1
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Sharma AL, Tyagi P, Khumallambam M, Tyagi M. Cocaine-induced DNA-PK relieves RNAP II pausing by promoting TRIM28 phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608673. [PMID: 39229050 PMCID: PMC11370412 DOI: 10.1101/2024.08.19.608673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK phosphorylation triggers the translocation of DNA-PK into the nucleus. The finding that cocaine promotes nuclear translocation of DNA-PK further validates our observation of enhanced DNA-PK recruitment at the HIV long terminal repeat (LTR) following cocaine exposure. By activating and facilitating the nuclear translocation of DNA-PK, cocaine effectively orchestrates multiple stages of HIV transcription, thereby promoting HIV replication. Additionally, our study indicates that cocaine-induced DNA-PK promotes hyper-phosphorylation of RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) at Ser5 and Ser2 sites, enhancing both initiation and elongation phases, respectively, of HIV transcription. Cocaine's enhancement of transcription initiation and elongation is further supported by its activation of cyclin-dependent kinase 7 (CDK7) and subsequent phosphorylation of CDK9, thereby promoting positive transcriptional elongation factor b (P-TEFb) activity. We demonstrate for the first time that cocaine, through DNA-PK activation, promotes the specific phosphorylation of TRIM28 at Serine 824 (p-TRIM28, S824). This modification converts TRIM28 from a transcriptional inhibitor to a transactivator for HIV transcription. Additionally, we observe that phosphorylation of TRIM28 (p-TRIM28, S824) promotes the transition from the pausing phase to the elongation phase of HIV transcription, thereby facilitating the production of full-length HIV genomic transcripts. This finding corroborates the observed enhanced RNAP II CTD phosphorylation at Ser2, a marker of transcriptional elongation, following cocaine exposure. Accordingly, upon cocaine treatment, we observed elevated recruitment of p-TRIM28-(S824) at the HIV LTR. Overall, our results have unraveled the intricate molecular mechanisms underlying cocaine-induced HIV transcription and gene expression. These findings hold promise for the development of highly targeted therapeutics aimed at mitigating the detrimental effects of cocaine in individuals living with HIV.
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Affiliation(s)
| | - Priya Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Meenata Khumallambam
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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2
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Liang F, Jin J, Li Q, Duan J, Jiang A, Chen X, Geng H, Wu K, Yu F, Zhao X, Zhou Y, Hu D, Chen L. DOT1L/H3K79me2 represses HIV-1 reactivation via recruiting DCAF1. Cell Rep 2024; 43:114368. [PMID: 38905100 DOI: 10.1016/j.celrep.2024.114368] [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: 01/03/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/23/2024] Open
Abstract
DOT1L mediates the methylation of histone H3 at lysine 79 and, in turn, the transcriptional activation or repression in a context-dependent manner, yet the regulatory mechanisms and functions of DOT1L/H3K79me remain to be fully explored. Following peptide affinity purification and proteomic analysis, we identified that DCAF1-a component of the E3 ligase complex involved in HIV regulation-is associated with H3K79me2 and DOT1L. Interestingly, blocking the expression or catalytic activity of DOT1L or repressing the expression of DCAF1 significantly enhances the tumor necrosis factor alpha (TNF-α)/nuclear factor κB (NF-κB)-induced reactivation of the latent HIV-1 genome. Mechanistically, upon TNF-α/NF-κB activation, DCAF1 is recruited to the HIV-1 long terminal repeat (LTR) by DOT1L and H3K79me2. Recruited DCAF1 subsequently induces the ubiquitination of NF-κB and restricts its accumulation at the HIV-1 LTR. Altogether, our findings reveal a feedback modulation of HIV reactivation by DOT1L-mediated histone modification regulation and highlight the potential of targeting the DOT1L/DCAF1 axis as a therapeutic strategy for HIV treatment.
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Affiliation(s)
- Fenfei Liang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiaxing Jin
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiming Li
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiangkai Duan
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ao Jiang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Wu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fei Yu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaolu Zhao
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Zhou
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Deqing Hu
- State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Cancer Institute and Hospital of Tianjin Medical University, Tianjin 300060, China.
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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3
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Song L, Li Q, Xia L, Sahay AE, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. Nat Commun 2024; 15:5937. [PMID: 39009564 PMCID: PMC11250843 DOI: 10.1038/s41467-024-50171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
How disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL's histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
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Affiliation(s)
- Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qinglan Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lingbo Xia
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arushi Eesha Sahay
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kotaro Sasaki
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Liling Wan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [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: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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5
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Yang Y, Ahmad E, Premkumar V, Liu A, Ashikur Rahman SM, Nikolovska‐Coleska Z. Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. Protein Sci 2024; 33:e5019. [PMID: 38747396 PMCID: PMC11094776 DOI: 10.1002/pro.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
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Affiliation(s)
- Yuting Yang
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Ejaz Ahmad
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Vidhya Premkumar
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Alicen Liu
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - S. M. Ashikur Rahman
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Zaneta Nikolovska‐Coleska
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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6
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Talukdar P, Pal S, Biswas D. Post-translational modification-dependent oligomerization switch in regulation of global transcription and DNA damage repair during genotoxic stress. Nat Commun 2024; 15:4128. [PMID: 38750015 PMCID: PMC11096357 DOI: 10.1038/s41467-024-48530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Mechanisms of functional cross-talk between global transcriptional repression and efficient DNA damage repair during genotoxic stress are poorly known. In this study, using human AF9 as representative of Super Elongation Complex (SEC) components, we delineate detailed mechanisms of these processes. Mechanistically, we describe that Poly-Serine domain-mediated oligomerization is pre-requisite for AF9 YEATS domain-mediated TFIID interaction-dependent SEC recruitment at the promoter-proximal region for release of paused RNA polymerase II. Interestingly, during genotoxic stress, CaMKII-mediated phosphorylation-dependent nuclear export of AF9-specific deacetylase HDAC5 enhances concomitant PCAF-mediated acetylation of K339 residue. This causes monomerization of AF9 and reduces TFIID interaction for transcriptional downregulation. Furthermore, the K339 acetylation-dependent enhanced AF9-DNA-PKc interaction leads to phosphorylation at S395 residue which reduces AF9-SEC interaction resulting in transcriptional downregulation and efficient repair of DNA damage. After repair, nuclear re-entry of HDAC5 reduces AF9 acetylation and restores its TFIID and SEC interaction to restart transcription.
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Affiliation(s)
| | - Sujay Pal
- CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India.
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7
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Song L, Li Q, Xia L, Sahay A, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L. Single-Cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.591709. [PMID: 38766219 PMCID: PMC11100752 DOI: 10.1101/2024.05.09.591709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cell differentiation during organogenesis relies on precise epigenetic and transcriptional control. Disruptions to this regulation can result in developmental abnormalities and malignancies, yet the underlying mechanisms are not well understood. Wilms tumors, a type of embryonal tumor closely linked to disrupted organogenesis, harbor mutations in epigenetic regulators in 30-50% of cases. However, the role of these regulators in kidney development and pathogenesis remains unexplored. By integrating mouse modeling, histological characterizations, and single-cell transcriptomics and chromatin accessibility profiling, we show that a Wilms tumor-associated mutation in the chromatin reader protein ENL disrupts kidney development trajectory by rewiring the gene regulatory landscape. Specifically, the mutant ENL promotes the commitment of nephron progenitors while simultaneously restricting their differentiation by dysregulating key transcription factor regulons, particularly the HOX clusters. It also induces the emergence of abnormal progenitor cells that lose their chromatin identity associated with kidney specification. Furthermore, the mutant ENL might modulate stroma-nephron interactions via paracrine Wnt signaling. These multifaceted effects caused by the mutation result in severe developmental defects in the kidney and early postnatal mortality in mice. Notably, transient inhibition of the histone acetylation binding activity of mutant ENL with a small molecule displaces transcriptional condensates formed by mutant ENL from target genes, abolishes its gene activation function, and restores developmental defects in mice. This work provides new insights into how mutations in epigenetic regulators can alter the gene regulatory landscape to disrupt kidney developmental programs at single-cell resolution in vivo . It also offers a proof-of-concept for the use of epigenetics-targeted agents to rectify developmental defects.
