1
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Mayse L, Wang Y, Ahmad M, Movileanu L. Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision. ACS NANO 2024; 18:20468-20481. [PMID: 39049818 PMCID: PMC11308778 DOI: 10.1021/acsnano.4c04857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Transcription factors often interact with other protein cofactors, regulating gene expression. Direct detection of these brief events using existing technologies remains challenging due to their transient nature. In addition, intrinsically disordered domains, intranuclear location, and lack of cofactor-dependent active sites of transcription factors further complicate the quantitative analysis of these critical processes. Here, we create a genetically encoded label-free sensor to identify the interaction between a motif of the MYC transcription factor, a primary cancer driver, and WDR5, a chromatin-associated protein hub. Using an engineered nanopore equipped with this motif, WDR5 is probed through reversible captures and releases in a one-by-one and time-resolved fashion. Our single-molecule kinetic measurements indicate a weak-affinity interaction arising from a relatively slow complex association and a fast dissociation of WDR5 from the tethered motif. Further, we validate this subtle interaction by determinations in an ensemble using single nanodisc-wrapped nanopores immobilized on a biolayer interferometry sensor. This study also provides the proof-of-concept for a sensor that reveals unique recognition signatures of different protein binding sites. Our foundational work may be further developed to produce sensing elements for analytical proteomics and cancer nanomedicine.
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Affiliation(s)
- Lauren
A. Mayse
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Yazheng Wang
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Mohammad Ahmad
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, 114 Life Sciences Complex, Syracuse, New York 13244, United States
- The
BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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2
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Yoo L, Mendoza D, Richard AJ, Stephens JM. KAT8 beyond Acetylation: A Survey of Its Epigenetic Regulation, Genetic Variability, and Implications for Human Health. Genes (Basel) 2024; 15:639. [PMID: 38790268 PMCID: PMC11121512 DOI: 10.3390/genes15050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Lysine acetyltransferase 8, also known as KAT8, is an enzyme involved in epigenetic regulation, primarily recognized for its ability to modulate histone acetylation. This review presents an overview of KAT8, emphasizing its biological functions, which impact many cellular processes and range from chromatin remodeling to genetic and epigenetic regulation. In many model systems, KAT8's acetylation of histone H4 lysine 16 (H4K16) is critical for chromatin structure modification, which influences gene expression, cell proliferation, differentiation, and apoptosis. Furthermore, this review summarizes the observed genetic variability within the KAT8 gene, underscoring the implications of various single nucleotide polymorphisms (SNPs) that affect its functional efficacy and are linked to diverse phenotypic outcomes, ranging from metabolic traits to neurological disorders. Advanced insights into the structural biology of KAT8 reveal its interaction with multiprotein assemblies, such as the male-specific lethal (MSL) and non-specific lethal (NSL) complexes, which regulate a wide range of transcriptional activities and developmental functions. Additionally, this review focuses on KAT8's roles in cellular homeostasis, stem cell identity, DNA damage repair, and immune response, highlighting its potential as a therapeutic target. The implications of KAT8 in health and disease, as evidenced by recent studies, affirm its importance in cellular physiology and human pathology.
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Affiliation(s)
- Lindsey Yoo
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David Mendoza
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Allison J. Richard
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
| | - Jacqueline M. Stephens
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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3
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Waldo JJ, Halmai JANM, Fink KD. Epigenetic editing for autosomal dominant neurological disorders. Front Genome Ed 2024; 6:1304110. [PMID: 38510848 PMCID: PMC10950933 DOI: 10.3389/fgeed.2024.1304110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Epigenetics refers to the molecules and mechanisms that modify gene expression states without changing the nucleotide context. These modifications are what encode the cell state during differentiation or epigenetic memory in mitosis. Epigenetic modifications can alter gene expression by changing the chromatin architecture by altering the affinity for DNA to wrap around histone octamers, forming nucleosomes. The higher affinity the DNA has for the histones, the tighter it will wrap and therefore induce a heterochromatin state, silencing gene expression. Several groups have shown the ability to harness the cell's natural epigenetic modification pathways to engineer proteins that can induce changes in epigenetics and consequently regulate gene expression. Therefore, epigenetic modification can be used to target and treat disorders through the modification of endogenous gene expression. The use of epigenetic modifications may prove an effective path towards regulating gene expression to potentially correct or cure genetic disorders.
