1
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Papp O, Jordán V, Hetey S, Balázs R, Kaszás V, Bartha Á, Ordasi NN, Kamp S, Farkas B, Mettetal J, Dry JR, Young D, Sidders B, Bulusu KC, Veres DV. Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors. NPJ Syst Biol Appl 2024; 10:68. [PMID: 38906870 PMCID: PMC11192759 DOI: 10.1038/s41540-024-00394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Combination therapy is well established as a key intervention strategy for cancer treatment, with the potential to overcome monotherapy resistance and deliver a more durable efficacy. However, given the scale of unexplored potential target space and the resulting combinatorial explosion, identifying efficacious drug combinations is a critical unmet need that is still evolving. In this paper, we demonstrate a network biology-driven, simulation-based solution, the Simulated Cell™. Integration of omics data with a curated signaling network enables the accurate and interpretable prediction of 66,348 combination-cell line pairs obtained from a large-scale combinatorial drug sensitivity screen of 684 combinations across 97 cancer cell lines (BAC = 0.62, AUC = 0.7). We highlight drug combination pairs that interact with DNA Damage Response pathways and are predicted to be synergistic, and deep network insight to identify biomarkers driving combination synergy. We demonstrate that the cancer cell 'avatars' capture the biological complexity of their in vitro counterparts, enabling the identification of pathway-level mechanisms of combination benefit to guide clinical translatability.
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Affiliation(s)
- Orsolya Papp
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | | | | | - Róbert Balázs
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Valér Kaszás
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Árpád Bartha
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Nóra N Ordasi
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | | | - Bálint Farkas
- Turbine Simulated Cell Technologies, Budapest, Hungary
| | - Jay Mettetal
- Oncology Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Jonathan R Dry
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Waltham, MA, USA
| | - Duncan Young
- Search and Evaluation, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ben Sidders
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Krishna C Bulusu
- Early Data Science, Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
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Yokoyama A, Niida H, Kutateladze TG, Côté J. HBO1, a MYSTerious KAT and its links to cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195045. [PMID: 38851533 DOI: 10.1016/j.bbagrm.2024.195045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
The histone acetyltransferase HBO1, also known as KAT7, is a major chromatin modifying enzyme responsible for H3 and H4 acetylation. It is found within two distinct tetrameric complexes, the JADE subunit-containing complex and BRPF subunit-containing complex. The HBO1-JADE complex acetylates lysine 5, 8 and 12 of histone H4, and the HBO1-BRPF complex acetylates lysine 14 of histone H3. HBO1 regulates gene transcription, DNA replication, DNA damage repair, and centromere function. It is involved in diverse signaling pathways and plays crucial roles in development and stem cell biology. Recent work has established a strong relationship of HBO1 with the histone methyltransferase MLL/KMT2A in acute myeloid leukemia. Here, we discuss functional and pathological links of HBO1 to cancer, highlighting the underlying mechanisms that may pave the way to the development of novel anti-cancer therapies.
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Affiliation(s)
- Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan.
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, United States of America.
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division-CHU de Québec-UL Research Center, Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada.
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3
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Gaurav N, Kanai A, Lachance C, Cox KL, Liu J, Grzybowski AT, Saksouk N, Klein BJ, Komata Y, Asada S, Ruthenburg AJ, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. Guiding the HBO1 complex function through the JADE subunit. Nat Struct Mol Biol 2024:10.1038/s41594-024-01245-2. [PMID: 38448574 DOI: 10.1038/s41594-024-01245-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024]
Abstract
JADE is a core subunit of the HBO1 acetyltransferase complex that regulates developmental and epigenetic programs and promotes gene transcription. Here we describe the mechanism by which JADE facilitates recruitment of the HBO1 complex to chromatin and mediates its enzymatic activity. Structural, genomic and complex assembly in vivo studies show that the PZP (PHD1-zinc-knuckle-PHD2) domain of JADE engages the nucleosome through binding to histone H3 and DNA and is necessary for the association with chromatin targets. Recognition of unmethylated H3K4 by PZP directs enzymatic activity of the complex toward histone H4 acetylation, whereas H3K4 hypermethylation alters histone substrate selectivity. We demonstrate that PZP contributes to leukemogenesis, augmenting transforming activity of the NUP98-JADE2 fusion. Our findings highlight biological consequences and the impact of the intact JADE subunit on genomic recruitment, enzymatic function and pathological activity of the HBO1 complex.
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Affiliation(s)
- Nitika Gaurav
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH, USA
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Adrian T Grzybowski
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Nehmé Saksouk
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan
| | - Shuhei Asada
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | | | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada.
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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4
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Sulzbach Denardin M, Bumiller-Bini Hoch V, Salviano-Silva A, Lobo-Alves SC, Adelman Cipolla G, Malheiros D, Augusto DG, Wittig M, Franke A, Pföhler C, Worm M, van Beek N, Goebeler M, Sárdy M, Ibrahim S, Busch H, Schmidt E, Hundt JE, Petzl-Erler ML, Beate Winter Boldt A. Genetic Association and Differential RNA Expression of Histone (De)Acetylation-Related Genes in Pemphigus Foliaceus-A Possible Epigenetic Effect in the Autoimmune Response. Life (Basel) 2023; 14:60. [PMID: 38255677 PMCID: PMC10821360 DOI: 10.3390/life14010060] [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: 11/28/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Pemphigus foliaceus (PF) is an autoimmune skin blistering disease characterized by antidesmoglein-1 IgG production, with an endemic form (EPF) in Brazil. Genetic and epigenetic factors have been associated with EPF, but its etiology is still not fully understood. To evaluate the genetic association of histone (de)acetylation-related genes with EPF susceptibility, we evaluated 785 polymorphisms from 144 genes, for 227 EPF patients and 194 controls. Carriers of HDAC4_rs4852054*A were more susceptible (OR = 1.79, p = 0.0038), whereas those with GSE1_rs13339618*A (OR = 0.57, p = 0.0011) and homozygotes for PHF21A_rs4756055*A (OR = 0.39, p = 0.0006) were less susceptible to EPF. These variants were not associated with sporadic PF (SPF) in German samples of 75 SPF patients and 150 controls, possibly reflecting differences in SPF and EPF pathophysiology. We further evaluated the expression of histone (de)acetylation-related genes in CD4+ T lymphocytes, using RNAseq. In these cells, we found a higher expression of KAT2B, PHF20, and ZEB2 and lower expression of KAT14 and JAD1 in patients with active EPF without treatment compared to controls from endemic regions. The encoded proteins cause epigenetic modifications related to immune cell differentiation and cell death, possibly affecting the immune response in patients with PF.
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Affiliation(s)
- Maiara Sulzbach Denardin
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
| | - Valéria Bumiller-Bini Hoch
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Amanda Salviano-Silva
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Sara Cristina Lobo-Alves
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Research Institut Pelé Pequeno Príncipe, Curitiba 80250-060, Brazil
| | - Gabriel Adelman Cipolla
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
| | - Danielle Malheiros
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Danillo G. Augusto
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Michael Wittig
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (M.W.); (A.F.)
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (M.W.); (A.F.)
| | - Claudia Pföhler
- Department of Dermatology, Saarland University Medical Center, 66421 Homburg, Germany;
| | - Margitta Worm
- Division of Allergy and Immunology, Department of Dermatology, Venerology and Allergy, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Nina van Beek
- Department of Dermatology, University of Lübeck, 23562 Lübeck, Germany; (N.v.B.); (E.S.)
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Miklós Sárdy
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80539 Munich, Germany;
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
| | - Saleh Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Enno Schmidt
- Department of Dermatology, University of Lübeck, 23562 Lübeck, Germany; (N.v.B.); (E.S.)
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Jennifer Elisabeth Hundt
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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Mah SY, Vanyai HK, Yang Y, Voss AK, Thomas T. The chromatin reader protein ING5 is required for normal hematopoietic cell numbers in the fetal liver. Front Immunol 2023; 14:1119750. [PMID: 37275850 PMCID: PMC10232820 DOI: 10.3389/fimmu.2023.1119750] [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: 12/09/2022] [Accepted: 04/18/2023] [Indexed: 06/07/2023] Open
Abstract
ING5 is a component of KAT6A and KAT7 histone lysine acetylation protein complexes. ING5 contains a PHD domain that binds to histone H3 lysine 4 when it is trimethylated, and so functions as a 'reader' and adaptor protein. KAT6A and KAT7 function are critical for normal hematopoiesis. To examine the function of ING5 in hematopoiesis, we generated a null allele of Ing5. Mice lacking ING5 during development had decreased foetal liver cellularity, decreased numbers of hematopoietic stem cells and perturbed erythropoiesis compared to wild-type control mice. Ing5-/- pups had hypoplastic spleens. Competitive transplantation experiments using foetal liver hematopoietic cells showed that there was no defect in long-term repopulating capacity of stem cells lacking ING5, suggesting that the defects during the foetal stage were not cell intrinsic. Together, these results suggest that ING5 function is dispensable for normal hematopoiesis but may be required for timely foetal hematopoiesis in a cell-extrinsic manner.
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Affiliation(s)
- Sophia Y.Y. Mah
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Hannah K. Vanyai
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Yuqing Yang
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Anne K. Voss
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tim Thomas
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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Ma Y, Chen X, Ding T, Zhang H, Zhang Q, Dai H, Zhang H, Tang J, Wang X. KAT7 promotes radioresistance through upregulating PI3K/AKT signaling in breast cancer. JOURNAL OF RADIATION RESEARCH 2023; 64:448-456. [PMID: 36724120 PMCID: PMC10036104 DOI: 10.1093/jrr/rrac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/03/2022] [Indexed: 05/27/2023]
Abstract
Chromatin-modifying enzymes are commonly altered in cancers, but the molecular mechanism by which they regulate cancers remains poorly understood. Herein, we demonstrated that Lysine acetyltransferase 7 (KAT7) was upregulated in breast cancer. KAT7 expression negatively correlated with the survival of breast cancer patients, and KAT7 silencing suppressed breast cancer radioresistance in vitro. Mechanistically, KAT7 activated Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) transcription, leading to enhanced PI3K/AKT signaling and radioresistance. Overexpression of AKT or PIK3CA restored radioresistance suppression induced by KAT7 inhibition. Moreover, overexpression of KAT7, but not KAT7 acetyltransferase activity-deficient mutants promoted AKT phosphorylation at the Ser473 site, PIK3CA expression and radioresistance suppression due to KAT7 inhibition. In conclusion, KAT7 has huge prospects for clinical application as a new target for predicting radioresistance in breast cancer patients.