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8
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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9
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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10
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Zhao J, Cato LD, Arora UP, Bao EL, Bryant SC, Williams N, Jia Y, Goldman SR, Nangalia J, Erb MA, Vos SM, Armstrong SA, Sankaran VG. Inherited blood cancer predisposition through altered transcription elongation. Cell 2024; 187:642-658.e19. [PMID: 38218188 PMCID: PMC10872907 DOI: 10.1016/j.cell.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/26/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies in a large population cohort to identify inherited predisposition genes for these blood cancers. CTR9, which encodes a key component of the PAF1 transcription elongation complex, is among the significant genes identified. The risk variants found in the cases cause loss of function and result in a ∼10-fold increased odds of acquiring a myeloid malignancy. Partial CTR9 loss of function expands human hematopoietic stem cells (HSCs) by increased super elongation complex-mediated transcriptional activity, which thereby increases the expression of key regulators of HSC self-renewal. By following up on insights from a human genetic study examining inherited predisposition to the myeloid malignancies, we define a previously unknown antagonistic interaction between the PAF1 and super elongation complexes. These insights could enable targeted approaches for blood cancer prevention.
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Affiliation(s)
- Jiawei Zhao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China.
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Uma P Arora
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicholas Williams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Yuemeng Jia
- Harvard Stem Cell Institute, Cambridge, MA, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Seth R Goldman
- Nascent Transcriptomics Core, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott A Armstrong
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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11
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Che Z, Liu X, Dai Q, Fang K, Guo C, Yue J, Fang H, Xie P, Luo Z, Lin C. Distinct roles of two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA polymerase II transcription elongation. J Mol Cell Biol 2024; 15:mjad049. [PMID: 37528066 PMCID: PMC11113081 DOI: 10.1093/jmcb/mjad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
The super elongation complex (SEC) containing positive transcription elongation factor b plays a critical role in regulating transcription elongation. AFF1 and AFF4, two members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. Here, we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSS, while AFF4 is enriched downstream of the TSS. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase II transcription.
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Affiliation(s)
- Zhuanzhuan Che
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Xiaoxu Liu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qian Dai
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Ke Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Chenghao Guo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Junjie Yue
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Haitong Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhuojuan Luo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Chengqi Lin
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
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12
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Erb MA. Small-molecule tools for YEATS domain proteins. Curr Opin Chem Biol 2023; 77:102404. [PMID: 37924571 PMCID: PMC10842393 DOI: 10.1016/j.cbpa.2023.102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/06/2023]
Abstract
Chromatin reader domains are protein folds that bind to post-translational modifications of histones and other chromatin-associated proteins. Compared to other families of reader domains, the discovery that YEATS domains bind to acylated lysines is relatively recent. Four human proteins harbor a YEATS domain, and each is present in protein complexes that regulate chromatin and transcription (ENL, AF9, YEATS2, and YEATS4). Without chemical tools to enable temporally resolved perturbations, it is often unclear how reader domains contribute to protein function. Here, we will discuss recent progress in developing small-molecule tools for YEATS domains and highlight their usefulness for making biological discoveries.
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Affiliation(s)
- Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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13
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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14
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Cameron DP, Grosser J, Ladigan S, Kuzin V, Iliopoulou E, Wiegard A, Benredjem H, Jackson K, Liffers ST, Lueong S, Cheung PF, Vangala D, Pohl M, Viebahn R, Teschendorf C, Wolters H, Usta S, Geng K, Kutter C, Arsenian-Henriksson M, Siveke JT, Tannapfel A, Schmiegel W, Hahn SA, Baranello L. Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription. SCIENCE ADVANCES 2023; 9:eadg5109. [PMID: 37831776 PMCID: PMC10575591 DOI: 10.1126/sciadv.adg5109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Pancreatic carcinoma lacks effective therapeutic strategies resulting in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC affects initiation, development, and survival of this tumor type. Using patient-derived xenografts of KRAS- and MYC-driven pancreatic carcinoma, we show that coinhibition of topoisomerase 1 (TOP1) and bromodomain-containing protein 4 (BRD4) synergistically induces tumor regression by targeting promoter pause release. Comparing the nascent transcriptome with the recruitment of elongation and termination factors, we found that coinhibition of TOP1 and BRD4 disrupts recruitment of transcription termination factors. Thus, RNA polymerases transcribe downstream of genes for hundreds of kilobases leading to readthrough transcription. This occurs during replication, perturbing replisome progression and inducing DNA damage. The synergistic effect of TOP1 + BRD4 inhibition is specific to cancer cells leaving normal cells unaffected, highlighting the tumor's vulnerability to transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of transcription and replication.
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Affiliation(s)
- Donald P. Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Swetlana Ladigan
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evanthia Iliopoulou
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hajar Benredjem
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn Jackson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sven T. Liffers
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Smiths Lueong
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Phyllis F. Cheung
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Deepak Vangala
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Michael Pohl
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Richard Viebahn
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Surgery, Bochum, Germany
| | | | - Heiner Wolters
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Selami Usta
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Wolff Schmiegel
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Stephan A. Hahn
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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15
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Li Z, Deeks SG, Ott M, Greene WC. Comprehensive synergy mapping links a BAF- and NSL-containing "supercomplex" to the transcriptional silencing of HIV-1. Cell Rep 2023; 42:113055. [PMID: 37682714 PMCID: PMC10591912 DOI: 10.1016/j.celrep.2023.113055] [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: 12/09/2022] [Revised: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Host repressors mediate HIV latency, but how they interactively silence the virus remains unclear. Here, we develop "reiterative enrichment and authentication of CRISPRi targets for synergies (REACTS)" to probe the genome for synergies between HIV transcription repressors. Using eight known host repressors as queries, we identify 32 synergies involving eleven repressors, including BCL7C, KANSL2, and SIRT2. Overexpression of these three proteins reduces HIV reactivation in Jurkat T cells and in CD4 T cells from people living with HIV on antiretroviral therapy (ART). We show that the BCL7C-containing BAF complex and the KANSL2-containing NSL complex form a "supercomplex" that increases inhibitory histone acetylation of the HIV long-terminal repeat (LTR) and its occupancy by the short variant of the acetyl-lysine reader Brd4. Collectively, we provide a validated platform for defining gene synergies genome wide, and the BAF-NSL "supercomplex" represents a potential target for overcoming HIV rebound after ART cessation.
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Affiliation(s)
- Zichong Li
- Gladstone Institute of Virology, San Francisco, CA 94158, USA.
| | - Steven G Deeks
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA
| | - Warner C Greene
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA.
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16
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Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun 2023; 14:5208. [PMID: 37626123 PMCID: PMC10457349 DOI: 10.1038/s41467-023-40981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT, and the loss of these factors abolishes enhancer-promoter contact. This work not only provides an additional model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK.
