1
|
Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Côté J, Nogales E. Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science 2024; 385:eadl5816. [PMID: 39088653 DOI: 10.1126/science.adl5816] [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: 11/03/2023] [Revised: 05/25/2024] [Accepted: 06/25/2024] [Indexed: 08/03/2024]
Abstract
The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
Collapse
Affiliation(s)
- Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, USA
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Arul Banerjea
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Amélie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Endocrinology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
2
|
Wong LH, Tremethick DJ. Multifunctional histone variants in genome function. Nat Rev Genet 2024:10.1038/s41576-024-00759-1. [PMID: 39138293 DOI: 10.1038/s41576-024-00759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 08/15/2024]
Abstract
Histones are integral components of eukaryotic chromatin that have a pivotal role in the organization and function of the genome. The dynamic regulation of chromatin involves the incorporation of histone variants, which can dramatically alter its structural and functional properties. Contrary to an earlier view that limited individual histone variants to specific genomic functions, new insights have revealed that histone variants exert multifaceted roles involving all aspects of genome function, from governing patterns of gene expression at precise genomic loci to participating in genome replication, repair and maintenance. This conceptual change has led to a new understanding of the intricate interplay between chromatin and DNA-dependent processes and how this connection translates into normal and abnormal cellular functions.
Collapse
Affiliation(s)
- Lee H Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capial Territory, Australia.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Park G, Patel AB, Wu C, Louder RK. Structures of H2A.Z-associated human chromatin remodelers SRCAP and TIP60 reveal divergent mechanisms of chromatin engagement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605802. [PMID: 39131301 PMCID: PMC11312561 DOI: 10.1101/2024.07.30.605802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
H2A.Z is a conserved histone variant that is localized to specific genomic regions where it plays important roles in transcription, DNA repair, and replication. Central to the biochemistry of human H2A.Z are the SRCAP and TIP60 chromatin remodelers, homologs of yeast SWR1 which catalyzes ATP-dependent H2A.Z exchange. Here, we use cryo-electron microscopy to resolve six structural states of the native SRCAP complex, uncovering conformational intermediates interpreted as a stepwise path to full nucleosome engagement. We also resolve the structure of the native TIP60 complex which consists of a structured core from which flexibly tethered chromatin binding domains emerge. Despite the shared subunit composition, the core of TIP60 displays divergent architectures from SRCAP that structurally disfavor nucleosome engagement, suggesting a distinct biochemical function.
Collapse
Affiliation(s)
- Giho Park
- Biochemistry, Cellular and Molecular Graduate Program, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
| | - Avinash B. Patel
- Department of Biophysics, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Carl Wu
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Robert K. Louder
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [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] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
Collapse
Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Yu L, Li Y, Song S, Zhang Y, Wang Y, Wang H, Yang Z, Wang Y. The dual role of sirtuins in cancer: biological functions and implications. Front Oncol 2024; 14:1384928. [PMID: 38947884 PMCID: PMC11211395 DOI: 10.3389/fonc.2024.1384928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024] Open
Abstract
Sirtuins are pivotal in orchestrating numerous cellular pathways, critically influencing cell metabolism, DNA repair, aging processes, and oxidative stress. In recent years, the involvement of sirtuins in tumor biology has garnered substantial attention, with a growing body of evidence underscoring their regulatory roles in various aberrant cellular processes within tumor environments. This article delves into the sirtuin family and its biological functions, shedding light on their dual roles-either as promoters or inhibitors-in various cancers including oral, breast, hepatocellular, lung, and gastric cancers. It further explores potential anti-tumor agents targeting sirtuins, unraveling the complex interplay between sirtuins, miRNAs, and chemotherapeutic drugs. The dual roles of sirtuins in cancer biology reflect the complexity of targeting these enzymes but also highlight the immense therapeutic potential. These advancements hold significant promise for enhancing clinical outcomes, marking a pivotal step forward in the ongoing battle against cancer.