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Affiliation(s)
| | | | | | - Hanqun Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, 730000, P. R. China
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, P.R. China
| | - Qiuning Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, P.R. China
- Lanzhou Heavy Ion Hospital, Lanzhou, Gansu, 730000, P.R. China
| | - Huanyu Dai
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu, 730000, P. R. China
| | - Haibo Zhang
- Oncology Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, 310014, P. R. China
| | - Jianming Tang
- Department of Radiation Oncology, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu, 730000, P. R. China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, Gansu, 730000, P. R. China
| | - Xiaohu Wang
- Corresponding author. The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, 730000, P. R. China. Tel: +8613909407551; E-mail:
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8
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Atypical histone targets of PHD fingers. J Biol Chem 2023; 299:104601. [PMID: 36907441 PMCID: PMC10124903 DOI: 10.1016/j.jbc.2023.104601] [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: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Plant homeodomain (PHD) fingers are structurally conserved zinc fingers that selectively bind unmodified or methylated at lysine 4 histone H3 tails. This binding stabilizes transcription factors and chromatin-modifying proteins at specific genomic sites, which is required for vital cellular processes, including gene expression and DNA repair. Several PHD fingers have recently been shown to recognize other regions of H3 or histone H4. In this review, we detail molecular mechanisms and structural features of the non-canonical histone recognition, discuss biological implications of the atypical interactions, highlight therapeutic potential of PHD fingers, and compare inhibition strategies.
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9
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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10
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Torres T, Barros S, Neuparth T, Ruivo R, Santos MM. Using zebrafish embryo bioassays to identify chemicals modulating the regulation of the epigenome: a case study with simvastatin. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:22913-22928. [PMID: 36307569 DOI: 10.1007/s11356-022-23683-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Contaminants of emerging concern have been increasingly associated with the modulation of the epigenome, leading to potentially inherited and persistent impacts on apical endpoints. Here, we address the performance of the OECD Test No. 236 FET (fish embryo acute toxicity) in the identification of chemicals able to modulate the epigenome. Using zebrafish (Danio rerio) embryos, acute and chronic exposures were performed with the pharmaceutical, simvastatin (SIM), a widely prescribed hypocholesterolemic drug reported to induce inter and transgenerational effects. In the present study, the epigenetic effects of environmentally relevant concentrations of SIM (from 8 ng/L to 2000 ng/L) were addressed following (1) an acute embryo assay based on OECD Test No. 236 FET, (2) a chronic partial life-cycle exposure using adult zebrafish (90 days), and (3) F1 embryos obtained from parental exposed animals. Simvastatin induced significant effects in gene expression of key epigenetic biomarkers (DNA methylation and histone acetylation/deacetylation) in the gonads of exposed adult zebrafish and in 80 hpf zebrafish embryos (acute and chronic parental intergenerational exposure), albeit with distinct effect profiles between biological samples. In the chronic exposure, SIM impacted particularly DNA methyltransferase genes in males and female gonads, whereas in F1 embryos SIM affected mostly genes associated with histone acetylation/deacetylation. In the embryo acute direct exposure, SIM modulated the expression of both genes involved in DNA methylation and histone deacetylase. These findings further support the use of epigenetic biomarkers in zebrafish embryos in a high throughput approach to identify and prioritize epigenome-modulating chemicals.
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Affiliation(s)
- Tiago Torres
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, 4169-007, Porto, Portugal
| | - Susana Barros
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Quinta de Prados, Ed. Blocos Laboratoriais C1.10, 5000-801, Vila Real, Portugal
| | - Teresa Neuparth
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
| | - Raquel Ruivo
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal.
| | - Miguel Machado Santos
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal.
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, 4169-007, Porto, Portugal.
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11
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Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7. Cell Rep 2023; 42:111980. [PMID: 36641753 DOI: 10.1016/j.celrep.2022.111980] [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: 02/25/2019] [Revised: 09/30/2022] [Accepted: 12/23/2022] [Indexed: 01/16/2023] Open
Abstract
In the conventional model of transcriptional activation, transcription factors bind to response elements and recruit co-factors, including histone acetyltransferases. Contrary to this model, we show that the histone acetyltransferase KAT7 (HBO1/MYST2) is required genome wide for histone H3 lysine 14 acetylation (H3K14ac). Examining neural stem cells, we find that KAT7 and H3K14ac are present not only at transcribed genes but also at inactive genes, intergenic regions, and in heterochromatin. KAT7 and H3K14ac were not required for the continued transcription of genes that were actively transcribed at the time of loss of KAT7 but indispensable for the activation of repressed genes. The absence of KAT7 abrogates neural stem cell plasticity, diverse differentiation pathways, and cerebral cortex development. Re-expression of KAT7 restored stem cell developmental potential. Overexpression of KAT7 enhanced neuron and oligodendrocyte differentiation. Our data suggest that KAT7 prepares chromatin for transcriptional activation and is a prerequisite for gene activation.
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12
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Viita T, Côté J. The MOZ-BRPF1 acetyltransferase complex in epigenetic crosstalk linked to gene regulation, development, and human diseases. Front Cell Dev Biol 2023; 10:1115903. [PMID: 36712963 PMCID: PMC9873972 DOI: 10.3389/fcell.2022.1115903] [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: 12/04/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Acetylation of lysine residues on histone tails is an important post-translational modification (PTM) that regulates chromatin dynamics to allow gene transcription as well as DNA replication and repair. Histone acetyltransferases (HATs) are often found in large multi-subunit complexes and can also modify specific lysine residues in non-histone substrates. Interestingly, the presence of various histone PTM recognizing domains (reader domains) in these complexes ensures their specific localization, enabling the epigenetic crosstalk and context-specific activity. In this review, we will cover the biochemical and functional properties of the MOZ-BRPF1 acetyltransferase complex, underlining its role in normal biological processes as well as in disease progression. We will discuss how epigenetic reader domains within the MOZ-BRPF1 complex affect its chromatin localization and the histone acetyltransferase specificity of the complex. We will also summarize how MOZ-BRPF1 is linked to development via controlling cell stemness and how mutations or changes in expression levels of MOZ/BRPF1 can lead to developmental disorders or cancer. As a last touch, we will review the latest drug candidates for these two proteins and discuss the therapeutic possibilities.
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13
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Lu PYT, Kirlin AC, Aristizabal MJ, Brewis HT, Lévesque N, Setiaputra DT, Avvakumov N, Benschop JJ, Groot Koerkamp M, Holstege FCP, Krogan NJ, Yip CK, Côté J, Kobor MS. A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans. Genetics 2022; 222:iyac136. [PMID: 36066422 PMCID: PMC9630986 DOI: 10.1093/genetics/iyac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 lysine acetyltransferase complex acetylates histone and nonhistone proteins and functions in transcription regulation, cell cycle progression, and DNA repair. NuA4 harbors an interesting duality in that its catalytic module can function independently and distinctly as picNuA4. At the molecular level, picNuA4 anchors to its bigger brother via physical interactions between the C-terminus of Epl1 and the HSA domain of Eaf1, the NuA4 central scaffolding subunit. This is reflected at the regulatory level, as picNuA4 can be liberated genetically from NuA4 by disrupting the Epl1-Eaf1 interaction. As such, removal of either Eaf1 or the Epl1 C-terminus offers a unique opportunity to elucidate the contributions of Eaf1 and Epl1 to NuA4 biology and in turn their roles in balancing picNuA4 and NuA4 activities. Using high-throughput genetic and gene expression profiling, and targeted functional assays to compare eaf1Δ and epl1-CΔ mutants, we found that EAF1 and EPL1 had both overlapping and distinct roles. Strikingly, loss of EAF1 or its HSA domain led to a significant decrease in the amount of picNuA4, while loss of the Epl1 C-terminus increased picNuA4 levels, suggesting starkly opposing effects on picNuA4 regulation. The eaf1Δ epl1-CΔ double mutants resembled the epl1-CΔ single mutants, indicating that Eaf1's role in picNuA4 regulation depended on the Epl1 C-terminus. Key aspects of this regulation were evolutionarily conserved, as truncating an Epl1 homolog in human cells increased the levels of other picNuA4 subunits. Our findings suggested a model in which distinct aspects of the Epl1-Eaf1 interaction regulated picNuA4 amount and activity.
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Affiliation(s)
- Phoebe Y T Lu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Alyssa C Kirlin
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hilary T Brewis
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nancy Lévesque
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Dheva T Setiaputra
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikita Avvakumov
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Joris J Benschop
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | | | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, The Netherlands
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacques Côté
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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14
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Zandian M, Jang SM, Lachance C, Acharya A, Byrareddy SN, Côté J, Kutateladze TG. Characterization of multiple interactions between the envelope E protein of SARS-CoV-2 and human BRD4. STAR Protoc 2022; 3:101853. [PMID: 36595918 PMCID: PMC9613806 DOI: 10.1016/j.xpro.2022.101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022] Open
Abstract
The SARS-CoV-2 envelope (E) protein hijacks human BRD4 (bromodomain and extra-terminal domain protein 4). Here, we describe a protocol to characterize the interaction of the acetylated E protein with BRD4 in vivo. We detail steps to use NMR spectroscopy to map the binding interface and include steps to monitor the effect of BRD4 inhibitors in SARS-CoV-2-infected human lung bronchial epithelial cells. This approach could be applied to study interactions involving other viral and human proteins. For complete details on the use and execution of this protocol, please refer to Vann et al. (2022).1.