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Dopico-Fernandez
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas Denny
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joseph C Hamley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicole E Jackson
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Catherine Chahrour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Simone Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kojo Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Anindita Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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17
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Basu S, Nandy A, Ghosh A, Mall DP, Biswas D. Degradation of CDK9 by Ubiquitin E3 Ligase STUB1 Regulates P-TEFb Level and Its Functions for Global Target Gene Expression within Mammalian Cells. Mol Cell Biol 2023; 43:451-471. [PMID: 37564002 PMCID: PMC10512928 DOI: 10.1080/10985549.2023.2239694] [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: 04/15/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
Positive transcription elongation factor b (P-TEFb) regulates expression of diverse sets of genes within mammalian cells that have implications in several human disease pathogeneses. However, mechanisms of functional regulation of P-TEFb complex through regulation of its stability are poorly known. In this study, we show an important role of C-terminus of Hsc70-interacting protein (CHIP aka STUB1) in regulation of overall level of CDK9 and thus P-TEFb complex within mammalian cells. STUB1 acts as a ubiquitin E3 ligase for proteasomal degradation of CDK9 involving N-terminal lysine 3 (K3) residue. Whereas, overexpression of STUB1 enhances, its knockdown reduces overall CDK9 degradation kinetics within mammalian cells. Interestingly, owing to the same region of binding within CDK9, CyclinT1 protects CDK9 from STUB1-mediated degradation. Factors that cooperatively bind with CyclinT1 to form functional complex also protects CDK9 from degradation by STUB1. Knockdown of STUB1 enhances CDK9 expression and thus P-TEFb complex formation that leads to global increase in RNA polymerase II CTD phosphorylation and transcriptional activation of diverse P-TEFb target genes. Thus, we describe an important functional role of STUB1 in regulation of transcription through modulation of overall level of P-TEFb complex formation within mammalian cells.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Nandy
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Avik Ghosh
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Dheerendra Pratap Mall
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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18
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Hu H, Muntean AG. The YEATS domain epigenetic reader proteins ENL and AF9 and their therapeutic value in leukemia. Exp Hematol 2023; 124:15-21. [PMID: 37295550 PMCID: PMC10527611 DOI: 10.1016/j.exphem.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Recent studies have uncovered similarities and differences between 2 highly homologous epigenetic reading proteins, namely, ENL (MLLT1) and AF9 (MLLT3) with therapeutic implications. The importance of these proteins has traditionally been exemplified by their involvement in chromosomal translocations with the mixed-lineage leukemia gene (MLL; aka KMT2a). MLL rearrangements occur in a subset of acute leukemias and generate potent oncogenic MLL-fusion proteins that impact epigenetic and transcriptional regulation. Leukemic patients with MLL rearrangements display intermediate-to-poor prognoses, necessitating further mechanistic research. Several protein complexes involved in regulating RNA polymerase II transcription and the epigenetic landscape are hijacked in MLL-r leukemia, which include ENL and AF9. Recent biochemical studies have defined a highly homologous YEATS domain in ENL and AF9 that binds acylated histones, which aids in the localization and retention of these proteins to transcriptional targets. In addition, detailed characterization of the homologous ANC-1 homology domain (AHD) on ENL and AF9 revealed differential association with transcriptional activating and repressing complexes. Importantly, CRISPR knockout screens have demonstrated a unique role for wild-type ENL in leukemic stem cell function, whereas AF9 appears important for normal hematopoietic stem cells. In this perspective, we examine the ENL and AF9 proteins with attention to recent work characterizing the epigenetic reading YEATS domains and AHD on both wild-type proteins and when fused to MLL. We summarized the drug development efforts and their therapeutic potential and assess ongoing research that has refined our understanding of how these proteins function, which continues to reveal new therapeutic avenues.
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Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
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19
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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20
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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21
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Wen H, Shi X. Histone Readers and Their Roles in Cancer. Cancer Treat Res 2023; 190:245-272. [PMID: 38113004 PMCID: PMC11395558 DOI: 10.1007/978-3-031-45654-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Histone proteins in eukaryotic cells are subjected to a wide variety of post-translational modifications, which are known to play an important role in the partitioning of the genome into distinctive compartments and domains. One of the major functions of histone modifications is to recruit reader proteins, which recognize the epigenetic marks and transduce the molecular signals in chromatin to downstream effects. Histone readers are defined protein domains with well-organized three-dimensional structures. In this Chapter, we will outline major histone readers, delineate their biochemical and structural features in histone recognition, and describe how dysregulation of histone readout leads to human cancer.
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Affiliation(s)
- Hong Wen
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Xiaobing Shi
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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22
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Wang X, Fan Y, Wu Q. The regulation of transcription elongation in embryonic stem cells. Front Cell Dev Biol 2023; 11:1145611. [PMID: 36875763 PMCID: PMC9978399 DOI: 10.3389/fcell.2023.1145611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Transcription elongation is a fundamental molecular process which is accurately regulated to ensure proper gene expression in cellular activities whereas its malfunction is associated with impaired cellular functions. Embryonic stem cells (ESCs) have significant value in regenerative medicine due to their self-renewal ability and their potential to differentiate to almost all types of cells. Therefore, dissection of the exact regulatory mechanism of transcription elongation in ESCs is crucial for both basic research and their clinical applications. In this review, we discuss the current understanding on the regulatory mechanisms of transcription elongation mediated by transcription factors and epigenetic modifications in ESCs.
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Affiliation(s)
- Xuepeng Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yudan Fan
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
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23
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Hu H, Saha N, Yang Y, Ahmad E, Lachowski L, Shrestha U, Premkumar V, Ropa J, Chen L, Teahan B, Grigsby S, Marschalek R, Nikolovska-Coleska Z, Muntean AG. The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia. Leukemia 2023; 37:190-201. [PMID: 36435883 PMCID: PMC11246743 DOI: 10.1038/s41375-022-01765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
MLL (KMT2a) translocations are found in ~10% of acute leukemia patients, giving rise to oncogenic MLL-fusion proteins. A common MLL translocation partner is ENL and associated with a poor prognosis in t(11;19) patients. ENL contains a highly conserved N-terminal YEATS domain that binds acetylated histones and interacts with the PAF1c, an epigenetic regulator protein complex essential for MLL-fusion leukemogenesis. Recently, wild-type ENL, and specifically the YEATS domain, was shown to be essential for leukemic cell growth. However, the inclusion and importance of the YEATS domain in MLL-ENL-mediated leukemogenesis remains unexplored. We found the YEATS domain is retained in 84.1% of MLL-ENL patients and crucial for MLL-ENL-mediated leukemogenesis in mouse models. Mechanistically, deletion of the YEATS domain impaired MLL-ENL fusion protein binding and decreased expression of pro-leukemic genes like Eya1 and Meis1. Point mutations that disrupt YEATS domain binding to acetylated histones decreased stem cell frequency and increased MLL-ENL-mediated leukemia latency. Therapeutically, YEATS containing MLL-ENL leukemic cells display increased sensitivity to the YEATS inhibitor SGC-iMLLT compared to control AML cells. Our results demonstrate that the YEATS domain is important for MLL-ENL fusion protein-mediated leukemogenesis and exposes an "Achilles heel" that may be therapeutically targeted for treating t(11;19) patients.
