local transcription factor binding site environment at PML::RARA bound positions to reveal distinct signatures that modulate how PML::RARA directs the transcriptional response.
Collapse
|
5
|
Sun H, Chen Y, Yan K, Shao Y, Zhang QC, Lin Y, Xi Q. Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates nodal signaling in mESCs. EMBO J 2023; 42:e112058. [PMID: 36524443 PMCID: PMC9890237 DOI: 10.15252/embj.2022112058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
TRIM33 is a chromatin reader required for mammalian mesendoderm differentiation after activation of Nodal signaling, while its role in mESCs is still elusive. Here, we report that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML-NBs) specifically in mESCs, to mediate Nodal signaling-directed transcription of Lefty1/2. We show that TRIM33 puncta formation in mESCs depends on PML and on specific assembly of PML-NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs, with both PML protein and formation of mESCs-specific PML-NBs being required for TRIM33 recruitment to these loci, and PML-NBs directly associating with the Lefty1/2 loci. Finally, a TurboID proximity-labeling experiment confirmed that TRIM33 is highly enriched only in mESCs-specific PML-NBs. Thus, our study supports a model in which TRIM33 condensates regulate Nodal signaling-directed transcription in mESCs and shows that PML-NBs can recruit distinct sets of client proteins in a cell-context-dependent manner.
Collapse
Affiliation(s)
- Hongyao Sun
- MOE Key Laboratory of Protein Sciences, School of Life SciencesTsinghua UniversityBeijingChina
- Joint Graduate Program of Peking‐Tsinghua‐NIBSTsinghua UniversityBeijingChina
| | - Yutong Chen
- IDG/McGovern Institute for Brain Research, School of Life SciencesTsinghua UniversityBeijingChina
| | - Kun Yan
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| | - Yanqiu Shao
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| | - Qiangfeng C Zhang
- Joint Graduate Program of Peking‐Tsinghua‐NIBSTsinghua UniversityBeijingChina
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Yi Lin
- IDG/McGovern Institute for Brain ResearchTsinghua‐Peking Joint Centre for Life SciencesBeijingChina
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| |
Collapse
|
6
|
Tian SZ, Yin P, Jing K, Yang Y, Xu Y, Huang G, Ning D, Fullwood MJ, Zheng M. MCI-frcnn: A deep learning method for topological micro-domain boundary detection. Front Cell Dev Biol 2022; 10:1050769. [DOI: 10.3389/fcell.2022.1050769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
Chromatin structural domains, or topologically associated domains (TADs), are a general organizing principle in chromatin biology. RNA polymerase II (RNAPII) mediates multiple chromatin interactive loops, tethering together as RNAPII-associated chromatin interaction domains (RAIDs) to offer a framework for gene regulation. RAID and TAD alterations have been found to be associated with diseases. They can be further dissected as micro-domains (micro-TADs and micro-RAIDs) by clustering single-molecule chromatin-interactive complexes from next-generation three-dimensional (3D) genome techniques, such as ChIA-Drop. Currently, there are few tools available for micro-domain boundary identification. In this work, we developed the MCI-frcnn deep learning method to train a Faster Region-based Convolutional Neural Network (Faster R-CNN) for micro-domain boundary detection. At the training phase in MCI-frcnn, 50 images of RAIDs from Drosophila RNAPII ChIA-Drop data, containing 261 micro-RAIDs with ground truth boundaries, were trained for 7 days. Using this well-trained MCI-frcnn, we detected micro-RAID boundaries for the input new images, with a fast speed (5.26 fps), high recognition accuracy (AUROC = 0.85, mAP = 0.69), and high boundary region quantification (genomic IoU = 76%). We further applied MCI-frcnn to detect human micro-TADs boundaries using human GM12878 SPRITE data and obtained a high region quantification score (mean gIoU = 85%). In all, the MCI-frcnn deep learning method which we developed in this work is a general tool for micro-domain boundary detection.