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Affiliation(s)
- Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA,Corresponding author
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada.
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA,Corresponding author
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15
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Barman S, Roy A, Padhan J, Sudhamalla B. Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain. Biochemistry 2022; 61:1774-1789. [PMID: 35976792 DOI: 10.1021/acs.biochem.2c00297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HBO1 [HAT bound to the origin recognition complex (ORC)], a member of the MYST family of histone acetyltransferases (HATs), was initially identified as a binding partner of ORC that acetylates free histone H3, H4, and nucleosomal H3. It functions as a quaternary complex with the BRPF (BRPF1/2/3) scaffolding protein and two accessory proteins, ING4/5 and Eaf6. Interaction of BRPF2 with HBO1 has been shown to be important for regulating H3K14 acetylation during embryonic development. However, how BRPF2 directs the HBO1 HAT complex to chromatin to regulate its HAT activity toward nucleosomal substrates remains unclear. Our findings reveal novel interacting partners of the BRPF2 bromodomain that recognizes different acetyllysine residues on the N-terminus of histone H4, H3, and H2A and preferentially binds to H4K5ac, H4K8ac, and H4K5acK12ac modifications. In addition, mutational analysis of the BRPF2 bromodomain coupled with isothermal titration calorimetry binding and pull-down assays on the histone substrates identified critical residues responsible for acetyllysine binding. Moreover, the BRPF2 bromodomain could enrich H4K5ac mark-bearing mononucleosomes compared to other acetylated H4 marks. Consistent with this, ChIP-seq analysis revealed that BRPF2 strongly co-localizes with HBO1 at histone H4K5ac and H4K8ac marks near the transcription start sites in the genome. Our study provides novel insights into how the histone binding function of the BRPF2 bromodomain directs the recruitment of the HBO1 HAT complex to chromatin to regulate gene expression.
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Affiliation(s)
- Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, West Bengal 741246, India
| | - Anirban Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, West Bengal 741246, India
| | - Jyotirmayee Padhan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, West Bengal 741246, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, West Bengal 741246, India
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16
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Devoucoux M, Fort V, Khelifi G, Xu J, Alerasool N, Galloy M, Wong N, Bourriquen G, Fradet-Turcotte A, Taipale M, Hope K, Hussein SMI, Côté J. Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active genes. Cell Rep 2022; 39:110947. [PMID: 35705031 DOI: 10.1016/j.celrep.2022.110947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 02/14/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022] Open
Abstract
A recurrent chromosomal translocation found in acute myeloid leukemia leads to an in-frame fusion of the transcription repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase complex. To understand the abnormal molecular events that ZMYND11-MBTD1 expression can create, we perform a biochemical and functional characterization comparison to each individual fusion partner. ZMYND11-MBTD1 is stably incorporated into the endogenous NuA4/TIP60 complex, leading to its mislocalization on the body of genes normally bound by ZMYND11. This can be correlated to increased chromatin acetylation and altered gene transcription, most notably on the MYC oncogene, and alternative splicing. Importantly, ZMYND11-MBTD1 expression favors Myc-driven pluripotency during embryonic stem cell differentiation and self-renewal of hematopoietic stem/progenitor cells. Altogether, these results indicate that the ZMYND11-MBTD1 fusion functions primarily by mistargeting the NuA4/TIP60 complex to the body of genes, altering normal transcription of specific genes, likely driving oncogenesis in part through the Myc regulatory network.
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Affiliation(s)
- Maëva Devoucoux
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Victoire Fort
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Gabriel Khelifi
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Joshua Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto ON, Canada
| | - Maxime Galloy
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Nicholas Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gaëlle Bourriquen
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Amelie Fradet-Turcotte
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto ON, Canada
| | - Kristin Hope
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Samer M I Hussein
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada.
| | - Jacques Côté
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada.
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17
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Cenik BK, Sze CC, Ryan CA, Das S, Cao K, Douillet D, Rendleman EJ, Zha D, Khan NH, Bartom E, Shilatifard A. A synthetic lethality screen reveals ING5 as a genetic dependency of catalytically dead Set1A/COMPASS in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2022; 119:e2118385119. [PMID: 35500115 PMCID: PMC9171609 DOI: 10.1073/pnas.2118385119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Embryonic stem cells (ESCs) are defined by their ability to self-renew and the potential to differentiate into all tissues of the developing organism. We previously demonstrated that deleting the catalytic SET domain of the Set1A/complex of proteins associated with SET1 histone methyltransferase (Set1A/COMPASS) in mouse ESCs does not impair their viability or ability to self-renew; however, it leads to defects in differentiation. The precise mechanisms by which Set1A executes these functions remain to be elucidated. In this study, we demonstrate that mice lacking the SET domain of Set1A are embryonic lethal at a stage that is unique from null alleles. To gain insight into Set1A function in regulating pluripotency, we conducted a CRISPR/Cas9-mediated dropout screen and identified the MOZ/MORF (monocytic leukaemia zinc finger protein/monocytic leukaemia zinc finger protein-related factor) and HBO1 (HAT bound to ORC1) acetyltransferase complex member ING5 as a synthetic perturbation to Set1A. The loss of Ing5 in Set1AΔSET mouse ESCs decreases the fitness of these cells, and the simultaneous loss of ING5 and in Set1AΔSET leads to up-regulation of differentiation-associated genes. Taken together, our results point toward Set1A/COMPASS and ING5 as potential coregulators of the self-renewal and differentiation status of ESCs.
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Affiliation(s)
- Bercin K. Cenik
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Christie C. Sze
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Caila A. Ryan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Kaixiang Cao
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Delphine Douillet
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Emily J. Rendleman
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Nabiha Haleema Khan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Elizabeth Bartom
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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18
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Yang Y, Kueh AJ, Grant ZL, Abeysekera W, Garnham AL, Wilcox S, Hyland CD, Di Rago L, Metcalf D, Alexander WS, Coultas L, Smyth GK, Voss AK, Thomas T. The histone lysine acetyltransferase HBO1 (KAT7) regulates hematopoietic stem cell quiescence and self-renewal. Blood 2022; 139:845-858. [PMID: 34724565 DOI: 10.1182/blood.2021013954] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/13/2021] [Indexed: 11/20/2022] Open
Abstract
The histone acetyltransferase HBO1 (MYST2, KAT7) is indispensable for postgastrulation development, histone H3 lysine 14 acetylation (H3K14Ac), and the expression of embryonic patterning genes. In this study, we report the role of HBO1 in regulating hematopoietic stem cell function in adult hematopoiesis. We used 2 complementary cre-recombinase transgenes to conditionally delete Hbo1 (Mx1-Cre and Rosa26-CreERT2). Hbo1-null mice became moribund due to hematopoietic failure with pancytopenia in the blood and bone marrow 2 to 6 weeks after Hbo1 deletion. Hbo1-deleted bone marrow cells failed to repopulate hemoablated recipients in competitive transplantation experiments. Hbo1 deletion caused a rapid loss of hematopoietic progenitors. The numbers of lineage-restricted progenitors for the erythroid, myeloid, B-, and T-cell lineages were reduced. Loss of HBO1 resulted in an abnormally high rate of recruitment of quiescent hematopoietic stem cells (HSCs) into the cell cycle. Cycling HSCs produced progenitors at the expense of self-renewal, which led to the exhaustion of the HSC pool. Mechanistically, genes important for HSC functions were downregulated in HSC-enriched cell populations after Hbo1 deletion, including genes essential for HSC quiescence and self-renewal, such as Mpl, Tek(Tie-2), Gfi1b, Egr1, Tal1(Scl), Gata2, Erg, Pbx1, Meis1, and Hox9, as well as genes important for multipotent progenitor cells and lineage-specific progenitor cells, such as Gata1. HBO1 was required for H3K14Ac through the genome and particularly at gene loci required for HSC quiescence and self-renewal. Our data indicate that HBO1 promotes the expression of a transcription factor network essential for HSC maintenance and self-renewal in adult hematopoiesis.
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Affiliation(s)
- Yuqing Yang
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Andrew J Kueh
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Zoe L Grant
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Waruni Abeysekera
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Alexandra L Garnham
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Stephen Wilcox
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
| | - Craig D Hyland
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
| | - Ladina Di Rago
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
| | - Don Metcalf
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Warren S Alexander
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Leigh Coultas
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Gordon K Smyth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; and
- Department of Medical Biology and
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19
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Grant ZL, Hickey PF, Abeysekera W, Whitehead L, Lewis SM, Symons RCA, Baldwin TM, Amann-Zalcenstein D, Garnham AL, Smyth GK, Thomas T, Voss AK, Coultas L. The histone acetyltransferase HBO1 promotes efficient tip cell sprouting during angiogenesis. Development 2021; 148:272249. [PMID: 34550360 DOI: 10.1242/dev.199581] [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: 03/04/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022]
Abstract
Blood vessel growth and remodelling are essential during embryonic development and disease pathogenesis. The diversity of endothelial cells (ECs) is transcriptionally evident and ECs undergo dynamic changes in gene expression during vessel growth and remodelling. Here, we investigated the role of the histone acetyltransferase HBO1 (KAT7), which is important for activating genes during development and for histone H3 lysine 14 acetylation (H3K14ac). Loss of HBO1 and H3K14ac impaired developmental sprouting angiogenesis and reduced pathological EC overgrowth in the retinal endothelium. Single-cell RNA sequencing of retinal ECs revealed an increased abundance of tip cells in Hbo1-deficient retinas, which led to EC overcrowding in the retinal sprouting front and prevented efficient tip cell migration. We found that H3K14ac was highly abundant in the endothelial genome in both intra- and intergenic regions, suggesting that HBO1 acts as a genome organiser that promotes efficient tip cell behaviour necessary for sprouting angiogenesis. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Zoe L Grant
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Waruni Abeysekera
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sabrina M Lewis
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Robert C A Symons
- Department of Optometry and Vision Sciences, University of Melbourne, Parkville, 3010, Australia.,Department of Surgery, University of Melbourne, Parkville, 3010, Australia.,Department of Ophthalmology, Royal Melbourne Hospital, Parkville, 3050, Australia
| | - Tracey M Baldwin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Daniela Amann-Zalcenstein
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Leigh Coultas
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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20
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Takahashi S, Kanai A, Okuda H, Miyamoto R, Komata Y, Kawamura T, Matsui H, Inaba T, Takaori-Kondo A, Yokoyama A. HBO1-MLL interaction promotes AF4/ENL/P-TEFb-mediated leukemogenesis. eLife 2021; 10:e65872. [PMID: 34431785 PMCID: PMC8387021 DOI: 10.7554/elife.65872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/12/2021] [Indexed: 12/27/2022] Open
Abstract
Leukemic oncoproteins cause uncontrolled self-renewal of hematopoietic progenitors by aberrant gene activation, eventually causing leukemia. However, the molecular mechanism underlying aberrant gene activation remains elusive. Here, we showed that leukemic MLL fusion proteins associate with the HBO1 histone acetyltransferase (HAT) complex through their trithorax homology domain 2 (THD2) in various human cell lines. MLL proteins associated with the HBO1 complex through multiple contacts mediated mainly by the ING4/5 and PHF16 subunits in a chromatin-bound context where histone H3 lysine 4 tri-methylation marks were present. Of the many MLL fusions, MLL-ELL particularly depended on the THD2-mediated association with the HBO1 complex for leukemic transformation. The C-terminal portion of ELL provided a binding platform for multiple factors including AF4, EAF1, and p53. MLL-ELL activated gene expression in murine hematopoietic progenitors by loading an AF4/ENL/P-TEFb (AEP) complex onto the target promoters wherein the HBO1 complex promoted the association with AEP complex over EAF1 and p53. Moreover, the NUP98-HBO1 fusion protein exerted its oncogenic properties via interaction with MLL but not its intrinsic HAT activity. Thus, the interaction between the HBO1 complex and MLL is an important nexus in leukemic transformation, which may serve as a therapeutic target for drug development.