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Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nirmalya Saha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yuting Yang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lauren Lachowski
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Uttar Shrestha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vidhya Premkumar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James Ropa
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - Lili Chen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Blaine Teahan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sierrah Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology / Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany
| | | | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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24
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Kenaston MW, Pham OH, Petit MJ, Shah PS. Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks. BMC Genomics 2022; 23:787. [PMID: 36451099 PMCID: PMC9713194 DOI: 10.1186/s12864-022-09013-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Sitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several microbial proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant. RESULTS Advancing past work, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression with broad analytical depth. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. With this model, we employ computational approaches to refine how PAF1 may contribute to both gene activation and suppression. Specifically focusing on transcriptional motifs and regulons, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Overall, our results suggest PAF1 is involved in innate immunity at several distinct axes of regulation. CONCLUSIONS By identifying PAF1-dependent gene expression across several pathogenic contexts, we confirm PAF1C to be a key mediator of innate immunity. Combining these transcriptomic profiles with potential regulatory networks corroborates the previously identified functions of PAF1C. With this, we foster new avenues for its study as a regulator of innate immunity, and our results will serve as a basis for targeted study of PAF1C in future validation studies.
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Affiliation(s)
- Matthew W. Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Oanh H. Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Marine J. Petit
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA ,grid.301713.70000 0004 0393 3981MRC-University of Glasgow, Centre for Virus Research, G61 1HQ, Glasgow, UK
| | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA ,Department of Chemical Engineering, University of California, Davis, Davis, California, USA
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25
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Liu Y, Li Q, Alikarami F, Barrett DR, Mahdavi L, Li H, Tang S, Khan TA, Michino M, Hill C, Song L, Yang L, Li Y, Pokharel SP, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Carroll M, Chen CW, Gardini A, Maillard I, Huggins DJ, Bernt KM, Wan L. Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia. Cancer Discov 2022; 12:2684-2709. [PMID: 36053276 PMCID: PMC9627135 DOI: 10.1158/2159-8290.cd-21-1307] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 02/06/2023]
Abstract
The chromatin reader eleven-nineteen leukemia (ENL) has been identified as a critical dependency in acute myeloid leukemia (AML), but its therapeutic potential remains unclear. We describe a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-11055, which displaces ENL from chromatin by blocking its YEATS domain interaction with acylated histones. Cell lines and primary patient samples carrying MLL rearrangements or NPM1 mutations are responsive to TDI-11055. A CRISPR-Cas9-mediated mutagenesis screen uncovers an ENL mutation that confers resistance to TDI-11055, validating the compound's on-target activity. TDI-11055 treatment rapidly decreases chromatin occupancy of ENL-associated complexes and impairs transcription elongation, leading to suppression of key oncogenic gene expression programs and induction of differentiation. In vivo treatment with TDI-11055 blocks disease progression in cell line- and patient-derived xenograft models of MLL-rearranged and NPM1-mutated AML. Our results establish ENL displacement from chromatin as a promising epigenetic therapy for molecularly defined AML subsets and support the clinical translation of this approach. SIGNIFICANCE AML is a poor-prognosis disease for which new therapeutic approaches are desperately needed. We developed an orally bioavailable inhibitor of ENL, demonstrated its potent efficacy in MLL-rearranged and NPM1-mutated AML, and determined its mechanisms of action. These biological and chemical insights will facilitate both basic research and clinical translation. This article is highlighted in the In This Issue feature, p. 2483.
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Affiliation(s)
- Yiman Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Qinglan Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fatemeh Alikarami
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Declan R. Barrett
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Leila Mahdavi
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hangpeng Li
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sylvia Tang
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tanweer A. Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Connor Hill
- Wistar Institute, Gene Expression and Regulation Program, Philadelphia, Pennsylvania.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Lele Song
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing, China
| | | | | | - Nigel Liverton
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | | | - Simon Taylor
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Gillian F. Watt
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Tammy Ladduwahetty
- Pharmaron Drug Discovery, Pharmaron UK, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire, United Kingdom
| | - Stacia Kargman
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Bridge Medicines, New York, New York
| | - Peter T. Meinke
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Michael A. Foley
- Tri-Institutional Therapeutics Discovery Institute, New York, New York
| | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, and Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Martin Carroll
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California
| | - Alessandro Gardini
- Wistar Institute, Gene Expression and Regulation Program, Philadelphia, Pennsylvania
| | - Ivan Maillard
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David J. Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, New York.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Kathrin M. Bernt
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Corresponding Authors: Liling Wan, University of Pennsylvania, BRB II/III, RM751, 421 Curie Boulevard, Philadelphia, PA 19104. Phone: 215-898-3116; E-mail: ; and Kathrin M. Bernt, Children's Hospital of Philadelphia, Colket Translational Research Center, Room 3064, 3501 Civic Center Boulevard, Philadelphia, PA 19104. Phone: 215-370-3171; E-mail:
| | - Liling Wan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Corresponding Authors: Liling Wan, University of Pennsylvania, BRB II/III, RM751, 421 Curie Boulevard, Philadelphia, PA 19104. Phone: 215-898-3116; E-mail: ; and Kathrin M. Bernt, Children's Hospital of Philadelphia, Colket Translational Research Center, Room 3064, 3501 Civic Center Boulevard, Philadelphia, PA 19104. Phone: 215-370-3171; E-mail:
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26
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Negative Feedback Loop Mechanism between EAF1/2 and DBC1 in Regulating ELL Stability and Functions. Mol Cell Biol 2022; 42:e0015122. [PMID: 36036574 PMCID: PMC9590304 DOI: 10.1128/mcb.00151-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although ELL-associated factors 1 and 2 (EAF1/2) have been shown to enhance RNA polymerase II-mediated transcription in vitro, their functional roles in vivo are poorly known. In this report, we show functions of these proteins in regulating ELL stability through their competitive binding with HDAC3 at the N terminus of ELL. Reduced HDAC3 binding to ELL causes increased acetylation leading to reduced ubiquitylation-mediated degradation. Similar functional roles played by DBC1 in regulating ELL stability further prompted in-depth analyses that demonstrated presence of negative feedback loop mechanisms between DBC1 and EAF1/2 in maintaining overall ELL level. Mechanistically, increased DBC1 reduces EAF1/2 level through increased ubiquitylation involving E3 ubiquitin ligase TRIM28, whereas increased EAF1/2 reduces DBC1 level through reduced transcription. Physiologically, after a few passages, ELL levels in either DBC1 or EAF1 knockdown cells are restored through enhanced expression of EAF1 and DBC1, respectively. Interestingly, for maintenance of ELL level, mammalian cells prefer the EAF1-dependent pathway during exposure to genotoxic stress, and the DBC1-dependent pathway during exposure to growth factors. Thus, we describe coordinated functions of multiple factors, including EAF1/2, HDAC3, DBC1, and TRIM28 in regulating ELL protein level for optimal target gene expression in a context-dependent manner within mammalian cells.
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27
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Tsukumo SI, Subramani PG, Seija N, Tabata M, Maekawa Y, Mori Y, Ishifune C, Itoh Y, Ota M, Fujio K, Di Noia JM, Yasutomo K. AFF3, a susceptibility factor for autoimmune diseases, is a molecular facilitator of immunoglobulin class switch recombination. SCIENCE ADVANCES 2022; 8:eabq0008. [PMID: 36001653 PMCID: PMC9401627 DOI: 10.1126/sciadv.abq0008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Immunoglobulin class switch recombination (CSR) plays critical roles in controlling infections and inflammatory tissue injuries. Here, we show that AFF3, a candidate gene for both rheumatoid arthritis and type 1 diabetes, is a molecular facilitator of CSR with an isotype preference. Aff3-deficient mice exhibit low serum levels of immunoglobulins, predominantly immunoglobulin G2c (IgG2c) followed by IgG1 and IgG3 but not IgM. Furthermore, Aff3-deficient mice show weak resistance to Plasmodium yoelii infection, confirming that Aff3 modulates immunity to this pathogen. Mechanistically, the AFF3 protein binds to the IgM and IgG1 switch regions via a C-terminal domain, and Aff3 deficiency reduces the binding of AID to the switch regions less efficiently. One AFF3 risk allele for rheumatoid arthritis is associated with high mRNA expression of AFF3, IGHG2, and IGHA2 in human B cells. These findings demonstrate that AFF3 directly regulates CSR by facilitating the recruitment of AID to the switch regions.
