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Liu Y, Li Q, Song L, Gong C, Tang S, Budinich KA, Vanderbeck A, Mathias KM, Wertheim GB, Nguyen SC, Outen R, Joyce EF, Maillard I, Wan L. Condensate-Promoting ENL Mutation Drives Tumorigenesis In Vivo Through Dynamic Regulation of Histone Modifications and Gene Expression. Cancer Discov 2024; 14:1522-1546. [PMID: 38655899 PMCID: PMC11294821 DOI: 10.1158/2159-8290.cd-23-0876] [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: 08/02/2023] [Revised: 02/21/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Gain-of-function mutations in the histone acetylation "reader" eleven-nineteen-leukemia (ENL), found in acute myeloid leukemia (AML) and Wilms tumor, are known to drive condensate formation and gene activation in cellular systems. However, their role in tumorigenesis remains unclear. Using a conditional knock-in mouse model, we show that mutant ENL perturbs normal hematopoiesis, induces aberrant expansion of myeloid progenitors, and triggers rapid onset of aggressive AML. Mutant ENL alters developmental and inflammatory gene programs in part by remodeling histone modifications. Mutant ENL forms condensates in hematopoietic stem/progenitor cells at key leukemogenic genes, and disrupting condensate formation via mutagenesis impairs its chromatin and oncogenic function. Moreover, treatment with an acetyl-binding inhibitor of the mutant ENL displaces these condensates from target loci, inhibits mutant ENL-induced chromatin changes, and delays AML initiation and progression in vivo. Our study elucidates the function of ENL mutations in chromatin regulation and tumorigenesis and demonstrates the potential of targeting pathogenic condensates in cancer treatment. Significance: A direct link between ENL mutations, condensate formation, and tumorigenesis is lacking. This study elucidates the function and mechanism of ENL mutations in leukemogenesis, establishing these mutations as bona fide oncogenic drivers. Our results also support the role of condensate dysregulation in cancer and reveal strategies to target pathogenic condensates.
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Affiliation(s)
- Yiman Liu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Qinglan Li
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Lele Song
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Chujie Gong
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Sylvia Tang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Krista A. Budinich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Cancer Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Ashley Vanderbeck
- VMD-PhD Program, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Kaeli M. Mathias
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Gerald B. Wertheim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Division of Hematopathology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Son C. Nguyen
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Riley Outen
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Eric F. Joyce
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Ivan Maillard
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Liling Wan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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2
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Wang Z, Zhao N, Zhang S, Wang D, Wang S, Liu N. YEATS domain-containing protein GAS41 regulates nuclear shape by working in concert with BRD2 and the mediator complex in colorectal cancer. Pharmacol Res 2024; 206:107283. [PMID: 38964523 DOI: 10.1016/j.phrs.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
The maintenance of nuclear shape is essential for cellular homeostasis and disruptions in this process have been linked to various pathological conditions, including cancer, laminopathies, and aging. Despite the significance of nuclear shape, the precise molecular mechanisms controlling it are not fully understood. In this study, we have identified the YEATS domain-containing protein 4 (GAS41) as a previously unidentified factor involved in regulating nuclear morphology. Genetic ablation of GAS41 in colorectal cancer cells resulted in significant abnormalities in nuclear shape and inhibited cancer cell proliferation both in vitro and in vivo. Restoration experiments revealed that wild-type GAS41, but not a YEATS domain mutant devoid of histone H3 lysine 27 acetylation or crotonylation (H3K27ac/cr) binding, rescued the aberrant nuclear phenotypes in GAS41-deficient cells, highlighting the importance of GAS41's binding to H3K27ac/cr in nuclear shape regulation. Further experiments showed that GAS41 interacts with H3K27ac/cr to regulate the expression of key nuclear shape regulators, including LMNB1, LMNB2, SYNE4, and LEMD2. Mechanistically, GAS41 recruited BRD2 and the Mediator complex to gene loci of these regulators, promoting their transcriptional activation. Disruption of GAS41-H3K27ac/cr binding caused BRD2, MED14 and MED23 to dissociate from gene loci, leading to nuclear shape abnormalities. Overall, our findings demonstrate that GAS41 collaborates with BRD2 and the Mediator complex to control the expression of crucial nuclear shape regulators.
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Affiliation(s)
- Zhengmin Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Zhao
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Deyu Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Shuai Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China.
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3
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Du N, Yi L, Wang J, Lei Y, Bo X, Guo F, Wang R, Chai J, Liu G. High expression of YEATS2 as a predictive factor of poor prognosis in patients with hepatocellular carcinoma. Sci Rep 2024; 14:17246. [PMID: 39060453 PMCID: PMC11282058 DOI: 10.1038/s41598-024-68348-0] [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: 04/30/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024] Open
Abstract
YEATS domain containing 2 (YEATS2), it may function as a proto-oncogene. This study aims to investigate if YEATS2 correlates with prognosis in hepatocellular carcinoma. The prognostic landscape of YEATS2 and its relationship with expression in hepatocellular carcinoma were deciphered with public databases, RT-qPCR and western-blot in tissue samples. The expression profiling and prognostic value of YEATS2 were explored using UALCAN, TIMER, OncoLnc database. Transcription and survival analyses of YEATS2 in hepatocellular carcinoma were investigated with cBioPortal database. The STRING database was explored to identify molecular functions and signaling pathways downstream of YEATS2. YEATS2 expression was significantly higher in hepatocellular carcinoma compared with adjacent non-malignant tissues. Promoter methylation of YEATS2 exhibited different patterns in hepatocellular carcinoma. High expression of YEATS2 was associated with poorer survival. Mechanistically, YEATS2 was involved in mediating multiple biological processes including morphogenesis and migration.
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Affiliation(s)
- Ning Du
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Lili Yi
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jiamu Wang
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Yongqiang Lei
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Xiaohui Bo
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Fangjie Guo
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Ruhao Wang
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jian Chai
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China.
| | - Guijie Liu
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China.
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4
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Ruan K, Bai G, Fang Y, Li D, Li T, Liu X, Lu B, Lu Q, Songyang Z, Sun S, Wang Z, Zhang X, Zhou W, Zhang H. Biomolecular condensates and disease pathogenesis. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2661-3. [PMID: 39037698 DOI: 10.1007/s11427-024-2661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Biomolecular condensates or membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.
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Affiliation(s)
- Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ge Bai
- Nanhu Brain-computer Interface Institute, Hangzhou, 311100, China.
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Qing Lu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuguo Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zheng Wang
- The Second Affiliated Hospital, School of Basic Medical Sciences, Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| | - Xin Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Song L, Li Q, Xia L, Sahay AE, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. Nat Commun 2024; 15:5937. [PMID: 39009564 PMCID: PMC11250843 DOI: 10.1038/s41467-024-50171-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: 10/31/2023] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
How disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL's histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
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Affiliation(s)
- Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qinglan Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lingbo Xia
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arushi Eesha Sahay
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Liling Wan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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6
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Tian G, Li X, Li XD. Genetically Encoded Epitope Tag for Probing Lysine Acylation-Mediated Protein-Protein Interactions. ACS Chem Biol 2024; 19:1376-1386. [PMID: 38829775 DOI: 10.1021/acschembio.4c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Histone lysine acetylation (Kac) and crotonylation (Kcr) marks mediate the recruitment of YEATS domains to chromatin. In this way, YEATS domain-containing proteins such as AF9 participate in the regulation of DNA-templated processes. Our previous study showed that the replacement of Kac/Kcr by a 2-furancarbonyllysine (Kfu) residue led to greatly enhanced affinity toward the AF9 YEATS domain, rendering Kfu-containing peptides useful chemical tools to probe the AF9 YEATS-Kac/Kcr interactions. Here, we report the genetic incorporation of Kfu in Escherichia coli and mammalian cells through the amber codon suppression technology. We develop a Kfu-containing epitope tag, termed RAY-tag, which can robustly and selectively engage with the AF9 YEATS domain in vitro and in cellulo. We further demonstrate that the fusion of RAY-tag to different protein modules, including fluorescent proteins and DNA binding proteins, can facilitate the interrogation of the histone lysine acylation-mediated recruitment of the AF9 YEATS domain in different biological contexts.
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Affiliation(s)
- Gaofei Tian
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
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7
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Chen C, Chen C, Wang A, Jiang Z, Zhao F, Li Y, Han Y, Niu Z, Tian S, Bai X, Zhang K, Zhai G. ENL reads histone β-hydroxybutyrylation to modulate gene transcription. Nucleic Acids Res 2024:gkae504. [PMID: 38880495 DOI: 10.1093/nar/gkae504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Histone modifications are typically recognized by chromatin-binding protein modules (referred to as 'readers') to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap should be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark, and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation led to the suppressed expression of genes such MYC that drive cell proliferation. Together, our work offered a chemoproteomics approach and identified ENL as a novel histone β-hydroxybutyrylation effector that regulates gene transcription, providing new insight into the regulation mechanism and function of histone Kbhb.
