1
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Zeng Y, Wei R, Bao L, Xue T, Qin Y, Ren M, Bai Q, Yao Q, Yu C, Chen C, Wei P, Yu B, Cao J, Li X, Zhang Q, Zhou X. Characteristics and Clinical Value of MYC , BCL2, and BCL6 Rearrangement Detected by Next-generation Sequencing in DLBCL. Am J Surg Pathol 2024; 48:919-929. [PMID: 38937822 PMCID: PMC11251499 DOI: 10.1097/pas.0000000000002258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
MYC , BCL2, and BCL6 rearrangements are clinically important events of diffuse large B-cell lymphoma (DLBCL). The ability and clinical value of targeted next-generation sequencing (NGS) in the detection of these rearrangements in DLBCL have not been fully determined. We performed targeted NGS (481-gene-panel) and break-apart FISH of MYC , BCL2, and BCL6 gene regions in 233 DLBCL cases. We identified 88 rearrangements (16 MYC ; 20 BCL2 ; 52 BCL6 ) using NGS and 96 rearrangements (28 MYC ; 20 BCL2 ; 65 BCL6 ) using FISH. The consistency rates between FISH and targeted NGS for the detection of MYC , BCL2, and BCL6 rearrangements were 93%, 97%, and 89%, respectively. FISH-cryptic rearrangements (NGS+/FISH-) were detected in 7 cases (1 MYC ; 3 BCL2 ; 2 BCL6 ; 1 MYC::BCL6 ), mainly caused by small chromosomal insertions and inversions. NGS-/FISH+ were detected in 38 cases (14 MYC ; 4 BCL2 ; 20 BCL6 ).To clarify the cause of the inconsistencies, we selected 17 from the NGS-/FISH+ rearrangements for further whole genome sequencing (WGS), and all 17 rearrangements were detected with break points by WGS. These break points were all located outside the region covered by the probe of targeted NGS, and most (16/17) were located in the intergenic region. These results indicated that targeted NGS is a powerful clinical diagnostics tool for comprehensive MYC , BCL2, and BCL6 rearrangement detection. Compared to FISH, it has advantages in describing the break point distribution, identifying uncharacterized partners, and detecting FISH-cryptic rearrangements. However, the lack of high-sensitivity caused by insufficient probe coverage is the main limitation of the current technology.
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Affiliation(s)
- Yupeng Zeng
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Longlong Bao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Yulan Qin
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Chengli Yu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Chen Chen
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Ping Wei
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Baohua Yu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Junning Cao
- Department of Oncology, Shanghai Medical College
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoqiu Li
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qunling Zhang
- Department of Oncology, Shanghai Medical College
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
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Watanabe A, Wang L, Tan TK, Urayama KY, Kizuki T, Komatsu C, Kagami K, Shinohara T, Kasai S, Tamai M, Harama D, Akahane K, Goi K, Goto H, Satou K, Kaname T, Sanda T, Inukai T. Acquired copy number amplification at the MYC enhancer in human B-precursor acute lymphoblastic leukemia cell lines. Cancer Sci 2024. [PMID: 38923173 DOI: 10.1111/cas.16260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/17/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Our study highlights the discovery of recurrent copy number alterations in noncoding regions, specifically blood enhancer cluster (BENC-CNA), in B-precursor acute lymphoblastic leukemia (BCP-ALL) cell lines. We demonstrate that BENC-CNA acts as a super-enhancer, driving MYC expression and possibly contributing to the immortalization and proliferative advantage of BCP-ALL cells in vitro.
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Affiliation(s)
- Atsushi Watanabe
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
- Department of Pediatrics, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Lu Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
| | - Kevin Y Urayama
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, Japan
- Graduate School of Public Health, St. Luke's International University, Tokyo, Japan
| | - Toshihiko Kizuki
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Chiaki Komatsu
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Keiko Kagami
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Tamao Shinohara
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Shin Kasai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Minori Tamai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Daisuke Harama
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kumiko Goi
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kazuhito Satou
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore City, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
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3
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Yao M, Cao Y, He J, Dong R, Liu G, Chen Y, Wang J, Zhou J. Single-cell transcriptomic analysis reveals heterogeneous features of myeloid-derived suppressor cells in newborns. Front Immunol 2024; 15:1367230. [PMID: 38919617 PMCID: PMC11196393 DOI: 10.3389/fimmu.2024.1367230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
The transitory emergence of myeloid-derived suppressor cells (MDSCs) in infants is important for the homeostasis of the immune system in early life. The composition and functional heterogeneity of MDSCs in newborns remain elusive, hampering the understanding of the importance of MDSCs in neonates. In this study, we unraveled the maturation trajectory of polymorphonuclear (PMN)-MDSCs from the peripheral blood of human newborns by performing single-cell RNA sequencing. Results indicated that neonatal PMN-MDSCs differentiated from self-renewal progenitors, antimicrobial PMN-MDSCs, and immunosuppressive PMN-MDSCs to late PMN-MDSCs with reduced antimicrobial capacity. We also established a simple framework to distinguish these distinct stages by CD177 and CXCR2. Importantly, preterm newborns displayed a reduced abundance of classical PMN-MDSCs but increased late PMN-MDSCs, consistent with their higher susceptibility to infections and inflammation. Furthermore, newborn PMN-MDSCs were distinct from those from cancer patients, which displayed minimum expression of genes about antimicrobial capacity. This study indicates that the heterogeneity of PMN-MDSCs is associated with the maturity of human newborns.
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Affiliation(s)
- Meng Yao
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yingjiao Cao
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Juan He
- Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Rui Dong
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Gaoyu Liu
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yingying Chen
- Department of Clinical Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Jun Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zhou
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Liu S, Dai W, Jin B, Jiang F, Huang H, Hou W, Lan J, Jin Y, Peng W, Pan J. Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets. Mol Cancer 2024; 23:122. [PMID: 38844984 PMCID: PMC11157854 DOI: 10.1186/s12943-024-02033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Metastasis remains the principal cause of cancer-related lethality despite advancements in cancer treatment. Dysfunctional epigenetic alterations are crucial in the metastatic cascade. Among these, super-enhancers (SEs), emerging as new epigenetic regulators, consist of large clusters of regulatory elements that drive the high-level expression of genes essential for the oncogenic process, upon which cancer cells develop a profound dependency. These SE-driven oncogenes play an important role in regulating various facets of metastasis, including the promotion of tumor proliferation in primary and distal metastatic organs, facilitating cellular migration and invasion into the vasculature, triggering epithelial-mesenchymal transition, enhancing cancer stem cell-like properties, circumventing immune detection, and adapting to the heterogeneity of metastatic niches. This heavy reliance on SE-mediated transcription delineates a vulnerable target for therapeutic intervention in cancer cells. In this article, we review current insights into the characteristics, identification methodologies, formation, and activation mechanisms of SEs. We also elaborate the oncogenic roles and regulatory functions of SEs in the context of cancer metastasis. Ultimately, we discuss the potential of SEs as novel therapeutic targets and their implications in clinical oncology, offering insights into future directions for innovative cancer treatment strategies.
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Affiliation(s)
- Shenglan Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wei Dai
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Bei Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Feng Jiang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Hao Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Wen Hou
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China
| | - Jinxia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, China
| | - Yanli Jin
- College of Pharmacy, Jinan University Institute of Tumor Pharmacology, Jinan University, Guangzhou, 510632, China
| | - Weijie Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Jiangxi Provincal Key Laboratory of Tissue Engineering, School of Pharmacy, Gannan Medical University, Ganzhou, 314000, China.
| | - Jingxuan Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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5
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Manguso N, Kim M, Joshi N, Al Mahmud MR, Aldaco J, Suzuki R, Cortes-Ledesma F, Cui X, Yamada S, Takeda S, Giuliano A, You S, Tanaka H. TDP2 is a regulator of estrogen-responsive oncogene expression. NAR Cancer 2024; 6:zcae016. [PMID: 38596431 PMCID: PMC11000318 DOI: 10.1093/narcan/zcae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 02/19/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
With its ligand estrogen, the estrogen receptor (ER) initiates a global transcriptional program, promoting cell growth. This process involves topoisomerase 2 (TOP2), a key protein in resolving topological issues during transcription by cleaving a DNA duplex, passing another duplex through the break, and repairing the break. Recent studies revealed the involvement of various DNA repair proteins in the repair of TOP2-induced breaks, suggesting potential alternative repair pathways in cases where TOP2 is halted after cleavage. However, the contribution of these proteins in ER-induced transcriptional regulation remains unclear. We investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme for the removal of halted TOP2 from the DNA ends, in the estrogen-induced transcriptome using both targeted and global transcription analyses. MYC activation by estrogen, a TOP2-dependent and transient event, became prolonged in the absence of TDP2 in both TDP2-deficient cells and mice. Bulk and single-cell RNA-seq analyses defined MYC and CCND1 as oncogenes whose estrogen response is tightly regulated by TDP2. These results suggest that TDP2 may inherently participate in the repair of estrogen-induced breaks at specific genomic loci, exerting precise control over oncogenic gene expression.
