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Zohourian N, Coll E, Dever M, Sheahan A, Burns-Lane P, Brown JAL. Evaluating the Cellular Roles of the Lysine Acetyltransferase Tip60 in Cancer: A Multi-Action Molecular Target for Precision Oncology. Cancers (Basel) 2024; 16:2677. [PMID: 39123405 PMCID: PMC11312108 DOI: 10.3390/cancers16152677] [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: 06/06/2024] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Precision (individualized) medicine relies on the molecular profiling of tumors' dysregulated characteristics (genomic, epigenetic, transcriptomic) to identify the reliance on key pathways (including genome stability and epigenetic gene regulation) for viability or growth, and then utilises targeted therapeutics to disrupt these survival-dependent pathways. Non-mutational epigenetic changes alter cells' transcriptional profile and are a key feature found in many tumors. In contrast to genetic mutations, epigenetic changes are reversable, and restoring a normal epigenetic profile can inhibit tumor growth and progression. Lysine acetyltransferases (KATs or HATs) protect genome stability and integrity, and Tip60 is an essential acetyltransferase due to its roles as an epigenetic and transcriptional regulator, and as master regulator of the DNA double-strand break response. Tip60 is commonly downregulated and mislocalized in many cancers, and the roles that mislocalized Tip60 plays in cancer are not well understood. Here we categorize and discuss Tip60-regulated genes, evaluate Tip60-interacting proteins based on cellular localization, and explore the therapeutic potential of Tip60-targeting compounds as epigenetic inhibitors. Understanding the multiple roles Tip60 plays in tumorigenesis will improve our understanding of tumor progression and will inform therapeutic options, including informing potential combinatorial regimes with current chemotherapeutics, leading to improvements in patient outcomes.
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Affiliation(s)
- Nazanin Zohourian
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Erin Coll
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Muiread Dever
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Anna Sheahan
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - Petra Burns-Lane
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
| | - James A. L. Brown
- Department of Biological Science, University of Limerick, V94 T9PX Limerick, Ireland; (N.Z.)
- Limerick Digital Cancer Research Centre (LDCRC), Health Research Institute (HRI), University of Limerick, V94 T9PX Limerick, Ireland
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2
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Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601745. [PMID: 39005446 PMCID: PMC11244972 DOI: 10.1101/2024.07.02.601745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remains unclear. Here, we systematically identified enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We found that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further showed that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.
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Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Grossi E, Hasson D, Bernstein E. H2A.Z chaperones converge on E2F target genes for melanoma cell proliferation. Genes Dev 2024; 38:336-353. [PMID: 38744503 PMCID: PMC11146596 DOI: 10.1101/gad.351318.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes SRCAP and P400-TIP60 in melanoma remains unclear. Here, we show that individual subunit depletion of SRCAP, P400, and VPS72 (YL1) results in not only the loss of H2A.Z deposition into chromatin but also a reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is particularly found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
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Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Saul Carcamo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Bioinformatics for Next-Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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4
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Xuan F, Xuan H, Huang M, He W, Xu H, Shi X, Wen H. The Tudor-knot Domain of KAT5 Regulates Nucleosomal Substrate Acetylation. J Mol Biol 2024; 436:168414. [PMID: 38141874 PMCID: PMC10957329 DOI: 10.1016/j.jmb.2023.168414] [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: 10/21/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
The lysine acetyltransferase KAT5 is a pivotal enzyme responsible for catalyzing histone H4 acetylation in cells. In addition to its indispensable HAT domain, KAT5 also encompasses a conserved Tudor-knot domain at its N-terminus. However, the function of this domain remains elusive, with conflicting findings regarding its role as a histone reader. In our study, we have employed a CRISPR tiling array approach and unveiled the Tudor-knot motif as an essential domain for cell survival. The Tudor-knot domain does not bind to histone tails and is not required for KAT5's chromatin occupancy. However, its absence leads to a global reduction in histone acetylation, accompanied with genome-wide alterations in gene expression that consequently result in diminished cell viability. Mechanistically, we find that the Tudor-knot domain regulates KAT5's HAT activity on nucleosomes by fine-tuning substrate accessibility. In summary, our study uncovers the Tudor-knot motif as an essential domain for cell survival and reveals its critical role in modulating KAT5's catalytic efficiency on nucleosome and KAT5-dependent transcriptional programs critical for cell viability.