Collapse
Affiliation(s)
- Lu Yu
- Department of Respiratory, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanjiao Li
- Department of Pharmacy, Qionglai Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Siyuan Song
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Yalin Zhang
- School of Medicine, University of Electronic Science and Technology of China, Center of Critical Care Medicine, Sichuan Academy of Medical Sciences, Chengdu, China
- Center of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Wang
- Center of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hailian Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science, Nanning, China
| | - Zhengteng Yang
- Department of Medicine, The First Affiliated Hospital of Guangxi University of Traditional Medicine, Nanning, China
| | - Yi Wang
- Center of Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science, Nanning, China
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Grossi E, Hasson D, Bernstein E. H2A.Z chaperones converge on E2F target genes for melanoma cell proliferation. Genes Dev 2024; 38:336-353. [PMID: 38744503 PMCID: PMC11146596 DOI: 10.1101/gad.351318.123] [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: 11/27/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes SRCAP and P400-TIP60 in melanoma remains unclear. Here, we show that individual subunit depletion of SRCAP, P400, and VPS72 (YL1) results in not only the loss of H2A.Z deposition into chromatin but also a reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is particularly found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
Collapse
Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Saul Carcamo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Zong Y, Weiss N, Wang K, Pagano AE, Heissel S, Perveen S, Huang J. Development of Complementary Photo-arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307526. [PMID: 38298064 PMCID: PMC11005723 DOI: 10.1002/advs.202307526] [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: 10/09/2023] [Revised: 12/03/2023] [Indexed: 02/02/2024]
Abstract
Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context-specific and transient effectors of these marks, while significant, have evaded study as detection methods have thus far not reached a standard to capture these ephemeral events. Herein, a pair of complementary photo-arginine/δ-photo-lysine (R-dz/K-dz) probes is developed and involve these into histone peptide, nucleosome, and chromatin substrates to capture and explore the interactomes of Arg and Lys hPTMs. By means of these developed tools, this study identifies that H3R2me2a can recruit MutS protein homolog 6 (MSH6), otherwise repelDouble PHD fingers 2 (DPF2), Retinoblastoma binding protein 4/7 (RBBP4/7). And it is disclosed that H3R2me2a inhibits the chromatin remodeling activity of the cBAF complex by blocking the interaction between DPF2 (one component of cBAF) and the nucleosome. In addition, the novel pairs of H4K5 PTMs and respective readers are highlighted, namely H4K5me-Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2), H4K5me2-L3MBTL2, and H4K5acK8ac-YEATS domain-containing protein 4 (YEATS4). These powerful tools pave the way for future investigation of related epigenetic mechanisms including but not limited to hPTMs.
Collapse
Affiliation(s)
- Yu Zong
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | - Nicole Weiss
- Program of PharmacologyWeill Cornell Medical College of Cornell UniversityNew York10065USA
| | - Ke Wang
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | | | - Søren Heissel
- Proteomics Resource CenterRockefeller UniversityNew York10065USA
| | - Sumera Perveen
- Structural Genomics ConsortiumUniversity of TorontoTorontoM5S3H2Canada
| | - Jian Huang
- Department of Molecular BiologyPrinceton UniversityPrinceton08544USA
| |
Collapse
|
14
|
Dashti P, Lewallen EA, Gordon JAR, Montecino MA, Davie JR, Stein GS, van Leeuwen JPTM, van der Eerden BCJ, van Wijnen AJ. Epigenetic regulators controlling osteogenic lineage commitment and bone formation. Bone 2024; 181:117043. [PMID: 38341164 DOI: 10.1016/j.bone.2024.117043] [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: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bone formation and homeostasis are controlled by environmental factors and endocrine regulatory cues that initiate intracellular signaling pathways capable of modulating gene expression in the nucleus. Bone-related gene expression is controlled by nucleosome-based chromatin architecture that limits the accessibility of lineage-specific gene regulatory DNA sequences and sequence-specific transcription factors. From a developmental perspective, bone-specific gene expression must be suppressed during the early stages of embryogenesis to prevent the premature mineralization of skeletal elements during fetal growth in utero. Hence, bone formation is initially inhibited by gene suppressive epigenetic regulators, while other epigenetic regulators actively support osteoblast differentiation. Prominent epigenetic regulators that stimulate or attenuate osteogenesis include lysine methyl transferases (e.g., EZH2, SMYD2, SUV420H2), lysine deacetylases (e.g., HDAC1, HDAC3, HDAC4, HDAC7, SIRT1, SIRT3), arginine methyl transferases (e.g., PRMT1, PRMT4/CARM1, PRMT5), dioxygenases (e.g., TET2), bromodomain proteins (e.g., BRD2, BRD4) and chromodomain proteins (e.g., CBX1, CBX2, CBX5). This narrative review provides a broad overview of the covalent modifications of DNA and histone proteins that involve hundreds of enzymes that add, read, or delete these epigenetic modifications that are relevant for self-renewal and differentiation of mesenchymal stem cells, skeletal stem cells and osteoblasts during osteogenesis.
Collapse
Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada; CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada.
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | | | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Andre J van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
| |
Collapse
|
15
|
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."
Collapse
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.
| |
Collapse
|
16
|
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).
Collapse
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.
| |
Collapse
|
17
|
Ma Q, Chen L, Feng K, Guo W, Huang T, Cai YD. Exploring Prognostic Gene Factors in Breast Cancer via Machine Learning. Biochem Genet 2024:10.1007/s10528-024-10712-w. [PMID: 38383836 DOI: 10.1007/s10528-024-10712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024]
Abstract
Breast cancer remains the most prevalent cancer in women. To date, its underlying molecular mechanisms have not been fully uncovered. The determination of gene factors is important to improve our understanding on breast cancer, which can correlate the specific gene expression and tumor staging. However, the knowledge in this regard is still far from complete. Thus, this study aimed to explore these knowledge gaps by analyzing existing gene expression profile data from 3149 breast cancer samples, where each sample was represented by the expression of 19,644 genes and classified into Nottingham histological grade (NHG) classes (Grade 1, 2, and 3). To this end, a machine learning-based framework was designed. First, the profile data were analyzed by using seven feature ranking algorithms to evaluate the importance of features (genes). Seven feature lists were generated, each of which sorted features in accordance with feature importance evaluated from a special aspect. Then, the incremental feature selection method was applied to each list to determine essential features for classification and building efficient classifiers. Consequently, overlapping genes, such as AURKA, CBX2, and MYBL2, were deemed as potentially related to breast cancer malignancy and prognosis, indicating that such genes were identified to be important by multiple feature ranking algorithms. In addition, the study formulated classification rules to reflect special gene expression patterns for three NHG classes. Some genes and rules were analyzed and supported by recent literature, providing new references for studying breast cancer.