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Affiliation(s)
- Satoshi Takahashi
- Tsuruoka Metabolomics Laboratory, National Cancer CenterTsuruokaJapan
- Department of Hematology and Oncology, Kyoto University Graduate School of MedicineKyotoJapan
| | - Akinori Kanai
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
| | - Hiroshi Okuda
- Tsuruoka Metabolomics Laboratory, National Cancer CenterTsuruokaJapan
| | - Ryo Miyamoto
- Tsuruoka Metabolomics Laboratory, National Cancer CenterTsuruokaJapan
| | - Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer CenterTsuruokaJapan
| | | | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto UniversityKumamotoJapan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima UniversityHiroshimaJapan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Kyoto University Graduate School of MedicineKyotoJapan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer CenterTsuruokaJapan
- Department of Hematology and Oncology, Kyoto University Graduate School of MedicineKyotoJapan
- Division of Hematological Malignancy, National Cancer Center Research InstituteTokyoJapan
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21
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Xiao Y, Li W, Yang H, Pan L, Zhang L, Lu L, Chen J, Wei W, Ye J, Li J, Li G, Zhang Y, Tan M, Ding J, Wong J. HBO1 is a versatile histone acyltransferase critical for promoter histone acylations. Nucleic Acids Res 2021; 49:8037-8059. [PMID: 34259319 PMCID: PMC8661427 DOI: 10.1093/nar/gkab607] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
Recent studies demonstrate that histones are subjected to a series of short-chain fatty acid modifications that is known as histone acylations. However, the enzymes responsible for histone acylations in vivo are not well characterized. Here, we report that HBO1 is a versatile histone acyltransferase that catalyzes not only histone acetylation but also propionylation, butyrylation and crotonylation both in vivo and in vitro and does so in a JADE or BRPF family scaffold protein-dependent manner. We show that the minimal HBO1/BRPF2 complex can accommodate acetyl-CoA, propionyl-CoA, butyryl-CoA and crotonyl-CoA. Comparison of CBP and HBO1 reveals that they catalyze histone acylations at overlapping as well as distinct sites, with HBO1 being the key enzyme for H3K14 acylations. Genome-wide chromatin immunoprecipitation assay demonstrates that HBO1 is highly enriched at and contributes to bulk histone acylations on the transcriptional start sites of active transcribed genes. HBO1 promoter intensity highly correlates with the level of promoter histone acylation, but has no significant correlation with level of transcription. We also show that HBO1 is associated with a subset of DNA replication origins. Collectively our study establishes HBO1 as a versatile histone acyltransferase that links histone acylations to promoter acylations and selection of DNA replication origins.
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Affiliation(s)
- Yanhui Xiao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Joint Center for Translational Medicine, School of Life Sciences, East China Normal University and Fengxian District Central Hospital, Shanghai 201499, China
| | - Wenjing Li
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Yang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Lulu Pan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jie Ye
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Joint Center for Translational Medicine, School of Life Sciences, East China Normal University and Fengxian District Central Hospital, Shanghai 201499, China
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22
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Shatnawi A, Abu Rabe DI, Frigo DE. Roles of the tumor suppressor inhibitor of growth family member 4 (ING4) in cancer. Adv Cancer Res 2021; 152:225-262. [PMID: 34353439 DOI: 10.1016/bs.acr.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inhibitor of growth family member 4 (ING4) is best known as a tumor suppressor that is frequently downregulated, deleted, or mutated in many cancers. ING4 regulates a broad array of tumor-related processes including proliferation, apoptosis, migration, autophagy, invasion, angiogenesis, DNA repair and chromatin remodeling. ING4 alters local chromatin structure by functioning as an epigenetic reader of H3K4 trimethylation histone marks (H3K4Me3) and regulating gene transcription through directing histone acetyltransferase (HAT) and histone deacetylase (HDAC) protein complexes. ING4 may serve as a useful prognostic biomarker for many cancer types and help guide treatment decisions. This review provides an overview of ING4's central functions in gene expression and summarizes current literature on the role of ING4 in cancer and its possible use in therapy.
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Affiliation(s)
- Aymen Shatnawi
- Department of Pharmaceutical and Administrative Sciences, University of Charleston School of Pharmacy, Charleston, WV, United States.
| | - Dina I Abu Rabe
- Integrated Bioscience Program, North Carolina Central University, Durham, NC, United States
| | - Daniel E Frigo
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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23
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Klein BJ, Cox KL, Jang SM, Singh RK, Côté J, Poirier MG, Kutateladze TG. Structural and biophysical characterization of the nucleosome-binding PZP domain. STAR Protoc 2021; 2:100479. [PMID: 33982013 PMCID: PMC8082262 DOI: 10.1016/j.xpro.2021.100479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The core subunit of the MORF acetyltransferase complex BRPF1 contains a unique combination of zinc fingers, including a plant homeodomain (PHD) finger followed by a zinc knuckle and another PHD finger, which together form a PZP domain (BRPF1PZP). BRPF1PZP has been shown to bind to the nucleosome and make contacts with both histone H3 tail and DNA. Here, we describe biophysical and structural methods for characterization of the interactions between BRPF1PZP, H3 tail, DNA, and the intact nucleosome. For complete details on the use and execution of this protocol, please refer to Klein et al. (2020).
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Affiliation(s)
- Brianna J. Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Khan L. Cox
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center - Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Rohit K. Singh
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center - Oncology Division, Quebec City, QC G1R 3S3, Canada
| | | | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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24
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Liang Y, Su Y, Xu C, Zhang N, Liu D, Li G, Tong T, Chen J. Protein kinase D1 phosphorylation of KAT7 enhances its protein stability and promotes replication licensing and cell proliferation. Cell Death Discov 2020; 6:89. [PMID: 33014433 PMCID: PMC7501302 DOI: 10.1038/s41420-020-00323-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/09/2020] [Accepted: 09/02/2020] [Indexed: 01/24/2023] Open
Abstract
The histone acetyltransferase (HAT) KAT7/HBO1/MYST2 plays a crucial role in the pre-replication complex (pre-RC) formation, DNA replication and cell proliferation via acetylation of histone H4 and H3. In a search for protein kinase D1 (PKD1)-interacting proteins, we have identified KAT7 as a potential PKD1 substrate. We show that PKD1 directly interacts and phosphorylates KAT7 at Thr97 and Thr331 in vitro and in vivo. PKD1-mediated phosphorylation of KAT7 enhances its expression levels and stability by reducing its ubiquitination-mediated degradation. Significantly, the phospho-defective mutant KAT7-Thr97/331A attenuates histone H4 acetylation levels, MCM2/6 loading on the chromatin, DNA replication and cell proliferation. Similarly, PKD1 knockdown decreases, whereas the constitutive active mutant PKD1-CA increases histone H4 acetylation levels and MCM2/6 loading on the chromatin. Overall, these results suggest that PKD1-mediated phosphorylation of KAT7 may be required for pre-RC formation and DNA replication.
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Affiliation(s)
- Yao Liang
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Yuanyuan Su
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Chenzhong Xu
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Na Zhang
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Doudou Liu
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Guodong Li
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Tanjun Tong
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191 China
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25
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NUP98-HBO1-fusion generates phenotypically and genetically relevant chronic myelomonocytic leukemia pathogenesis. Blood Adv 2020; 3:1047-1060. [PMID: 30944097 DOI: 10.1182/bloodadvances.2018025007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 02/27/2019] [Indexed: 12/18/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) constitutes a hematopoietic stem cell (HSC) disorder characterized by prominent monocytosis and myelodysplasia. Although genome sequencing has revealed the CMML mutation profile, the mechanism of disease development remains unclear. Here we show that aberrant histone acetylation by nucleoporin-98 (NUP98)-HBO1, a newly identified fusion in a patient with CMML, is sufficient to generate clinically relevant CMML pathogenesis. Overexpression of NUP98-HBO1 in murine HSC/progenitors (HSC/Ps) induced diverse CMML phenotypes, such as severe leukocytosis, increased CD115+ Ly6Chigh monocytes (an equivalent subpopulation to human classical CD14+ CD16- monocytes), macrocytic anemia, thrombocytopenia, megakaryocyte-lineage dysplasia, splenomegaly, and cachexia. A NUP98-HBO1-mediated transcriptional signature in human CD34+ cells was specifically activated in HSC/Ps from a CMML patient cohort. Besides critical determinants of monocytic cell fate choice in HSC/Ps, an oncogenic HOXA9 signature was significantly activated by NUP98-HBO1 fusion through aberrant histone acetylation. Increased HOXA9 gene expression level with disease progression was confirmed in our CMML cohort. Genetic disruption of NUP98-HBO1 histone acetyltransferase activity abrogated its leukemogenic potential and disease development in human cells and a mouse model. Furthermore, treatment of azacytidine was effective in our CMML mice. The recapitulation of CMML clinical phenotypes and gene expression profile by the HBO1 fusion suggests our new model as a useful platform for elucidating the central downstream mediators underlying diverse CMML-related mutations and testing multiple compounds, providing novel therapeutic potential.