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Affiliation(s)
- Nicholas Manguso
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Minhyung Kim
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Neeraj Joshi
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Md Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Aldaco
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Ryusuke Suzuki
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
| | - Felipe Cortes-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Sevilla, 41092, Spain
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Shintaro Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Armando Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Sungyong You
- Department of Urology and Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048 USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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Wu C, Huang J. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics 2024; 25:483. [PMID: 38750461 PMCID: PMC11097474 DOI: 10.1186/s12864-024-10408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Multiple enhancers co-regulating the same gene is prevalent and plays a crucial role during development and disease. However, how multiple enhancers coordinate the same gene expression across various cell types remains largely unexplored at genome scale. RESULTS We develop a computational approach that enables the quantitative assessment of enhancer specificity and selectivity across diverse cell types, leveraging enhancer-promoter (E-P) interactions data. We observe two well-known gene regulation patterns controlled by enhancer clusters, which regulate the same gene either in a limited number of cell types (Specific pattern, Spe) or in the majority of cell types (Conserved pattern, Con), both of which are enriched for super-enhancers (SEs). We identify a previously overlooked pattern (Variable pattern, Var) that multiple enhancers link to the same gene, but rarely coexist in the same cell type. These three patterns control the genes associating with distinct biological function and exhibit unique epigenetic features. Specifically, we discover a subset of Var patterns contains Shared enhancers with stable enhancer-promoter interactions in the majority of cell types, which might contribute to maintaining gene expression by recruiting abundant CTCF. CONCLUSIONS Together, our findings reveal three distinct E-P regulation patterns across different cell types, providing insights into deciphering the complexity of gene transcriptional regulation.
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Affiliation(s)
- Chengyi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
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8
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Li-Bao L, Díaz-Díaz C, Raiola M, Sierra R, Temiño S, Moya FJ, Rodriguez-Perales S, Santos E, Giovinazzo G, Bleckwehl T, Rada-Iglesias Á, Spitz F, Torres M. Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression. Nat Commun 2024; 15:3931. [PMID: 38729993 PMCID: PMC11087473 DOI: 10.1038/s41467-024-48258-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
MYC plays various roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency, the regulation of cell competition and the control of embryonic diapause. However, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~ 3-megabase gene desert with multiple cis-regulatory elements. Here we use genomic rearrangements, transgenesis and targeted mutation to analyse Myc regulation in early mouse embryos and pluripotent stem cells. We identify a topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the pre-implantation and early post-implantation embryo. Within this region, we identify elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially activate during naive and formative pluripotency. Deletion of pluripotency-specific enhancers dampens embryonic stem cell competitive ability. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.
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Affiliation(s)
- Lin Li-Bao
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro Andaluz de Biología del Desarrollo (CABD), Sevilla, Spain
| | - Covadonga Díaz-Díaz
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Morena Raiola
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Rocío Sierra
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Francisco J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Elisa Santos
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Giovanna Giovinazzo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Álvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Francois Spitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
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9
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Capelli D. FLT3-Mutated Leukemic Stem Cells: Mechanisms of Resistance and New Therapeutic Targets. Cancers (Basel) 2024; 16:1819. [PMID: 38791898 PMCID: PMC11119130 DOI: 10.3390/cancers16101819] [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: 03/18/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the availability of target drugs in the first and second line, only 30% of FLT3mut AMLs are cured. Among the multiple mechanisms of resistance, those of FLT3mut LSC are the most difficult to eradicate because of their metabolic and genomic characteristics. Reactivation of glycogen synthesis, inhibition of the RAS/MAPK pathway, and degradation of FLT3 may be potential aids to fight the resistance of LSC to FLT3i. LSC is also characterized by the expression of a CD34+/CD25+/CD123+/CD99+ immunophenotype. The receptor and ligand of FLT3, the natural killer group 2 member D ligand (NKGD2L), and CD123 are some of the targets of chimeric antigen receptor T cells (CAR-T), bispecific T-cell engager molecules (BiTEs), CAR-NK and nanoparticles recently designed and reported here. The combination of these new therapeutic options, hopefully in a minimal residual disease (MRD)-driven approach, could provide the future answer to the challenge of treating FLT3mut AML.
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Affiliation(s)
- Debora Capelli
- Department of Hematology, Azienda Ospedaliera Universitaria, Ospedali Riuniti di Ancona, Via Conca 71, 60126 Ancona, Italy
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Rojo D, Hael CE, Soria A, de Souza FSJ, Low MJ, Franchini LF, Rubinstein M. A mammalian tripartite enhancer cluster controls hypothalamic Pomc expression, food intake, and body weight. Proc Natl Acad Sci U S A 2024; 121:e2322692121. [PMID: 38652744 PMCID: PMC11067048 DOI: 10.1073/pnas.2322692121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/12/2024] [Indexed: 04/25/2024] Open
Abstract
Food intake and energy balance are tightly regulated by a group of hypothalamic arcuate neurons expressing the proopiomelanocortin (POMC) gene. In mammals, arcuate-specific POMC expression is driven by two cis-acting transcriptional enhancers known as nPE1 and nPE2. Because mutant mice lacking these two enhancers still showed hypothalamic Pomc mRNA, we searched for additional elements contributing to arcuate Pomc expression. By combining molecular evolution with reporter gene expression in transgenic zebrafish and mice, here, we identified a mammalian arcuate-specific Pomc enhancer that we named nPE3, carrying several binding sites also present in nPE1 and nPE2 for transcription factors known to activate neuronal Pomc expression, such as ISL1, NKX2.1, and ERα. We found that nPE3 originated in the lineage leading to placental mammals and remained under purifying selection in all mammalian orders, although it was lost in Simiiformes (monkeys, apes, and humans) following a unique segmental deletion event. Interestingly, ablation of nPE3 from the mouse genome led to a drastic reduction (>70%) in hypothalamic Pomc mRNA during development and only moderate (<33%) in adult mice. Comparison between double (nPE1 and nPE2) and triple (nPE1, nPE2, and nPE3) enhancer mutants revealed the relative contribution of nPE3 to hypothalamic Pomc expression and its importance in the control of food intake and adiposity in male and female mice. Altogether, these results demonstrate that nPE3 integrates a tripartite cluster of partially redundant enhancers that originated upon a triple convergent evolutionary process in mammals and that is critical for hypothalamic Pomc expression and body weight homeostasis.
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Affiliation(s)
- Daniela Rojo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
| | - Clara E. Hael
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
| | - Agustina Soria
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires1428, Argentina
| | - Flávio S. J. de Souza
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires1428, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
| | - Malcolm J. Low
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48105
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
| | - Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires1428, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires1428, Argentina
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48105
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11
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Cai H, Liang J, Jiang Y, Wang Z, Li H, Wang W, Wang C, Hou J. KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:69. [PMID: 38443991 PMCID: PMC10913600 DOI: 10.1186/s13046-024-02996-y] [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: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Head and neck squamous carcinoma (HNSCC) is known for its high aggressiveness and susceptibility to cervical lymph node metastasis, which greatly contributes to its poor prognosis. During tumorigenesis, many types of cancer cells acquire oncogenic super-enhancers (SEs) that drive the overexpression of oncogenes, thereby maintaining malignant progression. This study aimed to identify and validate the role of oncogenic SE-associated genes in the malignant progression of HNSCC. METHODS We identified HNSCC cell-specific SE-associated genes through H3K27Ac ChIP-seq and overlapped them with HNSCC-associated genes obtained from The Cancer Genome Atlas (TCGA) dataset and Gene Expression Omnibus (GEO) datasets using weighted gene coexpression network analysis (WGCNA) to identify hub genes. The expression of IGF2BP2 and KLF7 in HNSCC was detected using clinical samples. To determine the biological role of IGF2BP2, we performed CCK-8, colony formation assay, Transwell migration assay, invasion assay, and orthotopic xenograft model experiments. Furthermore, we utilized a CRISPR/Cas9 gene-editing system, small-molecule inhibitors, ChIP-qPCR, and dual-luciferase reporter assays to investigate the molecular mechanisms of IGF2BP2 and its upstream transcription factors. RESULTS Our study identified IGF2BP2 as a hub SE-associated gene that exhibited aberrant expression in HNSCC tissues. Increased expression of IGF2BP2 was observed to be linked with malignant progression and unfavorable prognosis in HNSCC patients. Both in vitro and in vivo experiments confirmed that IGF2BP2 promotes the tumorigenicity and metastasis of HNSCC by promoting cell proliferation, migration, and invasion. Mechanistically, the IGF2BP2-SE region displayed enrichment for H3K27Ac, BRD4, and MED1, which led to the inhibition of IGF2BP2 transcription and expression through deactivation of the SE-associated transcriptional program. Additionally, KLF7 was found to induce the transcription of IGF2BP2 and directly bind to its promoter and SE regions. Moreover, the abundance of KLF7 exhibited a positive correlation with the abundance of IGF2BP2 in HNSCC. Patients with high expression of both KLF7 and IGF2BP2 showed poorer prognosis. Lastly, we demonstrated that the small molecule inhibitor JQ1, targeting BRD4, attenuated the proliferation and metastatic abilities of HNSCC cells. CONCLUSIONS Our study reveals the critical role of IGF2BP2 overexpression mediated by SE and KLF7 in promoting HNSCC progression. Targeting SE-associated transcriptional programs may represent a potential therapeutic strategy in managing HNSCC.
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Affiliation(s)
- Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hongyu Li
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wenjin Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Cheng Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology,, Sun Yat-Sen University, Guangzhou, 51055, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China.