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Affiliation(s)
- Chen Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Cong Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Aiyuan Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zixin Jiang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Fei Zhao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Ziping Niu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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8
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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9
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Xie M, Zhou L, Li T, Lin Y, Zhang R, Zheng X, Zeng C, Zheng L, Zhong L, Huang X, Zou Y, Kang T, Wu Y. Targeting the KAT8/YEATS4 Axis Represses Tumor Growth and Increases Cisplatin Sensitivity in Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310146. [PMID: 38526153 PMCID: PMC11165526 DOI: 10.1002/advs.202310146] [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: 12/23/2023] [Revised: 02/13/2024] [Indexed: 03/26/2024]
Abstract
Bladder cancer (BC) is one of the most common tumors characterized by a high rate of relapse and a lack of targeted therapy. Here, YEATS domain-containing protein 4 (YEATS4) is an essential gene for BC cell viability using CRISPR-Cas9 library screening is reported, and that HUWE1 is an E3 ligase responsible for YEATS4 ubiquitination and proteasomal degradation by the Protein Stability Regulators Screening Assay. KAT8-mediated acetylation of YEATS4 impaired its interaction with HUWE1 and consequently prevented its ubiquitination and degradation. The protein levels of YEATS4 and KAT8 are positively correlated and high levels of these two proteins are associated with poor overall survival in BC patients. Importantly, suppression of YEATS4 acetylation with the KAT8 inhibitor MG149 decreased YEATS4 acetylation, reduced cell viability, and sensitized BC cells to cisplatin treatment. The findings reveal a critical role of the KAT8/YEATS4 axis in both tumor growth and cisplatin sensitivity in BC cells, potentially generating a novel therapeutic strategy for BC patients.
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Affiliation(s)
- Miner Xie
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of HematologyGuangzhou First People's HospitalSouth China University of TechnologyGuangzhou510060P. R. China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ting Li
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yujie Lin
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Xianchong Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cuiling Zeng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Li Zhong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Center of Digestive DiseaseScientific Research CenterThe Seventh Affiliated HospitalSun Yat‐sen UniversityShenzhen518107P. R. China
| | - Xiaodan Huang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yezi Zou
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- School of MedicineShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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10
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Zhang Z, Xu J, Liu J, Wang J, Lei L. SEC: A core hub during cell fate alteration. FASEB J 2024; 38:e23680. [PMID: 38758186 DOI: 10.1096/fj.202400514r] [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: 03/06/2024] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Pol II pause release is a rate-limiting step in gene transcription, influencing various cell fate alterations. Numerous proteins orchestrate Pol II pause release, thereby playing pivotal roles in the intricate process of cellular fate modulation. Super elongation complex (SEC), a large assembly comprising diverse protein components, has garnered attention due to its emerging significance in orchestrating physiological and pathological cellular identity changes by regulating the transcription of crucial genes. Consequently, SEC emerges as a noteworthy functional complex capable of modulating cell fate alterations. Therefore, a comprehensive review is warranted to systematically summarize the core roles of SEC in different types of cell fate alterations. This review focuses on elucidating the current understanding of the structural and functional basis of SEC. Additionally, we discuss the intricate regulatory mechanisms governing SEC in various models of cell fate alteration, encompassing both physiological and pathological contexts. Furthermore, leveraging the existing knowledge of SEC, we propose some insightful directions for future research, aiming to enhance our mechanistic and functional comprehension of SEC within the diverse landscape of cell fate alterations.
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Affiliation(s)
- Zhijing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jingyi Xu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiqiang Liu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
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11
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Song L, Li Q, Xia L, Sahay A, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.591709. [PMID: 38766219 PMCID: PMC11100752 DOI: 10.1101/2024.05.09.591709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly the HOX clusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolution in vivo . It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.
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12
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Chen PH, Guo XS, Zhang HE, Dubey GK, Geng ZZ, Fierke CA, Xu S, Hampton JT, Liu WR. Leveraging a Phage-Encoded Noncanonical Amino Acid: A Novel Pathway to Potent and Selective Epigenetic Reader Protein Inhibitors. ACS CENTRAL SCIENCE 2024; 10:782-792. [PMID: 38680566 PMCID: PMC11046469 DOI: 10.1021/acscentsci.3c01419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 05/01/2024]
Abstract
Epigenetic reader proteins interpret histone epigenetic marks to regulate gene expression. Given their vital roles and the link between their dysfunction and various diseases, these proteins present compelling targets for therapeutic interventions. Nevertheless, designing selective inhibitors for these proteins poses significant challenges, primarily due to their unique properties such as shallow binding sites and similarities with homologous proteins. To overcome these challenges, we propose an innovative strategy that uses phage display with a genetically encoded noncanonical amino acid (ncAA) containing an epigenetic mark. This ncAA guides binding to the reader protein's active site, allowing the identification of peptide inhibitors with enhanced affinity and selectivity. In this study, we demonstrate this novel approach's effectiveness by identifying potent inhibitors for the ENL YEATS domain that plays a critical role in leukemogenesis. Our strategy involved genetically incorporating Nε-butyryl-l-lysine (BuK), known for its binding to ENL YEATS, into a phage display library for enriching the pool of potent inhibitors. One resultant hit was further optimized by substituting BuK with other pharmacophores to exploit a unique π-π-π stacking interaction with ENL YEATS. This led to the creation of selective ENL YEATS inhibitors with a KD value of 2.0 nM and a selectivity 28 times higher for ENL YEATS than its close homologue AF9 YEATS. One such inhibitor, tENL-S1f, demonstrated robust cellular target engagement and on-target effects to inhibit leukemia cell growth and suppress the expression of ENL target genes. As a pioneering study, this work opens up extensive avenues for the development of potent and selective peptidyl inhibitors for a broad spectrum of epigenetic reader proteins.
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Affiliation(s)
- Peng-Hsun
Chase Chen
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xuejiao Shirley Guo
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hanyuan Eric Zhang
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Gopal K. Dubey
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zhi Zachary Geng
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Carol A. Fierke
- Department
of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Shiqing Xu
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Texas A&M
University, College
Station, Texas 77843, United States
| | - J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Texas A&M
University, College
Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
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13
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Abla O, Ries RE, Triche T, Gerbing RB, Hirsch B, Raimondi S, Cooper T, Farrar JE, Buteyn N, Harmon LM, Wen H, Deshpande AJ, Kolb EA, Gamis AS, Aplenc R, Alonzo T, Meshinchi S. Structural variants involving MLLT10 fusion are associated with adverse outcomes in pediatric acute myeloid leukemia. Blood Adv 2024; 8:2005-2017. [PMID: 38306602 PMCID: PMC11024924 DOI: 10.1182/bloodadvances.2023010805] [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: 05/23/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024] Open
Abstract
ABSTRACT MLLT10 gene rearrangements with KMT2A occur in pediatric acute myeloid leukemia (AML) and confer poor prognosis, but the prognostic impact of MLLT10 in partnership with other genes is unknown. We conducted a retrospective study with 2080 children and young adults with AML registered on the Children's Oncology Group AAML0531 (NCT00372593) and AAML1031 trials (NCT01371981). Transcriptome profiling and/or karyotyping were performed to identify leukemia-associated fusions associated with prognosis. Collectively, 127 patients (6.1%) were identified with MLLT10 fusions: 104 (81.9%) with KMT2A::MLLT10, 13 (10.2%) with PICALM::MLLT10, and 10 (7.9%) X::MLLT10: (2 each of DDX3X and TEC), with 6 partners (DDX3Y, CEP164, SCN2B, TREH, NAP1L1, and XPO1) observed in single patients. Patients with MLLT10 (n = 127) demonstrated adverse outcomes, with 5-year event-free survival (EFS) of 18.6% vs 49% in patients without MLLT10 (n = 1953, P < .001), inferior 5-year overall survival (OS) of 38.2% vs 65.7% (P ≤ .001), and a higher relapse risk of 76% vs 38.6% (P < .001). Patients with KMT2A::MLLT10 had an EFS from study entry of 19.5% vs 12.7% (P = .628), and an OS from study entry of 40.4% vs 27.6% (P = .361) in those with other MLLT10 fusion partners. Patients with PICALM::MLLT10 had an EFS of 9.2% vs 20% in other MLLT10- without PICALM (X::MLLT10; P = .788). Patients with PICALM::MLLT10 and X::MLLT10 fusions exhibit a DNA hypermethylation signature resembling NUP98::NSD1 fusions, whereas patients with KMT2A::MLLT10 bear aberrations primarily affecting distal regulatory elements. Regardless of the fusion partner, patients with AML harboring MLLT10 fusions exhibit very high-risk features and should be prioritized for alternative therapeutic interventions.
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Affiliation(s)
- Oussama Abla
- Division of Hematology/Oncology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Tim Triche
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI
| | | | - Betsy Hirsch
- Division of Laboratory Medicine, University of Minnesota Medical Center, Minneapolis, MN
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Todd Cooper
- Division of Hematology-Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Jason E. Farrar
- Department of Pediatrics, Hematology-Oncology Section, Arkansas Children's Research Institute, Little Rock, AR
| | | | | | - Hong Wen
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI
| | | | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders and Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Alan S. Gamis
- Division of Hematology, Oncology and Bone Marrow Transplantation, Children's Mercy Hospitals and Clinics, Kansas City, MO
| | | | - Todd Alonzo
- Department of Translational Genomics, University of Southern California, Los Angeles, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Hematology-Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
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14
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Chen Y, Ying Y, Ma W, Ma H, Shi L, Gao X, Jia M, Li M, Song X, Kong W, Chen W, Zheng X, Muluh TA, Wang X, Wang M, Shu XS. Targeting the Epigenetic Reader ENL Inhibits Super-Enhancer-Driven Oncogenic Transcription and Synergizes with BET Inhibition to Suppress Tumor Progression. Cancer Res 2024; 84:1237-1251. [PMID: 38241700 DOI: 10.1158/0008-5472.can-23-1836] [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: 06/20/2023] [Revised: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 01/21/2024]
Abstract
Epigenetic alterations at cis-regulatory elements (CRE) fine-tune transcriptional output. Epigenetic readers interact with CREs and can cooperate with other chromatin regulators to drive oncogene transcription. Here, we found that the YEATS domain-containing histone acetylation reader ENL (eleven-nineteen leukemia) acts as a key regulator of super-enhancers (SE), which are highly active distal CREs, across cancer types. ENL occupied the majority of SEs with substantially higher preference over typical enhancers, and the enrichment of ENL at SEs depended on its ability to bind acetylated histones. Rapid depletion of ENL by auxin-inducible degron tagging severely repressed the transcription of SE-controlled oncogenes, such as MYC, by inducing the decommissioning of their SEs, and restoring ENL protein expression largely reversed these effects. Additionally, ENL was indispensable for the rapid activation of SE-regulated immediate early genes in response to growth factor stimulation. Furthermore, ENL interacted with the histone chaperone FACT complex and was required for the deposition of FACT over CREs, which mediates nucleosome reorganization required for transcription initiation and elongation. Proper control of transcription by ENL and ENL-associated FACT was regulated by the histone reader BRD4. ENL was overexpressed in colorectal cancer and functionally contributed to colorectal cancer growth and metastasis. ENL degradation or inhibition synergized with BET inhibitors that target BRD4 in restraining colorectal cancer progression. These findings establish the essential role of epigenetic reader ENL in governing SE-driven oncogenic transcription and uncover the potential of ENL intervention to increase sensitivity to BET inhibition. SIGNIFICANCE ENL plays a key role in decoding epigenetic marks at highly active oncogenic super-enhancers and can be targeted in combination with BET inhibition as a promising synergistic strategy for optimizing cancer treatment.