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Affiliation(s)
- Shin-ichi Tsukumo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Noé Seija
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Mizuho Tabata
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoichi Maekawa
- Department of Parasitology and Infectious Diseases, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuya Mori
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Chieko Ishifune
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
| | - Yasushi Itoh
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Division of Experimental Medicine, McGill University, Montréal, QC, Canada
- Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Koji Yasutomo
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, Tokushima, Japan
- Department of Interdisciplinary Research on Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan
- The Research Cluster Program on Immunological Diseases, Tokushima University, Tokushima, Japan
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28
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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29
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Germano G, Porazzi P, Felix C. Leukemia‐associated transcription factor
mllt3
is important for primitive erythroid development in zebrafish embryogenesis. Dev Dyn 2022; 251:1728-1740. [DOI: 10.1002/dvdy.477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 03/15/2022] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Giuseppe Germano
- Division of Hematology/Oncology Institute of Pediatric Research Città Della Speranza Padova Italy
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center Thomas Jefferson University Philadelphia Pennsylvania USA
| | - Carolyn Felix
- Division of Oncology, Department of Pediatrics The Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
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30
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Li X, Yao Y, Wu F, Song Y. A proteolysis-targeting chimera molecule selectively degrades ENL and inhibits malignant gene expression and tumor growth. J Hematol Oncol 2022; 15:41. [PMID: 35395864 PMCID: PMC8994274 DOI: 10.1186/s13045-022-01258-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/18/2022] [Indexed: 02/07/2023] Open
Abstract
Background Chromosome translocations involving mixed lineage leukemia 1 (MLL1) cause acute leukemia in most infants and 5–10% children/adults with dismal clinical outcomes. Most frequent MLL1-fusion partners AF4/AFF4, AF9/ENL and ELL, together with CDK9/cyclin-T1, constitute super elongation complexes (SEC), which promote aberrant gene transcription, oncogenesis and maintenance of MLL1-rearranged (MLL1-r) leukemia. Notably, ENL, but not its paralog AF9, is essential for MLL1-r leukemia (and several other cancers) and therefore a drug target. Moreover, recurrent ENL mutations are found in Wilms tumor, the most common pediatric kidney cancer, and play critical roles in oncogenesis. Methods Proteolysis-Targeting Chimera (PROTAC) molecules were designed and synthesized to degrade ENL. Biological activities of these compounds were characterized in cell and mouse models of MLL1-r leukemia and other cancers. Results Compound 1 efficiently degraded ENL with DC50 of 37 nM and almost depleted it at ~ 500 nM in blood and solid tumor cells. AF9 (as well as other proteins in SEC) was not significantly decreased. Compound 1-mediated ENL reduction significantly suppressed malignant gene signatures, selectively inhibited cell proliferation of MLL1-r leukemia and Myc-driven cancer cells with EC50s as low as 320 nM, and induced cell differentiation and apoptosis. It exhibited significant antitumor activity in a mouse model of MLL1-r leukemia. Compound 1 can also degrade a mutant ENL in Wilms tumor and suppress its mediated gene transcription. Conclusion Compound 1 is a novel chemical probe for cellular and in vivo studies of ENL (including its oncogenic mutants) and a lead compound for further anticancer drug development. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-022-01258-8.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yuan Yao
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Fangrui Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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31
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Yi Y, Ge S. Targeting the histone H3 lysine 79 methyltransferase DOT1L in MLL-rearranged leukemias. J Hematol Oncol 2022; 15:35. [PMID: 35331314 PMCID: PMC8944089 DOI: 10.1186/s13045-022-01251-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 01/28/2023] Open
Abstract
Disrupting the methylation of telomeric silencing 1-like (DOT1L)-mediated histone H3 lysine 79 has been implicated in MLL fusion-mediated leukemogenesis. Recently, DOT1L has become an attractive therapeutic target for MLL-rearranged leukemias. Rigorous studies have been performed, and much progress has been achieved. Moreover, one DOT1L inhibitor, EPZ-5676, has entered clinical trials, but its clinical activity is modest. Here, we review the recent advances and future trends of various therapeutic strategies against DOT1L for MLL-rearranged leukemias, including DOT1L enzymatic activity inhibitors, DOT1L degraders, protein-protein interaction (PPI) inhibitors, and combinatorial interventions. In addition, the limitations, challenges, and prospects of these therapeutic strategies are discussed. In summary, we present a general overview of DOT1L as a target in MLL-rearranged leukemias to provide valuable guidance for DOT1L-associated drug development in the future. Although a variety of DOT1L enzymatic inhibitors have been identified, most of them require further optimization. Recent advances in the development of small molecule degraders, including heterobifunctional degraders and molecular glues, provide valuable insights and references for DOT1L degraders. However, drug R&D strategies and platforms need to be developed and preclinical experiments need to be performed with the purpose of blocking DOT1L-associated PPIs. DOT1L epigenetic-based combination therapy is worth considering and exploring, but the therapy should be based on a thorough understanding of the regulatory mechanism of DOT1L epigenetic modifications.
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Affiliation(s)
- Yan Yi
- Departments of Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Shenglei Ge
- Departments of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Street, Changsha, 410011, Hunan, People's Republic of China.
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Yeewa R, Chaiya P, Jantrapirom S, Shotelersuk V, Lo Piccolo L. Multifaceted roles of YEATS domain-containing proteins and novel links to neurological diseases. Cell Mol Life Sci 2022; 79:183. [PMID: 35279775 PMCID: PMC11071958 DOI: 10.1007/s00018-022-04218-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
The so-called Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins, hereafter referred to as YD proteins, take control over the transcription by multiple steps of regulation either involving epigenetic remodelling of chromatin or guiding the processivity of RNA polymerase II to facilitate elongation-coupled mRNA 3' processing. Interestingly, an increasing amount of evidence suggest a wider repertoire of YD protein's functions spanning from non-coding RNA regulation, RNA-binding proteins networking, post-translational regulation of a few signalling transduction proteins and the spindle pole formation. However, such a large set of non-canonical roles is still poorly characterized. Notably, four paralogous of human YEATS domain family members, namely eleven-nineteen-leukaemia (ENL), ALL1-fused gene from chromosome 9 protein (AF9), YEATS2 and glioma amplified sequence 41 (GAS41), have a strong link to cancer yet new findings also highlight a potential novel role in neurological diseases. Here, in an attempt to more comprehensively understand the complexity of four YD proteins and to gain more insight into the novel functions they may accomplish in the neurons, we summarized the YD protein's networks, systematically searched and reviewed the YD genetic variants associated with neurodevelopmental disorders and finally interrogated the model organism Drosophila melanogaster.
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Affiliation(s)
- Ranchana Yeewa
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pawita Chaiya
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Salinee Jantrapirom
- Drosophila Centre for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Vorasuk Shotelersuk
- Centre of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Centre for Genomics and Precision Medicine, The Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Luca Lo Piccolo
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Musculoskeletal Science and Translational Research Centre (MSTR), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai, 50200, Thailand.
