1
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Wu M, Wang W, Mao X, Wu Y, Jin Y, Liu T, Lu Y, Dai H, Zeng S, Huang W, Wang Y, Yao X, Che J, Ying M, Dong X. Discovery of a potent CDKs/FLT3 PROTAC with enhanced differentiation and proliferation inhibition for AML. Eur J Med Chem 2024; 275:116539. [PMID: 38878515 DOI: 10.1016/j.ejmech.2024.116539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/12/2024]
Abstract
AML is an aggressive malignancy of immature myeloid progenitor cells. Discovering effective treatments for AML through cell differentiation and anti-proliferation remains a significant challenge. Building on previous studies on CDK2 PROTACs with differentiation-inducing properties, this research aims to enhance CDKs degradation through structural optimization to facilitate the differentiation and inhibit the proliferation of AML cells. Compound C3, featuring a 4-methylpiperidine ring linker, effectively degraded CDK2 with a DC50 value of 18.73 ± 10.78 nM, and stimulated 72.77 ± 3.51 % cell differentiation at 6.25 nM in HL-60 cells. Moreover, C3 exhibited potent anti-proliferative activity against various AML cell types. Degradation selectivity analysis indicated that C3 could be endowed with efficient degradation of CDK2/4/6/9 and FLT3, especially FLT3-ITD in MV4-11 cells. These findings propose that C3 combined targeting CDK2/4/6/9 and FLT3 with enhanced differentiation and proliferation inhibition, which holds promise as a potential treatment for AML.
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Affiliation(s)
- Mingfei Wu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| | - Wei Wang
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences; Zhejiang University, Cancer Center; Zhejiang University School of Medicine Children'sHospital, Division of Hematology-Oncology, Hangzhou, 310058, PR China
| | - Xinfei Mao
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences; Zhejiang University, Cancer Center; Zhejiang University School of Medicine Children'sHospital, Division of Hematology-Oncology, Hangzhou, 310058, PR China
| | - Yiquan Wu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yuyuan Jin
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, 310058, PR China
| | - Tao Liu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yan Lu
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, PR China
| | - Haibin Dai
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, PR China
| | - Shenxin Zeng
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, 310058, PR China
| | - Wenhai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, 310058, PR China
| | - Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, PR China
| | - Xiaojun Yao
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau, 999078, PR China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| | - Meidan Ying
- Institute of Pharmacology and Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences; Zhejiang University, Cancer Center; Zhejiang University School of Medicine Children'sHospital, Division of Hematology-Oncology, Hangzhou, 310058, PR China.
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China; Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, PR China.
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2
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Walker RL, Hornicek FJ, Duan Z. Transcriptional regulation and therapeutic potential of cyclin-dependent kinase 9 (CDK9) in sarcoma. Biochem Pharmacol 2024; 226:116342. [PMID: 38848777 DOI: 10.1016/j.bcp.2024.116342] [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: 04/01/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Sarcomas include various subtypes comprising two significant groups - soft tissue and bone sarcomas. Although the survival rate for some sarcoma subtypes has improved over time, the current methods of treatment remain efficaciously limited, as recurrent, and metastatic diseases remain a major obstacle. There is a need for better options and therapeutic strategies in treating sarcoma. Cyclin dependent kinase 9 (CDK9) is a transcriptional kinase and has emerged as a promising target for treating various cancers. The aberrant expression and activation of CDK9 have been observed in several sarcoma subtypes, including rhabdomyosarcoma, synovial sarcoma, osteosarcoma, Ewing sarcoma, and chordoma. Enhanced CDK9 expression has also been correlated with poorer prognosis in sarcoma patients. As a master regulator of transcription, CDK9 promotes transcription elongation by phosphorylation and releasing RNA polymerase II (RNAPII) from its promoter proximal pause. Release of RNAPII from this pause induces transcription of critical genes in the tumor cell. Overexpression and activation of CDK9 have been observed to lead to the expression of oncogenes, including MYC and MCL-1, that aid sarcoma development and progression. Inhibition of CDK9 in sarcoma has been proven to reduce these oncogenes' expression and decrease proliferation and growth in different sarcoma cells. Currently, there are several CDK9 inhibitors in preclinical and clinical investigations. This review aims to highlight the recent discovery and results on the transcriptional role and therapeutic potential of CDK9 in sarcoma.
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Affiliation(s)
- Robert L Walker
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Francis J Hornicek
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Zhenfeng Duan
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA.
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3
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Taghizadeh MS, Taherishirazi M, Niazi A, Afsharifar A, Moghadam A. Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction. Front Pharmacol 2024; 15:1327820. [PMID: 38808256 PMCID: PMC11130503 DOI: 10.3389/fphar.2024.1327820] [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: 10/25/2023] [Accepted: 01/18/2024] [Indexed: 05/30/2024] Open
Abstract
CDK9 (cyclin-dependent kinase 9) plays a significant role in numerous pathological conditions, such as HIV-1 infection and cancer. The interaction between CDK9 and cyclin T1 is crucial for maintaining the kinase's active state. Therefore, targeting this protein-protein interaction offers a promising strategy for inhibiting CDK9. In this study, we aimed to design and characterize a library of mutant peptides based on the binding region of cyclin T1 to CDK9. Using Osprey software, a total of 7,776 mutant peptides were generated. After conducting a comprehensive analysis, three peptides, namely, mp3 (RAADVEGQRKRRE), mp20 (RAATVEGQRKRRE), and mp29 (RAADVEGQDKRRE), were identified as promising inhibitors that possess the ability to bind to CDK9 with high affinity and exhibit low free binding energy. These peptides exhibited favorable safety profiles and displayed promising dynamic behaviors. Notably, our findings revealed that the mp3 and mp29 peptides interacted with a conserved sequence in CDK9 (residues 60-66). In addition, by designing the structure of potential peptides in the plasmid vector pET28a (+), we have been able to pave the way for facilitating the process of their recombinant production in an Escherichia coli expression system in future studies. Predictions indicated good solubility upon overexpression, further supporting their potential for downstream applications. While these results demonstrate the promise of the designed peptides as blockers of CDK9 with high affinity, additional experimental studies are required to validate their biological activity and assess their selectivity. Such investigations will provide valuable insights into their therapeutic potential and pave the way for the future development of peptide-based inhibitors targeting the CDK9-cyclin T1 complex.