Collapse
Affiliation(s)
- QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, 510507, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200030, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| |
Collapse
|
18
|
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y. Structural insights into histone exchange by human SRCAP complex. Cell Discov 2024; 10:15. [PMID: 38331872 PMCID: PMC10853557 DOI: 10.1038/s41421-023-00640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024] Open
Abstract
Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeFx-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.
Collapse
Affiliation(s)
- Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Fengrui Sui
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Feng Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuang He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
| |
Collapse
|
19
|
Gao J, Lu Q, Zhong J, Li Z, Pan L, Feng C, Tang S, Wang X, Tao Y, Zhou X, Wang Q. Identification and validation of an H2AZ1-based index model: a novel prognostic tool for hepatocellular carcinoma. Aging (Albany NY) 2024; 16:2542-2562. [PMID: 38305811 PMCID: PMC10911386 DOI: 10.18632/aging.205497] [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: 03/28/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024]
Abstract
The H2A.Z variant histone 1 (H2AZ1) is aberrantly expressed in various tumors, correlating with an unfavorable prognosis. However, its role in hepatocellular carcinoma (HCC) remains unclear. We aimed to elucidate the pathways affected by H2AZ1 and identify promising therapeutic targets for HCC. Following bioinformatic analysis of gene expression and clinical data from The Cancer Genome Atlas and Gene Expression Omnibus database, we found 6,344 dysregulated genes related to H2AZ1 overexpression in HCC tissues (P < 0.05). We performed weighted gene co-expression network analysis to identify the gene module most related to H2AZ1. The H2AZ1-based index was further developed using Cox regression analysis, which revealed that the poor prognosis in the high H2AZ1-based index group could be attributed to elevated tumor stemness (P < 0.05). Moreover, the clinical model showed good prognostic potential (AUC > 0.7). We found that H2AZ1 knockdown led to reduced superoxide dismutase (SOD) activity, elevated malondialdehyde (MDA) levels, and increased apoptosis rate in tumor cells (P < 0.001). Thus, we developed an H2AZ1-based index model with the potential to predict the prognosis of patients with HCC. Our findings provide initial evidence that H2AZ1 overexpression plays a pivotal role in HCC initiation and progression.
Collapse
Affiliation(s)
- Jiamin Gao
- Laboratory of Infectious Disease, Nanning Infectious Disease Hospital Affiliated to Guangxi Medical University and The Fourth People’s Hospital of Nanning, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Qinchen Lu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Jialing Zhong
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhijian Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lixin Pan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Chao Feng
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Shaomei Tang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Xi Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Xianguo Zhou
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
- Department of Blood Transfusion, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
21
|
Lin X, Ma Q, Chen L, Guo W, Huang Z, Huang T, Cai YD. Identifying genes associated with resistance to KRAS G12C inhibitors via machine learning methods. Biochim Biophys Acta Gen Subj 2023; 1867:130484. [PMID: 37805078 DOI: 10.1016/j.bbagen.2023.130484] [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: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Targeted therapy has revolutionized cancer treatment, greatly improving patient outcomes and quality of life. Lung cancer, specifically non-small cell lung cancer, is frequently driven by the G12C mutation at the KRAS locus. The development of KRAS inhibitors has been a breakthrough in the field of cancer research, given the crucial role of KRAS mutations in driving tumor growth and progression. However, over half of patients with cancer bypass inhibition show limited response to treatment. The mechanisms underlying tumor cell resistance to this treatment remain poorly understood. METHODS To address above gap in knowledge, we conducted a study aimed to elucidate the differences between tumor cells that respond positively to KRAS (G12C) inhibitor therapy and those that do not. Specifically, we analyzed single-cell gene expression profiles from KRAS G12C-mutant tumor cell models (H358, H2122, and SW1573) treated with KRAS G12C (ARS-1620) inhibitor, which contained 4297 cells that continued to proliferate under treatment and 3315 cells that became quiescent. Each cell was represented by the expression levels on 8687 genes. We then designed an innovative machine learning based framework, incorporating seven feature ranking algorithms and four classification algorithms to identify essential genes and establish quantitative rules. RESULTS Our analysis identified some top-ranked genes, including H2AFZ, CKS1B, TUBA1B, RRM2, and BIRC5, that are known to be associated with the progression of multiple cancers. CONCLUSION Above genes were relevant to tumor cell resistance to targeted therapy. This study provides important insights into the molecular mechanisms underlying tumor cell resistance to KRAS inhibitor treatment.
Collapse
Affiliation(s)
- Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Clinical Oncology School of Fujian Medical University and Fujian Cancer Hospital, Fuzhou 350014, China.