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Zhou K, Zhuang S, Liu F, Chen Y, Li Y, Wang S, Li Y, Wen H, Lin X, Wang J, Huang Y, He C, Xu N, Li Z, Xu L, Zhang Z, Chen LF, Chen R, Liu M. Disrupting the Cdk9/Cyclin T1 heterodimer of 7SK snRNP for the Brd4 and AFF1/4 guided reconstitution of active P-TEFb. Nucleic Acids Res 2021; 50:750-762. [PMID: 34935961 PMCID: PMC8789079 DOI: 10.1093/nar/gkab1228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 01/16/2023] Open
Abstract
P-TEFb modulates RNA polymerase II elongation through alternative interaction with negative and positive regulation factors. While inactive P-TEFbs are mainly sequestered in the 7SK snRNP complex in a chromatin-free state, most of its active forms are in complex with its recruitment factors, Brd4 and SEC, in a chromatin-associated state. Thus, switching from inactive 7SK snRNP to active P-TEFb (Brd4/P-TEFb or SEC/P-TEFb) is essential for global gene expression. Although it has been shown that cellular signaling stimulates the disruption of 7SK snRNP, releasing dephosphorylated and catalytically inactive P-TEFb, little is known about how the inactive released P-TEFb is reactivated. Here, we show that the Cdk9/CycT1 heterodimer released from 7SK snRNP is completely dissociated into monomers in response to stress. Brd4 or SEC then recruits monomerized Cdk9 and CycT1 to reassemble the core P-TEFb. Meanwhile, the binding of monomeric dephosphorylated Cdk9 to either Brd4 or SEC induces the autophosphorylation of T186 of Cdk9. Finally, the same mechanism is employed during nocodazole released entry into early G1 phase of cell cycle. Therefore, our studies demonstrate a novel mechanism by which Cdk9 and CycT1 monomers are reassembled on chromatin to form active P-TEFb by its interaction with Brd4 or SEC to regulate transcription.
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Affiliation(s)
- Kai Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Songkuan Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Fulong Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yanheng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - You Li
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Shihui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yuxuan Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Huixin Wen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xiaohua Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Jie Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Yue Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Cailing He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Nan Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Zongshu Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Lang Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Zixuan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
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34
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Characterizing the Interaction between the HTLV-1 Transactivator Tax-1 with Transcription Elongation Factor ELL2 and Its Impact on Viral Transactivation. Int J Mol Sci 2021; 22:ijms222413597. [PMID: 34948391 PMCID: PMC8705299 DOI: 10.3390/ijms222413597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The human T-cell leukemia virus type 1 (HTLV-1)-encoded transactivator and oncoprotein Tax-1 is essential for HTLV-1 replication. We recently found that Tax-1 interacts with transcription elongation factor for RNA polymerase II 2, ELL2, which enhances Tax-1-mediated transactivation of the HTLV-1 promotor. Here, we characterize the Tax-1:ELL2 interaction and its impact on viral transactivation by confocal imaging, co-immunoprecipitation, and luciferase assays. We found that Tax-1 and ELL2 not only co-precipitate, but also co-localize in dot-like structures in the nucleus. Tax-1:ELL2 complex formation occurred independently of Tax-1 point mutations, which are crucial for post translational modifications (PTMs) of Tax-1, suggesting that these PTMs are irrelevant for Tax-1:ELL2 interaction. In contrast, Tax-1 deletion mutants lacking either N-terminal (aa 1-37) or C-terminal regions (aa 150-353) of Tax-1 were impaired in interacting with ELL2. Contrary to Tax-1, the related, non-oncogenic Tax-2B from HTLV-2B did not interact with ELL2. Finally, we found that ELL2-R1 (aa 1-353), which carries an RNA polymerase II binding domain, and ELL2-R3 (aa 515-640) are sufficient to interact with Tax-1; however, only ELL2-truncations expressing R1 could enhance Tax-1-mediated transactivation of the HTLV-1 promoter. Together, this study identifies domains in Tax-1 and ELL2 being required for Tax-1:ELL2 complex formation and for viral transactivation.
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Li J, Wang X, Ding J, Zhu Y, Min W, Kuang W, Yuan K, Sun C, Yang P. Development and clinical advancement of small molecules for ex vivo expansion of hematopoietic stem cell. Acta Pharm Sin B 2021; 12:2808-2831. [PMID: 35755294 PMCID: PMC9214065 DOI: 10.1016/j.apsb.2021.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
Hematopoietic stem cell (HSC) transplantation is the only curative therapy for many diseases. HSCs from umbilical cord blood (UCB) source have many advantages over from bone marrow. However, limited HSC dose in a single CB unit restrict its widespread use. Over the past two decades, ex vivo HSC expansion with small molecules has been an effective approach for obtaining adequate HSCs. Till now, several small-molecule compounds have entered the phase I/II trials, showing safe and favorable pharmacological profiles. As HSC expansion has become a hot topic over recent years, many newly identified small molecules along with novel biological mechanisms for HSC expansion would help solve this challenging issue. Here, we will give an overview of HSC biology, discovery and medicinal chemistry development of small molecules, natural products targeting for HSC expansion, and their recent clinical progresses, as well as potential protein targets for HSC expansion.
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36
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Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling. Nat Commun 2021; 12:6318. [PMID: 34732721 PMCID: PMC8566496 DOI: 10.1038/s41467-021-26604-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/17/2021] [Indexed: 11/20/2022] Open
Abstract
RNA Polymerase II (Pol II) transcriptional recycling is a mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of putative RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. Proof-of-principle experiments identified PAF1 complex components among recycling factors and detected defective transcriptional output from Pol II recycling following PAF1 depletion. Dynamic ChIP-seq confirmed PAF1 silencing triggered defective Pol II recycling in human cells. Prostate tumors exhibited enhanced transcriptional recycling, which was attenuated by antibody-based PAF1 depletion. These findings identify Pol II recycling as a potential target in cancer and demonstrate the applicability of in vitro and cellular transcription assays to characterize Pol II recycling in other disease states. RNA Polymerase II (Pol II) recycling can influence transcription efficiency. Here the authors describe an approach aimed at facilitating the identification of factors involved in Pol II recycling and identify PAF1 complex components as mediators of recycling.
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37
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Chen Y, Qiang R, Zhang Y, Cao W, Wu L, Jiang P, Ai J, Ma X, Dong Y, Gao X, Li H, Lu L, Zhang S, Chai R. The Expression and Roles of the Super Elongation Complex in Mouse Cochlear Lgr5+ Progenitor Cells. Front Cell Neurosci 2021; 15:735723. [PMID: 34658793 PMCID: PMC8519586 DOI: 10.3389/fncel.2021.735723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/14/2021] [Indexed: 12/04/2022] Open
Abstract
The super elongation complex (SEC) has been reported to play a key role in the proliferation and differentiation of mouse embryonic stem cells. However, the expression pattern and function of the SEC in the inner ear has not been investigated. Here, we studied the inner ear expression pattern of three key SEC components, AFF1, AFF4, and ELL3, and found that these three proteins are all expressed in both cochlear hair cells (HCs)and supporting cells (SCs). We also cultured Lgr5+ inner ear progenitors in vitro for sphere-forming assays and differentiation assays in the presence of the SEC inhibitor flavopiridol. We found that flavopiridol treatment decreased the proliferation ability of Lgr5+ progenitors, while the differentiation ability of Lgr5+ progenitors was not affected. Our results suggest that the SEC might play important roles in regulating inner ear progenitors and thus regulating HC regeneration. Therefore, it will be very meaningful to further investigate the detailed roles of the SEC signaling pathway in the inner ear in vivo in order to develop effective treatments for sensorineural hearing loss.