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12
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Li X, Zeng S, Chen L, Zhang Y, Li X, Zhang B, Su D, Du Q, Zhang J, Wang H, Zhong Z, Zhang J, Li P, Jiang A, Long K, Li M, Ge L. An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation. Cell Prolif 2024; 57:e13552. [PMID: 37905345 PMCID: PMC10905358 DOI: 10.1111/cpr.13552] [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: 04/24/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 11/02/2023] Open
Abstract
Cebpa is a master transcription factor gene for adipogenesis. However, the mechanisms of enhancer-promoter chromatin interactions controlling Cebpa transcriptional regulation during adipogenic differentiation remain largely unknown. To reveal how the three-dimensional structure of Cebpa changes during adipogenesis, we generated high-resolution chromatin interactions of Cebpa in 3T3-L1 preadipocytes and 3T3-L1 adipocytes using circularized chromosome conformation capture sequencing (4C-seq). We revealed dramatic changes in chromatin interactions and chromatin status at interaction sites during adipogenic differentiation. Based on this, we identified five active enhancers of Cebpa in 3T3-L1 adipocytes through epigenomic data and luciferase reporter assays. Next, epigenetic repression of Cebpa-L1-AD-En2 or -En3 by the dCas9-KRAB system significantly down-regulated Cebpa expression and inhibited adipocyte differentiation. Furthermore, experimental depletion of cohesin decreased the interaction intensity between Cebpa-L1-AD-En2 and the Cebpa promoter and down-regulated Cebpa expression, indicating that long-range chromatin loop formation was mediated by cohesin. Two transcription factors, RXRA and PPARG, synergistically regulate the activity of Cebpa-L1-AD-En2. To test whether Cebpa-L1-AD-En2 plays a role in adipose tissue development, we injected dCas9-KRAB-En2 lentivirus into the inguinal white adipose tissue (iWAT) of mice to suppress the activity of Cebpa-L1-AD-En2. Repression of Cebpa-L1-AD-En2 significantly decreased Cebpa expression and adipocyte size, altered iWAT transcriptome, and affected iWAT development. We identified functional enhancers regulating Cebpa expression and clarified the crucial roles of Cebpa-L1-AD-En2 and Cebpa promoter interaction in adipocyte differentiation and adipose tissue development.
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Affiliation(s)
- Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sha Zeng
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Li Chen
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Xuemin Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Biwei Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Duo Su
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qinjiao Du
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haoming Wang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Zhining Zhong
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jinwei Zhang
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and GeneticsSichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Anan Jiang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Chongqing Academy of Animal SciencesChongqingChina
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Liangpeng Ge
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
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13
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Zhu X, Zhang Y, Yin Z, Ye Z, Qin Y, Cheng Z, Shen Y, Yin Z, Ma J, Tang Y, Ding H, Guo Y, Hou G, Shen N. Three-Dimensional Chromosomal Landscape Revealing miR-146a Dysfunctional Enhancer in Lupus and Establishing a CRISPR-Mediated Approach to Inhibit the Interferon Pathway. Arthritis Rheumatol 2024; 76:384-395. [PMID: 37728419 DOI: 10.1002/art.42703] [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: 02/05/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVE The diminished expression of microRNA-146a (miR-146a) in systemic lupus erythematosus (SLE) contributes to the aberrant activation of the interferon pathway. Despite its significance, the underlying mechanism driving this reduced expression remains elusive. Considering the integral role of enhancers in steering gene expression, our study seeks to pinpoint the SLE-affected enhancers responsible for modulating miR-146a expression. Additionally, we aim to elucidate the mechanisms by which these enhancers influence the contribution of miR-146a to the activation of the interferon pathway. METHODS Circular chromosome conformation capture sequencing and epigenomic profiles were applied to identify candidate enhancers of miR-146a. CRISPR activation was performed to screen functional enhancers. Differential analysis of chromatin accessibility was used to identify SLE-dysregulated enhancers, and the mechanism underlying enhancer dysfunction was investigated by analyzing transcription factor binding. The therapeutic value of a lupus-related enhancer was further evaluated by targeting it in the peripheral blood mononuclear cells (PBMCs) of patients with SLE through a CRISPR activation approach. RESULTS We identified shared and cell-specific enhancers of miR-146a in distinct immune cells. An enhancer 32.5 kb downstream of miR-146a possesses less accessibility in SLE, and its chromatin openness was negatively correlated with SLE disease activity. Moreover, CCAAT/enhancer binding protein α, a down-regulated transcription factor in patients with SLE, binds to the 32.5-kb enhancer and induces the epigenomic change of this locus. Furthermore, CRISPR-based activation of this enhancer in SLE PBMCs could inhibit the activity of interferon pathway. CONCLUSION Our work defines a promising target for SLE intervention. We adopted integrative approaches to define cell-specific and functional enhancers of the SLE critical gene and investigated the mechanism underlying its dysregulation mediated by a lupus-related enhancer.
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Affiliation(s)
- Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Yutong Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zihang Yin
- Sheng Yushou Center of Cell Biology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaorui Cheng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwei Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China, and Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
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14
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Zhang C, Stelloo E, Barrans S, Cucco F, Jiang D, Tzioni MM, Chen Z, Li Y, Swennenhuis JF, Makker J, Rásó-Barnett L, Liu H, El-Daly H, Soilleux E, Shah N, Nagumantry SK, Kyaw M, Prahladan MP, Tooze R, Westhead DR, Feitsma H, Davies AJ, Burton C, Johnson PWM, Du MQ. Non-IG::MYC in diffuse large B-cell lymphoma confers variable genomic configurations and MYC transactivation potential. Leukemia 2024; 38:621-629. [PMID: 38184753 PMCID: PMC10912016 DOI: 10.1038/s41375-023-02134-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
MYC translocation occurs in 8-14% of diffuse large B-cell lymphoma (DLBCL), and may concur with BCL2 and/or BCL6 translocation, known as double-hit (DH) or triple-hit (TH). DLBCL-MYC/BCL2-DH/TH are largely germinal centre B-cell like subtype, but show variable clinical outcome, with IG::MYC fusion significantly associated with inferior survival. While DLBCL-MYC/BCL6-DH are variable in their cell-of-origin subtypes and clinical outcome. Intriguingly, only 40-50% of DLBCL with MYC translocation show high MYC protein expression (>70%). We studied 186 DLBCLs with MYC translocation including 32 MYC/BCL2/BCL6-TH, 75 MYC/BCL2-DH and 26 MYC/BCL6-DH. FISH revealed a MYC/BCL6 fusion in 59% of DLBCL-MYC/BCL2/BCL6-TH and 27% of DLBCL-MYC/BCL6-DH. Targeted NGS showed a similar mutation profile and LymphGen genetic subtype between DLBCL-MYC/BCL2/BCL6-TH and DLBCL-MYC/BCL2-DH, but variable LymphGen subtypes among DLBCL-MYC/BCL6-DH. MYC protein expression is uniformly high in DLBCL with IG::MYC, but variable in those with non-IG::MYC including MYC/BCL6-fusion. Translocation breakpoint analyses of 8 cases by TLC-based NGS showed no obvious genomic configuration that enables MYC transactivation in 3 of the 4 cases with non-IG::MYC, while a typical promoter substitution or IGH super enhancer juxtaposition in the remaining cases. The findings potentially explain variable MYC expression in DLBCL with MYC translocation, and also bear practical implications in its routine assessment.
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Affiliation(s)
- Chunye Zhang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | | | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Francesco Cucco
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
- Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Dan Jiang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Maria-Myrsini Tzioni
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yan Li
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Haematology, Hebei General Hospital, Shijiazhuang, PR China
| | | | - Jasmine Makker
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Lívia Rásó-Barnett
- The Haematopathology and Oncology Diagnostic Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hongxiang Liu
- East Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hesham El-Daly
- Cellular Pathology Department, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - Elizabeth Soilleux
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Nimish Shah
- Department of Haematology, Norfolk and Norwich University Foundation Hospital, Norwich, UK
| | | | - Maw Kyaw
- Department of Haematology, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, UK
| | | | - Reuben Tooze
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Andrew J Davies
- Southampton NIHR/Cancer Research UK Experimental Cancer Medicine Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK
| | - Peter W M Johnson
- Southampton NIHR/Cancer Research UK Experimental Cancer Medicine Centre and Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.
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15
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Feng P, Pang P, Sun Z, Xie Z, Chen T, Wang S, Cao Q, Mi R, Zeng C, Lu Y, Yu W, Shen H, Wu Y. Enhancer-mediated FOXO3 expression promotes MSC adipogenic differentiation by activating autophagy. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166975. [PMID: 38043828 DOI: 10.1016/j.bbadis.2023.166975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) are pluripotent stem cells capable of differentiating into osteocytes, adipocytes and chondrocytes. However, in osteoporosis, the balance of differentiation is tipped toward adipogenesis and the key mechanism is controversial. Researches have shown that, as upstream regulatory elements of gene expression, enhancers ar involved in the expression of identity genes. In this study, we identified enhancers-mediated gene FOXO3 promoting MSC adipogenic differentiation by activating autophagy. METHODS We integrated data of RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq) and ATAC-sequencing (ATAC-seq) to find the identity gene FOXO3. The expression of FOXO3 protein, adipogenic transcription factors and the substrate of autophagy were measured by western blotting. The Oil Red O (ORO) staining was used to visualize the adipogenesis of MSCs. Immunohistochemistry was used to visualize the FOXO3 expression in adipocytes in bone marrow. Immunofluorescence was used to detect the expression of PPARγ and LC3B. RESULTS During adipogenesis, enhancers redistribute to genes associated with adipogenic differentiation, among which we identified the pivotal identity gene FOXO3. FOXO3 could promote the expression of the adipogenic transcription factors PPARγ, CEBPα, and CEBPβ during adipogenic differentiation, while PPARγ, CEBPα, and CEBPβ could in turn bind to FOXO3 and continue to promote FOXO3 expression to form a positive feedback loop. Consistently elevated FOXO3 expression promotes autophagy by activating the PI3K-AKT pathway which mediates adipogenic differentiation. CONCLUSIONS Pivotal identity gene FOXO3 promotes autophagy by activating PI3K-AKT pathway, which provokes adipogenic differentiation of MSCs. Enhancer-regulated adipogenic identity gene FOXO3 could be an attractive treatment for osteoporosis.
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Affiliation(s)
- Pei Feng
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Peizhuo Pang
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Zehang Sun
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Zhongyu Xie
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Tingting Chen
- Department of Ophthalmology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, PR China
| | - Shan Wang
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Qian Cao
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Rujia Mi
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Chenying Zeng
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Yixuan Lu
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China
| | - Wenhui Yu
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China.
| | - Huiyong Shen
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China.
| | - Yanfeng Wu
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, PR China.