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Affiliation(s)
- Yongheng Chen
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Graduate Program of Pharmaceutical Sciences, Shenzhen University Medical School, Shenzhen, China
| | - Ying Ying
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Wenlong Ma
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Hongchao Ma
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Liang Shi
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Xuefeng Gao
- Integrative Microecology Center, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Min Jia
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Meiqi Li
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Xiaoman Song
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Weixiao Kong
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Wei Chen
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiangyi Zheng
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Tobias Achu Muluh
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
| | - Xiaobin Wang
- Southern University of Science and Technology Hospital, Shenzhen, China
| | - Maolin Wang
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xing-Sheng Shu
- Department of Physiology, Shenzhen University Medical School, Shenzhen, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Graduate Program of Pharmaceutical Sciences, Shenzhen University Medical School, Shenzhen, China
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15
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Michino M, Khan TA, Miller MW, Fukase Y, Vendome J, Adura C, Glickman JF, Liu Y, Wan L, Allis CD, Stamford AW, Meinke PT, Renzetti LM, Kargman S, Liverton NJ, Huggins DJ. Lead Optimization of Small Molecule ENL YEATS Inhibitors to Enable In Vivo Studies: Discovery of TDI-11055. ACS Med Chem Lett 2024; 15:524-532. [PMID: 38628784 PMCID: PMC11017412 DOI: 10.1021/acsmedchemlett.4c00016] [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: 01/10/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
Eleven-nineteen leukemia (ENL) is an epigenetic reader protein that drives oncogenic transcriptional programs in acute myeloid leukemia (AML). AML is one of the deadliest hematopoietic malignancies, with an overall 5-year survival rate of 27%. The epigenetic reader activity of ENL is mediated by its YEATS domain that binds to acetyl and crotonyl marks on histone tails and colocalizes with promoters of actively transcribed genes that are essential for leukemia. Prior to the discovery of TDI-11055, existing inhibitors of ENL YEATS showed in vitro potency, but had not shown efficacy in in vivo animal models. During the course of the medicinal chemistry campaign described here, we identified ENL YEATS inhibitor TDI-11055 that has an improved pharmacokinetic profile and is appropriate for in vivo evaluation of the ENL YEATS inhibition mechanism in AML.
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Affiliation(s)
- Mayako Michino
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Tanweer A. Khan
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Michael W. Miller
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Yoshiyuki Fukase
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Jeremie Vendome
- Schrödinger,
Inc., 1540 Broadway,
24th Floor, New York, New
York 10036, United States
| | - Carolina Adura
- Fisher
Drug Discovery Resource Center, The Rockefeller
University, New York, New York 10065, United States
| | - J. Fraser Glickman
- Fisher
Drug Discovery Resource Center, The Rockefeller
University, New York, New York 10065, United States
| | - Yiman Liu
- Department
of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Liling Wan
- Department
of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - C. David Allis
- Laboratory
of Chromatin Biology and Epigenetics, The
Rockefeller University, New York, New York 10065, United States
| | - Andrew W. Stamford
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Peter T. Meinke
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Department
of Pharmacology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Louis M. Renzetti
- Bridge
Medicines, The Rockefeller University, 1230 York Avenue, Smith Hall Annex,
C-Floor, New York, New York 10065, United States
| | - Stacia Kargman
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Bridge
Medicines, The Rockefeller University, 1230 York Avenue, Smith Hall Annex,
C-Floor, New York, New York 10065, United States
| | - Nigel J. Liverton
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - David J. Huggins
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10021, United States
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16
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Konuma T, Zhou MM. Distinct Histone H3 Lysine 27 Modifications Dictate Different Outcomes of Gene Transcription. J Mol Biol 2024; 436:168376. [PMID: 38056822 DOI: 10.1016/j.jmb.2023.168376] [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: 09/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Site-specific histone modifications have long been recognized to play an important role in directing gene transcription in chromatin in biology of health and disease. However, concrete illustration of how different histone modifications in a site-specific manner dictate gene transcription outcomes, as postulated in the influential "Histone code hypothesis", introduced by Allis and colleagues in 2000, has been lacking. In this review, we summarize our latest understanding of the dynamic regulation of gene transcriptional activation, silence, and repression in chromatin that is directed distinctively by histone H3 lysine 27 acetylation, methylation, and crotonylation, respectively. This represents a special example of a long-anticipated verification of the "Histone code hypothesis."
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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17
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Wang Z, Yang X, Chen D, Liu Y, Li Z, Duan S, Zhang Z, Jiang X, Stockwell BR, Gu W. GAS41 modulates ferroptosis by anchoring NRF2 on chromatin. Nat Commun 2024; 15:2531. [PMID: 38514704 PMCID: PMC10957913 DOI: 10.1038/s41467-024-46857-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: 09/11/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
YEATS domain-containing protein GAS41 is a histone reader and oncogene. Here, through genome-wide CRISPR-Cas9 screenings, we identify GAS41 as a repressor of ferroptosis. GAS41 interacts with NRF2 and is critical for NRF2 to activate its targets such as SLC7A11 for modulating ferroptosis. By recognizing the H3K27-acetylation (H3K27-ac) marker, GAS41 is recruited to the SLC7A11 promoter, independent of NRF2 binding. By bridging the interaction between NRF2 and the H3K27-ac marker, GAS41 acts as an anchor for NRF2 on chromatin in a promoter-specific manner for transcriptional activation. Moreover, the GAS41-mediated effect on ferroptosis contributes to its oncogenic role in vivo. These data demonstrate that GAS41 is a target for modulating tumor growth through ferroptosis. Our study reveals a mechanism for GAS41-mediated regulation in transcription by anchoring NRF2 on chromatin, and provides a model in which the DNA binding activity on chromatin by transcriptional factors (NRF2) can be directly regulated by histone markers (H3K27-ac).
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Affiliation(s)
- Zhe Wang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Xin Yang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Delin Chen
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yanqing Liu
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Genetics and Development, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Wei Gu
- Institute for Cancer Genetics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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18
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Chan AK, Han L, Delaney CD, Wang X, Mukhaleva E, Li M, Yang L, Pokharel SP, Mattson N, Garcia M, Wang B, Xu X, Zhang L, Singh P, Elsayed Z, Chen R, Kuang B, Wang J, Yuan YC, Chen B, Chan LN, Rosen ST, Horne D, Müschen M, Chen J, Vaidehi N, Armstrong SA, Su R, Chen CW. Therapeutic targeting Tudor domains in leukemia via CRISPR-Scan Assisted Drug Discovery. SCIENCE ADVANCES 2024; 10:eadk3127. [PMID: 38394203 PMCID: PMC10889360 DOI: 10.1126/sciadv.adk3127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Epigenetic dysregulation has been reported in multiple cancers including leukemias. Nonetheless, the roles of the epigenetic reader Tudor domains in leukemia progression and therapy remain unexplored. Here, we conducted a Tudor domain-focused CRISPR screen and identified SGF29, a component of SAGA/ATAC acetyltransferase complexes, as a crucial factor for H3K9 acetylation, ribosomal gene expression, and leukemogenesis. To facilitate drug development, we integrated the CRISPR tiling scan with compound docking and molecular dynamics simulation, presenting a generally applicable strategy called CRISPR-Scan Assisted Drug Discovery (CRISPR-SADD). Using this approach, we identified a lead inhibitor that selectively targets SGF29's Tudor domain and demonstrates efficacy against leukemia. Furthermore, we propose that the structural genetics approach used in our study can be widely applied to diverse fields for de novo drug discovery.
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Affiliation(s)
- Anthony K.N. Chan
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Christopher D. Delaney
- Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Xueer Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nicole Mattson
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Michelle Garcia
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Bintao Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Leisi Zhang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Priyanka Singh
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zeinab Elsayed
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Benjamin Kuang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Yate-Ching Yuan
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bryan Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lai N. Chan
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - David Horne
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Scott A. Armstrong
- Department of Pediatrics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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19
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Barbosa K, Deshpande A, Perales M, Xiang P, Murad R, Pramod AB, Minkina A, Robertson N, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, Humphries RK, Ruppin E, Shendure J, Mali P, Adams PD, Deshpande AJ. Transcriptional control of leukemogenesis by the chromatin reader SGF29. Blood 2024; 143:697-712. [PMID: 38048593 PMCID: PMC10900139 DOI: 10.1182/blood.2023021234] [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: 05/31/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
ABSTRACT Aberrant expression of stem cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators coordinately controlled the transcription of several AML oncogenes. In particular, we identified a novel role for the Tudor-domain-containing chromatin reader protein SGF29 in the transcription of AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes in multiple AML subtype models. Our studies reveal a novel role for SGF29 as a nononcogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery.