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Affiliation(s)
- Fan Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hongwen Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Mengying Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hong Wen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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5
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Aryal S, Lu R. HOXA9 Regulome and Pharmacological Interventions in Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:405-430. [PMID: 39017854 DOI: 10.1007/978-3-031-62731-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
HOXA9, an important transcription factor (TF) in hematopoiesis, is aberrantly expressed in numerous cases of both acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) and is a strong indicator of poor prognosis in patients. HOXA9 is a proto-oncogene which is both sufficient and necessary for leukemia transformation. HOXA9 expression in leukemia correlates with patient survival outcomes and response to therapy. Chromosomal transformations (such as NUP98-HOXA9), mutations, epigenetic dysregulation (e.g., MLL- MENIN -LEDGF complex or DOT1L/KMT4), transcription factors (such as USF1/USF2), and noncoding RNA (such as HOTTIP and HOTAIR) regulate HOXA9 mRNA and protein during leukemia. HOXA9 regulates survival, self-renewal, and progenitor cell cycle through several of its downstream target TFs including LMO2, antiapoptotic BCL2, SOX4, and receptor tyrosine kinase FLT3 and STAT5. This dynamic and multilayered HOXA9 regulome provides new therapeutic opportunities, including inhibitors targeting DOT1L/KMT4, MENIN, NPM1, and ENL proteins. Recent findings also suggest that HOXA9 maintains leukemia by actively repressing myeloid differentiation genes. This chapter summarizes the recent advances understanding biochemical mechanisms underlying HOXA9-mediated leukemogenesis, the clinical significance of its abnormal expression, and pharmacological approaches to treat HOXA9-driven leukemia.
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Affiliation(s)
- Sajesan Aryal
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
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6
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Jostes S, Vardabasso C, Dong J, Carcamo S, Singh R, Phelps R, Meadows A, Hasson D, Bernstein E. H2A.Z chaperones converge on histone H4 acetylation for melanoma cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568747. [PMID: 38076914 PMCID: PMC10705243 DOI: 10.1101/2023.11.26.568747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes, SRCAP and P400-TIP60, in melanoma remains unclear. Here, we show that individual depletion of SRCAP, P400, and VPS72 (YL1) not only results in loss of H2A.Z deposition into chromatin, but also a striking reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a highly coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
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Affiliation(s)
- Sina Jostes
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saul Carcamo
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Phelps
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Austin Meadows
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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7
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Hattori A, Takamatsu-Ichihara E, Yamamoto Y, Fujita S, Yamagata K, Katsumoto T, Machida Y, Shinohara H, Murakami R, Kitabayashi I. Genetic and chemical targeting of the ATPase complex TIP48 and 49 impairs acute myeloid leukemia. Leukemia 2023; 37:1812-1829. [PMID: 37491463 DOI: 10.1038/s41375-023-01971-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/01/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
The chromatin-associated AAA+ ATPases Tip48 and Tip49 are the core components of various complexes implicated in diverse nuclear events such as DNA repair and gene regulation. Although they are frequently overexpressed in many human cancers, their functional significance remains unclear. Here, we show that loss of Tip49 triggered p53-dependent apoptosis and inhibited leukemia development in vivo. To examine the impact of chemical inhibition of this complex on leukemia, we have developed the novel compound DS-4950, which interferes with the ATPase activity of the Tip48/49. Administration of DS-4950 was well-tolerated in healthy mice, and the drug effectively reduced tumor burden and improved survival. We also provide evidence that the dependency on Tip48/49 is widely conserved in non-hematologic malignancies with wild type p53. These results demonstrated that the Tip48/49 ATPases are functionally necessary and therapeutically targetable for the treatment of human cancers.
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Affiliation(s)
- Ayuna Hattori
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan.
- Division of Cell Fate Dynamics and Therapeutics, Department of Biosystems Science, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan.
| | - Emi Takamatsu-Ichihara
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshiki Yamamoto
- Division of Cell Fate Dynamics and Therapeutics, Department of Biosystems Science, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Shuhei Fujita
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazutsune Yamagata
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuo Katsumoto
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Yukino Machida
- Department of Veterinary Pathology, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Haruka Shinohara
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan
| | - Ryo Murakami
- Oncology Research Laboratory II, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Issay Kitabayashi
- Division of Hematological Malignancy, National Cancer Center Research Institute, Tokyo, Japan.
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8
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Kirkiz E, Meers O, Grebien F, Buschbeck M. Histone Variants and Their Chaperones in Hematological Malignancies. Hemasphere 2023; 7:e927. [PMID: 37449197 PMCID: PMC10337764 DOI: 10.1097/hs9.0000000000000927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Epigenetic regulation occurs on the level of compacting DNA into chromatin. The functional unit of chromatin is the nucleosome, which consists of DNA wrapped around a core of histone proteins. While canonical histone proteins are incorporated into chromatin through a replication-coupled process, structural variants of histones, commonly named histone variants, are deposited into chromatin in a replication-independent manner. Specific chaperones and chromatin remodelers mediate the locus-specific deposition of histone variants. Although histone variants comprise one of the least understood layers of epigenetic regulation, it has been proposed that they play an essential role in directly regulating gene expression in health and disease. Here, we review the emerging evidence suggesting that histone variants have a role at different stages of hematopoiesis, with a particular focus on the histone variants H2A, H3, and H1. Moreover, we discuss the current knowledge on how the dysregulation of histone variants can contribute to hematopoietic malignancies.