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Zhiyi Huang
- College of Chemistry, Fuzhou University, Fuzhou 350000, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| |
Collapse
|
22
|
Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Hasson D, Bernstein E. H2A.Z chaperones converge on histone H4 acetylation for melanoma cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568747. [PMID: 38076914 PMCID: PMC10705243 DOI: 10.1101/2023.11.26.568747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes, SRCAP and P400-TIP60, in melanoma remains unclear. Here, we show that individual depletion of SRCAP, P400, and VPS72 (YL1) not only results in loss of H2A.Z deposition into chromatin, but also a striking reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a highly coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
Collapse
Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saul Carcamo
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Ji K, Li L, Liu H, Shen Y, Jiang J, Zhang M, Teng H, Yan X, Zhang Y, Cai Y, Zhou H. Unveiling the role of GAS41 in cancer progression. Cancer Cell Int 2023; 23:245. [PMID: 37853482 PMCID: PMC10583379 DOI: 10.1186/s12935-023-03098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
GAS41, a member of the human YEATS domain family, plays a pivotal role in human cancer development. It serves as a highly promising epigenetic reader, facilitating precise regulation of cell growth and development by recognizing essential histone modifications, including histone acetylation, benzoylation, succinylation, and crotonylation. Functional readouts of these histone modifications often coincide with cancer progression. In addition, GAS41 functions as a novel oncogene, participating in numerous signaling pathways. Here, we summarize the epigenetic functions of GAS41 and its role in the carcinoma progression. Moving forward, elucidating the downstream target oncogenes regulated by GAS41 and the developing small molecule inhibitors based on the distinctive YEATS recognition properties will be pivotal in advancing this research field.
Collapse
Affiliation(s)
- Kangkang Ji
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Li Li
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hui Liu
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yucheng Shen
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Jian Jiang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Minglei Zhang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hongwei Teng
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Xun Yan
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yanhua Zhang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yong Cai
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hai Zhou
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China.
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T. Epigenetic mechanisms to propagate histone acetylation by p300/CBP. Nat Commun 2023; 14:4103. [PMID: 37460559 DOI: 10.1038/s41467-023-39735-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone N-terminal tail acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization.
Collapse
Affiliation(s)
- Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Satoshi Morita
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Masatoshi Wakamori
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Tomomi Uchikubo-Kamo
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Xian Q, Song Y, Gui C, Zhou Y. Mechanistic insights into genomic structure and functions of a novel oncogene YEATS4. Front Cell Dev Biol 2023; 11:1192139. [PMID: 37435030 PMCID: PMC10332269 DOI: 10.3389/fcell.2023.1192139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
As a novel oncogene, the role of YEATS domain-containing protein 4 (YEATS4) in the occurrence, development, and treatment of tumors is now beginning to be appreciated. YEATS4 plays an important role in regulating DNA repair during replication. The upregulation of YEAST4 promotes DNA damage repair and prevents cell death, whereas its downregulation inhibits DNA replication and induces apoptosis. Additionally, accumulating evidence indicates that the aberrant activation of YEATS4 leads to changes in drug resistance, epithelial-mesenchymal transition and also in the migration and invasion capacity of tumor cells. Therefore, specific inhibition of the expression or activity of YEATS4 protein may be an effective strategy for inhibiting the proliferation, motility, differentiation, and/or survival of tumor cells. Taken together, YEATS4 has emerged as a potential target for multiple cancers and is an attractive protein for the development of small-molecule inhibitors. However, research on YEAST4 in tumor-related fields is limited and its biological functions, metabolism, and the regulatory mechanism of YEATS4 in numerous cancers remain undetermined. This review comprehensively and extensively summarizes the functions, structure and oncogenic roles of YEATS4 in cancer progression and aims to further contribute to the study of its underlying molecular mechanism and targeted drugs.