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26
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Macromolecular Crowding Increases the Affinity of the PHD of ING4 for the Histone H3K4me3 Mark. Biomolecules 2020; 10:biom10020234. [PMID: 32033221 PMCID: PMC7072245 DOI: 10.3390/biom10020234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The five members of the family of tumor suppressors ING contain a Plant Homeodomain (PHD) that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) with an affinity in the low micromolar range. Here, we use NMR to show that in the presence of 15% Ficoll 70, an inert macromolecular crowding agent, the mode of binding does not change but the affinity increases by one order of magnitude. The affinity increases also for unmethylated histone H3 tail, but the difference with H3K4me3 is larger in the presence of Ficoll. These results indicate that in the cellular milieu, the affinity of the ING proteins for their chromatin target is larger than previously thought.
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27
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Kueh AJ, Eccles S, Tang L, Garnham AL, May RE, Herold MJ, Smyth GK, Voss AK, Thomas T. HBO1 (KAT7) Does Not Have an Essential Role in Cell Proliferation, DNA Replication, or Histone 4 Acetylation in Human Cells. Mol Cell Biol 2020; 40:e00506-19. [PMID: 31767635 PMCID: PMC6996278 DOI: 10.1128/mcb.00506-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/11/2019] [Indexed: 01/01/2023] Open
Abstract
HBO1 (MYST2/KAT7) is essential for histone 3 lysine 14 acetylation (H3K14ac) but is dispensable for H4 acetylation and DNA replication in mouse tissues. In contrast, previous studies using small interfering RNA (siRNA) knockdown in human cell lines have suggested that HBO1 is essential for DNA replication. To determine if HBO1 has distinctly different roles in immortalized human cell lines and normal mouse cells, we performed siRNA knockdown of HBO1. In addition, we used CRISPR/Cas9 to generate 293T, MCF7, and HeLa cell lines lacking HBO1. Using both techniques, we show that HBO1 is essential for all H3K14ac in human cells and is unlikely to have a direct effect on H4 acetylation and only has minor effects on cell proliferation. Surprisingly, the loss of HBO1 and H3K14ac in HeLa cells led to the secondary loss of almost all H4 acetylation after 4 weeks. Thus, HBO1 is dispensable for DNA replication and cell proliferation in immortalized human cells. However, while cell proliferation proceeded without HBO1 and H3K14ac, HBO1 gene deletion led to profound changes in cell adhesion, particularly in 293T cells. Consistent with this phenotype, the loss of HBO1 in both 293T and HeLa principally affected genes mediating cell adhesion, with comparatively minor effects on other cellular processes.
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Affiliation(s)
- Andrew J Kueh
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Samantha Eccles
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Leonie Tang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexandra L Garnham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Rose E May
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Gordon K Smyth
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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28
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Chen L, Luo L, Kang N, He X, Li T, Chen Y. The Protective Effect of HBO1 on Cigarette Smoke Extract-Induced Apoptosis in Airway Epithelial Cells. Int J Chron Obstruct Pulmon Dis 2020; 15:15-24. [PMID: 32021140 PMCID: PMC6954103 DOI: 10.2147/copd.s234634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose Epigenetic modification is one of most important mechanisms underlying the pathogenesis of chronic obstructive pulmonary disease (COPD). The purpose of this study was to determine whether histone acetyltransferase binding to ORC1 (HBO1) can protect against cigarette smoke (CS)-induced cell apoptosis and sustain normal histone acetylation in COPD. Methods Human lung tissue samples were obtained from patients who underwent lung resection. The emphysema mouse model and HBO1 overexpressing mice were each established by intraperitoneal injection with cigarette smoke extract (CSE) or intratracheal lentiviral vectors instillation. TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) assays were used to assess apoptotic ratio in mice. The apoptosis of human bronchial epithelial cells (HBECs) was assayed by flow cytometry. HBO1, B-cell lymphoma-2 (BCL-2), and H3K14ac protein expression were detected by Western blotting. HBO1 mRNA expression was measured by quantitative real-time polymerase chain reaction. Results Protein expression of HBO1 was decreased significantly in lung tissue from COPD patients and CSE-treated emphysema mouse models. Overexpression of HBO1 attenuated CSE-induced emphysematous changes, as well as apoptosis in the lungs of COPD mice. In vitro, the HBO1 protein degraded in a time- and dose-dependent course with CSE treatment. With flow cytometry, we proved that HBO1 could reverse the apoptosis of HBECs induced by CSE. Furthermore, HBO1 overexpression promoted the expression of anti-apoptotic BCL-2 protein and enhanced H3K14 acetylation in airway epithelial cells. Conclusion These findings demonstrate that the key histone modulator HBO1 plays a protective role in COPD pathogenesis that may shed light on potential therapeutic targets to inhibit the progress of COPD.
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Affiliation(s)
- Lin Chen
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
| | - Lijuan Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
| | - Naixin Kang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
| | - Xue He
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
| | - Tiao Li
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
| | - Yan Chen
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People's Republic of China.,Research Unit of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China.,Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha 410011, Hunan, People's Republic of China
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29
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Espinosa-Cores L, Bouza-Morcillo L, Barrero-Gil J, Jiménez-Suárez V, Lázaro A, Piqueras R, Jarillo JA, Piñeiro M. Insights Into the Function of the NuA4 Complex in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:125. [PMID: 32153620 PMCID: PMC7047200 DOI: 10.3389/fpls.2020.00125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 05/14/2023]
Abstract
Chromatin remodeling plays a key role in the establishment and maintenance of gene expression patterns essential for plant development and responses to environmental factors. Post-translational modification of histones, including acetylation, is one of the most relevant chromatin remodeling mechanisms that operate in eukaryotic cells. Histone acetylation is an evolutionarily conserved chromatin signature commonly associated with transcriptional activation. Histone acetylation levels are tightly regulated through the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In plants, different families of HATs are present, including the MYST family, which comprises homologs of the catalytic subunit of the Nucleosome Acetyltransferase of H4 (NuA4) complex in yeast. This complex mediates acetylation of histones H4, H2A, and H2A.Z, and is involved in transcriptional regulation, heterochromatin silencing, cell cycle progression, and DNA repair in yeast. In Arabidopsis and, other plant species, homologs for most of the yeast NuA4 subunits are present and although the existence of this complex has not been demonstrated yet, compelling evidence supports the notion that this type of HAT complex functions from mosses to angiosperms. Recent proteomic studies show that several Arabidopsis homologs of NuA4 components, including the assembly platform proteins and the catalytic subunit, are associated in vivo with additional members of this complex suggesting that a NuA4-like HAT complex is present in plants. Furthermore, the functional characterization of some Arabidopsis NuA4 subunits has uncovered the involvement of these proteins in the regulation of different plant biological processes. Interestingly, for most of the mutant plants deficient in subunits of this complex characterized so far, conspicuous defects in flowering time are observed, suggesting a role for NuA4 in the control of this plant developmental program. Moreover, the participation of Arabidopsis NuA4 homologs in other developmental processes, such as gametophyte development, as well as in cell proliferation and stress and hormone responses, has also been reported. In this review, we summarize the current state of knowledge on plant putative NuA4 subunits and discuss the latest progress concerning the function of this chromatin modifying complex.
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30
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Trinh DA, Shirakawa R, Kimura T, Sakata N, Goto K, Horiuchi H. Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis. Sci Rep 2019; 9:17235. [PMID: 31754246 PMCID: PMC6872537 DOI: 10.1038/s41598-019-53767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/30/2019] [Indexed: 01/29/2023] Open
Abstract
Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.