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Affiliation(s)
- Yin Chen
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Ruiying Qiang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Yuan Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Wei Cao
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Hospital of Anhui Medical University, Hefei, China
| | - Leilei Wu
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Pei Jiang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Jingru Ai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Xiangyu Ma
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Ying Dong
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Xia Gao
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - He Li
- Department of Otolaryngology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ling Lu
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Shasha Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
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38
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Ma XR, Xu L, Xu S, Klein BJ, Wang H, Das S, Li K, Yang KS, Sohail S, Chapman A, Kutateladze TG, Shi X, Liu WR, Wen H. Discovery of Selective Small-Molecule Inhibitors for the ENL YEATS Domain. J Med Chem 2021; 64:10997-11013. [PMID: 34279931 DOI: 10.1021/acs.jmedchem.1c00367] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Eleven-nineteen leukemia (ENL) protein is a histone acetylation reader essential for disease maintenance in acute leukemias, in particular, the mixed-lineage leukemia (MLL)-rearranged leukemia. In this study, we carried out high-throughput screening of a small-molecule library to identify inhibitors for the ENL YEATS domain. Structure-activity relationship studies of the hits and structure-based inhibitor design led to two compounds, 11 and 24, with IC50 values below 100 nM in inhibiting the ENL-acetyl-H3 interaction. Both compounds, and their precursor compound 7, displayed strong selectivity toward the ENL YEATS domain over all other human YEATS domains. Moreover, 7 exhibited on-target inhibition of ENL in cultured cells and a synergistic effect with the bromodomain and extraterminal domain inhibitor JQ1 in killing leukemia cells. Together, we have developed selective chemical probes for the ENL YEATS domain, providing the basis for further medicinal chemistry-based optimization to advance both basic and translational research of ENL.
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Affiliation(s)
- Xinyu R Ma
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Longxia Xu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Hongkuan Wang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Sukant Das
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kuai Li
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Kai S Yang
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sana Sohail
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Andrew Chapman
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.,Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas 77030, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
| | - Hong Wen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, United States
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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Chantkran W, Hsieh YC, Zheleva D, Frame S, Wheadon H, Copland M. Interrogation of novel CDK2/9 inhibitor fadraciclib (CYC065) as a potential therapeutic approach for AML. Cell Death Dis 2021; 7:137. [PMID: 34112754 PMCID: PMC8192769 DOI: 10.1038/s41420-021-00496-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 02/05/2023]
Abstract
Over the last 50 years, there has been a steady improvement in the treatment outcome of acute myeloid leukemia (AML). However, median survival in the elderly is still poor due to intolerance to intensive chemotherapy and higher numbers of patients with adverse cytogenetics. Fadraciclib (CYC065), a novel cyclin-dependent kinase (CDK) 2/9 inhibitor, has preclinical efficacy in AML. In AML cell lines, myeloid cell leukemia 1 (MCL-1) was downregulated following treatment with fadraciclib, resulting in a rapid induction of apoptosis. In addition, RNA polymerase II (RNAPII)-driven transcription was suppressed, rendering a global gene suppression. Rapid induction of apoptosis was observed in primary AML cells after treatment with fadraciclib for 6-8 h. Twenty-four hours continuous treatment further increased efficacy of fadraciclib. Although preliminary results showed that AML cell lines harboring KMT2A rearrangement (KMT2A-r) are more sensitive to fadraciclib, we found that the drug can induce apoptosis and decrease MCL-1 expression in primary AML cells, regardless of KMT2A status. Importantly, the diversity of genetic mutations observed in primary AML patient samples was associated with variable response to fadraciclib, confirming the need for patient stratification to enable a more effective and personalized treatment approach. Synergistic activity was demonstrated when fadraciclib was combined with the BCL-2 inhibitor venetoclax, or the conventional chemotherapy agents, cytarabine, or azacitidine, with the combination of fadraciclib and azacitidine having the most favorable therapeutic window. In summary, these results highlight the potential of fadraciclib as a novel therapeutic approach for AML.
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Affiliation(s)
- Wittawat Chantkran
- grid.8756.c0000 0001 2193 314XPaul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK ,grid.10223.320000 0004 1937 0490Department of Pathology, Phramongkutklao College of Medicine, Bangkok, Thailand
| | - Ya-Ching Hsieh
- grid.8756.c0000 0001 2193 314XPaul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Sheelagh Frame
- grid.481607.c0000 0004 0397 2104Cyclacel Limited, Dundee, UK
| | - Helen Wheadon
- grid.8756.c0000 0001 2193 314XPaul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mhairi Copland
- grid.8756.c0000 0001 2193 314XPaul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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41
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Mandal R, Becker S, Strebhardt K. Targeting CDK9 for Anti-Cancer Therapeutics. Cancers (Basel) 2021; 13:2181. [PMID: 34062779 PMCID: PMC8124690 DOI: 10.3390/cancers13092181] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Cyclin Dependent Kinase 9 (CDK9) is one of the most important transcription regulatory members of the CDK family. In conjunction with its main cyclin partner-Cyclin T1, it forms the Positive Transcription Elongation Factor b (P-TEFb) whose primary function in eukaryotic cells is to mediate the positive transcription elongation of nascent mRNA strands, by phosphorylating the S2 residues of the YSPTSPS tandem repeats at the C-terminus domain (CTD) of RNA Polymerase II (RNAP II). To aid in this process, P-TEFb also simultaneously phosphorylates and inactivates a number of negative transcription regulators like 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) Sensitivity-Inducing Factor (DSIF) and Negative Elongation Factor (NELF). Significantly enhanced activity of CDK9 is observed in multiple cancer types, which is universally associated with significantly shortened Overall Survival (OS) of the patients. In these cancer types, CDK9 regulates a plethora of cellular functions including proliferation, survival, cell cycle regulation, DNA damage repair and metastasis. Due to the extremely critical role of CDK9 in cancer cells, inhibiting its functions has been the subject of intense research, resulting the development of multiple, increasingly specific small-molecule inhibitors, some of which are presently in clinical trials. The search for newer generation CDK9 inhibitors with higher specificity and lower potential toxicities and suitable combination therapies continues. In fact, the Phase I clinical trials of the latest, highly specific CDK9 inhibitor BAY1251152, against different solid tumors have shown good anti-tumor and on-target activities and pharmacokinetics, combined with manageable safety profile while the phase I and II clinical trials of another inhibitor AT-7519 have been undertaken or are undergoing. To enhance the effectiveness and target diversity and reduce potential drug-resistance, the future of CDK9 inhibition would likely involve combining CDK9 inhibitors with inhibitors like those against BRD4, SEC, MYC, MCL-1 and HSP90.
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Affiliation(s)
- Ranadip Mandal
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Sven Becker
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Klaus Strebhardt
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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42
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Efficacy of combined CDK9/BET inhibition in preclinical models of MLL-rearranged acute leukemia. Blood Adv 2021; 4:296-300. [PMID: 31971998 DOI: 10.1182/bloodadvances.2019000586] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/27/2019] [Indexed: 12/30/2022] Open
Abstract
Key Points
Cyclin-dependent kinase 9 and bromodomain and extraterminal inhibitors are synergistic in MLL-rearranged leukemia. Multiple AML driver genes are downregulated by the combined therapy suggesting broad applicability for this subtype.