Collapse
Affiliation(s)
- Qingqing Xian
- Department of Clinical Laboratory Diagnosis, Shandong University, Jinan, Shandong, China
| | - Yiying Song
- Department of Clinical Laboratory Diagnosis, Shandong University, Jinan, Shandong, China
| | - Chengzhi Gui
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong, China
| | - Yunying Zhou
- Department of Clinical Laboratory Diagnosis, Shandong University, Jinan, Shandong, China
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong, China
- Medical Research and Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| |
Collapse
|
30
|
Zhu X, Luo X, Long X, Jiang S, Xie X, Zhang Q, Wang H. CircAGO2 promotes colorectal cancer progression by inhibiting heat shock protein family B (small) member 8 via miR-1-3p/retinoblastoma binding protein 4 axis. Funct Integr Genomics 2023; 23:78. [PMID: 36881338 DOI: 10.1007/s10142-023-00990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023]
Abstract
This paper was to uncover the mechanism of circular RNA Argonaute 2 (circAGO2) in colorectal cancer (CRC) progression. The expression of circAGO2 was detected in CRC cells and tissues, and the relationship between clinicopathological features of CRC and circAGO2 level was evaluated. The growth and invasion of CRC cells and subcutaneous xenograft of nude mice were measured to evaluate the effect of circAGO2 on CRC development. Bioinformatics databases were applied to analyze levels of retinoblastoma binding protein 4 (RBBP4) and heat shock protein family B 8 (HSPB8) in cancer tissues. The relevance of circAGO2 and RBBP4 expression and the relationship between RBBP4 and HSPB8 during histone acetylation were assessed. The targeting relationship between miR-1-3p and circAGO2 or RBBP4 was predicted and confirmed. The effects of miR-1-3p and RBBP4 on biological functions of CRC cells were also verified. CircAGO2 was upregulated in CRC. CircAGO2 promoted the growth and invasion of CRC cells. CircAGO2 competitively bound to miR-1-3p and regulated RBBP4 expression, thus inhibiting HSPB8 transcription by promoting histone deacetylation. Silencing circAGO2 enhanced miR-1-3p expression and reduced RBBP4 expression, while suppression of miR-1-3p downgraded levels of miR-1-3p, up-regulated RBBP4, and facilitated cell proliferation and invasion in the presence of silencing circAGO2. RBBP4 silencing decreased RBBP4 expression and reduced proliferation and invasion of cells where circAGO2 and miR-1-3p were silenced. CircAGO2 overexpression decoyed miR-1-3p to increase RBBP4 expression, which inhibited HSPB8 transcription via histone deacetylation in HSPB8 promoter region, promoting proliferation and invasion of CRC cells.
Collapse
Affiliation(s)
- Xijia Zhu
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Xishun Luo
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Xiangkai Long
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Shiyu Jiang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Xinyang Xie
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Qiqi Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China
| | - Haipeng Wang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, Guangxi, 541100, People's Republic of China.
| |
Collapse
|
31
|
Hsiao YL, Chen HW, Chen KH, Tan BCM, Chen CH, Pi H. Actin-related protein 6 facilitates proneural protein-induced gene activation for rapid neural differentiation. Development 2023; 150:297055. [PMID: 36897355 DOI: 10.1242/dev.201034] [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: 06/21/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023]
Abstract
Neurogenesis is initiated by basic helix-loop-helix proneural proteins. Here, we show that Actin-related protein 6 (Arp6), a core component of the H2A.Z exchange complex SWR1, interacts with proneural proteins and is crucial for efficient onset of proneural protein target gene expression. Arp6 mutants exhibit reduced transcription in sensory organ precursors (SOPs) downstream of the proneural protein patterning event. This leads to retarded differentiation and division of SOPs and smaller sensory organs. These phenotypes are also observed in proneural gene hypomorphic mutants. Proneural protein expression is not reduced in Arp6 mutants. Enhanced proneural gene expression fails to rescue retarded differentiation in Arp6 mutants, suggesting that Arp6 acts downstream of or in parallel with proneural proteins. H2A.Z mutants display Arp6-like retardation in SOPs. Transcriptomic analyses demonstrate that loss of Arp6 and H2A.Z preferentially decreases expression of proneural protein-activated genes. H2A.Z enrichment in nucleosomes around the transcription start site before neurogenesis correlates highly with greater activation of proneural protein target genes by H2A.Z. We propose that upon proneural protein binding to E-box sites, H2A.Z incorporation around the transcription start site allows rapid and efficient activation of target genes, promoting rapid neural differentiation.
Collapse
Affiliation(s)
- Yun-Ling Hsiao
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Hui-Wen Chen
- Gradulate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Kuan-Han Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Gradulate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chia-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| | - Haiwei Pi
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Gradulate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| |
Collapse
|
32
|
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.
Collapse
|
33
|
Bignoux MJ, Otgaar TC, Bernert M, Weiss SFT, Ferreira E. Downregulation of LRP/LR with siRNA inhibits several cancer hallmarks in lung cancer cells. FEBS Open Bio 2023; 13:323-340. [PMID: 36579897 PMCID: PMC9900088 DOI: 10.1002/2211-5463.13544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
The incidence and mortality rates of cancer are growing rapidly worldwide, with lung cancer being the most commonly occurring cancer in males. Human carcinomas circumvent the inhibitory pathways induced by DNA damage and senescence through the upregulation of telomerase activity. The 37 kDa/67 kDa laminin receptor (LRP/LR) is a cell surface receptor which plays a role in several cancer hallmarks, including metastasis, angiogenesis, cell viability maintenance, apoptotic evasion, and mediating telomerase activity. We have previously shown that the knockdown of LRP/LR with an LRP-specific siRNA significantly impedes adhesion and invasion, induces apoptosis, and inhibits telomerase activity in various cancer cell lines in vitro. Here, we investigated the effect of downregulating LRP/LR with LRP-specific siRNA in A549 lung cancer cells. Downregulation of LRP/LR resulted in a significant decrease in cell viability, migration potential, and telomerase activity, as well as a significant increase in apoptosis. Proteomic analysis further suggested the re-establishment of immune control over the lung cancer cells, a previously unidentified facet of LRP downregulation in cancer. Altogether, we suggest that targeting LRP/LR for downregulation may have therapeutic potential for inhibiting several cancer hallmarks.