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Affiliation(s)
- Karina Barbosa
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anagha Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Marlenne Perales
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Ping Xiang
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rabi Murad
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Akula Bala Pramod
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anna Minkina
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Neil Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xue Lei
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Younguk Sun
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Adam Brown
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | | | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA
| | - Peter D. Adams
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Aniruddha J. Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
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20
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Wu Q, Zheng Q, Yuan L, Gao D, Hu Y, Jiang X, Zhai Q, Liu M, Xu L, Xu H, Ye J, Zhang F. Repression of YEATS2 induces cellular senescence in hepatocellular carcinoma and inhibits tumor growth. Cell Cycle 2024; 23:478-494. [PMID: 38619971 PMCID: PMC11174065 DOI: 10.1080/15384101.2024.2342714] [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: 11/29/2023] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the third leading cause of cancer-related fatalities globally. In this study, we observed a significant increase in the expression level of the YEATS2 gene in HCC patients, and it is negatively correlated with the patients' survival rate. While we have previously identified the association between YEATS2 and the survival of pancreatic cancer cells, the regulatory mechanisms and significance in HCC are still to be fully elucidated. Our study shows that knockdown (KD) of YEATS2 expression leads to DNA damage, which in turn results in an upregulation of γ-H2A.X expression and activation of the canonical senescence-related pathway p53/p21Cip1. Moreover, our transcriptomic analysis reveals that YEATS2 KD cells can enhance the expression of p21Cip1 via the c-Myc/miR-93-5p pathway, consequently fostering the senescence of HCC cells. The initiation of cellular senescence through dual-channel activation suggests that YEATS2 plays a pivotal regulatory role in the process of cell proliferation. Ultimately, our in vivo research utilizing a nude mouse tumor model revealed a notable decrease in both tumor volume and weight after the suppression of YEATS2 expression. This phenomenon is likely attributable to the attenuation of proliferative cell activity, coupled with a concurrent augmentation in the population of natural killer (NK) cells. In summary, our research results have supplemented the understanding of the regulatory mechanisms of HCC cell proliferation and indicated that targeting YEATS2 may potentially inhibit liver tumor growth.
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Affiliation(s)
- Qi Wu
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Quan Zheng
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Lei Yuan
- Department of Hepatobiliary Surgery, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Dandan Gao
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yabing Hu
- School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xinqing Jiang
- The Joint Innovation Center for Engineering in Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiaocheng Zhai
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Ming Liu
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Lifeng Xu
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Heng Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jinlin Ye
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Feng Zhang
- The Joint Innovation Center for Engineering in Medicine, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
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21
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Zhao J, Cato LD, Arora UP, Bao EL, Bryant SC, Williams N, Jia Y, Goldman SR, Nangalia J, Erb MA, Vos SM, Armstrong SA, Sankaran VG. Inherited blood cancer predisposition through altered transcription elongation. Cell 2024; 187:642-658.e19. [PMID: 38218188 PMCID: PMC10872907 DOI: 10.1016/j.cell.2023.12.016] [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: 06/06/2023] [Revised: 11/26/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies in a large population cohort to identify inherited predisposition genes for these blood cancers. CTR9, which encodes a key component of the PAF1 transcription elongation complex, is among the significant genes identified. The risk variants found in the cases cause loss of function and result in a ∼10-fold increased odds of acquiring a myeloid malignancy. Partial CTR9 loss of function expands human hematopoietic stem cells (HSCs) by increased super elongation complex-mediated transcriptional activity, which thereby increases the expression of key regulators of HSC self-renewal. By following up on insights from a human genetic study examining inherited predisposition to the myeloid malignancies, we define a previously unknown antagonistic interaction between the PAF1 and super elongation complexes. These insights could enable targeted approaches for blood cancer prevention.
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Affiliation(s)
- Jiawei Zhao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China.
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Uma P Arora
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicholas Williams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Yuemeng Jia
- Harvard Stem Cell Institute, Cambridge, MA, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Seth R Goldman
- Nascent Transcriptomics Core, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott A Armstrong
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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22
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Neja S, Dashwood WM, Dashwood RH, Rajendran P. Histone Acyl Code in Precision Oncology: Mechanistic Insights from Dietary and Metabolic Factors. Nutrients 2024; 16:396. [PMID: 38337680 PMCID: PMC10857208 DOI: 10.3390/nu16030396] [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: 12/30/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Cancer etiology involves complex interactions between genetic and non-genetic factors, with epigenetic mechanisms serving as key regulators at multiple stages of pathogenesis. Poor dietary habits contribute to cancer predisposition by impacting DNA methylation patterns, non-coding RNA expression, and histone epigenetic landscapes. Histone post-translational modifications (PTMs), including acyl marks, act as a molecular code and play a crucial role in translating changes in cellular metabolism into enduring patterns of gene expression. As cancer cells undergo metabolic reprogramming to support rapid growth and proliferation, nuanced roles have emerged for dietary- and metabolism-derived histone acylation changes in cancer progression. Specific types and mechanisms of histone acylation, beyond the standard acetylation marks, shed light on how dietary metabolites reshape the gut microbiome, influencing the dynamics of histone acyl repertoires. Given the reversible nature of histone PTMs, the corresponding acyl readers, writers, and erasers are discussed in this review in the context of cancer prevention and treatment. The evolving 'acyl code' provides for improved biomarker assessment and clinical validation in cancer diagnosis and prognosis.
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Affiliation(s)
- Sultan Neja
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
| | - Wan Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
| | - Roderick H. Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Antibody & Biopharmaceuticals Core, Texas A&M Health, Houston, TX 77030, USA
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23
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Raux B, Buchan KA, Bennett J, Christott T, Dowling MS, Farnie G, Fedorov O, Gamble V, Gileadi C, Giroud C, Huber KVM, Korczynska M, Limberakis C, Narayanan A, Owen DR, Sáez LD, Stock IA, Londregan AT. Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3. Bioorg Med Chem Lett 2024; 98:129546. [PMID: 37944866 DOI: 10.1016/j.bmcl.2023.129546] [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: 08/31/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Epigenetic proteins containing YEATS domains (YD) are an emerging target class in drug discovery. Described herein are the discovery and characterization efforts associated with PFI-6, a new chemical probe for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). For hit identification, fragment-like mimetics of endogenous YD ligands (crotonylated histone-containing proteins), were synthesized via parallel medicinal chemistry (PMC) and screened for MLLT1 binding. Subsequent SAR studies led to iterative MLLT1/3 binding and selectivity improvements, culminating in the discovery of PFI-6. PFI-6 demonstrates good affinity and selectivity for MLLT1/3 vs. other human YD proteins (YEATS2/4) and engages MLLT3 in cells. Small-molecule X-ray co-crystal structures of two molecules, including PFI-6, bound to the YD of MLLT1/3 are also described. PFI-6 may be a useful tool molecule to better understand the biological effects associated with modulation of MLLT1/3.
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Affiliation(s)
- Brigitt Raux
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Karly A Buchan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - James Bennett
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Thomas Christott
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Gillian Farnie
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Vicki Gamble
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Carina Gileadi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Charline Giroud
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Chris Limberakis
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Allyn T Londregan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA.
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24
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Long Q, Xiang M, Xiao L, Wang J, Guan X, Liu J, Liao C. The Biological Significance of AFF4: Promoting Transcription Elongation, Osteogenic Differentiation and Tumor Progression. Comb Chem High Throughput Screen 2024; 27:1403-1412. [PMID: 37815186 DOI: 10.2174/0113862073241079230920082056] [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: 12/20/2022] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 10/11/2023]
Abstract
As a member of the AF4/FMR2 (AFF) family, AFF4 is a scaffold protein in the superelongation complex (SEC). In this mini-view, we discuss the role of AFF4 as a transcription elongation factor that mediates HIV activation and replication and stem cell osteogenic differentiation. AFF4 also promotes the progression of head and neck squamous cell carcinoma, leukemia, breast cancer, bladder cancer and other malignant tumors. The biological function of AFF4 is largely achieved through SEC assembly, regulates SRY-box transcription factor 2 (SOX2), MYC, estrogen receptor alpha (ESR1), inhibitor of differentiation 1 (ID1), c-Jun and noncanonical nuclear factor-κB (NF-κB) transcription and combines with fusion in sarcoma (FUS), unique regulatory cyclins (CycT1), or mixed lineage leukemia (MLL). We explore the prospects of using AFF4 as a therapeutic in Acquired immunodeficiency syndrome (AIDS) and malignant tumors and its potential as a stemness regulator.