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16
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Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M. An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Comput Biol 2024; 20:e1011873. [PMID: 38335222 PMCID: PMC10883583 DOI: 10.1371/journal.pcbi.1011873] [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: 07/11/2023] [Revised: 02/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Super enhancers (SE), large genomic elements that activate transcription and drive cell identity, have been found with cancer-specific gene regulation in human cancers. Recent studies reported the importance of understanding the cooperation and function of SE internal components, i.e., the constituent enhancers (CE). However, there are no pan-cancer studies to identify cancer-specific SE signatures at the constituent level. Here, by revisiting pan-cancer SE activities with H3K27Ac ChIP-seq datasets, we report fingerprint SE signatures for 28 cancer types in the NCI-60 cell panel. We implement a mixture model to discriminate active CEs from inactive CEs by taking into consideration ChIP-seq variabilities between cancer samples and across CEs. We demonstrate that the model-based estimation of CE states provides improved functional interpretation of SE-associated regulation. We identify cancer-specific CEs by balancing their active prevalence with their capability of encoding cancer type identities. We further demonstrate that cancer-specific CEs have the strongest per-base enhancer activities in independent enhancer sequencing assays, suggesting their importance in understanding critical SE signatures. We summarize fingerprint SEs based on the cancer-specific statuses of their component CEs and build an easy-to-use R package to facilitate the query, exploration, and visualization of fingerprint SEs across cancers.
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Affiliation(s)
- Xiang Liu
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Nancy Gillis
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Chang Jiang
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Anthony McCofie
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Aik-Choon Tan
- Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah, United States of America
| | - Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lixin Wan
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
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17
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Rogers BB, Anderson AG, Lauzon SN, Davis MN, Hauser RM, Roberts SC, Rodriguez-Nunez I, Trausch-Lowther K, Barinaga EA, Hall PI, Knuesel MT, Taylor JW, Mackiewicz M, Roberts BS, Cooper SJ, Rizzardi LF, Myers RM, Cochran JN. Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements. Am J Hum Genet 2024; 111:259-279. [PMID: 38232730 PMCID: PMC10870142 DOI: 10.1016/j.ajhg.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Tauopathies are a group of neurodegenerative diseases defined by abnormal aggregates of tau, a microtubule-associated protein encoded by MAPT. MAPT expression is near absent in neural progenitor cells (NPCs) and increases during differentiation. This temporally dynamic expression pattern suggests that MAPT expression could be controlled by transcription factors and cis-regulatory elements specific to differentiated cell types. Given the relevance of MAPT expression to neurodegeneration pathogenesis, identification of such elements is relevant to understanding disease risk and pathogenesis. Here, we performed chromatin conformation assays (HiC & Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27ac and CTCF in NPCs and differentiated neurons to nominate candidate cis-regulatory elements (cCREs). We assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects on MAPT expression. Finally, we integrated cCRE annotations into an analysis of genetic variation in neurodegeneration-affected individuals and control subjects. We identified both proximal and distal regulatory elements for MAPT and confirmed the regulatory function for several regions, including three regions centromeric to MAPT beyond the H1/H2 haplotype inversion breakpoint. We also found that rare and predicted damaging genetic variation in nominated CREs was nominally depleted in dementia-affected individuals relative to control subjects, consistent with the hypothesis that variants that disrupt MAPT enhancer activity, and thereby reduced MAPT expression, may be protective against neurodegenerative disease. Overall, this study provides compelling evidence for pursuing detailed knowledge of CREs for genes of interest to permit better understanding of disease risk.
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Affiliation(s)
- Brianne B Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Shelby N Lauzon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - M Natalie Davis
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Rebecca M Hauser
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sydney C Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Erin A Barinaga
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Paige I Hall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jared W Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
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18
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Klein DC, Lardo SM, Hainer SJ. The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. CANCER RESEARCH COMMUNICATIONS 2024; 4:237-252. [PMID: 38126767 PMCID: PMC10831031 DOI: 10.1158/2767-9764.crc-23-0382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites. SIGNIFICANCE The bromodomain-containing protein BRD9 is essential for AML cell viability, but it is unclear whether this requirement is due to the protein's role as an epigenetic reader. We inhibited this activity and identified altered gene-distal chromatin regulation and transcription consistent with a more mature myeloid cell state.
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Affiliation(s)
- David C. Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Santana M. Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
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19
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Lemma RB, Fuglerud BM, Frampton J, Gabrielsen OS. MYB: A Key Transcription Factor in the Hematopoietic System Subject to Many Levels of Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:3-29. [PMID: 39017837 DOI: 10.1007/978-3-031-62731-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
MYB is a master regulator and pioneer factor highly expressed in hematopoietic progenitor cells (HPCs) where it contributes to the reprogramming processes operating during hematopoietic development. MYB plays a complex role being involved in several lineages of the hematopoietic system. At the molecular level, the MYB gene is subject to intricate regulation at many levels through several enhancer and promoter elements, through transcriptional elongation control, as well as post-transcriptional regulation. The protein is modulated by post-translational modifications (PTMs) such as SUMOylation restricting the expression of its downstream targets. Together with a range of interaction partners, cooperating transcription factors (TFs) and epigenetic regulators, MYB orchestrates a fine-tuned symphony of genes expressed during various stages of haematopoiesis. At the same time, the complex MYB system is vulnerable, being a target for unbalanced control and cancer development.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | | | - Jon Frampton
- Department of Cancer & Genomic Sciences, College of Medicine & Health, University of Birmingham, Edgbaston, Birmingham, UK
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20
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Qian H, Zhu M, Tan X, Zhang Y, Liu X, Yang L. Super-enhancers and the super-enhancer reader BRD4: tumorigenic factors and therapeutic targets. Cell Death Discov 2023; 9:470. [PMID: 38135679 PMCID: PMC10746725 DOI: 10.1038/s41420-023-01775-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Transcriptional super-enhancers and the BET bromodomain protein BRD4 are emerging as critical drivers of tumorigenesis and therapeutic targets. Characterized by substantial accumulation of histone H3 lysine 27 acetylation (H3K27ac) signals at the loci of cell identity genes and critical oncogenes, super-enhancers are recognized, bound and activated by BRD4, resulting in considerable oncogene over-expression, malignant transformation, cancer cell proliferation, survival, tumor initiation and progression. Small molecule compound BRD4 BD1 and BD2 bromodomain inhibitors block BRD4 binding to super-enhancers, suppress oncogene transcription and expression, reduce cancer cell proliferation and survival, and repress tumor progression in a variety of cancer types. Like other targeted therapy agents, BRD4 inhibitors show moderate anticancer effects on their own, and exert synergistic anticancer effects in vitro and in preclinical models, when combined with other anticancer agents including CDK7 inhibitors, CBP/p300 inhibitors and histone deacetylase inhibitors. More recently, BRD4 BD2 bromodomain selective inhibitors, proteolysis-targeting chimera (PROTAC) BRD4 protein degraders, and dual BRD4 and CBP/p300 bromodomain co-inhibitors have been developed and shown better anticancer efficacy and/or safety profile. Importantly, more than a dozen BRD4 inhibitors have entered clinical trials in patients with cancer of various organ origins. In summary, super-enhancers and their reader BRD4 are critical tumorigenic drivers, and BRD4 BD1 and BD2 bromodomain inhibitors, BRD4 BD2 bromodomain selective inhibitors, PROTAC BRD4 protein degraders, and dual BRD4 and CBP/p300 bromodomain co-inhibitors are promising novel anticancer agents for clinical translation.
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Affiliation(s)
- Haihong Qian
- Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Min Zhu
- Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Xinyu Tan
- Department of Dentistry, Kunming Medical University, Kunming, 650032, China
| | - Yixing Zhang
- Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Xiangning Liu
- Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China
| | - Li Yang
- Yangpu Hospital, School of Medicine, Tongji University, Shanghai, 200090, China.
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21
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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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22
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Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
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Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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23
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Nishida Y, Ishizawa J, Ayoub E, Montoya RH, Ostermann LB, Muftuoglu M, Ruvolo VR, Patsilevas T, Scruggs DA, Khazaei S, Mak PY, Tao W, Carter BZ, Boettcher S, Ebert BL, Daver NG, Konopleva M, Seki T, Kojima K, Andreeff M. Enhanced TP53 reactivation disrupts MYC transcriptional program and overcomes venetoclax resistance in acute myeloid leukemias. SCIENCE ADVANCES 2023; 9:eadh1436. [PMID: 38019903 PMCID: PMC10686564 DOI: 10.1126/sciadv.adh1436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
The tumor suppressor TP53 is frequently inactivated in a mutation-independent manner in cancers and is reactivated by inhibiting its negative regulators. We here cotarget MDM2 and the nuclear exporter XPO1 to maximize transcriptional activity of p53. MDM2/XPO1 inhibition accumulated nuclear p53 and elicited a 25- to 60-fold increase of its transcriptional targets. TP53 regulates MYC, and MDM2/XPO1 inhibition disrupted the c-MYC-regulated transcriptome, resulting in the synergistic induction of apoptosis in acute myeloid leukemia (AML). Unexpectedly, venetoclax-resistant AMLs express high levels of c-MYC and are vulnerable to MDM2/XPO1 inhibition in vivo. However, AML cells persisting after MDM2/XPO1 inhibition exhibit a quiescence- and stress response-associated phenotype. Venetoclax overcomes that resistance, as shown by single-cell mass cytometry. The triple inhibition of MDM2, XPO1, and BCL2 was highly effective against venetoclax-resistant AML in vivo. Our results propose a novel, highly translatable therapeutic approach leveraging p53 reactivation to overcome nongenetic, stress-adapted venetoclax resistance.