Collapse
Affiliation(s)
- Monique J. Bignoux
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Tyrone C. Otgaar
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Martin Bernert
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Stefan F. T. Weiss
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Eloise Ferreira
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Wen H, Shi X. Histone Readers and Their Roles in Cancer. Cancer Treat Res 2023; 190:245-272. [PMID: 38113004 PMCID: PMC11395558 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] [Grants] [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.
Collapse
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.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Mol Cell 2022; 82:4627-4646.e14. [PMID: 36417913 PMCID: PMC9779922 DOI: 10.1016/j.molcel.2022.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
Collapse
Affiliation(s)
- Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacklyn H Luu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moritz Mall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Han Ng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuhao Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Neumayer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
38
|
Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun 2022; 13:7052. [PMID: 36396651 PMCID: PMC9672302 DOI: 10.1038/s41467-022-34861-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.
Collapse
Affiliation(s)
- Jiayi Fan
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Interdisciplinary Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Andrew T. Moreno
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Alexander S. Baier
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Joseph J. Loparo
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Craig L. Peterson
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| |
Collapse
|
39
|
Liu Y, Li Q, Alikarami F, Barrett DR, Mahdavi L, Li H, Tang S, Khan TA, Michino M, Hill C, Song L, Yang L, Li Y, Pokharel SP, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Carroll M, Chen CW, Gardini A, Maillard I, Huggins DJ, Bernt KM, Wan L. Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia. Cancer Discov 2022; 12:2684-2709. [PMID: 36053276 PMCID: PMC9627135 DOI: 10.1158/2159-8290.cd-21-1307] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 02/06/2023]
Abstract
The chromatin reader eleven-nineteen leukemia (ENL) has been identified as a critical dependency in acute myeloid leukemia (AML), but its therapeutic potential remains unclear. We describe a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-11055, which displaces ENL from chromatin by blocking its YEATS domain interaction with acylated histones. Cell lines and primary patient samples carrying MLL rearrangements or NPM1 mutations are responsive to TDI-11055. A CRISPR-Cas9-mediated mutagenesis screen uncovers an ENL mutation that confers resistance to TDI-11055, validating the compound's on-target activity. TDI-11055 treatment rapidly decreases chromatin occupancy of ENL-associated complexes and impairs transcription elongation, leading to suppression of key oncogenic gene expression programs and induction of differentiation. In vivo treatment with TDI-11055 blocks disease progression in cell line- and patient-derived xenograft models of MLL-rearranged and NPM1-mutated AML. Our results establish ENL displacement from chromatin as a promising epigenetic therapy for molecularly defined AML subsets and support the clinical translation of this approach. SIGNIFICANCE AML is a poor-prognosis disease for which new therapeutic approaches are desperately needed. We developed an orally bioavailable inhibitor of ENL, demonstrated its potent efficacy in MLL-rearranged and NPM1-mutated AML, and determined its mechanisms of action. These biological and chemical insights will facilitate both basic research and clinical translation. This article is highlighted in the In This Issue feature, p. 2483.
Collapse
Affiliation(s)
- Yiman Liu
- Department of Cancer Biology, 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, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fatemeh Alikarami
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Declan R. Barrett
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Leila Mahdavi
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hangpeng Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sylvia Tang
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tanweer A. Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Connor Hill
- Wistar Institute, Gene Expression and Regulation Program, Philadelphia, Pennsylvania.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing, China
| | | | | | - Nigel Liverton
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | | | - Simon Taylor
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Gillian F. Watt
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Tammy Ladduwahetty
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Stacia Kargman
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Bridge Medicines, New York, New York
| | - Peter T. Meinke
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Michael A. Foley
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Junwei Shi
- Department of Cancer Biology, 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
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Martin Carroll
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California
| | - Alessandro Gardini
- Wistar Institute, Gene Expression and Regulation Program, Philadelphia, Pennsylvania
| | - Ivan Maillard
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David J. Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Kathrin M. Bernt
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Corresponding Authors: Liling Wan, University of Pennsylvania, BRB II/III, RM751, 421 Curie Boulevard, Philadelphia, PA 19104. Phone: 215-898-3116; E-mail: ; and Kathrin M. Bernt, Children's Hospital of Philadelphia, Colket Translational Research Center, Room 3064, 3501 Civic Center Boulevard, Philadelphia, PA 19104. Phone: 215-370-3171; E-mail:
| | - Liling Wan
- Department of Cancer Biology, 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.,Corresponding Authors: Liling Wan, University of Pennsylvania, BRB II/III, RM751, 421 Curie Boulevard, Philadelphia, PA 19104. Phone: 215-898-3116; E-mail: ; and Kathrin M. Bernt, Children's Hospital of Philadelphia, Colket Translational Research Center, Room 3064, 3501 Civic Center Boulevard, Philadelphia, PA 19104. Phone: 215-370-3171; E-mail:
| |
Collapse
|
40
|
Wang W, Shen Y, Zhang P, Liu L, Sha X, Li H, Wang S, Zhang H, Zhou Y, Shi J. Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients. J Thorac Dis 2022; 14:3886-3902. [PMID: 36389327 PMCID: PMC9641363 DOI: 10.21037/jtd-22-1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. METHODS In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. RESULTS We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. CONCLUSIONS Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.