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43
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Hsu E, Zemke NR, Berk AJ. Promoter-specific changes in initiation, elongation, and homeostasis of histone H3 acetylation during CBP/p300 inhibition. eLife 2021; 10:63512. [PMID: 33704060 PMCID: PMC8009678 DOI: 10.7554/elife.63512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Regulation of RNA polymerase II (Pol2) elongation in the promoter-proximal region is an important and ubiquitous control point for gene expression in metazoans. We report that transcription of the adenovirus 5 E4 region is regulated during the release of paused Pol2 into productive elongation by recruitment of the super-elongation complex, dependent on promoter H3K18/27 acetylation by CBP/p300. We also establish that this is a general transcriptional regulatory mechanism that applies to ~7% of expressed protein-coding genes in primary human airway epithelial cells. We observed that a homeostatic mechanism maintains promoter, but not enhancer, H3K18/27ac in response to extensive inhibition of CBP/p300 acetyl transferase activity by the highly specific small molecule inhibitor A-485. Further, our results suggest a function for BRD4 association at enhancers in regulating paused Pol2 release at nearby promoters. Taken together, our results uncover the processes regulating transcriptional elongation by promoter region histone H3 acetylation and homeostatic maintenance of promoter, but not enhancer, H3K18/27ac in response to inhibition of CBP/p300 acetyl transferase activity.
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Affiliation(s)
- Emily Hsu
- Molecular Biology Institute, UCLA, Los Angeles, United States
| | - Nathan R Zemke
- Molecular Biology Institute, UCLA, Los Angeles, United States
| | - Arnold J Berk
- Molecular Biology Institute, UCLA, Los Angeles, United States.,Department of Microbiology, UCLA, Los Angeles, United States
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44
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Zhu C, Kim SJ, Mooradian A, Wang F, Li Z, Holohan S, Collins PL, Wang K, Guo Z, Hoog J, Ma CX, Oltz EM, Held JM, Shao J. Cancer-associated exportin-6 upregulation inhibits the transcriptionally repressive and anticancer effects of nuclear profilin-1. Cell Rep 2021; 34:108749. [PMID: 33596420 PMCID: PMC8006859 DOI: 10.1016/j.celrep.2021.108749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 12/29/2020] [Accepted: 01/21/2021] [Indexed: 01/22/2023] Open
Abstract
Aberrant expression of nuclear transporters and deregulated subcellular localization of their cargo proteins are emerging as drivers and therapeutic targets of cancer. Here, we present evidence that the nuclear exporter exportin-6 and its cargo profilin-1 constitute a functionally important and frequently deregulated axis in cancer. Exportin-6 upregulation occurs in numerous cancer types and is associated with poor patient survival. Reducing exportin-6 level in breast cancer cells triggers antitumor effects by accumulating nuclear profilin-1. Mechanistically, nuclear profilin-1 interacts with eleven-nineteen-leukemia protein (ENL) within the super elongation complex (SEC) and inhibits the ability of the SEC to drive transcription of numerous pro-cancer genes including MYC. XPO6 and MYC are positively correlated across diverse cancer types including breast cancer. Therapeutically, exportin-6 loss sensitizes breast cancer cells to the bromodomain and extra-terminal (BET) inhibitor JQ1. Thus, exportin-6 upregulation is a previously unrecognized cancer driver event by spatially inhibiting nuclear profilin-1 as a tumor suppressor.
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Affiliation(s)
- Cuige Zhu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sun-Joong Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Arshag Mooradian
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Faliang Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ziqian Li
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Sean Holohan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrick L Collins
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Keren Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhanfang Guo
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeremy Hoog
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cynthia X Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jieya Shao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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45
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Zheng B, Aoi Y, Shah AP, Iwanaszko M, Das S, Rendleman EJ, Zha D, Khan N, Smith ER, Shilatifard A. Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression. Genes Dev 2021; 35:273-285. [PMID: 33446572 PMCID: PMC7849361 DOI: 10.1101/gad.346106.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression catalyzed by RNA polymerase II (Pol II) requires a host of accessory factors to ensure cell growth, differentiation, and survival under environmental stress. Here, using the auxin-inducible degradation (AID) system to study transcriptional activities of the bromodomain and extraterminal domain (BET) and super elongation complex (SEC) families, we found that the CDK9-containing BRD4 complex is required for the release of Pol II from promoter-proximal pausing for most genes, while the CDK9-containing SEC is required for activated transcription in the heat shock response. By using both the proteolysis targeting chimera (PROTAC) dBET6 and the AID system, we found that dBET6 treatment results in two major effects: increased pausing due to BRD4 loss, and reduced enhancer activity attributable to BRD2 loss. In the heat shock response, while auxin-mediated depletion of the AFF4 subunit of the SEC has a more severe defect than AFF1 depletion, simultaneous depletion of AFF1 and AFF4 leads to a stronger attenuation of the heat shock response, similar to treatment with the SEC inhibitor KL-1, suggesting a possible redundancy among SEC family members. This study highlights the usefulness of orthogonal acute depletion/inhibition strategies to identify distinct and redundant biological functions among Pol II elongation factor paralogs.
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Affiliation(s)
- Bin Zheng
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nabiha Khan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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46
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Jiang Y, Chen G, Li XM, Liu S, Tian G, Li Y, Li X, Li H, Li XD. Selective Targeting of AF9 YEATS Domain by Cyclopeptide Inhibitors with Preorganized Conformation. J Am Chem Soc 2020; 142:21450-21459. [DOI: 10.1021/jacs.0c10324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yixiang Jiang
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Guochao Chen
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Meng Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Sha Liu
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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47
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Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
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Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
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48
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Mori L, Valente ST. Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:E529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The "block-and-lock" approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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Affiliation(s)
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA;
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49
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Ui A, Chiba N, Yasui A. Relationship among DNA double-strand break (DSB), DSB repair, and transcription prevents genome instability and cancer. Cancer Sci 2020; 111:1443-1451. [PMID: 32232911 PMCID: PMC7226179 DOI: 10.1111/cas.14404] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 12/28/2022] Open
Abstract
DNA double‐strand break (DSB) is a serious type of DNA damage and is known to trigger multiple responses within cells. In these responses, novel relationships among DSB, DSB repair, and transcription machineries are created. First, transcription is repressed if DSB occurs near or at the transcription site, termed DSB‐induced transcriptional repression, which contributes to DSB repair with the aid of DNA damage‐signaling pathways, ATM‐ or DNA‐PKcs‐signaling pathways. DSB‐induced transcriptional repression is also regulated by transcriptional factors TLP1, NELF, and ENL, as well as chromatin remodeling and organizing factors ZMYND8, CDYL1, PBAF, and cohesin. Second, transcription and RNA promote DSB repair for genome integrity. Transcription factors such as LEDGF, SETD2, and transcriptionally active histone modification, H3K36, facilitate homologous recombination to overcome DSB. At transcriptional active sites, DNA:RNA hybrids, termed R‐loops, which are formed by DSB, are processed by RAD52 and XPG leading to an activation of the homologous recombination pathway. Even in a transcriptionally inactive non‐genic sites, noncoding RNAs that are produced by RNA polymerase II, DICER, and DROSHA, help to recruit DSB repair proteins at the DSB sites. Third, transcriptional activation itself, however, can induce DSB. Transcriptional activation often generates specific DNA structures such as R‐loops and topoisomerase‐induced DSBs, which cause genotoxic stress and may lead to genome instability and consequently to cancer. Thus, transcription and DSB repair machineries interact and cooperate to prevent genome instability and cancer.
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Affiliation(s)
- Ayako Ui
- Genome Regulation and Molecular Pharmacogenomics, School of Bioscience and Biotechnology, Tokyo University of Technology, Hachijoji, Japan.,Department of Molecular Oncology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan.,Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Natsuko Chiba
- Department of Cancer Biology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Akira Yasui
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
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50
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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