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Affiliation(s)
- Qian Long
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Mingli Xiang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Linlin Xiao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jiajia Wang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Xiaoyan Guan
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jianguo Liu
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Chengcheng Liao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
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25
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Tubío-Santamaría N, Jayavelu AK, Schnoeder TM, Eifert T, Hsu CJ, Perner F, Zhang Q, Wenge DV, Hansen FM, Kirkpatrick JM, Jyotsana N, Lane SW, von Eyss B, Deshpande AJ, Kühn MWM, Schwaller J, Cammann C, Seifert U, Ebstein F, Krüger E, Hochhaus A, Heuser M, Ori A, Mann M, Armstrong SA, Heidel FH. Immunoproteasome function maintains oncogenic gene expression in KMT2A-complex driven leukemia. Mol Cancer 2023; 22:196. [PMID: 38049829 PMCID: PMC10694946 DOI: 10.1186/s12943-023-01907-7] [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: 06/17/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
Pharmacologic targeting of chromatin-associated protein complexes has shown significant responses in KMT2A-rearranged (KMT2A-r) acute myeloid leukemia (AML) but resistance frequently develops to single agents. This points to a need for therapeutic combinations that target multiple mechanisms. To enhance our understanding of functional dependencies in KMT2A-r AML, we have used a proteomic approach to identify the catalytic immunoproteasome subunit PSMB8 as a specific vulnerability. Genetic and pharmacologic inactivation of PSMB8 results in impaired proliferation of murine and human leukemic cells while normal hematopoietic cells remain unaffected. Disruption of immunoproteasome function drives an increase in transcription factor BASP1 which in turn represses KMT2A-fusion protein target genes. Pharmacologic targeting of PSMB8 improves efficacy of Menin-inhibitors, synergistically reduces leukemia in human xenografts and shows preserved activity against Menin-inhibitor resistance mutations. This identifies and validates a cell-intrinsic mechanism whereby selective disruption of proteostasis results in altered transcription factor abundance and repression of oncogene-specific transcriptional networks. These data demonstrate that the immunoproteasome is a relevant therapeutic target in AML and that targeting the immunoproteasome in combination with Menin-inhibition could be a novel approach for treatment of KMT2A-r AML.
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Affiliation(s)
- Nuria Tubío-Santamaría
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | - Ashok Kumar Jayavelu
- Max-Planck-Institute of Biochemistry, Munich, Germany
- Proteomics and Cancer Cell Signaling Group, DKFZ, Heidelberg, Germany
| | - Tina M Schnoeder
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | - Theresa Eifert
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | - Chen-Jen Hsu
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | - Florian Perner
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | - Qirui Zhang
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | - Daniela V Wenge
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard University, Boston, MA, 02215, USA
| | - Fynn M Hansen
- Max-Planck-Institute of Biochemistry, Munich, Germany
| | | | - Nidhi Jyotsana
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Steven W Lane
- Queensland Institute for Medical Research (QIMR), Brisbane, Australia
| | - Björn von Eyss
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | | | - Michael W M Kühn
- Medizinische Klinik 3, Hämatologie, Onkologie und Pneumologie, Universitätsmedizin Mainz, Mainz, Germany
| | - Juerg Schwaller
- Department of Biomedicine, University Children's Hospital of Basel, Basel, Switzerland
| | - Clemens Cammann
- Friedrich Loeffler-Institut für Medizinische Mikrobiologie - Virologie, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | - Ulrike Seifert
- Friedrich Loeffler-Institut für Medizinische Mikrobiologie - Virologie, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | - Frédéric Ebstein
- Department of Biochemistry, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | - Elke Krüger
- Department of Biochemistry, Universitätsmedizin Greifswald, 17475, Greifswald, Germany
| | | | - Michael Heuser
- Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany
| | - Alessandro Ori
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany
| | - Matthias Mann
- Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard University, Boston, MA, 02215, USA
| | - Florian H Heidel
- Innere Medizin C, Universitätsmedizin Greifswald, 17475, Greifswald, Germany.
- Leibniz Institute On Aging, Fritz-Lipmann Institute, 07745, Jena, Germany.
- Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany.
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26
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Erb MA. Small-molecule tools for YEATS domain proteins. Curr Opin Chem Biol 2023; 77:102404. [PMID: 37924571 PMCID: PMC10842393 DOI: 10.1016/j.cbpa.2023.102404] [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: 08/09/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/06/2023]
Abstract
Chromatin reader domains are protein folds that bind to post-translational modifications of histones and other chromatin-associated proteins. Compared to other families of reader domains, the discovery that YEATS domains bind to acylated lysines is relatively recent. Four human proteins harbor a YEATS domain, and each is present in protein complexes that regulate chromatin and transcription (ENL, AF9, YEATS2, and YEATS4). Without chemical tools to enable temporally resolved perturbations, it is often unclear how reader domains contribute to protein function. Here, we will discuss recent progress in developing small-molecule tools for YEATS domains and highlight their usefulness for making biological discoveries.
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Affiliation(s)
- Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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27
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Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C. Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens. Nat Commun 2023; 14:7464. [PMID: 38016946 PMCID: PMC10684515 DOI: 10.1038/s41467-023-43264-5] [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: 10/20/2022] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Accumulating evidence indicates that HOXA9 dysregulation is necessary and sufficient for leukemic transformation and maintenance. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes. Here, we conduct dropout CRISPR screens against 229 HOXA9-bound peaks identified by ChIP-seq. Integrative data analysis identifies reproducible noncoding hits, including those located in the distal enhancer of FLT3 and intron of CDK6. The Cas9-editing and dCas9-KRAB silencing of the HOXA9-bound sites significantly reduce corresponding gene transcription and impair cell proliferation in vitro, and in vivo by transplantation into NSG female mice. In addition, RNA-seq, Q-PCR analysis, chromatin accessibility change, and chromatin conformation evaluation uncover the noncoding regulation mechanism of HOXA9 and its functional downstream genes. In summary, our work improves our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency.
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Affiliation(s)
- Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xujie Zhao
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shelby Mryncza
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhenling Liu
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Siqi Yi
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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28
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Bilgin N, Türkmen VA, Hammami N, Christensen NR, Hintzen JCJ, Mecinović J. Reading and erasing of histone crotonyllysine mimics by the AF9 YEATS domain and SIRT2 deacylase. Bioorg Med Chem 2023; 95:117500. [PMID: 37839329 DOI: 10.1016/j.bmc.2023.117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Lysine acylations on histones and their recognition by chromatin-binding reader domains and removal by histone deacylases function as an important mechanism for eukaryotic gene regulation. Histone lysine crotonylation (Kcr) is an epigenetic mark associated with active transcription, and its installation and removal are dynamically regulated by cellular epigenetic enzymes. Here, we report binding studies and enzyme assays with histone H3K9 peptides bearing simplest Kcr analogs with varying hydrocarbon chain length, bulkiness, rigidity and polarity. We demonstrate that the AF9 YEATS domain displays selectivity for binding of different acylation modifications on histone H3K9 peptides and exhibits preference for bulkier cinnamoylated lysine over crotonylated lysine and its mimics. SIRT2 shows deacylase activity against most of acylated H3K9 peptides bearing different crotonyllysine mimics, however, it displays a poor ability for the removal of cinnamoyl and trifluorocrotonyl groups. These results demonstrate different substrate selectivities of epigenetic proteins acting on crotonyllysine and pave the way for rational design and development of AF9 YEATS and SIRT2 inhibitors for treatment of human diseases, including cancer.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nesrin Hammami
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nadja R Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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29
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Li X, Wu X, Nie S, Zhao J, Yao Y, Wu F, Mishra CB, Ashraf-Uz-Zaman M, Moku BK, Song Y. Discovery, Structure-Activity Relationship and In Vitro Anticancer Activity of Small-Molecule Inhibitors of the Protein-Protein Interactions between AF9/ENL and AF4 or DOT1L. Cancers (Basel) 2023; 15:5283. [PMID: 37958457 PMCID: PMC10650850 DOI: 10.3390/cancers15215283] [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: 10/10/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Chromosomal translocations involving the mixed lineage leukemia (MLL) gene cause 5-10% acute leukemias with poor clinical outcomes. Protein-protein interactions (PPI) between the most frequent MLL fusion partner proteins AF9/ENL and AF4 or histone methyltransferase DOT1L are drug targets for MLL-rearranged (MLL-r) leukemia. Several benzothiophene-carboxamide compounds were identified as novel inhibitors of these PPIs with IC50 values as low as 1.6 μM. Structure-activity relationship studies of 77 benzothiophene and related indole and benzofuran compounds show that a 4-piperidin-1-ylphenyl or 4-pyrrolidin-1-ylphenyl substituent is essential for the activity. The inhibitors suppressed expression of MLL target genes HoxA9, Meis1 and Myc, and selectively inhibited proliferation of MLL-r and other acute myeloid leukemia cells with EC50 values as low as 4.7 μM. These inhibitors are useful chemical probes for biological studies of AF9/ENL, as well as pharmacological leads for further drug development against MLL-r and other leukemias.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Xiaowei Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Shenyou Nie
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Jidong Zhao
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Yuan Yao
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Fangrui Wu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Chandra Bhushan Mishra
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Md Ashraf-Uz-Zaman
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Bala Krishna Moku
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (X.L.); (X.W.); (S.N.); (J.Z.); (Y.Y.); (F.W.); (C.B.M.); (M.A.-U.-Z.); (B.K.M.)