Collapse
Affiliation(s)
- Wenmiao Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Yao Shen
- School of Medicine, Nantong University, Nantong, China
| | - Peng Zhang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Lei Liu
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Xinyu Sha
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Houqiang Li
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Silin Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China;,School of Public Health, Nantong University, Nantong, China
| |
Collapse
|
41
|
Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
Collapse
Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| |
Collapse
|
42
|
Dijkwel Y, Tremethick DJ. The Role of the Histone Variant H2A.Z in Metazoan Development. J Dev Biol 2022; 10:jdb10030028. [PMID: 35893123 PMCID: PMC9326617 DOI: 10.3390/jdb10030028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 12/10/2022] Open
Abstract
During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.
Collapse
|
43
|
Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles. J Biol Chem 2022; 298:102164. [PMID: 35732209 PMCID: PMC9293779 DOI: 10.1016/j.jbc.2022.102164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 01/02/2023] Open
Abstract
Acetylated lysine residues (Kac) in histones are recognized by epigenetic reader proteins, such as Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins. Human YEATS domains bind to the acetylated N-terminal tail of histone H3; however, their Kac-binding preferences at the level of the nucleosome are unknown. Through genetic code reprogramming, here, we established a nucleosome core particle (NCP) array containing histones that were acetylated at specific residues and used it to compare the Kac-binding preferences of human YEATS domains. We found that AF9-YEATS showed basal binding to the unmodified NCP and that it bound stronger to the NCP containing a single acetylation at one of K4, K9, K14, or K27 of H3, or to histone H4 multi-acetylated between K5 and K16. Crystal structures of AF9-YEATS in complex with an H4 peptide diacetylated either at K5/K8 or K8/K12 revealed that the aromatic cage of the YEATS domain recognized the acetylated K8 residue. Interestingly, E57 and D103 of AF9, both located outside of the aromatic cage, were shown to interact with acetylated K5 and K12 of H4, respectively, consistent with the increase in AF9-YEATS binding to the H4K8-acetylated NCP upon additional acetylation at K5 or K12. Finally, we show that a mutation of E57 to alanine in AF9-YEATS reduced the binding affinity for H4 multiacetylated NCPs containing H4K5ac. Our data suggest that the Kac-binding affinity of AF9-YEATS increases additively with the number of Kac in the histone tail.
Collapse
|
44
|
Han S, Cao C, Liu R, Yuan Y, Pan L, Xu M, Hu C, Zhang X, Li M, Zhang X. GAS41 mediates proliferation and GEM chemoresistance via H2A.Z.2 and Notch1 in pancreatic cancer. Cell Oncol (Dordr) 2022; 45:429-446. [PMID: 35503594 DOI: 10.1007/s13402-022-00675-8] [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] [Accepted: 04/11/2022] [Indexed: 12/09/2022] Open
Abstract
PURPOSE GAS41 is a YEATS domain protein that binds to acetylated histone H3 to promote the chromatin deposition of H2A.Z in non-small cell lung cancer. The role of GAS41 in pancreatic cancer is still unknown. Here, we aimed to reveal this role. METHODS GAS41 expression in pancreatic cancer tissues and cell lines was examined using qRT-PCR, Western blotting and immunohistochemistry. MTT, colony formation, spheroid formation and in vivo tumorigenesis assays were performed to assess the proliferation, tumorigenesis, stemness and gemcitabine (GEM) resistance of pancreatic cancer cells. Mechanistically, co-immunoprecipitation (co-IP) and chromatin immunoprecipitation (ChIP) assays were used to evaluate the roles of GAS41, H2A.Z.2 and Notch1 in pancreatic cancer. RESULTS We found that GAS41 is overexpressed in human pancreatic cancer tissues and cell lines, and that its expression increases following the acquisition of GEM resistance. We also found that GAS41 up-regulates Notch, as well as pancreatic cancer cell stemness and GEM resistance in vitro and in vivo. We show that GAS41 binds to H2A.Z.2 and activates Notch and its downstream mediators, thereby regulating stemness and drug resistance. Depletion of GAS41 or H2A.Z.2 was found to down-regulate Notch and to sensitize pancreatic cancer cells to GEM. CONCLUSION Our data indicate that GAS41 mediates proliferation and GEM resistance in pancreatic cancer cells via H2A.Z.2 and Notch1.
Collapse
Affiliation(s)
- Shilong Han
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Chuanwu Cao
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Rui Liu
- Shanghai Tenth People's Hospital of Tongji University, Tongji University Cancer Center, Shanghai, 200072, China
| | - YiFeng Yuan
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Long Pan
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Minjie Xu
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Chao Hu
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Xiaojun Zhang
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China
| | - Maoquan Li
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China.
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China.
| | - Xiaoping Zhang
- Department of Intervention and Vascular Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 50 Chifeng Road, Yangpu, Shanghai, 200072, China.