Collapse
|
7
|
Lee LM, Christodoulou EG, Shyamsunder P, Chen BJ, Lee KL, Fung TK, So CWE, Wong GC, Petretto E, Rackham OJL, Tiong Ong S. A novel network pharmacology approach for leukaemia differentiation therapy using Mogrify ®. Oncogene 2022; 41:5160-5175. [PMID: 36271030 DOI: 10.1038/s41388-022-02505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) is a rapidly fatal blood cancer that is characterised by the accumulation of immature myeloid cells in the blood and bone marrow as a result of blocked differentiation. Methods which identify master transcriptional regulators of AML subtype-specific leukaemia cell states and their combinations could be critical for discovering novel differentiation-inducing therapies. In this proof-of-concept study, we demonstrate a novel utility of the Mogrify® algorithm in identifying combinations of transcription factors (TFs) and drugs, which recapitulate granulocytic differentiation of the NB4 acute promyelocytic leukaemia (APL) cell line, using two different approaches. In the first approach, Connectivity Map (CMAP) analysis of these TFs and their target networks outperformed standard approaches, retrieving ATRA as the top hit. We identify dimaprit and mebendazole as a drug combination which induces myeloid differentiation. In the second approach, we show that genetic manipulation of specific Mogrify®-identified TFs (MYC and IRF1) leads to co-operative induction of APL differentiation, as does pharmacological targeting of these TFs using currently available compounds. We also show that loss of IRF1 blunts ATRA-mediated differentiation, and that MYC represses IRF1 expression through recruitment of PML-RARα, the driver fusion oncoprotein in APL, to the IRF1 promoter. Finally, we demonstrate that these drug combinations can also induce differentiation of primary patient-derived APL cells, and highlight the potential of targeting MYC and IRF1 in high-risk APL. Thus, these results suggest that Mogrify® could be used for drug discovery or repositioning in leukaemia differentiation therapy for other subtypes of leukaemia or cancers.
Collapse
MESH Headings
- Humans
- Tretinoin/pharmacology
- Tretinoin/therapeutic use
- Network Pharmacology
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Cell Differentiation/genetics
- Transcription Factors/genetics
Collapse
Affiliation(s)
- Lin Ming Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Eleni G Christodoulou
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Pavithra Shyamsunder
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Bei Jun Chen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Kian Leong Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Tsz Kan Fung
- Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, London, UK
| | - Chi Wai Eric So
- Comprehensive Cancer Centre, King's College London, London, UK
- Department of Haematological Medicine, King's College Hospital, London, UK
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Enrico Petretto
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College London, Faculty of Medicine, London, UK.
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, China.
| | - Owen J L Rackham
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - S Tiong Ong
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
- Department of Haematology, Singapore General Hospital, Singapore, Singapore.
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore.
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
8
|
Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
Collapse
Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| |
Collapse
|
9
|
Defining the Transcriptional Control of Pediatric AML Highlights RARA as a Super-Enhancer Regulated Druggable Dependency. Blood Adv 2021; 5:4864-4876. [PMID: 34543389 PMCID: PMC9153032 DOI: 10.1182/bloodadvances.2020003737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/11/2021] [Indexed: 11/26/2022] Open
Abstract
The first enhancer mapping of pediatric AML reveals that the most common SE-associated signature is one driven by RARA. A RARA SE is common in pediatric AML and correlates to sensitivity to the retinoid tamibarotene both in vitro and in vivo.
Somatic mutations are rare in pediatric acute myeloid leukemia (pAML), indicating that alternate strategies are needed to identify targetable dependencies. We performed the first enhancer mapping of pAML in 22 patient samples. Generally, pAML samples were distinct from adult AML samples, and MLL (KMT2A)–rearranged samples were also distinct from non–KMT2A-rearranged samples. Focusing specifically on superenhancers (SEs), we identified SEs associated with many known leukemia regulators. The retinoic acid receptor alpha (RARA) gene was differentially regulated in our cohort, and a RARA-associated SE was detected in 64% of the study cohort across all cytogenetic and molecular subtypes tested. RARA SE+ pAML cell lines and samples exhibited high RARA messenger RNA levels. These samples were specifically sensitive to the synthetic RARA agonist tamibarotene in vitro, with slowed proliferation, apoptosis induction, differentiation, and upregulated retinoid target gene expression, compared with RARA SE− samples. Tamibarotene prolonged survival and suppressed the leukemia burden of an RARA SE+ pAML patient-derived xenograft mouse model compared with a RARA SE− patient-derived xenograft. Our work shows that examining chromatin regulation can identify new, druggable dependencies in pAML and provides a rationale for a pediatric tamibarotene trial in children with RARA-high AML.