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Affiliation(s)
- Duc-Anh Trinh
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan.,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kimura
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Research Center for Molecular Genetics, Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, Yamagata, Yamagata, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisanori Horiuchi
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan. .,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
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31
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Klein BJ, Cox KL, Jang SM, Côté J, Poirier MG, Kutateladze TG. Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin. Structure 2019; 28:105-110.e3. [PMID: 31711755 DOI: 10.1016/j.str.2019.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]
Abstract
The assembly of human histone acetyltransferase MOZ/MORF complexes relies on the scaffolding bromodomain plant homeodomain (PHD) finger 1 (BRPF1) subunit. The PHD-zinc-knuckle-PHD module of BRPF1 (BRPF1PZP) has been shown to associate with the histone H3 tail and DNA; however, the molecular mechanism underlying recognition of H3 and the relationship between the histone and DNA-binding activities remain unclear. In this study, we report the crystal structure of BRPF1PZP bound to the H3 tail and characterize the role of the bipartite interaction in the engagement of BRPF1PZP with the nucleosome core particle (NCP). We find that although both interactions of BRPF1PZP with the H3 tail and DNA are required for tight binding to NCP and for acetyltransferase function of the BRPF1-MORF-ING5-MEAF6 complex, binding to extranucleosomal DNA dominates. Our findings suggest that functionally active BRPF1PZP might be important in stabilization of the MOZ/MORF complexes at chromatin with accessible DNA.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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32
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Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, Thomas T, Garcia BA, Liu WR, Strahl BD, Kono H, Li W, Shi X, Côté J, Kutateladze TG. Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nat Commun 2019; 10:4724. [PMID: 31624313 PMCID: PMC6797804 DOI: 10.1038/s41467-019-12551-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Wenyi Mi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jie Lyu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shun Sakuraba
- Molecular Modeling and Simulation Group, National Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Wesley W Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Simone Sidoli
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Xiaolu Wang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Becka M Warfield
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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33
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Ormaza G, Rodríguez JA, Ibáñez de Opakua A, Merino N, Villate M, Gorroño I, Rábano M, Palmero I, Vilaseca M, Kypta R, Vivanco MDM, Rojas AL, Blanco FJ. The Tumor Suppressor ING5 Is a Dimeric, Bivalent Recognition Molecule of the Histone H3K4me3 Mark. J Mol Biol 2019; 431:2298-2319. [PMID: 31026448 DOI: 10.1016/j.jmb.2019.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
The INhibitor of Growth (ING) family of tumor suppressors regulates the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at lysine 4 (H3K4me3). This modification is recognized by the plant homeodomain (PHD) present at the C-terminus of the five ING proteins. ING5 facilitates histone H3 acetylation by the HBO1 complex, and also H4 acetylation by the MOZ/MORF complex. We show that ING5 forms homodimers through its N-terminal domain, which folds independently into an elongated coiled-coil structure. The central region of ING5, which contains the nuclear localization sequence, is flexible and disordered, but it binds dsDNA with micromolar affinity. NMR analysis of the full-length protein reveals that the two PHD fingers of the dimer are chemically equivalent and independent of the rest of the molecule, and they bind H3K4me3 in the same way as the isolated PHD. We have observed that ING5 can form heterodimers with the highly homologous ING4, and that two of three primary tumor-associated mutants in the N-terminal domain strongly destabilize the coiled-coil structure. They also affect cell proliferation and cell cycle phase distribution, suggesting a driver role in cancer progression.
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Affiliation(s)
- Georgina Ormaza
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Maider Villate
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Irantzu Gorroño
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Miriam Rábano
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Ignacio Palmero
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Robert Kypta
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | | | - Adriana L Rojas
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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34
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A chemical toolbox for the study of bromodomains and epigenetic signaling. Nat Commun 2019; 10:1915. [PMID: 31015424 PMCID: PMC6478789 DOI: 10.1038/s41467-019-09672-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
Bromodomains (BRDs) are conserved protein interaction modules which recognize (read) acetyl-lysine modifications, however their role(s) in regulating cellular states and their potential as targets for the development of targeted treatment strategies is poorly understood. Here we present a set of 25 chemical probes, selective small molecule inhibitors, covering 29 human bromodomain targets. We comprehensively evaluate the selectivity of this probe-set using BROMOscan and demonstrate the utility of the set identifying roles of BRDs in cellular processes and potential translational applications. For instance, we discovered crosstalk between histone acetylation and the glycolytic pathway resulting in a vulnerability of breast cancer cell lines under conditions of glucose deprivation or GLUT1 inhibition to inhibition of BRPF2/3 BRDs. This chemical probe-set will serve as a resource for future applications in the discovery of new physiological roles of bromodomain proteins in normal and disease states, and as a toolset for bromodomain target validation. Bromodomains are conserved protein interaction modules that recognize acetyl-lysine modifications. Here the authors present a set of 25 selective small molecule inhibitors covering 29 human bromodomain targets and comprehensively evaluate the selectivity of this probe-set.
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35
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Quintela M, Sieglaff DH, Gazze AS, Zhang A, Gonzalez D, Francis L, Webb P, Conlan RS. HBO1 directs histone H4 specific acetylation, potentiating mechano-transduction pathways and membrane elasticity in ovarian cancer cells. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 17:254-265. [DOI: 10.1016/j.nano.2019.01.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/15/2022]
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36
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Mouche A, Archambeau J, Ricordel C, Chaillot L, Bigot N, Guillaudeux T, Grenon M, Pedeux R. ING3 is required for ATM signaling and DNA repair in response to DNA double strand breaks. Cell Death Differ 2019; 26:2344-2357. [PMID: 30804473 DOI: 10.1038/s41418-019-0305-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 01/16/2023] Open
Abstract
Inhibitor of Growth 3 (ING3) is a candidate tumor suppressor gene whose expression is lost in tumors such as hepatocellular carcinoma, head and neck squamous cell carcinoma and melanoma. In the present study, we show that ING3-depleted human cells and yeast cells deleted for its ortholog YNG2 are sensitive to DNA damage suggesting a conserved role in response to such stress. In human cells, ING3 is recruited to DNA double strand breaks and is required for ATM activation. Remarkably, in response to doxorubicin, ATM activation is dependent on ING3 but not on TIP60, whose recruitment to DNA breaks also depends on ING3. These events lead to ATM-mediated phosphorylation of NBS1 and the subsequent recruitment of RNF8, RNF168, 53BP1, and BRCA1, which are major mediators of the DNA damage response. Accordingly, upon genotoxic stress, DNA repair by non-homologous end joining (NHEJ) or homologous recombination (HR) were impaired in absence of ING3. Finally, immunoglobulin class switch recombination (CSR), a physiological mechanism requiring NHEJ repair, was impaired in the absence of ING3. Since deregulation of DNA double strand break repair is associated with genomic instability, we propose a novel function of ING3 as a caretaker tumor suppressor involved in the DNA damage signaling and repair.
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Affiliation(s)
- Audrey Mouche
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France
| | - Jérôme Archambeau
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Charles Ricordel
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Laura Chaillot
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Nicolas Bigot
- Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Thierry Guillaudeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Muriel Grenon
- Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Rémy Pedeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France. .,Université de Rennes 1, Rennes, France.
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37
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The essential role of tumor suppressor gene ING4 in various human cancers and non-neoplastic disorders. Biosci Rep 2019; 39:BSR20180773. [PMID: 30643005 PMCID: PMC6356015 DOI: 10.1042/bsr20180773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/19/2018] [Accepted: 01/13/2019] [Indexed: 12/21/2022] Open
Abstract
Inhibitor of growth 4 (ING4), a member of the ING family discovered in 2003, has been shown to act as a tumor suppressor and is frequently down-regulated in various human cancers. Numerous published in vivo and in vitro studies have shown that ING4 is responsible for important cancer hallmarks such as pathologic cell cycle arrest, apoptosis, autophagy, contact inhibition, and hypoxic adaptation, and also affects tumor angiogenesis, invasion, and metastasis. These characteristics are typically associated with regulation through chromatin acetylation by binding histone H3 trimethylated at lysine 4 (H3K4me3) and through transcriptional activity of transcription factor P53 and NF-κB. In addition, emerging evidence has indicated that abnormalities in ING4 expression and function play key roles in non-neoplastic disorders. Here, we provide an overview of ING4-modulated chromosome remodeling and transcriptional function, as well as the functional consequences of different genetic variants. We also present the current understanding concerning the role of ING4 in the development of neoplastic and non-neoplastic diseases. These studies offer inspiration for pursuing novel therapeutics for various cancers.
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38
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Regulat-INGs in tumors and diseases: Focus on ncRNAs. Cancer Lett 2019; 447:66-74. [PMID: 30673590 DOI: 10.1016/j.canlet.2019.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/21/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022]
Abstract
ING family genes (Inhibitor of Growth) are tumor suppressor genes that play a vital role in cell homeostasis. It has been shown that their expression is lost or diminished in many cancers and other diseases. The main mechanisms by which they are regulated in oncogenesis have not yet been fully elucidated. The involvement of non-coding RNAs (ncRNAs) and in particular microRNAs (miRNAs) in post-transcriptional gene regulation is well established. miRNAs are short sequences (18-25 nucleotides) that can bind to the 3 'UTR sequence of the targeted messenger RNA (mRNA), leading to its degradation or translational repression. Interactions between the ING family and miRNAs have been described in some cancers but also in other diseases. The involvement of miRNAs in ING family regulation opens up new fields of investigation, particularly for targeted therapies. In this review, we will summarize the regulatory mechanisms at the RNA and protein level of the ING family and focus on the interactions with ncRNAs.
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39
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Ricketts MD, Han J, Szurgot MR, Marmorstein R. Molecular basis for chromatin assembly and modification by multiprotein complexes. Protein Sci 2018; 28:329-343. [PMID: 30350439 DOI: 10.1002/pro.3535] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 12/29/2022]
Abstract
Epigenetic regulation of the chromatin landscape is often orchestrated through modulation of nucleosomes. Nucleosomes are composed of two copies each of the four core histones, H2A, H2B, H3, and H4, wrapped in ~150 bp of DNA. We focus this review on recent structural studies that further elucidate the mechanisms used by macromolecular complexes to mediate histone modification and nucleosome assembly. Nucleosome assembly, spacing, and variant histone incorporation are coordinated by chromatin remodeler and histone chaperone complexes. Several recent structural studies highlight how disparate families of histone chaperones and chromatin remodelers share similar features that underlie how they interact with their respective histone or nucleosome substrates. Post-translational modification of histone residues is mediated by enzymatic subunits within large complexes. Until recently, relatively little was known about how association with auxiliary subunits serves to modulate the activity and specificity of the enzymatic subunit. Analysis of several recent structures highlights the different modes that auxiliary subunits use to influence enzymatic activity or direct specificity toward individual histone residues.
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Affiliation(s)
- M Daniel Ricketts
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Joseph Han
- Department of Chemistry Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Mary R Szurgot
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Department of Chemistry Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104
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40
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Voss AK, Thomas T. Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals. Bioessays 2018; 40:e1800078. [PMID: 30144132 DOI: 10.1002/bies.201800078] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/01/2018] [Indexed: 01/08/2023]
Abstract
Histone acetylation has been recognized as an important post-translational modification of core nucleosomal histones that changes access to the chromatin to allow gene transcription, DNA replication, and repair. Histone acetyltransferases were initially identified as co-activators that link DNA-binding transcription factors to the general transcriptional machinery. Over the years, more chromatin-binding modes have been discovered suggesting direct interaction of histone acetyltransferases and their protein complex partners with histone proteins. While much progress has been made in characterizing histone acetyltransferase complexes biochemically, cell-free activity assay results are often at odds with in-cell histone acetyltransferase activities. In-cell studies suggest specific histone lysine targets, but broad recruitment modes, apparently not relying on specific DNA sequences, but on chromatin of a specific functional state. Here we review the evidence for general versus specific roles of individual nuclear lysine acetyltransferases in light of in vivo and in vitro data in the mammalian system.