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Affiliation(s)
| | | | - Kyle D. Fink
- Neurology Department, Stem Cell Program and Gene Therapy Center, MIND Institute, UC Davis Health System, Sacramento, CA, United States
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4
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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5
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Weissmiller AM, Fesik SW, Tansey WP. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think. J Clin Med 2024; 13:274. [PMID: 38202281 PMCID: PMC10779565 DOI: 10.3390/jcm13010274] [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: 12/04/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
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Affiliation(s)
- April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, USA;
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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6
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Fields JK, Hicks CW, Wolberger C. Diverse modes of regulating methyltransferase activity by histone ubiquitination. Curr Opin Struct Biol 2023; 82:102649. [PMID: 37429149 PMCID: PMC10527252 DOI: 10.1016/j.sbi.2023.102649] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/29/2023] [Accepted: 06/11/2023] [Indexed: 07/12/2023]
Abstract
Post-translational modification of histones plays a central role in regulating transcription. Methylation of histone H3 at lysines 4 (H3K4) and 79 (H3K79) play roles in activating transcription whereas methylation of H3K27 is a repressive mark. These modifications, in turn, depend upon prior monoubiquitination of specific histone residues in a phenomenon known as histone crosstalk. Earlier work had provided insights into the mechanism by which monoubiquitination histone H2BK120 stimulates H3K4 methylation by COMPASS/MLL1 and H3K79 methylation by DOT1L, and monoubiquitinated H2AK119 stimulates methylation of H3K27 by the PRC2 complex. Recent studies have shed new light on the role of individual subunits and paralogs in regulating the activity of PRC2 and how additional post-translational modifications regulate yeast Dot1 and human DOT1L, as well as provided new insights into the regulation of MLL1 by H2BK120ub.
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Affiliation(s)
- James K Fields
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Chad W Hicks
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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7
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Lomov NA, Viushkov VS, Rubtsov MA. Mechanisms of Secondary Leukemia Development Caused by Treatment with DNA Topoisomerase Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:892-911. [PMID: 37751862 DOI: 10.1134/s0006297923070040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 09/28/2023]
Abstract
Leukemia is a blood cancer originating in the blood and bone marrow. Therapy-related leukemia is associated with prior chemotherapy. Although cancer therapy with DNA topoisomerase II inhibitors is one of the most effective cancer treatments, its side effects include development of secondary leukemia characterized by the chromosomal rearrangements affecting AML1 or MLL genes. Recurrent chromosomal translocations in the therapy-related leukemia differ from chromosomal rearrangements associated with other neoplasias. Here, we reviewed the factors that drive chromosomal translocations induced by cancer treatment with DNA topoisomerase II inhibitors, such as mobility of ends of double-strand DNA breaks formed before the translocation and gain of function of fusion proteins generated as a result of translocation.
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Affiliation(s)
- Nikolai A Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Vladimir S Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119435, Russia
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8
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Jain K, Marunde MR, Burg JM, Gloor SL, Joseph FM, Poncha KF, Gillespie ZB, Rodriguez KL, Popova IK, Hall NW, Vaidya A, Howard SA, Taylor HF, Mukhsinova L, Onuoha UC, Patteson EF, Cooke SW, Taylor BC, Weinzapfel EN, Cheek MA, Meiners MJ, Fox GC, Namitz KEW, Cowles MW, Krajewski K, Sun ZW, Cosgrove MS, Young NL, Keogh MC, Strahl BD. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. eLife 2023; 12:e82596. [PMID: 37204295 PMCID: PMC10229121 DOI: 10.7554/elife.82596] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/18/2023] [Indexed: 05/20/2023] Open
Abstract
In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
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Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | | | - Faith M Joseph
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Karl F Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | | | | | | | | | | | | | | | - Spencer W Cooke
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | - Bethany C Taylor
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | - Geoffrey C Fox
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | | | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, Upstate Medical UniversitySyracuseUnited States
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
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9