Collapse
|
10
|
Wang P, Feng Y, Zhu K, Chai H, Chang YT, Yang X, Liu X, Shen C, Gega E, Lee B, Kim M, Ruan X, Ruan Y. In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing. Curr Protoc 2021; 1:e174. [PMID: 34351700 DOI: 10.1002/cpz1.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is an established method to map protein-mediated chromatin interactions. A limitation, however, is that it requires a hundred million cells per experiment, which hampers its broad application in biomedical research, particularly in studies in which it is impractical to obtain a large number of cells from rare samples. To reduce the required input cell number while retaining high data quality, we developed an in situ ChIA-PET protocol, which requires as few as 1 million cells. Here, we describe detailed step-by-step procedures for performing in situ ChIA-PET from cultured cells, including both an experimental protocol for sample preparation and data generation and a computational protocol for data processing and visualization using the ChIA-PIPE pipeline. As the protocol significantly simplifies the experimental procedure, reduces ligation noise, and decreases the required input of cells compared to previous versions of ChIA-PET protocols, it can be applied to generate high-resolution chromatin contact maps mediated by various protein factors for a wide range of human and mouse primary cells. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample preparation and data generation Support Protocol: Bridge linker preparation Basic Protocol 2: Data processing and visualization.
Collapse
Affiliation(s)
- Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Yuliang Feng
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmacy, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Kun Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Ya-Ting Chang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Department of Translational Research and Cellular Therapeutics, City of Hope, Duarte, California
| | - Xiaofei Yang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chen Shen
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Eva Gega
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
| |
Collapse
|
11
|
CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA. J Biol Chem 2021; 296:100413. [PMID: 33581110 PMCID: PMC7960549 DOI: 10.1016/j.jbc.2021.100413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
Proper expression of Homeobox A cluster genes (HoxA) is essential for embryonic stem cell (ESC) differentiation and individual development. However, mechanisms controlling precise spatiotemporal expression of HoxA during early ESC differentiation remain poorly understood. Herein, we identified a functional CTCF-binding element (CBE+47) closest to the 3'-end of HoxA within the same topologically associated domain (TAD) in ESC. CRISPR-Cas9-mediated deletion of CBE+47 significantly upregulated HoxA expression and enhanced early ESC differentiation induced by retinoic acid (RA) relative to wild-type cells. Mechanistic analysis by chromosome conformation capture assay (Capture-C) revealed that CBE+47 deletion decreased interactions between adjacent enhancers, enabling formation of a relatively loose enhancer-enhancer interaction complex (EEIC), which overall increased interactions between that EEIC and central regions of HoxA chromatin. These findings indicate that CBE+47 organizes chromatin interactions between its adjacent enhancers and HoxA. Furthermore, deletion of those adjacent enhancers synergistically inhibited HoxA activation, suggesting that these enhancers serve as an EEIC required for RA-induced HoxA activation. Collectively, these results provide new insight into RA-induced HoxA expression during early ESC differentiation, also highlight precise regulatory roles of the CTCF-binding element in orchestrating high-order chromatin structure.
Collapse
|
12
|
Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. Genome Biol 2020; 21:110. [PMID: 32393309 PMCID: PMC7212609 DOI: 10.1186/s13059-020-02030-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/27/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis remain largely unknown. RESULTS Using an inducible system, we comprehensively analyze the 3D genome organization in myeloid cells and its reorganization after PML-RARα induction and perform additional analyses in patient-derived APL cells with native PML-RARα. We discover that PML-RARα mediates extensive chromatin interactions genome-wide. Globally, it redefines the chromatin topology of the myeloid genome toward a more condensed configuration in APL cells; locally, it intrudes RNAPII-associated interaction domains, interrupts myeloid-specific transcription factors binding at enhancers and super-enhancers, and leads to transcriptional repression of genes critical for myeloid differentiation and maturation. CONCLUSIONS Our results not only provide novel topological insights for the roles of PML-RARα in transforming myeloid cells into leukemia cells, but further uncover a topological framework of a molecular mechanism for oncogenic fusion proteins in cancers.
Collapse
Affiliation(s)
- Ping Wang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Present Address: Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Jacqueline Jufen Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030, USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Przemyslaw Szalaj
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Simon Zhongyuan Tian
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030, USA.
| |
Collapse
|