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Affiliation(s)
- Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rafael Heinz Montoya
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren B. Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muharrem Muftuoglu
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vivian R Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tallie Patsilevas
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darah A. Scruggs
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shayaun Khazaei
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wenjing Tao
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bing Z. Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steffen Boettcher
- Department of Medical Oncology and Haematology, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, The Broad Institute, Boston, MA 02115, USA
| | - Benjamin L. Ebert
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, The Broad Institute, Boston, MA 02115, USA
| | - Naval G. Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Section of Leukemia Biology Research, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kensuke Kojima
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematology, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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24
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Edrei Y, Levy R, Kaye D, Marom A, Radlwimmer B, Hellman A. Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation. Genome Biol 2023; 24:264. [PMID: 38012713 PMCID: PMC10683314 DOI: 10.1186/s13059-023-03094-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation. RESULTS In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. Under experimental conditions, DNA methylation induces enhancers to alter their enhancing effects or convert into silencers, while silencers are affected inversely. High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). Upon increased methylation of these units, their target-genes either increased or decreased in expression. Gene-enhancing and silencing units constitute cis-regulatory networks of genes. Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. Methylation variation in these sites effectively describe inter-patient expression variation and, compared with DNA sequence-alterations, appears as a major contributor of gene-expression variation among glioblastoma patients. CONCLUSIONS We describe complex cis-regulatory networks, which determine gene expression by summing the effects of positive and negative transcriptional inputs. In these networks, DNA methylation induces both enhancing and silencing effects, depending on the context. The revealed mechanism sheds light on the regulatory role of DNA methylation, explains inter-individual gene-expression variation, and opens the way for monitoring the driving forces behind deferential courses of cancer and other diseases.
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Affiliation(s)
- Yifat Edrei
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Revital Levy
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Daniel Kaye
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Anat Marom
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asaf Hellman
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel.
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25
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Spolski R, Li P, Chandra V, Shin B, Goel S, Sakamoto K, Liu C, Oh J, Ren M, Enomoto Y, West EE, Christensen SM, Wan ECK, Ge M, Lin JX, Yan B, Kazemian M, Yu ZX, Nagao K, Vijayanand P, Rothenberg EV, Leonard WJ. Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function. Sci Immunol 2023; 8:eadi8217. [PMID: 37922339 PMCID: PMC10832512 DOI: 10.1126/sciimmunol.adi8217] [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: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/05/2023]
Abstract
The IL-2 receptor α chain (IL-2Rα/CD25) is constitutively expressed on double-negative (DN2/DN3 thymocytes and regulatory T cells (Tregs) but induced by IL-2 on T and natural killer (NK) cells, with Il2ra expression regulated by a STAT5-dependent super-enhancer. We investigated CD25 regulation and function using a series of mice with deletions spanning STAT5-binding elements. Deleting the upstream super-enhancer region mainly affected constitutive CD25 expression on DN2/DN3 thymocytes and Tregs, with these mice developing autoimmune alopecia, whereas deleting an intronic region decreased IL-2-induced CD25 on peripheral T and NK cells. Thus, distinct super-enhancer elements preferentially control constitutive versus inducible expression in a cell type-specific manner. The mediator-1 coactivator colocalized with specific STAT5-binding sites. Moreover, both upstream and intronic regions had extensive chromatin interactions, and deletion of either region altered the super-enhancer structure in mature T cells. These results demonstrate differential functions for distinct super-enhancer elements, thereby indicating previously unknown ways to manipulate CD25 expression in a cell type-specific fashion.
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Affiliation(s)
- Rosanne Spolski
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peng Li
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivek Chandra
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shubham Goel
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keiko Sakamoto
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Hamamatsu University School of Medicine, Department of Dermatology, Hamamatsu, Japan
| | - Chengyu Liu
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jangsuk Oh
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Min Ren
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yutaka Enomoto
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erin E West
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Christensen
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edwin C K Wan
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Meili Ge
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Zu-Xi Yu
- Pathology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keisuke Nagao
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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26
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Mulet-Lazaro R, Delwel R. From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. Hemasphere 2023; 7:e969. [PMID: 37953829 PMCID: PMC10635615 DOI: 10.1097/hs9.0000000000000969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
Blood comprises a wide array of specialized cells, all of which share the same genetic information and ultimately derive from the same precursor, the hematopoietic stem cell (HSC). This diversity of phenotypes is underpinned by unique transcriptional programs gradually acquired in the process known as hematopoiesis. Spatiotemporal regulation of gene expression depends on many factors, but critical among them are enhancers-sequences of DNA that bind transcription factors and increase transcription of genes under their control. Thus, hematopoiesis involves the activation of specific enhancer repertoires in HSCs and their progeny, driving the expression of sets of genes that collectively determine morphology and function. Disruption of this tightly regulated process can have catastrophic consequences: in hematopoietic malignancies, dysregulation of transcriptional control by enhancers leads to misexpression of oncogenes that ultimately drive transformation. This review attempts to provide a basic understanding of enhancers and their role in transcriptional regulation, with a focus on normal and malignant hematopoiesis. We present examples of enhancers controlling master regulators of hematopoiesis and discuss the main mechanisms leading to enhancer dysregulation in leukemia and lymphoma.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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27
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Wu Y, Chen S, Shao Y, Su Y, Li Q, Wu J, Zhu J, Wen H, Huang Y, Zheng Z, Chen X, Ju X, Huang S, Wu X, Hu Z. KLF5 Promotes Tumor Progression and Parp Inhibitor Resistance in Ovarian Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304638. [PMID: 37702443 PMCID: PMC10625120 DOI: 10.1002/advs.202304638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/16/2023] [Indexed: 09/14/2023]
Abstract
One major characteristic of tumor cells is the aberrant activation of epigenetic regulatory elements, which remodel the tumor transcriptome and ultimately promote cancer progression and drug resistance. However, the oncogenic functions and mechanisms of ovarian cancer (OC) remain elusive. Here, super-enhancer (SE) regulatory elements that are aberrantly activated in OC are identified and it is found that SEs drive the relative specific expression of the transcription factor KLF5 in OC patients and poly(ADP-ribose) polymerase inhibitor (PARPi)-resistant patients. KLF5 expression is associated with poor outcomes in OC patients and can drive tumor progression in vitro and in vivo. Mechanistically, KLF5 forms a transcriptional complex with EHF and ELF3 and binds to the promoter region of RAD51 to enhance its transcription, strengthening the homologous recombination repair (HRR) pathway. Notably, the combination of suberoylanilide hydroxamic acid (SAHA) and olaparib significantly inhibits tumor growth and metastasis of PARPi-resistant OC cells with high KLF5. In conclusion, it is discovered that SEs-driven KLF5 is a key regulatory factor in OC progression and PARPi resistance; and potential therapeutic strategies for OC patients with PARPi resistance and high KLF5 are identified.
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Affiliation(s)
- Yong Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Siyu Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yang Shao
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Su
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qin Li
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jiangchun Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jun Zhu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Hao Wen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yan Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Zhong Zheng
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xiaojun Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xingzhu Ju
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Shenglin Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Xiaohua Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhixiang Hu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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28
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López-Pérez A, Remeseiro S, Hörnblad A. Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice. Sci Rep 2023; 13:18666. [PMID: 37907668 PMCID: PMC10618177 DOI: 10.1038/s41598-023-45614-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023] Open
Abstract
Several preclinical models have been recently developed for metabolic associated fatty liver disease (MAFLD) and associated hepatocellular carcinoma (HCC) but comprehensive analysis of the regulatory and transcriptional landscapes underlying disease in these models are still missing. We investigated the regulatory and transcriptional landscape in fatty livers and liver tumours from DIAMOND mice that faithfully mimic human HCC development in the context of MAFLD. RNA-sequencing and ChIP-sequencing revealed rewiring of the Wnt/β-catenin regulatory network in DIAMOND tumours, as manifested by chromatin remodelling and associated switching in the expression of the canonical TCF/LEF downstream effectors. We identified splicing as a major mechanism leading to constitutive oncogenic activation of β-catenin in a large subset of DIAMOND tumours, a mechanism that is independent on somatic mutations in the locus and that has not been previously shown. Similar splicing events were found in a fraction of human HCC and hepatoblastoma samples.
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Affiliation(s)
- Ana López-Pérez
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 90187, Umeå, Sweden
| | - Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 90187, Umeå, Sweden.
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29
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Wang H, Sun H, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Zhao S, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S, Liu Y. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia. Nat Commun 2023; 14:6792. [PMID: 37880218 PMCID: PMC10600232 DOI: 10.1038/s41467-023-42565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.
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Affiliation(s)
- Han Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bilin Liang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghua Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Hu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Wu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiao Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kefei Wu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Xie
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
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30
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Jha RK, Kouzine F, Levens D. MYC function and regulation in physiological perspective. Front Cell Dev Biol 2023; 11:1268275. [PMID: 37941901 PMCID: PMC10627926 DOI: 10.3389/fcell.2023.1268275] [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: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
MYC, a key member of the Myc-proto-oncogene family, is a universal transcription amplifier that regulates almost every physiological process in a cell including cell cycle, proliferation, metabolism, differentiation, and apoptosis. MYC interacts with several cofactors, chromatin modifiers, and regulators to direct gene expression. MYC levels are tightly regulated, and deregulation of MYC has been associated with numerous diseases including cancer. Understanding the comprehensive biology of MYC under physiological conditions is an utmost necessity to demark biological functions of MYC from its pathological functions. Here we review the recent advances in biological mechanisms, functions, and regulation of MYC. We also emphasize the role of MYC as a global transcription amplifier.
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Affiliation(s)
| | | | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, United States
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31
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Chakraborty C, Nissen I, Vincent CA, Hägglund AC, Hörnblad A, Remeseiro S. Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication. Nat Commun 2023; 14:6446. [PMID: 37833281 PMCID: PMC10576091 DOI: 10.1038/s41467-023-41919-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Chromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regulatory landscape of glioblastoma, the most aggressive primary brain tumour. Our data reveals profound rewiring of promoter-enhancer interactions, chromatin accessibility and redistribution of histone marks in glioblastoma. This leads to loss of long-range regulatory interactions and overall activation of promoters, which orchestrate changes in the expression of genes associated to glutamatergic synapses, axon guidance, axonogenesis and chromatin remodelling. SMAD3 and PITX1 emerge as major transcription factors controlling genes related to synapse organization and axon guidance. Inhibition of SMAD3 and neuronal activity stimulation cooperate to promote proliferation of glioblastoma cells in co-culture with glutamatergic neurons, and in mice bearing patient-derived xenografts. Our findings provide mechanistic insight into the regulatory networks that mediate neurogliomal synaptic communication.