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Affiliation(s)
- Ecem Kirkiz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- PhD Programme in Biomedicine, University of Barcelona, Spain
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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9
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Sporrij A, Choudhuri A, Prasad M, Muhire B, Fast EM, Manning ME, Weiss JD, Koh M, Yang S, Kingston RE, Tolstorukov MY, Clevers H, Zon LI. PGE 2 alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fate. Proc Natl Acad Sci U S A 2023; 120:e2220613120. [PMID: 37126722 PMCID: PMC10175842 DOI: 10.1073/pnas.2220613120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/13/2023] [Indexed: 05/03/2023] Open
Abstract
Prostaglandin E2 (PGE2) and 16,16-dimethyl-PGE2 (dmPGE2) are important regulators of hematopoietic stem and progenitor cell (HSPC) fate and offer potential to enhance stem cell therapies [C. Cutler et al. Blood 122, 3074-3081(2013); W. Goessling et al. Cell Stem Cell 8, 445-458 (2011); W. Goessling et al. Cell 136, 1136-1147 (2009)]. Here, we report that PGE2-induced changes in chromatin at enhancer regions through histone-variant H2A.Z permit acute inflammatory gene induction to promote HSPC fate. We found that dmPGE2-inducible enhancers retain MNase-accessible, H2A.Z-variant nucleosomes permissive of CREB transcription factor (TF) binding. CREB binding to enhancer nucleosomes following dmPGE2 stimulation is concomitant with deposition of histone acetyltransferases p300 and Tip60 on chromatin. Subsequent H2A.Z acetylation improves chromatin accessibility at stimuli-responsive enhancers. Our findings support a model where histone-variant nucleosomes retained within inducible enhancers facilitate TF binding. Histone-variant acetylation by TF-associated nucleosome remodelers creates the accessible nucleosome landscape required for immediate enhancer activation and gene induction. Our work provides a mechanism through which inflammatory mediators, such as dmPGE2, lead to acute transcriptional changes and modify HSPC behavior to improve stem cell transplantation.
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Affiliation(s)
- Audrey Sporrij
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Avik Choudhuri
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Meera Prasad
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Brejnev Muhire
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | - Eva M. Fast
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Margot E. Manning
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Jodi D. Weiss
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Michelle Koh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
| | - Robert E. Kingston
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | | | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht3584 CT, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht3584 CS, The Netherlands
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA02115
- HHMI, Harvard Stem Cell Institute, Boston, MA02115
- Harvard Medical School, Harvard Stem Cell Institute, Boston, MA02115
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10
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VRK1 Kinase Activity Modulating Histone H4K16 Acetylation Inhibited by SIRT2 and VRK-IN-1. Int J Mol Sci 2023; 24:ijms24054912. [PMID: 36902348 PMCID: PMC10003087 DOI: 10.3390/ijms24054912] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The accessibility of DNA to different cellular functions requires a dynamic regulation of chromatin organization that is mediated by different epigenetic modifications, which regulate chromatin accessibility and degree of compaction. These epigenetic modifications, particularly the acetylation of histone H4 in lysine 14 (H4K16ac), determine the degree of chromatin accessibility to different nuclear functions, as well as to DNA damage drugs. H4K16ac is regulated by the balance between two alternative histone modifications, acetylation and deacetylation, which are mediated by acetylases and deacetylases. Tip60/KAT5 acetylates, and SIRT2 deacetylates histone H4K16. However, the balance between these two epigenetic enzymes is unknown. VRK1 regulates the level of H4K16 acetylation by activating Tip60. We have shown that the VRK1 and SIRT2 are able to form a stable protein complex. For this work, we used in vitro interaction, pull-down and in vitro kinase assays. In cells, their interaction and colocalization were detected by immunoprecipitation and immunofluorescence. The kinase activity of VRK1 is inhibited by a direct interaction of its N-terminal kinase domain with SIRT2 in vitro. This interaction causes a loss of H4K16ac similarly to the effect of a novel VRK1 inhibitor (VRK-IN-1) or VRK1 depletion. The use of specific SIRT2 inhibitors in lung adenocarcinoma cells induces H4K16ac, contrary to the novel VRK-IN-1 inhibitor, which prevents H4K16ac and a correct DNA damage response. Therefore, the inhibition of SIRT2 can cooperate with VRK1 in the accessibility of drugs to chromatin in response to DNA damage caused by doxorubicin.
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Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Mol Cell 2022; 82:4627-4646.e14. [PMID: 36417913 PMCID: PMC9779922 DOI: 10.1016/j.molcel.2022.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
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Affiliation(s)
- Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacklyn H Luu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moritz Mall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Han Ng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuhao Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Neumayer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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