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Affiliation(s)
- Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 3 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
| | - Tim Thomas
- Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
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41
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Abstract
The temporal activation of kinases and timely ubiquitin-mediated degradation is central to faithful mitosis. Here we present evidence that acetylation controlled by Coenzyme A synthase (COASY) and acetyltransferase CBP constitutes a novel mechanism that ensures faithful mitosis. We found that COASY knockdown triggers prolonged mitosis and multinucleation. Acetylome analysis reveals that COASY inactivation leads to hyper-acetylation of proteins associated with mitosis, including CBP and an Aurora A kinase activator, TPX2. During early mitosis, a transient CBP-mediated TPX2 acetylation is associated with TPX2 accumulation and Aurora A activation. The recruitment of COASY inhibits CBP-mediated TPX2 acetylation, promoting TPX2 degradation for mitotic exit. Consistently, we detected a stage-specific COASY-CBP-TPX2 association during mitosis. Remarkably, pharmacological and genetic inactivation of CBP effectively rescued the mitotic defects caused by COASY knockdown. Together, our findings uncover a novel mitotic regulation wherein COASY and CBP coordinate an acetylation network to enforce productive mitosis.
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42
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Yan MS, Turgeon PJ, Man HSJ, Dubinsky MK, Ho JJD, El-Rass S, Wang YD, Wen XY, Marsden PA. Histone acetyltransferase 7 (KAT7)-dependent intragenic histone acetylation regulates endothelial cell gene regulation. J Biol Chem 2018; 293:4381-4402. [PMID: 29414790 DOI: 10.1074/jbc.ra117.001383] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/26/2018] [Indexed: 12/12/2022] Open
Abstract
Although the functional role of chromatin marks at promoters in mediating cell-restricted gene expression has been well characterized, the role of intragenic chromatin marks is not well understood, especially in endothelial cell (EC) gene expression. Here, we characterized the histone H3 and H4 acetylation profiles of 19 genes with EC-enriched expression via locus-wide chromatin immunoprecipitation followed by ultra-high-resolution (5 bp) tiling array analysis in ECs versus non-ECs throughout their genomic loci. Importantly, these genes exhibit differential EC enrichment of H3 and H4 acetylation in their promoter in ECs versus non-ECs. Interestingly, VEGFR-2 and VEGFR-1 show EC-enriched acetylation across broad intragenic regions and are up-regulated in non-ECs by histone deacetylase inhibition. It is unclear which histone acetyltransferases (KATs) are key to EC physiology. Depletion of KAT7 reduced VEGFR-2 expression and disrupted angiogenic potential. Microarray analysis of KAT7-depleted ECs identified 263 differentially regulated genes, many of which are key for growth and angiogenic potential. KAT7 inhibition in zebrafish embryos disrupted vessel formation and caused loss of circulatory integrity, especially hemorrhage, all of which were rescued with human KAT7. Notably, perturbed EC-enriched gene expression, especially the VEGFR-2 homologs, contributed to these vascular defects. Mechanistically, KAT7 participates in VEGFR-2 transcription by mediating RNA polymerase II binding, H3 lysine 14, and H4 acetylation in its intragenic region. Collectively, our findings support the importance of differential histone acetylation at both promoter and intragenic regions of EC genes and reveal a previously underappreciated role of KAT7 and intragenic histone acetylation in regulating VEGFR-2 and endothelial function.
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Affiliation(s)
- Matthew S Yan
- From the Departments of Medical Biophysics and.,Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Laboratory Medicine and Pathobiology
| | - Hon-Sum Jeffrey Man
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and
| | - Michelle K Dubinsky
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and
| | - J J David Ho
- the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 31336, and.,the Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida 31336
| | - Suzan El-Rass
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and
| | - You-Dong Wang
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and
| | - Xiao-Yan Wen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and
| | - Philip A Marsden
- From the Departments of Medical Biophysics and .,Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, and.,Institute of Medical Science, and.,Department of Medicine, University of Toronto, Toronto, Ontario M5B 1T8, Canada
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43
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Han J, Lachance C, Ricketts MD, McCullough CE, Gerace M, Black BE, Côté J, Marmorstein R. The scaffolding protein JADE1 physically links the acetyltransferase subunit HBO1 with its histone H3-H4 substrate. J Biol Chem 2018; 293:4498-4509. [PMID: 29382722 DOI: 10.1074/jbc.ra117.000677] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
The human enzyme histone acetyltransferase binding to ORC1 (HBO1) regulates DNA replication, cell proliferation, and development. HBO1 is part of a multiprotein histone acetyltransferase (HAT) complex that also contains inhibitor of growth family member (ING) 4/5, MYST/Esa1-associated factor (MEAF) 6, and the scaffolding proteins Jade family PHD finger (JADE) 1/2/3 or bromodomain and PHD finger-containing protein (BRPF) 2/3 to acetylate histone H4 H4K5/8/12 or H3K14, respectively. Within this four-protein complex, JADE1 determines histone H4 substrate specificity of the HBO1-HAT complex. However, the mechanism by which JADE1 controls the H4-specific acetyltransferase activity of HBO1 is unknown. Here we used recombinant proteins in vitro to dissect the specific regions and activities of HBO1 and JADE1 that mediate histone H3-H4 acetylation via the HBO1-HAT domain. We found that JADE1 increases the catalytic efficiency of HBO1 acetylation of an H3-H4 substrate by about 5-fold through an N-terminal, 21-residue HBO1- and histone-binding domain and a nearby second histone core-binding domain. We also demonstrate that HBO1 contains an N-terminal histone-binding domain (HBD) that makes additional contacts with H3-H4 independent of JADE1 interactions with histones and that the HBO1 HBD does not significantly contribute to HBO1's overall HAT activity. Experiments with JADE1 deletions in vivo recapitulated these in vitro interactions and their roles in HBO1 histone acetylation activity. Together, these results indicate that the N-terminal region of JADE1 functions as a platform that brings together the catalytic HBO1 subunit with its cognate H3-H4 substrate for histone acetylation.
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Affiliation(s)
- Joseph Han
- From the Department of Biochemistry and Biophysics.,Abramson Family Cancer Research Institute, and.,Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | - Catherine Lachance
- the Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Quebec G1R 3S3, Canada
| | - M Daniel Ricketts
- From the Department of Biochemistry and Biophysics.,Abramson Family Cancer Research Institute, and.,Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, and
| | - Cheryl E McCullough
- From the Department of Biochemistry and Biophysics.,Abramson Family Cancer Research Institute, and.,Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | | | - Ben E Black
- From the Department of Biochemistry and Biophysics
| | - Jacques Côté
- the Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Quebec G1R 3S3, Canada
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics, .,Abramson Family Cancer Research Institute, and.,Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
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44
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Tao Y, Zhong C, Zhu J, Xu S, Ding J. Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2. Nucleic Acids Res 2017; 45:5707-5719. [PMID: 28334966 PMCID: PMC5449618 DOI: 10.1093/nar/gkx142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
HBO1, a member of the MYST family of histone acetyltransferases (HATs), is required for global acetylation of histone H3K14 and embryonic development. It functions as a catalytic subunit in multisubunit complexes comprising a BRPF1/2/3 or JADE1/2/3 scaffold protein, and two accessory proteins. BRPF2 has been shown to be important for the HAT activity of HBO1 toward H3K14. Here we demonstrated that BRPF2 can regulate the HAT activity of HBO1 toward free H3 and H4, and nucleosomal H3. Particularly, a short N-terminal region of BRPF2 is sufficient for binding to HBO1 and can potentiate its activity toward H3K14. The crystal structure of the HBO1 MYST domain in complex with this segment of BRPF2 together with the biochemical and cell biological data revealed the key residues responsible for the HBO1–BRPF2 interaction. Our structural and functional data together indicate that the N-terminal region of BRPF2 plays an important role in the binding of HBO1 and a minor role in the binding of nucleosomes, which provide new mechanistic insights into the regulation of the HAT activity of HBO1 by BRPF2.
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Affiliation(s)
- Ye Tao
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Chen Zhong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Junjun Zhu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Shutong Xu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.,Shanghai Science Research Center, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Road, Shanghai 200438, China
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45
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Pardo M, Yu L, Shen S, Tate P, Bode D, Letney BL, Quelle DE, Skarnes W, Choudhary JS. Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells. Sci Rep 2017; 7:8157. [PMID: 28811661 PMCID: PMC5557939 DOI: 10.1038/s41598-017-08456-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/10/2017] [Indexed: 12/28/2022] Open
Abstract
MYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse embryonic stem cells by affinity purification coupled to mass spectrometry. This study confirms that in embryonic stem cells Myst2 is part of H3 and H4 histone acetylation complexes similar to those described in somatic cells. We identify a novel Myst2-associated protein, the tumour suppressor protein Niam (Nuclear Interactor of ARF and Mdm2). Human NIAM is involved in chromosome segregation, p53 regulation and cell proliferation in somatic cells, but its role in embryonic stem cells is unknown. We describe the first Niam embryonic stem cell interactome, which includes proteins with roles in DNA replication and repair, transcription, splicing and ribosome biogenesis. Many of Myst2 and Niam binding partners are required for correct embryonic development, implicating Myst2 and Niam in the cooperative regulation of this process and suggesting a novel role for Niam in embryonic biology. The data provides a useful resource for exploring Myst2 and Niam essential cellular functions and should contribute to deeper understanding of organism early development and survival as well as cancer. Data are available via ProteomeXchange with identifier PXD005987.