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Affiliation(s)
- Chaitali Chakraborty
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Itzel Nissen
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Craig A Vincent
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Anna-Carin Hägglund
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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32
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Liu M, Wang W, Zhang H, Bi J, Zhang B, Shi T, Su G, Zheng Y, Fan S, Huang X, Chen B, Song Y, Zhao Z, Shi J, Li P, Lu W, Zhang L. Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis. Int J Mol Sci 2023; 24:14945. [PMID: 37834393 PMCID: PMC10574000 DOI: 10.3390/ijms241914945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Ferroptosis is an iron-dependent form of cell death, which is reported to be associated with glioma progression and drug sensitivity. Targeting ferroptosis is a potential therapeutic approach for glioma. However, the molecular mechanism of glioma cell ferroptosis is not clear. In this study, we profile the change of 3D chromatin structure in glioblastoma ferroptosis by using HiChIP and study the 3D gene regulation network in glioblastoma ferroptosis. A combination of an analysis of HiChIP and RNA-seq data suggests that change of chromatin loops mediated by 3D chromatin structure regulates gene expressions in glioblastoma ferroptosis. Genes that are regulated by 3D chromatin structures include genes that were reported to function in ferroptosis, like HDM2 and TXNRD1. We propose a new regulatory mechanism governing glioblastoma cell ferroptosis by 3D chromatin structure.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; (M.L.); (W.W.); (H.Z.); (J.B.); (B.Z.); (T.S.); (G.S.); (Y.Z.); (S.F.); (X.H.); (B.C.); (Y.S.); (Z.Z.); (J.S.); (P.L.)
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; (M.L.); (W.W.); (H.Z.); (J.B.); (B.Z.); (T.S.); (G.S.); (Y.Z.); (S.F.); (X.H.); (B.C.); (Y.S.); (Z.Z.); (J.S.); (P.L.)
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33
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Pan X, Chang Y, Ruan G, Wei F, Jiang H, Jiang Q, Huang X, Zhao X. Prognostic impact of FLT3-ITD mutation on NPM1 + acute myeloid leukaemia patients and related molecular mechanisms. Br J Haematol 2023; 203:212-223. [PMID: 37621257 DOI: 10.1111/bjh.18973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 08/26/2023]
Abstract
The prognosis of acute myeloid leukaemia (AML) patients carrying NPM1 mutations is significantly worse when accompanied by FLT3-ITD mutations. However, accurate quantitative detection of FLT3-ITD mutations remains challenging. To identify a novel biomarker in NPM1+ FLT3-ITD+ AML patients for more accurate stratification, we analysed the differential gene expression between the NPM1+ FLT3-ITD+ and NPM1+ FLT3-ITD- groups in five public AML datasets and identified a biomarker by taking the intersection of differentially expressed genes. We validated this biomarker in bone marrow samples from NPM1+ AML patients at the Peking University Institute of Haematology and analysed its prognostic significance. BCAT1 expression was higher in the NPM1+ FLT3-ITD+ group than in the NPM1+ FLT3-ITD- group in all seven cohorts. BCAT1 was able to predict the prognosis of NPM1+ FLT3-ITD+ AML patients, and its predictive ability was superior to that of the FLT3-ITD allelic ratio (AR). FLT3-targeted inhibitor quizartinib reduced BCAT1 expression. BCAT1 knockdown using lentiviral vectors led to the downregulation of MYC expression. Thus, we identified BCAT1 as a novel biomarker for NPM1+ FLT3-ITD+ AML patients. The FLT3-ITD/BCAT1/MYC signalling pathway may play a biological role in promoting the occurrence and development of AML in FLT3-ITD+ cell lines.
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Affiliation(s)
- Xin'an Pan
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Yingjun Chang
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Guorui Ruan
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Fangfang Wei
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Hao Jiang
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Qian Jiang
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
| | - Xiaojun Huang
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaosu Zhao
- National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University Institute of Hematology, Peking University People's Hospital, Beijing, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, China
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Yuan J, Liu X, Zhao H, Wang Y, Wei X, Wang P, Zhan J, Liu L, Li F, Ge X. GhRCD1 regulates cotton somatic embryogenesis by modulating the GhMYC3-GhMYB44-GhLBD18 transcriptional cascade. THE NEW PHYTOLOGIST 2023; 240:207-223. [PMID: 37434324 DOI: 10.1111/nph.19120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023]
Abstract
Plant somatic embryogenesis (SE) is a multifactorial developmental process where embryos that can develop into whole plants are produced from somatic cells rather than through the fusion of gametes. The molecular regulation of plant SE, which involves the fate transition of somatic cells into embryogenic cells, is intriguing yet remains elusive. We deciphered the molecular mechanisms by which GhRCD1 interacts with GhMYC3 to regulate cell fate transitions during SE in cotton. While silencing of GhMYC3 had no discernible effect on SE, its overexpression accelerated callus formation, and proliferation. We identified two of GhMYC3 downstream SE regulators, GhMYB44 and GhLBD18. GhMYB44 overexpression was unconducive to callus growth but bolstered EC differentiation. However, GhLBD18 can be triggered by GhMYC3 but inhibited by GhMYB44, which positively regulates callus growth. On top of the regulatory cascade, GhRCD1 antagonistically interacts with GhMYC3 to inhibit the transcriptional function of GhMYC3 on GhMYB44 and GhLBD18, whereby a CRISPR-mediated rcd1 mutation expedites cell fate transition, resembling the effects of GhMYC3 overexpression. Furthermore, we showed that reactive oxygen species (ROS) are involved in SE regulation. Our findings elucidated that SE homeostasis is maintained by the tetrapartite module, GhRCD1-GhMYC3-GhMYB44-GhLBD18, which acts to modulate intracellular ROS in a temporal manner.
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Affiliation(s)
- Jiachen Yuan
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xingxing Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hang Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Ye Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xi Wei
- Research Base of State Key Laboratory of Cotton Biology, Henan Normal University, Xinxiang, 453000, China
| | - Peng Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Feng Q, Cui N, Li S, Cao J, Chen Q, Wang H. Upregulation of SOX9 promotes the self-renewal and tumorigenicity of cervical cancer through activating the Wnt/β-catenin signaling pathway. FASEB J 2023; 37:e23174. [PMID: 37668416 DOI: 10.1096/fj.202201596rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 07/30/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
Sry-box9 (SOX9) maintains stem cell properties and plays crucial roles in many cancers. However, whether SOX9 is correlated with cervical cancer cell stemness and its detailed mechanism remains obscure. We studied the relationship between SOX9 and prognosis of cervical cancer through public database, and SOX9 was related to poor prognosis of cervical cancer. Elevated SOX9 expression enhanced the self-renewal properties and promotes tumorigenicity in cervical cancer. Overexpression of SOX9 could promote the expression of stem cell-related factors in cervical cancer cells and xenografts. Meanwhile, overexpression of SOX9 could also enhance the expressions of FZD10, β-catenin, and c-Myc in cervical cancer cells and xenografts, while inhibiting the expression of DDK1. The activation of Wnt pathway by chir-99 021 raised the tumor spheroid ability of SOX9 knockdown HeLa cells. In addition, SOX9 could transcriptional inhibit DKK1 and activate FZD10 and MYC by binding to their promoters to affect the Wnt/β-catenin pathway. These results demonstrated SOX9 regulated the self-renewal and tumorigenicity of cervical cancer through Wnt/β-catenin pathway by directly transcriptional activation of FZD10, MYC and transcriptional inhibition of DKK1.
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Affiliation(s)
- Qian Feng
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Nan Cui
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Shan Li
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Jing Cao
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Qian Chen
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Haiyan Wang
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, Xi'an, China
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Das ND, Chang JC, Hon CC, Kelly ST, Ito S, Lizio M, Kaczkowski B, Watanabe H, Katsushima K, Natsume A, Koseki H, Kondo Y, Minoda A, Umehara T. Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties. BMC Genomics 2023; 24:574. [PMID: 37759202 PMCID: PMC10523799 DOI: 10.1186/s12864-023-09659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Super-enhancers (SEs), which activate genes involved in cell-type specificity, have mainly been defined as genomic regions with top-ranked enrichment(s) of histone H3 with acetylated K27 (H3K27ac) and/or transcription coactivator(s) including a bromodomain and extra-terminal domain (BET) family protein, BRD4. However, BRD4 preferentially binds to multi-acetylated histone H4, typically with acetylated K5 and K8 (H4K5acK8ac), leading us to hypothesize that SEs should be defined by high H4K5acK8ac enrichment at least as well as by that of H3K27ac. RESULTS Here, we conducted genome-wide profiling of H4K5acK8ac and H3K27ac, BRD4 binding, and the transcriptome by using a BET inhibitor, JQ1, in three human glial cell lines. When SEs were defined as having the top ranks for H4K5acK8ac or H3K27ac signal, 43% of H4K5acK8ac-ranked SEs were distinct from H3K27ac-ranked SEs in a glioblastoma stem-like cell (GSC) line. CRISPR-Cas9-mediated deletion of the H4K5acK8ac-preferred SEs associated with MYCN and NFIC decreased the stem-like properties in GSCs. CONCLUSIONS Collectively, our data highlights H4K5acK8ac's utility for identifying genes regulating cell-type specificity.