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He H, Li X, Shen J, Bai S, Li C, Shi H. Bisphenol A exposure causes testicular toxicity by targeting DPY30-mediated post-translational modification of PI3K/AKT signaling in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:113996. [PMID: 36030680 DOI: 10.1016/j.ecoenv.2022.113996] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/22/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA), one of the chemicals with the highest volume of production worldwide, has been demonstrated to cause testicular toxicity via different pathways. However, there is little evidence concerning the mechanism of BPA exposure induced histone modification alterations, especially regarding the effect on the histone H3 lysine 4 (H3K4) epigenetic modification. Our results demonstrated a new epigenetic regulation of BPA exposure on testicular damage using both cell culture and mouse models. With BPA treatment, disordered and shrunken seminiferous tubules and poor sperm quality were observed in vivo, and mouse spermatogonial germ cell proliferation was inhibited in vitro. BPA attenuated PI3K expression inducing phospho-AKT inhibition in vivo and in vitro. DPY30 was the only downregulated subunit in BPA and MEK2206 (AKT inhibitor) treated cells, which contributed to reducing H3K4me3 recruitment at the PIK3CA transcriptional start site (TSS) in BPA treated cells. The toxicity caused by BPA exposure was relieved after the transduction of adenoviruses expressing DPY30 transgenes, which resulted in the stimulation of PI3K/AKT with H3K4me3 enriched at the PI3KCA TSS. DPY30 promoted cell glycolysis via AMPK and proliferation through AKT/P21. DPY30 was mainly located in the round and elongated spermatids for energy accumulation in mature sperm in AD-DPY30-treated mice which showed higher sperm quality. Overall, our results indicated that BPA exposure causes testicular toxicity through a DPY30-mediated H3K4me3 epigenetic modification, which serves to regulate the PI3K/AKT/P21 pathway.
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Affiliation(s)
- Huanshan He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianing Shen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuying Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huaiping Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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10
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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11
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Luo JF, Yao YD, Cheng CS, Lio CK, Liu JX, Huang YF, He F, Xie Y, Liu L, Liu ZQ, Zhou H. Sinomenine increases the methylation level at specific GCG site in mPGES-1 promoter to facilitate its specific inhibitory effect on mPGES-1. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194813. [PMID: 35417776 DOI: 10.1016/j.bbagrm.2022.194813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/08/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Prostaglandin E2 (PGE2) in cancer and inflammatory diseases is a key mediator of disease progression. Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used to inhibit the expression of PGE2 by depressing cyclooxygenase (COX) in inflammatory treatments. However, the inhibition to COXs may cause serious side effects. Thus, it is urgent to develop new anti-inflammatory drugs aiming new targets to inhibit PGE2 production. Microsomal prostaglandin E synthase 1 (mPGES-1) catalyzes the final step of PGE2 biosynthesis. Therefore, the selective inhibition of mPGES-1 has become a promising strategy in the treatments of cancer and inflammatory diseases. Our previous studies confirmed that sinomenine (SIN) is a specific mPGES-1 inhibitor. However, the exact mechanism by which SIN inhibits mPGES-1 remains unknown. This study aimed to explain the regulation effect of SIN to mPGES-1 gene expression by its DNA methylation induction effect. We found that the demethylating agent 5-azacytidine (5-AzaC) reversed the inhibitory effect of SIN to mPGES-1. Besides, SIN selectively increased the methylation level of the promoter region in the mPGES-1 gene while the pretreatment of 5-AzaC suppressed this effect. The results also shows that pretreatment with SIN increased the methylation level of specific GCG sites in the promoter region of mPGES-1. This specific methylation site may become a new biomarker for predicting and diagnosing RA and cancer with high expression of mPGES-1. Also, our research provides new ideas and solutions for clinical diagnosis and treatment of diseases related to mPGES-1 and for targeted methylation strategy in drug development.
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Affiliation(s)
- Jin-Fang Luo
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Basic Medical College, Guizhou University of Traditional Chinese Medicine, Guian District, Guiyang, Guizhou, PR China
| | - Yun-Da Yao
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China
| | - Chun-Song Cheng
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant, Lushan Botanical Garden, Chinese Academy of Science, Jiujiang City, Jiangxi Province, PR China
| | - Chon-Kit Lio
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China
| | - Jian-Xin Liu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, Hunan, PR China
| | - Yu-Feng Huang
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China
| | - Fan He
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China
| | - Ying Xie
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China.
| | - Liang Liu
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China.
| | - Zhong-Qiu Liu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China.
| | - Hua Zhou
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China; Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China.