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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30
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Kikuchi M, Takase S, Konuma T, Noritsugu K, Sekine S, Ikegami T, Ito A, Umehara T. GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain. Proc Natl Acad Sci U S A 2023; 120:e2304103120. [PMID: 37844223 PMCID: PMC10614846 DOI: 10.1073/pnas.2304103120] [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: 03/12/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
Glioma amplified sequence 41 (GAS41), which has the Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain that recognizes lysine acetylation (Kac), regulates gene expression as a subunit of the SRCAP (SNF2-related CREBBP activator protein) complex that deposits histone H2A.Z at promoters in eukaryotes. The YEATS domains of the proteins AF9 and ENL recognize Kac by hydrogen bonding the aromatic cage to arginine situated just before K9ac or K27ac in the N-terminal tail of histone H3. Curiously, the YEATS domain of GAS41 binds most preferentially to the sequence that contains K14ac of H3 (H3K14ac) but lacks the corresponding arginine. Here, we biochemically and structurally elucidated the molecular mechanism by which GAS41 recognizes H3K14ac. First, stable binding of the GAS41 YEATS domain to H3K14ac required the N terminus of H3 (H3NT). Second, we revealed a pocket in the GAS41 YEATS domain responsible for the H3NT binding by crystallographic and NMR analyses. This pocket is away from the aromatic cage that recognizes Kac and is unique to GAS41 among the YEATS family. Finally, we showed that E109 of GAS41, a residue essential for the formation of the H3NT-binding pocket, was crucial for chromatin occupancy of H2A.Z and GAS41 at H2A.Z-enriched promoter regions. These data suggest that binding of GAS41 to H3NT via its YEATS domain is essential for its intracellular function.
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Affiliation(s)
- Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama230-0045, Japan
| | - Shohei Takase
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Tsuyoshi Konuma
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Kota Noritsugu
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Saaya Sekine
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Takahisa Ikegami
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Akihiro Ito
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama230-0045, Japan
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31
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Ji P, Zhang G, Guo Y, Song H, Yuan X, Hu X, Guo Z, Xia P, Shen R, Wang D. Protein crotonylation: An emerging regulator in DNA damage response. Life Sci 2023; 331:122059. [PMID: 37652154 DOI: 10.1016/j.lfs.2023.122059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DNA damage caused by internal or external factors lead to increased genomic instability and various diseases. The DNA damage response (DDR) is a crucial mechanism that maintaining genomic stability through detecting and repairing DNA damage timely. Post-translational modifications (PTMs) play significant roles in regulation of DDR. Among the present PTMs, crotonylation has emerged as a novel identified modification that is involved in a wide range of biological processes including gene expression, spermatogenesis, cell cycle, and the development of diverse diseases. In the past decade, numerous crotonylation sites have been identified in histone and non-histone proteins, leading to a more comprehensive and deep understanding of the function and mechanisms in protein crotonylation. This review provides a comprehensive overview of the regulatory mechanisms of protein crotonylation and the effect of crotonylation in DDR. Furthermore, the effect of protein crotonylation in tumor development and progression is presented, to inspire and explore the novel strategies for tumor therapy.
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Affiliation(s)
- Pengfei Ji
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Guokun Zhang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Yanan Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Haoyun Song
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xinyi Yuan
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xiaohui Hu
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Zhao Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Peng Xia
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Rong Shen
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Degui Wang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China; NHC Key Laboratory of diagnosis and therapy of Gastrointestinal Tumor, Lanzhou, Gansu Province 730000, China.
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32
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Bishop TR, Subramanian C, Bilotta EM, Garnar-Wortzel L, Ramos AR, Zhang Y, Asiaban JN, Ott CJ, Rock CO, Erb MA. Acetyl-CoA biosynthesis drives resistance to histone acetyltransferase inhibition. Nat Chem Biol 2023; 19:1215-1222. [PMID: 37127754 PMCID: PMC10538425 DOI: 10.1038/s41589-023-01320-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Histone acetyltransferases (HATs) are implicated as both oncogene and nononcogene dependencies in diverse human cancers. Acetyl-CoA-competitive HAT inhibitors have emerged as potential cancer therapeutics and the first clinical trial for this class of drugs is ongoing (NCT04606446). Despite these developments, the potential mechanisms of therapeutic response and evolved drug resistance remain poorly understood. Having discovered that multiple regulators of de novo coenzyme A (CoA) biosynthesis can modulate sensitivity to CBP/p300 HAT inhibition (PANK3, PANK4 and SLC5A6), we determined that elevated acetyl-CoA concentrations can outcompete drug-target engagement to elicit acquired drug resistance. This not only affects structurally diverse CBP/p300 HAT inhibitors, but also agents related to an investigational KAT6A/B HAT inhibitor that is currently in Phase 1 clinical trials. Altogether, this work uncovers CoA metabolism as an unexpected liability of anticancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.
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Affiliation(s)
- Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Bilotta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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33
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Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nat Struct Mol Biol 2023; 30:1592-1606. [PMID: 37679565 DOI: 10.1038/s41594-023-01087-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia.
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Neville
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel T Ferguson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- EMBL-Australia, Clayton, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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Xu L, Xuan H, He W, Zhang L, Huang M, Li K, Wen H, Xu H, Shi X. TAZ2 truncation confers overactivation of p300 and cellular vulnerability to HDAC inhibition. Nat Commun 2023; 14:5362. [PMID: 37660055 PMCID: PMC10475075 DOI: 10.1038/s41467-023-41245-2] [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: 04/26/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
The histone acetyltransferase p300/CBP is composed of several conserved domains, among which, the TAZ2 domain is known as a protein-protein interaction domain that binds to E1A and various transcription factors. Here we show that TAZ2 has a HAT autoinhibitory function. Truncating p300/CBP at TAZ2 leads to hyperactive HAT and elevated histone H3K27 and H3K18 acetylation in cells. Mechanistically, TAZ2 cooperates with other HAT neighboring domains to maintain the HAT active site in a 'closed' state. Truncating TAZ2 or binding of transcription factors to TAZ2 induces a conformational change that 'opens' the active site for substrate acetylation. Importantly, genetic mutations that lead to p300/CBP TAZ2 truncations are found in human cancers, and cells with TAZ2 truncations are vulnerable to histone deacetylase inhibitors. Our study reveals a function of the TAZ2 domain in HAT autoinhibitory regulation and provides a potential therapeutic strategy for the treatment of cancers harboring p300/CBP TAZ2 truncations.
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Affiliation(s)
- Longxia Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hongwen Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mengying Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kuai Li
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hong Wen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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Wang H, Qiu Y, Zhang H, Chang N, Hu Y, Chen J, Hu R, Liao P, Li Z, Yang Y, Cen Q, Ding X, Li M, Xie X, Li Y. Histone acetylation by HBO1 (KAT7) activates Wnt/β-catenin signaling to promote leukemogenesis in B-cell acute lymphoblastic leukemia. Cell Death Dis 2023; 14:498. [PMID: 37542030 PMCID: PMC10403501 DOI: 10.1038/s41419-023-06019-0] [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: 11/26/2022] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023]
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) is an aggressive hematological disorder with a dismal prognosis. The dysregulation of histone acetylation is of great significance in the pathogenesis and progression of B-ALL. Regarded as a fundamental acetyltransferase gene, the role of HBO1 (lysine acetyltransferase 7/KAT7) in B-ALL has not been investigated. Herein, we found that HBO1 expression was elevated in human B-ALL cells and associated with poor disease-free survival. Strikingly, HBO1 knockdown inhibited viability, proliferation, and G1-S cycle progression in B-ALL cells, while provoking apoptosis. In contrast, ectopic overexpression of HBO1 enhanced cell viability and proliferation but inhibited apoptotic activation. The results of in vivo experiments also certificated the inhibitory effect of HBO1 knockdown on tumor growth. Mechanistically, HBO1 acetylated histone H3K14, H4K8, and H4K12, followed by upregulating CTNNB1 expression, resulting in activation of the Wnt/β-catenin signaling pathway. Moreover, a novel small molecule inhibitor of HBO1, WM-3835, potently inhibited the progression of B-ALL. Our data identified HBO1 as an efficacious regulator of CTNNB1 with therapeutic potential in B-ALL.
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Affiliation(s)
- Hao Wang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yingqi Qiu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Honghao Zhang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
| | - Ning Chang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yuxing Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Jianyu Chen
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Rong Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Peiyun Liao
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Zhongwei Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Yulu Yang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Qingyan Cen
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Xiangyang Ding
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Meifang Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China
| | - Xiaoling Xie
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, P. R. China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, P. R. China.
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36
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Hu H, Muntean AG. The YEATS domain epigenetic reader proteins ENL and AF9 and their therapeutic value in leukemia. Exp Hematol 2023; 124:15-21. [PMID: 37295550 PMCID: PMC10527611 DOI: 10.1016/j.exphem.2023.06.001] [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: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Recent studies have uncovered similarities and differences between 2 highly homologous epigenetic reading proteins, namely, ENL (MLLT1) and AF9 (MLLT3) with therapeutic implications. The importance of these proteins has traditionally been exemplified by their involvement in chromosomal translocations with the mixed-lineage leukemia gene (MLL; aka KMT2a). MLL rearrangements occur in a subset of acute leukemias and generate potent oncogenic MLL-fusion proteins that impact epigenetic and transcriptional regulation. Leukemic patients with MLL rearrangements display intermediate-to-poor prognoses, necessitating further mechanistic research. Several protein complexes involved in regulating RNA polymerase II transcription and the epigenetic landscape are hijacked in MLL-r leukemia, which include ENL and AF9. Recent biochemical studies have defined a highly homologous YEATS domain in ENL and AF9 that binds acylated histones, which aids in the localization and retention of these proteins to transcriptional targets. In addition, detailed characterization of the homologous ANC-1 homology domain (AHD) on ENL and AF9 revealed differential association with transcriptional activating and repressing complexes. Importantly, CRISPR knockout screens have demonstrated a unique role for wild-type ENL in leukemic stem cell function, whereas AF9 appears important for normal hematopoietic stem cells. In this perspective, we examine the ENL and AF9 proteins with attention to recent work characterizing the epigenetic reading YEATS domains and AHD on both wild-type proteins and when fused to MLL. We summarized the drug development efforts and their therapeutic potential and assess ongoing research that has refined our understanding of how these proteins function, which continues to reveal new therapeutic avenues.