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Affiliation(s)
- Nando D Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Jen-Chien Chang
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, RIKEN IMS, Yokohama, Japan
| | - S Thomas Kelly
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN IMS, Yokohama, Japan
| | - Marina Lizio
- Laboratory for Genome Information Analysis, RIKEN IMS, Yokohama, Japan
| | - Bogumil Kaczkowski
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN IMS, Yokohama, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN IMS, Yokohama, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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37
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Wong H, Sugimura R. Immune-epigenetic crosstalk in haematological malignancies. Front Cell Dev Biol 2023; 11:1233383. [PMID: 37808081 PMCID: PMC10551137 DOI: 10.3389/fcell.2023.1233383] [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: 06/02/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Haematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms which can arise during any stage of haematopoiesis in the bone marrow. Accumulating evidence suggests that chronic inflammation generated by inflammatory cytokines secreted by tumour and the tumour-associated cells within the bone marrow microenvironment initiates signalling pathways in malignant cells, resulting in activation of master transcription factors including Smads, STAT3, and NF-κB which confer cancer stem cell phenotypes and drive disease progression. Deciphering the molecular mechanisms for how immune cells interact with malignant cells to induce such epigenetic modifications, specifically DNA methylation, histone modification, expression of miRNAs and lnRNAs to perturbate haematopoiesis could provide new avenues for developing novel targeted therapies for haematological malignancies. Here, the complex positive and negative feedback loops involved in inflammatory cytokine-induced cancer stem cell generation and drug resistance are reviewed to highlight the clinical importance of immune-epigenetic crosstalk in haematological malignancies.
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Affiliation(s)
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Lee Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Selleri L, Rijli FM. Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. Nat Rev Genet 2023; 24:610-626. [PMID: 37095271 DOI: 10.1038/s41576-023-00594-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Major differences in facial morphology distinguish vertebrate species. Variation of facial traits underlies the uniqueness of human individuals, and abnormal craniofacial morphogenesis during development leads to birth defects that significantly affect quality of life. Studies during the past 40 years have advanced our understanding of the molecular mechanisms that establish facial form during development, highlighting the crucial roles in this process of a multipotent cell type known as the cranial neural crest cell. In this Review, we discuss recent advances in multi-omics and single-cell technologies that enable genes, transcriptional regulatory networks and epigenetic landscapes to be closely linked to the establishment of facial patterning and its variation, with an emphasis on normal and abnormal craniofacial morphogenesis. Advancing our knowledge of these processes will support important developments in tissue engineering, as well as the repair and reconstruction of the abnormal craniofacial complex.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA.
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA.
| | - Filippo M Rijli
- Laboratory of Developmental Neuroepigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Lv M, Gong Y, Liu X, Wang Y, Wu Q, Chen J, Min Q, Zhao D, Li X, Chen D, Yang D, Yeerken D, Liu R, Li J, Zhang W, Zhan Q. CDK7-YAP-LDHD axis promotes D-lactate elimination and ferroptosis defense to support cancer stem cell-like properties. Signal Transduct Target Ther 2023; 8:302. [PMID: 37582812 PMCID: PMC10427695 DOI: 10.1038/s41392-023-01555-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/09/2023] [Accepted: 06/28/2023] [Indexed: 08/17/2023] Open
Abstract
Reprogrammed cellular metabolism is essential for maintaining cancer stem cells (CSCs) state. Here, we report that mitochondrial D-lactate catabolism is a necessary initiating oncogenic event during tumorigenesis of esophageal squamous cell carcinoma (ESCC). We discover that cyclin-dependent kinase 7 (CDK7) phosphorylates nuclear Yes-associated protein 1 (YAP) at S127 and S397 sites and enhances its transcription function, which promotes D-lactate dehydrogenase (LDHD) protein expression. Moreover, LDHD is enriched significantly in ESCC-CSCs rather than differentiated tumor cells and high LDHD status is connected with poor prognosis in ESCC patients. Mechanistically, the CDK7-YAP-LDHD axis helps ESCC-CSCs escape from ferroptosis induced by D-lactate and generates pyruvate to satisfy energetic demands for their elevated self-renewal potential. Hence, we conclude that esophageal CSCs adopt a D-lactate elimination and pyruvate accumulation mode dependent on CDK7-YAP-LDHD axis, which drives stemness-associated hallmarks of ESCC-CSCs. Reasonably, targeting metabolic checkpoints may serve as an effective strategy for ESCC therapy.
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Affiliation(s)
- Mengzhu Lv
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Ying Gong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Xuesong Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China
| | - Qingnan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China
| | - Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dongyu Zhao
- Peking University International Cancer Institute, Beijing, 100191, China
| | - Xianfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dongshao Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Di Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Danna Yeerken
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Rui Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518036, China.
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China.
- Peking University International Cancer Institute, Beijing, 100191, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
- Soochow University Cancer Institute, Suzhou, 215127, China.
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Zhu S, Zhao Y, Xing C, Guo W, Huang Z, Zhang H, Yin L, Ruan X, Li H, Cheng Z, Wang Z, Peng H. Immune infiltration and drug specificity analysis of different subtypes based on functional status in angioimmunoblastic T-cell lymphoma. Heliyon 2023; 9:e18836. [PMID: 37576233 PMCID: PMC10412840 DOI: 10.1016/j.heliyon.2023.e18836] [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: 02/28/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
Angioimmunoblastic T-cell lymphoma (AITL) is a subtype of peripheral T-cell lymphoma (PTCL) strongly correlated with worse clinical outcomes. However, the role of characteristic pathway-related genes in patients with AITL (e.g., subtype typing and pathogenesis) remains unknown. In this study, we intended to understand the potential role and prognostic value of characteristic pathways in AITL and identified a model for subtype identification based on pathway-related functional status. Transcriptomic (RNA-seq) data were obtained from the Gene Expression Omnibus database for three sets of tumor tissues from AITL patients. AITL was divided into three clusters based on the pathway profile of patients and the best clustering k = 3, and differentially expressed genes (DEGs) in the three clusters were analyzed. The top 45 important variables associated with characteristic pathways, such as Huntington's disease, VEGF signaling pathway, nucleotide excision repair, ubiquitin-mediated proteolysis, purine metabolism, olfactory transduction, etc., were used to construct a subtype identification model. The model was experimentally validated and proved to possess good predictive efficacy. In addition, pathway-related subtype typing was significantly associated with different immune cell infiltration in AITL. Further analysis revealed that the drug IC50 values predicted also differed markedly among the different subtypes, thus further identifying some subtype-specific drugs. Our study indicates a potential role of characteristic pathways in AITL staging for the first time, provides novel insights for future research targeting AITL, and points to potential therapeutic options for patients with different subtypes of AITL.
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Affiliation(s)
- Shicong Zhu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Wancheng Guo
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zineng Huang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Huifang Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Le Yin
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Xueqin Ruan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Heng Li
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zhao Cheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zhihua Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan 410011, China
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Ober-Reynolds B, Wang C, Ko JM, Rios EJ, Aasi SZ, Davis MM, Oro AE, Greenleaf WJ. Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. Nat Genet 2023; 55:1288-1300. [PMID: 37500727 PMCID: PMC11190942 DOI: 10.1038/s41588-023-01445-4] [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: 09/01/2022] [Accepted: 06/17/2023] [Indexed: 07/29/2023]
Abstract
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. We generated matched single-cell chromatin profiles and transcriptomes from scalp tissue from healthy controls and patients with alopecia areata, identifying diverse cell types of the hair follicle niche. By interrogating these datasets at multiple levels of cellular resolution, we infer 50-100% more enhancer-gene links than previous approaches and show that aggregate enhancer accessibility for highly regulated genes predicts expression. We use these gene-regulatory maps to prioritize cell types, genes and causal variants implicated in the pathobiology of androgenetic alopecia (AGA), eczema and other complex traits. AGA genome-wide association studies signals are enriched in dermal papilla regulatory regions, supporting the role of these cells as drivers of AGA pathogenesis. Finally, we train machine learning models to nominate single-nucleotide polymorphisms that affect gene expression through disruption of transcription factor binding, predicting candidate functional single-nucleotide polymorphism for AGA and eczema.
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Affiliation(s)
| | - Chen Wang
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Justin M Ko
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Eon J Rios
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - Sumaira Z Aasi
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anthony E Oro
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Tang ZC, Qu Q, Teng XQ, Zhuang HH, Xu WX, Qu J. Bibliometric analysis of evolutionary trends and hotspots of super-enhancers in cancer. Front Pharmacol 2023; 14:1192855. [PMID: 37576806 PMCID: PMC10415222 DOI: 10.3389/fphar.2023.1192855] [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: 03/24/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: In the past decade, super-enhancer (SE) has become a research hotspot with increasing attention on cancer occurrence, development, and prognosis. To illustrate the hotspots of SE in cancer research and its evolutionary tendency, bibliometric analysis was carried out for this topic. Methods: Literature published before Dec 31, 2022, in WOSCC, was systematically classified, and Citespace, bibliometric.com/app, and GraphPad Prism analyzed the data. Results: After screening out inappropriate documents and duplicate data, 911 publications were selected for further bibliometric analysis. The top five research areas were Oncology (257, 28.211%), Cell Biology (210, 23.052%), Biochemistry Molecular Biology (209, 22.942%), Science Technology Other Topics (138, 15.148%), and Genetics Heredity (132, 14.490%). The United States of America (United States) has the highest number of documents (462, 50.71%), followed by China (303, 33.26%). Among the most productive institutions, four of which are from the United States and one from Singapore, the National University of Singapore. Harvard Medical School (7.68%) has the highest percentage of articles. Young, Richard A, with 32 publications, ranks first in the number of articles. The top three authors came from Whitehead Institute for Biomedical Research as a research team. More than two-thirds of the research are supported by the National Institutes of Health of the United States (337, 37.654%) and the United States Department of Health Human Services (337, 37.654%). And "super enhancer" (525), "cell identity" (258), "expression" (223), "cancer" (205), and "transcription factor" (193) account for the top 5 occurrence keywords. Discussion: Since 2013, SE and cancer related publications have shown a rapid growth trend. The United States continues to play a leading role in this field, as the top literature numbers, affiliations, funding agencies, and authors were all from the United States, followed by China and European countries. A high degree of active cooperation is evident among a multitude of countries. The role of SEs in cell identity, gene transcription, expression, and inhibition, as well as the relationship between SEs and TFs, and the selective inhibition of SEs, have received much attention, suggesting that they are hot issues for research.