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12
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Ayoub A, Park SH, Lee YT, Cho US, Dou Y. Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes. Biochemistry 2021; 61:1-9. [DOI: 10.1021/acs.biochem.1c00603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Young-Tae Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
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Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
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14
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DOT1L complex regulates transcriptional initiation in human erythroleukemic cells. Proc Natl Acad Sci U S A 2021; 118:2106148118. [PMID: 34187895 DOI: 10.1073/pnas.2106148118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DOT1L, the only H3K79 methyltransferase in human cells and a homolog of the yeast Dot1, normally forms a complex with AF10, AF17, and ENL or AF9, is dysregulated in most cases of mixed-lineage leukemia (MLLr), and has been believed to regulate transcriptional elongation on the basis of its colocalization with RNA polymerase II (Pol II), the sharing of subunits (AF9 and ENL) between the DOT1L and super elongation complexes, and the distribution of H3K79 methylation on both promoters and transcribed regions of active genes. Here we show that DOT1L depletion in erythroleukemic cells reduces its global occupancy without affecting the traveling ratio or the elongation rate (assessed by 4sUDRB-seq) of Pol II, suggesting that DOT1L does not play a major role in elongation in these cells. In contrast, analyses of transcription initiation factor binding reveal that DOT1L and ENL depletions each result in reduced TATA binding protein (TBP) occupancies on thousands of genes. More importantly, DOT1L and ENL depletions concomitantly reduce TBP and Pol II occupancies on a significant fraction of direct (DOT1L-bound) target genes, indicating a role for the DOT1L complex in transcription initiation. Mechanistically, proteomic and biochemical studies suggest that the DOT1L complex may regulate transcriptional initiation by facilitating the recruitment or stabilization of transcription factor IID, likely in a monoubiquitinated H2B (H2Bub1)-enhanced manner. Additional studies show that DOT1L enhances H2Bub1 levels by limiting recruitment of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex. These results advance our understanding of roles of the DOT1L complex in transcriptional regulation and have important implications for MLLr leukemias.
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15
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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16
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Dölle A, Adhikari B, Krämer A, Weckesser J, Berner N, Berger LM, Diebold M, Szewczyk MM, Barsyte-Lovejoy D, Arrowsmith CH, Gebel J, Löhr F, Dötsch V, Eilers M, Heinzlmeir S, Kuster B, Sotriffer C, Wolf E, Knapp S. Design, Synthesis, and Evaluation of WD-Repeat-Containing Protein 5 (WDR5) Degraders. J Med Chem 2021; 64:10682-10710. [PMID: 33980013 DOI: 10.1021/acs.jmedchem.1c00146] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Histone H3K4 methylation serves as a post-translational hallmark of actively transcribed genes and is introduced by histone methyltransferase (HMT) and its regulatory scaffolding proteins. One of these is the WD-repeat-containing protein 5 (WDR5) that has also been associated with controlling long noncoding RNAs and transcription factors including MYC. The wide influence of dysfunctional HMT complexes and the typically upregulated MYC levels in diverse tumor types suggested WDR5 as an attractive drug target. Indeed, protein-protein interface inhibitors for two protein interaction interfaces on WDR5 have been developed. While such compounds only inhibit a subset of WDR5 interactions, chemically induced proteasomal degradation of WDR5 might represent an elegant way to target all oncogenic functions. This study presents the design, synthesis, and evaluation of two diverse WDR5 degrader series based on two WIN site binding scaffolds and shows that linker nature and length strongly influence degradation efficacy.
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Affiliation(s)
- Anja Dölle
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas Krämer
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Janik Weckesser
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Nicola Berner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lena-Marie Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Mathias Diebold
- Institut für Pharmazie und Lebensmittelchemie, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Jakob Gebel
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Frank Löhr
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Christoph Sotriffer
- Institut für Pharmazie und Lebensmittelchemie, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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17
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Wang Z, Schwartz RJ, Liu J, Sun F, Li Q, Ma Y. Smyd1 Orchestrates Early Heart Development Through Positive and Negative Gene Regulation. Front Cell Dev Biol 2021; 9:654682. [PMID: 33869215 PMCID: PMC8047137 DOI: 10.3389/fcell.2021.654682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/17/2021] [Indexed: 01/09/2023] Open
Abstract
SET and MYND domain-containing protein 1 (Smyd1) is a striated muscle-specific histone methyltransferase. Our previous work demonstrated that deletion of Smyd1 in either cardiomyocytes or the outflow tract (OFT) resulted in embryonic lethality at E9.5, with cardiac structural defects such as truncation of the OFT and right ventricle and impaired expansion and proliferation of the second heart field (SHF). The cardiac phenotype was accompanied by the downregulation of ISL LIM Homeobox 1 (Isl1) and upregulation of atrial natriuretic factor (ANF). However, the mechanisms of Smyd1 regulating Isl1 and ANF during embryonic heart development remain to be elucidated. Here, we employed various biochemical and molecular biological approaches including chromatin immunoprecipitation polymerase chain reaction (ChIP-PCR), pGL3 fluorescence reporter system, and co-immunoprecipitation (CoIP) and found that Smyd1 interacted with absent small homeotic-2-like protein (ASH2L) and activated the promoter of Isl1 by trimethylating H3K4. We also found that Smyd1 associated with HDAC to repress ANF expression using trichostatin A (TSA), a deacetylase inhibitor. In conclusion, Smyd1 participates in early heart development by upregulating the expression of Isl1 and downregulating the expression of ANF.