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Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
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37
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Han H, Lv F, Liu Z, Chen T, Xue T, Liang W, Liu M. BcTaf14 regulates growth and development, virulence, and stress responses in the phytopathogenic fungus Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2023; 24:849-865. [PMID: 37026690 PMCID: PMC10346378 DOI: 10.1111/mpp.13331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
TATA box-binding protein (TBP)-associated factor 14 (Taf14), a transcription-associated factor containing a conserved YEATS domain and an extra-terminal (ET) domain, is a multifunctional protein in Saccharomyces cerevisiae. However, the role of Taf14 in filamentous phytopathogenic fungi is not well understood. In this study, the homologue of ScTaf14 in Botrytis cinerea (named BcTaf14), a destructive phytopathogen causing grey mould, was investigated. The BcTaf14 deletion strain (ΔBcTaf14) showed pleiotropic defects, including slow growth, abnormal colony morphology, reduced conidiation, abnormal conidial morphology, reduced virulence, and altered responses to various stresses. The ΔBcTaf14 strain also exhibited differential expression of numerous genes compared to the wild-type strain. BcTaf14 could interact with the crotonylated H3K9 peptide, and mutation of two key sites (G80 and W81) in the YEATS domain disrupted this interaction. The mutation of G80 and W81 affected the regulatory effect of BcTaf14 on mycelial growth and virulence but did not affect the production and morphology of conidia. The absence of the ET domain at the C-terminus rendered BcTaf14 unable to localize to the nucleus, and the defects of ΔBcTaf14 were not recovered to wild-type levels when BcTaf14 without the ET domain was expressed. Our results provide insight into the regulatory roles of BcTaf14 and its two conserved domains in B. cinerea and will be helpful for understanding the function of the Taf14 protein in plant-pathogenic fungi.
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Affiliation(s)
- Hongjia Han
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Fangjiao Lv
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Zhishan Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tongge Chen
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tianzi Xue
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Wenxing Liang
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Mengjie Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
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38
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Liu N, Konuma T, Sharma R, Wang D, Zhao N, Cao L, Ju Y, Liu D, Wang S, Bosch A, Sun Y, Zhang S, Ji D, Nagatoishi S, Suzuki N, Kikuchi M, Wakamori M, Zhao C, Ren C, Zhou TJ, Xu Y, Meslamani J, Fu S, Umehara T, Tsumoto K, Akashi S, Zeng L, Roeder RG, Walsh MJ, Zhang Q, Zhou MM. Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin. Mol Cell 2023; 83:2206-2221.e11. [PMID: 37311463 PMCID: PMC11138481 DOI: 10.1016/j.molcel.2023.05.022] [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: 07/06/2022] [Revised: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023]
Abstract
Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.
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Affiliation(s)
- Nan Liu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China.
| | - Tsuyoshi Konuma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Rajal Sharma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deyu Wang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Nan Zhao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Lingling Cao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Ying Ju
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Di Liu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Shuai Wang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Almudena Bosch
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Satoru Nagatoishi
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Noa Suzuki
- School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Masaki Kikuchi
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | | | - Chengcheng Zhao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Chunyan Ren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas Jiachi Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yaoyao Xu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Jamel Meslamani
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shibo Fu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China
| | - Takashi Umehara
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Kouhei Tsumoto
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New Nork, NY 10065, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China.
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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39
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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40
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Yang X, Gao Y, Cao F, Wang S. Molecular Dynamics Simulations Combined with Markov Model to Explore the Effect of Allosteric Inhibitor Binding on Bromodomain-Containing Protein 4. Int J Mol Sci 2023; 24:10831. [PMID: 37446009 DOI: 10.3390/ijms241310831] [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: 05/23/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Bromodomain-Containing Protein 4 (BRD4) can play an important role in gene transcriptional regulation of tumor development and survival by participating in histone modification epigenetic mechanism. Although it has been reported that novel allosteric inhibitors such as ZL0590 have a high affinity with target protein BRD4 and good efficacy, their inhibitory mechanism has not been studied further. The aim of this study was to reveal the inhibition mechanism of allosteric inhibitor ZL0590 on Free-BRD4 and BRD4 binding MS436 (orthosteric inhibitor) by molecular dynamics simulation combined with a Markov model. Our results showed that BRD4-ZL0590 led to α-helices formation of 100-105 compared with Free-BRD4; the combination of MS436 caused residues 30-40 and 95-105 to form α-helices, while the combination of allosteric inhibitors untangled the α-helices formed by the MS436. The results of Markov flux analysis showed that the binding process of inhibitors mainly involved changes in the degree of α-helices at ZA loop. The binding of ZL0590 reduced the distance between ZA loop and BC loop, blocked the conformation at the active site, and inhibited the binding of MS436. After the allosteric inhibitor binding, the MS436 that could normally penetrate into the interior of the pocket was floating on the edge of the active pocket and did not continue to penetrate into the active pocket as expected. In summary, we provide a theoretical basis for the inhibition mechanism of ZL0590 against BRD4, which can be used as a reference for improving the development of drug targets for cancer therapy.
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Affiliation(s)
- Xiaotang Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yilin Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Song Wang
- The Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2 Liutiao Road, Changchun 130012, China
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41
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Bilgin N, Moesgaard L, Rahman MM, Türkmen VA, Kongsted J, Mecinović J. Molecular Recognition of Methacryllysine and Crotonyllysine by the AF9 YEATS Domain. Int J Mol Sci 2023; 24:ijms24087002. [PMID: 37108167 PMCID: PMC10138300 DOI: 10.3390/ijms24087002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Histone lysine methacrylation and crotonylation are epigenetic marks that play important roles in human gene regulation. Here, we explore the molecular recognition of histone H3 peptides possessing methacryllysine and crotonyllysine at positions 18 and 9 (H3K18 and H3K9) by the AF9 YEATS domain. Our binding studies demonstrate that the AF9 YEATS domain displays a higher binding affinity for histones possessing crotonyllysine than the isomeric methacryllysine, indicating that AF9 YEATS distinguishes between the two regioisomers. Molecular dynamics simulations reveal that the crotonyllysine/methacryllysine-mediated desolvation of the AF9 YEATS domain provides an important contribution to the recognition of both epigenetic marks. These results provide important knowledge for the development of AF9 YEATS inhibitors, an area of biomedical interest.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Mohammad M Rahman
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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42
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Komata Y, Kanai A, Maeda T, Inaba T, Yokoyama A. MOZ/ENL complex is a recruiting factor of leukemic AF10 fusion proteins. Nat Commun 2023; 14:1979. [PMID: 37031220 PMCID: PMC10082848 DOI: 10.1038/s41467-023-37712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
Changes in the transcriptional machinery cause aberrant self-renewal of non-stem hematopoietic progenitors. AF10 fusions, such as CALM-AF10, are generated via chromosomal translocations, causing malignant leukemia. In this study, we demonstrate that AF10 fusion proteins cause aberrant self-renewal via ENL, which binds to MOZ/MORF lysine acetyltransferases (KATs). The interaction of ENL with MOZ, via its YEATS domain, is critical for CALM-AF10-mediated leukemic transformation. The MOZ/ENL complex recruits DOT1L/AF10 fusion complexes and maintains their chromatin retention via KAT activity. Therefore, inhibitors of MOZ/MORF KATs directly suppress the functions of AF10 fusion proteins, thereby exhibiting strong antitumor effects on AF10 translocation-induced leukemia. Combinatorial inhibition of MOZ/MORF and DOT1L cooperatively induces differentiation of CALM-AF10-leukemia cells. These results reveal roles for the MOZ/ENL complex as an essential recruiting factor of the AF10 fusion/DOT1L complex, providing a rationale for using MOZ/MORF KAT inhibitors in AF10 translocation-induced leukemia.
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Affiliation(s)
- Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan
| | - Akinori Kanai
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
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Baweja L, Wereszczynski J. Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks. J Chem Inf Model 2023; 63:1229-1238. [PMID: 36786550 PMCID: PMC10332472 DOI: 10.1021/acs.jcim.2c01660] [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] [Indexed: 02/15/2023]
Abstract
Histone post-translational modifications (PTMs) are interpreted by multiple reader domains and proteins to regulate gene expression. The eleven-nineteen-leukemia (ENL) YEATS domain is a prototypical PTM reader that recognizes multiple lysine acetylation marks on the histone H3 tails as a way of recruiting chromatin remodellers. Two ENL YEATS mutations have been identified which have been linked with leukemia, Wilms tumor, and other forms of cancer and result in either an insertion or deletion of residues in the loop connecting beta sheets distant from the protein active site. In vitro experiments have shown that these mutations modulate the selectivities of YEATS domains for various lysine acetylation marks, although different experiments have provided contrasting views on the abilities of the insertion and deletion mutants to discern specific PTMs. Here, we have performed multiple molecular dynamics simulations of wild-type and insertion and deletion mutant YEATS domains free from and in complex with two PTM peptides: one that is acetylated at K9 of H3 and the other that is acetylated at residue K27 of H3. Results show that these two peptides have distinct flexibilities and binding energetics when bound to YEATS domains and that these properties are affected by interactions with residues within and outside of the peptide consensus motif. Furthermore, these properties are modulated by the YEATS insertion and deletion mutants, which results in disparate binding effects in these systems. Together, these results suggest that only the partial exposure of histone tails is sufficient in the context of nucleosomes for YEATS-mediated recognition of acetylation marks on histone tails. They also caution against the overinterpretation of results obtained from experiments on reader domain-histone peptide binding in isolation and not in the full-length nucleosome context.