- National Center Clinical Research for Interventional Medicine, Shanghai Tenth People's Hospital, 50 Chifeng Road, Yangpu, Shanghai, 200072, China.
| |
Collapse
|
45
|
Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
Collapse
Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
| |
Collapse
|
46
|
Yeewa R, Chaiya P, Jantrapirom S, Shotelersuk V, Lo Piccolo L. Multifaceted roles of YEATS domain-containing proteins and novel links to neurological diseases. Cell Mol Life Sci 2022; 79:183. [PMID: 35279775 PMCID: PMC11071958 DOI: 10.1007/s00018-022-04218-0] [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: 11/17/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
The so-called Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins, hereafter referred to as YD proteins, take control over the transcription by multiple steps of regulation either involving epigenetic remodelling of chromatin or guiding the processivity of RNA polymerase II to facilitate elongation-coupled mRNA 3' processing. Interestingly, an increasing amount of evidence suggest a wider repertoire of YD protein's functions spanning from non-coding RNA regulation, RNA-binding proteins networking, post-translational regulation of a few signalling transduction proteins and the spindle pole formation. However, such a large set of non-canonical roles is still poorly characterized. Notably, four paralogous of human YEATS domain family members, namely eleven-nineteen-leukaemia (ENL), ALL1-fused gene from chromosome 9 protein (AF9), YEATS2 and glioma amplified sequence 41 (GAS41), have a strong link to cancer yet new findings also highlight a potential novel role in neurological diseases. Here, in an attempt to more comprehensively understand the complexity of four YD proteins and to gain more insight into the novel functions they may accomplish in the neurons, we summarized the YD protein's networks, systematically searched and reviewed the YD genetic variants associated with neurodevelopmental disorders and finally interrogated the model organism Drosophila melanogaster.
Collapse
Affiliation(s)
- Ranchana Yeewa
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pawita Chaiya
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Salinee Jantrapirom
- Drosophila Centre for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Vorasuk Shotelersuk
- Centre of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Centre for Genomics and Precision Medicine, The Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Luca Lo Piccolo
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Musculoskeletal Science and Translational Research Centre (MSTR), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai, 50200, Thailand.
| |
Collapse
|
47
|
Li X, Liu S, Li X, Li XD. YEATS Domains as Novel Epigenetic Readers: Structures, Functions, and Inhibitor Development. ACS Chem Biol 2022; 18:994-1013. [PMID: 35041380 DOI: 10.1021/acschembio.1c00945] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interpretation of the histone posttranslational modifications (PTMs) by effector proteins, or readers, is an important epigenetic mechanism to regulate gene function. YEATS domains have been recently identified as novel readers of histone lysine acetylation and a variety of nonacetyl acylation marks. Accumulating evidence has revealed the association of dysregulated interactions between YEATS domains and histone PTMs with human diseases, suggesting the therapeutic potential of YEATS domain inhibition. Here, we discuss the molecular mechanisms adopted by YEATS domains in recognizing their preferred histone marks and the biological significance of such recognitions in normal cell physiology and pathogenesis of human diseases. Recent progress in the development of YEATS domain inhibitors is also discussed.
Collapse
Affiliation(s)
- Xin Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Sha Liu
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| |
Collapse
|
48
|
Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 284] [Impact Index Per Article: 142.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
Collapse
Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
| |
Collapse
|
49
|
Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals. Comput Struct Biotechnol J 2022; 20:353-367. [PMID: 35035788 PMCID: PMC8741409 DOI: 10.1016/j.csbj.2021.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
|
50
|
Yuan C, Liu J, Liu L, Jia H, Gao Q, Wang X, Zhao J. TRIM7 suppresses cell invasion and migration through inhibiting HIF-1α accumulation in clear cell renal cell carcinoma. Cell Biol Int 2021; 46:554-567. [PMID: 34936717 DOI: 10.1002/cbin.11750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 01/14/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is one frequent form of urologic malignancy characterized by deregulated hypoxia-inducible factor signaling, genetic and epigenetic alterations. Metastasis is the leading cause of mortality from ccRCC, and understanding the underlying mechanism of this event will provide better strategies for its management. Here, we identify tripartite motif containing 7 (TRIM7) as a tumor suppressor in ccRCC cells, which negatively regulates hypoxia-inducible factor 1α (HIF-1α) signaling through targeting the proto-oncogene Src. We observed the downregulated expression of TRIM7 in clinical ccRCC tissues and its correlation with the poor prognosis. In Caki-1 cells, depletion of TRIM7 increased cell migration and invasion under normoxic and hypoxic conditions. TRIM7 markedly reduced the abundance of Src protein via the ubiquitin-proteasome pathway. Further study showed that TRIM7 affected HIF-1α accumulation through targeting either the Src-triggered PI3K/AKT/mTOR signaling pathway or reactive oxygen species production. Overall, our findings highlight a novel mechanism for negative regulation of HIF-1 signaling pathway by TRIM7 and define a promising therapeutic strategy for ccRCC by modulating TRIM7.
Collapse
Affiliation(s)
- Chao Yuan
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Junli Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ling Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hongying Jia
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qi Gao
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiaoyan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jingjie Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|