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Affiliation(s)
- Mercedes Pardo
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
| | - Lu Yu
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Shihpei Shen
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Cold Genesys Inc., Santa Ana, CA, USA
| | - Peri Tate
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Daniel Bode
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Wellcome Trust PhD Program, Cambridge Stem Cell Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Blake L Letney
- Departments of Pharmacology and Pathology, The University of Iowa and Holden Comprehensive Cancer Center, Iowa City, IA, 52242, USA
| | - Dawn E Quelle
- Departments of Pharmacology and Pathology, The University of Iowa and Holden Comprehensive Cancer Center, Iowa City, IA, 52242, USA
| | - William Skarnes
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jyoti S Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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46
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Wright DG, Marchal C, Hoang K, Ankney JA, Nguyen ST, Rushing AW, Polakowski N, Miotto B, Lemasson I. Human T-cell leukemia virus type-1-encoded protein HBZ represses p53 function by inhibiting the acetyltransferase activity of p300/CBP and HBO1. Oncotarget 2016; 7:1687-706. [PMID: 26625199 PMCID: PMC4811490 DOI: 10.18632/oncotarget.6424] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/15/2015] [Indexed: 01/31/2023] Open
Abstract
Adult T-cell leukemia (ATL) is an often fatal malignancy caused by infection with the complex retrovirus, human T-cell Leukemia Virus, type 1 (HTLV-1). In ATL patient samples, the tumor suppressor, p53, is infrequently mutated; however, it has been shown to be inactivated by the viral protein, Tax. Here, we show that another HTLV-1 protein, HBZ, represses p53 activity. In HCT116 p53+/+ cells treated with the DNA-damaging agent, etoposide, HBZ reduced p53-mediated activation of p21/CDKN1A and GADD45A expression, which was associated with a delay in G2 phase-arrest. These effects were attributed to direct inhibition of the histone acetyltransferase (HAT) activity of p300/CBP by HBZ, causing a reduction in p53 acetylation, which has be linked to decreased p53 activity. In addition, HBZ bound to, and inhibited the HAT activity of HBO1. Although HBO1 did not acetylate p53, it acted as a coactivator for p53 at the p21/CDKN1A promoter. Therefore, through interactions with two separate HAT proteins, HBZ impairs the ability of p53 to activate transcription. This mechanism may explain how p53 activity is restricted in ATL cells that do not express Tax due to modifications of the HTLV-1 provirus, which accounts for a majority of patient samples.
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Affiliation(s)
- Diana G Wright
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Claire Marchal
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France
| | - Kimson Hoang
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - John A Ankney
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie T Nguyen
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Amanda W Rushing
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Nicholas Polakowski
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Benoit Miotto
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France.,INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Lemasson
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
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47
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Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome. Mol Cell Biol 2016; 36:2768-2781. [PMID: 27550811 DOI: 10.1128/mcb.00112-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 08/17/2016] [Indexed: 12/12/2022] Open
Abstract
Recognition of histone marks by reader modules is thought to be at the heart of epigenetic mechanisms. These protein domains are considered to function by targeting regulators to chromosomal loci carrying specific histone modifications. This is important for proper gene regulation as well as propagation of epigenetic information. The NuA4 acetyltransferase complex contains two of these reader modules, an H3K4me3-specific plant homeodomain (PHD) within the Yng2 subunit and an H3K36me2/3-specific chromodomain in the Eaf3 subunit. While each domain showed a close functional interaction with the respective histone mark that it recognizes, at the biochemical level, genetic level (as assessed with epistatic miniarray profile screens), and phenotypic level, cells with the combined loss of both readers showed greatly enhanced phenotypes. Chromatin immunoprecipitation coupled with next-generation sequencing experiments demonstrated that the Yng2 PHD specifically directs H4 acetylation near the transcription start site of highly expressed genes, while Eaf3 is important downstream on the body of the genes. Strikingly, the recruitment of the NuA4 complex to these loci was not significantly affected. Furthermore, RNA polymerase II occupancy was decreased only under conditions where both PHD and chromodomains were lost, generally in the second half of the gene coding regions. Altogether, these results argue that methylated histone reader modules in NuA4 are not responsible for its recruitment to the promoter or coding regions but, rather, are required to orient its acetyltransferase catalytic site to the methylated histone 3-bearing nucleosomes in the surrounding chromatin, cooperating to allow proper transition from transcription initiation to elongation.
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48
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Guo LL, Yu SY, Li M. Functional analysis of HBO1 in tumor development and inhibitor screening. Int J Mol Med 2016; 38:300-4. [PMID: 27247147 DOI: 10.3892/ijmm.2016.2617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 04/21/2016] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to explore the functions of histone acetyltransferase binding to origin recog-nition complex (ORC) 1 (HBO1) during tumor development and to screen for HBO1 inhibitors. The chromatin immuno-precipitation sequencing (ChIP-seq) data of HBO1 in the RKO human colon cancer cell line (GSE33007) were downloaded from the Gene Expression Omnibus (GEO) database. The reads were then mapped back to a reference genome hg19. The PCR duplicate reads were removed by using SAMtools software and the shift was calculated using SPP and MaSC software. The peak calling was carried out using MACS 1.4.0 software. Furthermore, the inhibitors of HBO1 were screened out from the Specs database using Dock 6.6 software. The binding sites of HBO1 were mainly distributed in the intergenic, intronic and 3'-end regions. Further analysis revealed that a total of 9,467 target genes was identified around HBO1 binding sites in the RKO cell lines and those genes mainly participated in the cell cycle, biosynthetic process, as well as other processes. Finally, 5 inhibitors with best binding affinity in the positively charged cavity of HBO1 were screened out: i) 5-[(2-hydroxybenzylidene)amino] -2-(2‑{4‑[(2‑hydroxy-benzylidene)amino]-2-sulfonatophenyl}vinyl)benzenesulfonate, ii) 3-[4-(3-bromo-4-{2-[4-(ethoxycarbonyl)anilino]-2-oxo-ethoxy}-5-methoxybenzylidene)‑3‑methyl‑5‑oxo -4,5-dihydro-1H-pyrazol-1-yl]benzoic acid, iii) 4-(4-{3-iodo‑5‑ methoxy‑4-[2-(2-methoxyanilino)-2-oxoethoxy]benzylidene}-3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)benzoic acid, iv) 5-chloro-1,3-bis{[3,5,6-trihydroxy-4-(octyloxy)tetrahydro-2H-pyran-2-yl]methyl}-1,3-dihydro-2H-benzimidazol-2-one and v) 4-{[4-(tetradecylamino)-1-naphthyl]diazenyl}benzoic acid. As a whole, in this study, we identified the possible binding sites and biological functions of HBO1. The potential inhibitors of HBO1 were also screened, which prove to be helpful for the inhibition of HBO1 during tumor development.
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Affiliation(s)
- Ling-Li Guo
- Department of Colorectal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Su-Yang Yu
- Department of Colorectal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Meng Li
- Department of Colorectal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
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49
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Panchenko MV. Structure, function and regulation of jade family PHD finger 1 (JADE1). Gene 2016; 589:1-11. [PMID: 27155521 DOI: 10.1016/j.gene.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 12/24/2022]
Abstract
The family of JADE proteins includes three paralogues encoded by individual genes and designated PHF17 (JADE1), PHF16 (JADE2), and PHF15 (JADE3). All three JADE proteins bear in tandem two Plant Homeo-domains (PHD) which are zinc finger domains. This review focuses on one member of the JADE family, JADE1. Studies addressing the biochemical, cellular and biological role of JADE1 are discussed. Recent discoveries of JADE1 function in the regulation of the epithelial cell cycle with potential relevance to disease are presented. Unresolved questions and future directions are formulated.
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Affiliation(s)
- Maria V Panchenko
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, United States.
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50
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Zhang F, Zhang X, Meng J, Zhao Y, Liu X, Liu Y, Wang Y, Li Y, Sun Y, Wang Z, Mei Q, Zhang T. ING5 inhibits cancer aggressiveness via preventing EMT and is a potential prognostic biomarker for lung cancer. Oncotarget 2016; 6:16239-52. [PMID: 25938545 PMCID: PMC4599267 DOI: 10.18632/oncotarget.3842] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/20/2015] [Indexed: 11/25/2022] Open
Abstract
The proteins of the Inhibitor of Growth (ING) candidate tumor suppressor family are involved in multiple cellular functions such as cell cycle regulation, apoptosis, and chromatin remodeling. ING5 is the new member of the family whose actual role in tumor suppression is not known. Here we show that ING5 overexpression in lung cancer A549 cells inhibited cell proliferation and invasiveness, while ING5 knockdown in lung cancer H1299 cells promoted cell aggressiveness. ING5 overexpression also abrogated tumor growth and invasive abilities of lung cancer cells in mouse xenograft models. Further study showed that ING5 overexpression inhibited EMT indicated by increase of E-cadherin and decrease of N-cadherin, Snail and slug at mRNA and protein levels, which was accompanied with morphological changes. cDNA microarray and subsequent qRT-PCR validation revealed that ING5 significantly downregulated expression of EMT (epithelial to mesenchymal transition)-inducing genes including CEACAM6, BMP2 and CDH11. Clinical study by tissue microarray showed that nuclear ING5 negatively correlated with clinical stages and lymph node metastasis of lung cancer. Furthermore, high level of nuclear ING5 was associated with a better prognosis. Taken together, these findings uncover an important role for ING5 as a potent tumor suppressor in lung cancer growth and metastasis.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Xutao Zhang
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Jin Meng
- Department of Oncology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China.,Department of Pharmacy, No. 309 Hospital of PLA, Beijing, China
| | - Yong Zhao
- Laboratory Animal Center, Fourth Military Medical University, Xi'an, China
| | - Xinli Liu
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Yanxia Liu
- National Engineering Center for Biochip, Shanghai, China
| | - Yukun Wang
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Yuhua Li
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Yang Sun
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Zhipeng Wang
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Qibing Mei
- Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Tao Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
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