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Affiliation(s)
- Lokesh Baweja
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois 60616, United States
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jeff Wereszczynski
- Departments of Physics and Biology, Illinois Institute of Technology, Chicago, Illinois 60616, United States
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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44
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Design, synthesis of novel benzimidazole derivatives as ENL inhibitors suppressing leukemia cells viability via downregulating the expression of MYC. Eur J Med Chem 2023; 248:115093. [PMID: 36645983 DOI: 10.1016/j.ejmech.2023.115093] [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: 10/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023]
Abstract
Eleven-Nineteen-Leukemia Protein (ENL) containing YEATS domain, a potential drug target, has emerged as a reader of lysine acetylation. SGC-iMLLT bearing with benzimidazole scaffold was identified as an effective ENL inhibitor, but with weak activity against mixed-lineage leukemia (MLL)-rearranged cells proliferation. In this study, a series of compounds were designed and synthesized by structural optimization on SGC-iMLLT. All the compounds have been evaluated for their ENL inhibitory activities. The results showed that compounds 13, 23 and 28 are the most potential ones with the IC50 values of 14.5 ± 3.0 nM, 10.7 ± 5.3 nM, and 15.4 ± 2.2 nM, respectively, similar with that of SGC-iMLLT. They could interact with ENL protein and strengthen its thermal stability in vitro. Among them, compound 28 with methyl phenanthridinone moiety replacement of indazole in SGC-iMLLT, exhibited significantly inhibitory activities towards MV4-11 and MOLM-13 cell lines with IC50 values of 4.8 μM and 8.3 μM, respectively, exhibiting ∼7 folds and ∼9 folds more potent inhibition of cell growth than SGC-iMLLT. It could also increase the ENL thermal stability while SGC-iMLLT had no obvious effect on leukemia cells. Moreover, compound 28 could downregulate the expression of target gene MYC either alone or in combination with JQ-1 in cells, which was more effective than SGC-iMLLT. Besides, in vivo pharmacokinetic studies showed that the PK properties for compound 28 was much improved over that of SGC-iMLLT. These observations suggested compound 28 was a potential ligand for ENL-related MLL chemotherapy.
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45
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Londregan AT, Aitmakhanova K, Bennett J, Byrnes LJ, Canterbury DP, Cheng X, Christott T, Clemens J, Coffey SB, Dias JM, Dowling MS, Farnie G, Fedorov O, Fennell KF, Gamble V, Gileadi C, Giroud C, Harris MR, Hollingshead BD, Huber K, Korczynska M, Lapham K, Loria PM, Narayanan A, Owen DR, Raux B, Sahasrabudhe PV, Ruggeri RB, Sáez LD, Stock IA, Thuma BA, Tsai A, Varghese AE. Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4. J Med Chem 2023; 66:460-472. [PMID: 36562986 DOI: 10.1021/acs.jmedchem.2c01421] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.
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Affiliation(s)
- Allyn T Londregan
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | | | - James Bennett
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Daniel P Canterbury
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Xiayun Cheng
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Thomas Christott
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Jennifer Clemens
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Steven B Coffey
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - João M Dias
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Gillian Farnie
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Kimberly F Fennell
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Vicki Gamble
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Carina Gileadi
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Charline Giroud
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Michael R Harris
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brett D Hollingshead
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kilian Huber
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Magdalena Korczynska
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kimberly Lapham
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Paula M Loria
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Brigitt Raux
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Benjamin A Thuma
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Andy Tsai
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Alison E Varghese
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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Wu X, Xie Y, Zhao K, Lu J. Targeting the super elongation complex for oncogenic transcription driven tumor malignancies: Progress in structure, mechanisms and small molecular inhibitor discovery. Adv Cancer Res 2023; 158:387-421. [PMID: 36990537 DOI: 10.1016/bs.acr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oncogenic transcription activation is associated with tumor development and resistance derived from chemotherapy or target therapy. The super elongation complex (SEC) is an important complex regulating gene transcription and expression in metazoans closely related to physiological activities. In normal transcriptional regulation, SEC can trigger promoter escape, limit proteolytic degradation of transcription elongation factors and increase the synthesis of RNA polymerase II (POL II), and regulate many normal human genes to stimulate RNA elongation. Dysregulation of SEC accompanied by multiple transcription factors in cancer promotes rapid transcription of oncogenes and induce cancer development. In this review, we summarized recent progress in understanding the mechanisms of SEC in regulating normal transcription, and importantly its roles in cancer development. We also highlighted the discovery of SEC complex target related inhibitors and their potential applications in cancer treatment.
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Affiliation(s)
- Xinyu Wu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
| | - Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
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47
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Wen H, Shi X. Histone Readers and Their Roles in Cancer. Cancer Treat Res 2023; 190:245-272. [PMID: 38113004 DOI: 10.1007/978-3-031-45654-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Histone proteins in eukaryotic cells are subjected to a wide variety of post-translational modifications, which are known to play an important role in the partitioning of the genome into distinctive compartments and domains. One of the major functions of histone modifications is to recruit reader proteins, which recognize the epigenetic marks and transduce the molecular signals in chromatin to downstream effects. Histone readers are defined protein domains with well-organized three-dimensional structures. In this Chapter, we will outline major histone readers, delineate their biochemical and structural features in histone recognition, and describe how dysregulation of histone readout leads to human cancer.
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Affiliation(s)
- Hong Wen
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Xiaobing Shi
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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48
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Aryal S, Zhang Y, Wren S, Li C, Lu R. Molecular regulators of HOXA9 in acute myeloid leukemia. FEBS J 2023; 290:321-339. [PMID: 34743404 DOI: 10.1111/febs.16268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/30/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
Dysregulation of the oncogenic transcription factor HOXA9 is a prominent feature for most aggressive acute myeloid leukemia cases and a strong indicator of poor prognosis in patients. Leukemia subtypes with hallmark overexpression of HOXA9 include those carrying MLL gene rearrangements, NPM1c mutations, and other genetic alternations. A growing body of evidence indicates that HOXA9 dysregulation is both sufficient and necessary for leukemic transformation. The HOXA9 mRNA and protein regulation includes multilayered controls by transcription factors (such as CDX2/4 and USF2/1), epigenetic factors (such as MLL-menin-LEDGF, DOT1L, ENL, HBO1, NPM1c-XPO1, and polycomb proteins), microRNAs (such as miR-126 and miR-196b), long noncoding RNAs (such as HOTTIP), three-dimensional chromatin interactions, and post-translational protein modifications. Recently, insights into the dynamic regulation of HOXA9 have led to an advanced understanding of the HOXA9 regulome and provided new cancer therapeutic opportunities, including developing inhibitors targeting DOT1L, menin, and ENL proteins. This review summarizes recent advances in understanding the molecular mechanisms controlling HOXA9 regulation and the pharmacological approaches that target HOXA9 regulators to treat HOXA9-driven acute myeloid leukemia.
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Affiliation(s)
- Sajesan Aryal
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Yang Zhang
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Wren
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
| | - Chunliang Li
- Department of Tumor Cell Biology & Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rui Lu
- Division of Hematology and Oncology & O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, AL, USA
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49
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Hu H, Saha N, Yang Y, Ahmad E, Lachowski L, Shrestha U, Premkumar V, Ropa J, Chen L, Teahan B, Grigsby S, Marschalek R, Nikolovska-Coleska Z, Muntean AG. The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia. Leukemia 2023; 37:190-201. [PMID: 36435883 PMCID: PMC11246743 DOI: 10.1038/s41375-022-01765-0] [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: 02/01/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
MLL (KMT2a) translocations are found in ~10% of acute leukemia patients, giving rise to oncogenic MLL-fusion proteins. A common MLL translocation partner is ENL and associated with a poor prognosis in t(11;19) patients. ENL contains a highly conserved N-terminal YEATS domain that binds acetylated histones and interacts with the PAF1c, an epigenetic regulator protein complex essential for MLL-fusion leukemogenesis. Recently, wild-type ENL, and specifically the YEATS domain, was shown to be essential for leukemic cell growth. However, the inclusion and importance of the YEATS domain in MLL-ENL-mediated leukemogenesis remains unexplored. We found the YEATS domain is retained in 84.1% of MLL-ENL patients and crucial for MLL-ENL-mediated leukemogenesis in mouse models. Mechanistically, deletion of the YEATS domain impaired MLL-ENL fusion protein binding and decreased expression of pro-leukemic genes like Eya1 and Meis1. Point mutations that disrupt YEATS domain binding to acetylated histones decreased stem cell frequency and increased MLL-ENL-mediated leukemia latency. Therapeutically, YEATS containing MLL-ENL leukemic cells display increased sensitivity to the YEATS inhibitor SGC-iMLLT compared to control AML cells. Our results demonstrate that the YEATS domain is important for MLL-ENL fusion protein-mediated leukemogenesis and exposes an "Achilles heel" that may be therapeutically targeted for treating t(11;19) patients.
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Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nirmalya Saha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yuting Yang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lauren Lachowski
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Uttar Shrestha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vidhya Premkumar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James Ropa
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - Lili Chen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Blaine Teahan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sierrah Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology / Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany
| | | | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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50
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Travis CR, Francis DY, Williams DC, Waters ML. Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain. Protein Sci 2023; 32:e4533. [PMID: 36482045 PMCID: PMC9793969 DOI: 10.1002/pro.4533] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Amide-π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide-π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide-π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere-π interaction. We show that compared to the amide-π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea-containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post-translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.
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Affiliation(s)
- Christopher R. Travis
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Denver Y. Francis
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, CB 7525University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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