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Affiliation(s)
- Zhen Wang
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China
| | - Robert J Schwartz
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Jing Liu
- Department of Reproductive Medicine Center, Zhengzhou University, Zhengzhou, China
| | - Fei Sun
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China
| | - Qi Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China.,Haikou Key Laboratory for Preservation of Human Genetic Resource, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, China
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18
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Pereira BMV, Katakia YT, Majumder S, Thieme K. Unraveling the epigenetic landscape of glomerular cells in kidney disease. J Mol Med (Berl) 2021; 99:785-803. [PMID: 33763722 DOI: 10.1007/s00109-021-02066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023]
Abstract
Chronic kidney disease (CKD) is a major public health concern and its prevalence and incidence are rising quickly. It is a non-communicable disease primarily caused by diabetes and/or hypertension and is associated with high morbidity and mortality. Despite decades of research efforts, the pathogenesis of CKD remains a puzzle with missing pieces. Understanding the cellular and molecular mechanisms that govern the loss of kidney function is crucial. Abrupt regulation of gene expression in kidney cells is apparent in CKD and shown to be responsible for disease onset and progression. Gene expression regulation extends beyond DNA sequence and involves epigenetic mechanisms including changes in DNA methylation and post-translational modifications of histones, driven by the activity of specific enzymes. Recent advances demonstrate the essential participation of epigenetics in kidney (patho)physiology, as its actions regulate both the integrity of cells but also triggers deleterious signaling pathways. Here, we review the known epigenetic processes regulating the complex filtration unit of the kidney, the glomeruli. The review will elaborate on novel insights into how epigenetics contributes to cell injury in the CKD setting majorly focusing on kidney glomerular cells: the glomerular endothelial cells, the mesangial cells, and the specialized and terminally differentiated podocyte cells.
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Affiliation(s)
- Beatriz Maria Veloso Pereira
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Yash T Katakia
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Karina Thieme
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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19
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Voutsadakis IA. Amplification of 8p11.23 in cancers and the role of amplicon genes. Life Sci 2020; 264:118729. [PMID: 33166592 DOI: 10.1016/j.lfs.2020.118729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023]
Abstract
Copy number alterations are widespread in cancer genomes and are part of the genomic instability underlying the pathogenesis of neoplastic diseases. Recurrent copy number alterations of specific chromosomal loci may result in gains of oncogenes or losses of tumor suppressor genes and become entrenched in the genomic framework of certain types of cancers. The locus at chromosome 8p11.23 presents recurrent amplifications most commonly in squamous lung carcinomas, breast cancers, squamous esophageal carcinomas, and urothelial carcinomas. Amplification is rare in other cancers. The amplified segment involves several described oncogenes that may promote cancer cell survival and proliferation, as well as less well characterized genes that could also contribute to neoplastic processes. Genes proposed to be "drivers" in 8p11.23 amplifications include ZNF703, FGFR1 and PLPP5. Additional genes in the locus that could be functionally important in neoplastic networks include co-chaperone BAG4, lysine methyltransferase NSD3, ASH2L, a member of another methyltransferase complex, MLL and the mRNA processing and translation regulators LSM1 and EIF4EBP1. In this paper, genes located in the amplified segment of 8p11.23 will be examined for their role in cancer and data arguing for their importance for cancers with the amplification will be presented.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, Ontario, Canada; Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada.
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