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Affiliation(s)
- Zhen-Chu Tang
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Hospital Management, Central South University, Changsha, China
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, China
| | - Xin-Qi Teng
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Hai-Hui Zhuang
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Wei-Xin Xu
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, China
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Guo W, Wang X, Lu B, Yu J, Xu M, Huang R, Cheng M, Yang M, Zhao W, Zou C. Super-enhancer-driven MLX mediates redox balance maintenance via SLC7A11 in osteosarcoma. Cell Death Dis 2023; 14:439. [PMID: 37460542 DOI: 10.1038/s41419-023-05966-y] [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: 01/09/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Osteosarcoma (OS) is a common type of bone tumor for which there has been limited therapeutic progress over the past three decades. The prevalence of transcriptional addiction in cancer cells emphasizes the biological significance and clinical relevance of super-enhancers. In this study, we found that Max-like protein X (MLX), a member of the Myc-MLX network, is driven by super-enhancers. Upregulation of MLX predicts a poor prognosis in osteosarcoma. Knockdown of MLX impairs growth and metastasis of osteosarcoma in vivo and in vitro. Transcriptomic sequencing has revealed that MLX is involved in various metabolic pathways (e.g., lipid metabolism) and can induce metabolic reprogramming. Furthermore, knockdown of MLX results in disturbed transport and storage of ferrous iron, leading to an increase in the level of cellular ferrous iron and subsequent induction of ferroptosis. Mechanistically, MLX regulates the glutamate/cystine antiporter SLC7A11 to promote extracellular cysteine uptake required for the biosynthesis of the essential antioxidant GSH, thereby detoxifying reactive oxygen species (ROS) and maintaining the redox balance of osteosarcoma cells. Importantly, sulfasalazine, an FDA-approved anti-inflammatory drug, can inhibit SLC7A11, disrupt redox balance, and induce massive ferroptosis, leading to impaired tumor growth in vivo. Taken together, this study reveals a novel mechanism in which super-enhancer-driven MLX positively regulates SLC7A11 to meet the alleviated demand for cystine and maintain the redox balance, highlighting the feasibility and clinical promise of targeting SLC7A11 in osteosarcoma.
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Affiliation(s)
- Weitang Guo
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Xin Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Bing Lu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Jiaming Yu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Mingxian Xu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Renxuan Huang
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Mingzhe Cheng
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Meiling Yang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Wei Zhao
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Changye Zou
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
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Zhou RW, Parsons RE. Etiology of super-enhancer reprogramming and activation in cancer. Epigenetics Chromatin 2023; 16:29. [PMID: 37415185 DOI: 10.1186/s13072-023-00502-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by changes in the super-enhancer landscape. These aberrant super-enhancers commonly form to activate proto-oncogenes, or other genes upon which cancer cells depend, that initiate tumorigenesis, promote tumor proliferation, and increase the fitness of cancer cells to survive in the tumor microenvironment. These include well-recognized master regulators of proliferation in the setting of cancer, such as the transcription factor MYC which is under the control of numerous super-enhancers gained in cancer compared to normal tissues. This Review will cover the expanding cell-intrinsic and cell-extrinsic etiology of these super-enhancer changes in cancer, including somatic mutations, copy number variation, fusion events, extrachromosomal DNA, and 3D chromatin architecture, as well as those activated by inflammation, extra-cellular signaling, and the tumor microenvironment.
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Affiliation(s)
- Royce W Zhou
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Molecular Medicine Program, University of California San Francisco Internal Medicine Residency, San Francisco, CA, USA
| | - Ramon E Parsons
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Yashar WM, Curtiss BM, Coleman DJ, VanCampen J, Kong G, Macaraeg J, Estabrook J, Demir E, Long N, Bottomly D, McWeeney SK, Tyner JW, Druker BJ, Maxson JE, Braun TP. Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia. Mol Cancer Res 2023; 21:631-647. [PMID: 36976323 PMCID: PMC10330306 DOI: 10.1158/1541-7786.mcr-22-0745] [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: 09/20/2022] [Revised: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Mutations in Fms-like tyrosine kinase 3 (FLT3) are common drivers in acute myeloid leukemia (AML) yet FLT3 inhibitors only provide modest clinical benefit. Prior work has shown that inhibitors of lysine-specific demethylase 1 (LSD1) enhance kinase inhibitor activity in AML. Here we show that combined LSD1 and FLT3 inhibition induces synergistic cell death in FLT3-mutant AML. Multi-omic profiling revealed that the drug combination disrupts STAT5, LSD1, and GFI1 binding at the MYC blood superenhancer, suppressing superenhancer accessibility as well as MYC expression and activity. The drug combination simultaneously results in the accumulation of repressive H3K9me1 methylation, an LSD1 substrate, at MYC target genes. We validated these findings in 72 primary AML samples with the nearly every sample demonstrating synergistic responses to the drug combination. Collectively, these studies reveal how epigenetic therapies augment the activity of kinase inhibitors in FLT3-ITD (internal tandem duplication) AML. IMPLICATIONS This work establishes the synergistic efficacy of combined FLT3 and LSD1 inhibition in FLT3-ITD AML by disrupting STAT5 and GFI1 binding at the MYC blood-specific superenhancer complex.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University; Portland, OR, 97239, USA
- These authors contributed equally to this work
| | - Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- These authors contributed equally to this work
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jake VanCampen
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Garth Kong
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Emek Demir
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd; Portland, OR 97239, USA
- Pacific Northwest National Laboratories; Richland, WA 99354, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Shannon K. McWeeney
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jeffrey W. Tyner
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
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Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
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Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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47
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Heer M, Giudice L, Mengoni C, Giugno R, Rico D. Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers. Nucleic Acids Res 2023; 51:e55. [PMID: 37021559 PMCID: PMC10250221 DOI: 10.1093/nar/gkad229] [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: 08/05/2022] [Revised: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. We present Esearch3D, a new method that exploits network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bidirectional CAGE-seq, STARR-seq, P300, RNA polymerase II and expression quantitative trait loci (eQTLs). Esearch3D leverages the relationship between chromatin architecture and transcription, allowing the prediction of active enhancers and an understanding of the complex underpinnings of regulatory networks. The method is available at: https://github.com/InfOmics/Esearch3D and https://doi.org/10.5281/zenodo.7737123.
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Affiliation(s)
- Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Luca Giudice
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Claudia Mengoni
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM. A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. Nat Commun 2023; 14:3242. [PMID: 37277355 DOI: 10.1038/s41467-023-38953-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
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Affiliation(s)
- Sandra Kessler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- INSERM UMR 1121, Université de Strasbourg, Faculté de Chirurgie Dentaire, 8, rue Sainte Elisabeth, 67 000, Strasbourg, France
| | - Onkar Joshi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Yousra Ben Zouari
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Fiona Ross
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nathalie Vilain
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Adwait Salvi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joachim Wolff
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Söderholm S, Jauregi-Miguel A, Pagella P, Ghezzi V, Zambanini G, Nordin A, Cantù C. Single-cell response to Wnt signaling activation reveals uncoupling of Wnt target gene expression. Exp Cell Res 2023:113646. [PMID: 37271249 DOI: 10.1016/j.yexcr.2023.113646] [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: 12/21/2022] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023]
Abstract
Wnt signaling drives nuclear translocation of β-catenin and its subsequent association with the DNA-bound TCF/LEF transcription factors, which dictate target gene specificity by recognizing Wnt responsive elements across the genome. β-Catenin target genes are therefore thought to be collectively activated upon Wnt pathway stimulation. However, this appears in contrast with the non-overlapping patterns of Wnt target gene expression in several contexts, including early mammalian embryogenesis. Here we followed Wnt target gene expression in human embryonic stem cells after Wnt pathway stimulation at a single-cell resolution. Cells changed gene expression program over time consistent with three key developmental events: i) loss of pluripotency, ii) induction of Wnt target genes, and iii) mesoderm specification. Contrary to our expectation, not all cells displayed equal amplitude of Wnt target gene activation; rather, they distributed in a continuum from strong to weak responders when ranked based on the expression of the target AXIN2. Moreover, high AXIN2 did not always correspond to elevated expression of other Wnt targets, which were activated in different proportions in individual cells. The uncoupling of Wnt target gene expression was also identified in single cell transcriptomics profiling of other Wnt-responding cell types, including HEK293T, murine developing forelimbs, and human colorectal cancer. Our finding underlines the necessity to identify additional mechanisms that explain the heterogeneity of the Wnt/β-catenin-mediated transcriptional outputs in single cells.
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Affiliation(s)
- Simon Söderholm
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Amaia Jauregi-Miguel
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Valeria Ghezzi
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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Iyer AR, Gurumurthy A, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rausch D, Gupta J, Hall CN, Runge JS, Weiss M, Rahmat M, Anyoha R, Fulco CP, Ghobrial IM, Engreitz J, Cieslik MP, Ryan RJH. Selective Enhancer Dependencies in MYC -Intact and MYC -Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538892. [PMID: 37205448 PMCID: PMC10187217 DOI: 10.1101/2023.05.02.538892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC -intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer ( BCL6 -SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6 -SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3' enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3' rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene. Key points CRISPR-interference screens identify a conserved germinal center B cell MYC enhancer that is essential for GCB-DLBCL lacking MYC rearrangements. Functional profiling of MYC partner loci reveals principles of MYC enhancer-hijacking activation by non-immunoglobulin rearrangements.
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