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Affiliation(s)
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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4
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Zhang Y, Shan L, Tang W, Ge Y, Li C, Zhang J. Recent Discovery and Development of Inhibitors that Target CDK9 and Their Therapeutic Indications. J Med Chem 2024; 67:5185-5215. [PMID: 38564299 DOI: 10.1021/acs.jmedchem.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
CDK9 is a cyclin-dependent kinase that plays pivotal roles in multiple cellular functions including gene transcription, cell cycle regulation, DNA damage repair, and cellular differentiation. Targeting CDK9 is considered an attractive strategy for antitumor therapy, especially for leukemia and lymphoma. Several potent small molecule inhibitors, exemplified by TG02 (4), have progressed to clinical trials. However, many of them face challenges such as low clinical efficacy and multiple adverse reactions and may necessitate the exploration of novel strategies to lead to success in the clinic. In this perspective, we present a comprehensive overview of the structural characteristics, biological functions, and preclinical status of CDK9 inhibitors. Our focus extends to various types of inhibitors, including pan-inhibitors, selective inhibitors, dual-target inhibitors, degraders, PPI inhibitors, and natural products. The discussion encompasses chemical structures, structure-activity relationships (SARs), biological activities, selectivity, and therapeutic potential, providing detailed insight into the diverse landscape of CDK9 inhibitors.
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Affiliation(s)
- Yuming Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- West China College of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Lianhai Shan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 Sichuan, China
| | - Wentao Tang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Yating Ge
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - ChengXian Li
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
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5
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Cisneros WJ, Walter M, Soliman SH, Simons LM, Cornish D, Halle AW, Kim EY, Wolinsky SM, Shilatifard A, Hultquist JF. Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582881. [PMID: 38464055 PMCID: PMC10925308 DOI: 10.1101/2024.03.01.582881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The persistence of HIV-1 in long-lived latent reservoirs during suppressive antiretroviral therapy (ART) remains one of the principal barriers to a functional cure. Blocks to transcriptional elongation play a central role in maintaining the latent state, and several latency reversal strategies focus on the release of positive transcription elongation factor b (P-TEFb) from sequestration by negative regulatory complexes, such as the 7SK complex and BRD4. Another major cellular reservoir of P-TEFb is in Super Elongation Complexes (SECs), which play broad regulatory roles in host gene expression. Still, it is unknown if the release of P-TEFb from SECs is a viable latency reversal strategy. Here, we demonstrate that the SEC is not required for HIV-1 replication in primary CD4+ T cells and that a small molecular inhibitor of the P-TEFb/SEC interaction (termed KL-2) increases viral transcription. KL-2 acts synergistically with other latency reversing agents (LRAs) to reactivate viral transcription in several cell line models of latency in a manner that is, at least in part, dependent on the viral Tat protein. Finally, we demonstrate that KL-2 enhances viral reactivation in peripheral blood mononuclear cells (PBMCs) from people living with HIV on suppressive ART, most notably in combination with inhibitor of apoptosis protein antagonists (IAPi). Taken together, these results suggest that the release of P-TEFb from cellular SECs may be a novel route for HIV-1 latency reactivation.
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Affiliation(s)
- William J. Cisneros
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miriam Walter
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shimaa H.A. Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Daphne Cornish
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ariel W. Halle
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Department of Medicine, 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
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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6
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Zhang Q, Chen Y, Teng Z, Lin Z, Liu H. CDK11 facilitates centromeric transcription to maintain centromeric cohesion during mitosis. Mol Biol Cell 2024; 35:ar18. [PMID: 38019613 PMCID: PMC10881149 DOI: 10.1091/mbc.e23-08-0303] [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: 08/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Actively-transcribing RNA polymerase (RNAP)II is remained on centromeres to maintain centromeric cohesion during mitosis, although it is largely released from chromosome arms. This pool of RNAPII plays an important role in centromere functions. However, the mechanism of RNAPII retention on mitotic centromeres is poorly understood. We here demonstrate that Cyclin-dependent kinase (Cdk)11 is involved in RNAPII regulation on mitotic centromeres. Consistently, we show that Cdk11 knockdown induces centromeric cohesion defects and decreases Bub1 on kinetochores, but the centromeric cohesion defects are partially attributed to Bub1. Furthermore, Cdk11 knockdown and the expression of its kinase-dead version significantly reduce both RNAPII and elongating RNAPII (pSer2) levels on centromeres and decrease centromeric transcription. Importantly, the overexpression of centromeric α-satellite RNAs fully rescues Cdk11-knockdown defects. These results suggest that the maintenance of centromeric cohesion requires Cdk11-facilitated centromeric transcription. Mechanistically, Cdk11 localizes on centromeres where it binds and phosphorylates RNAPII to promote transcription. Remarkably, mitosis-specific degradation of G2/M Cdk11-p58 recapitulates Cdk11-knockdown defects. Altogether, our findings establish Cdk11 as an important regulator of centromeric transcription and as part of the mechanism for retaining RNAPII on centromeres during mitosis.
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Affiliation(s)
- Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Teng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA 70112
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7
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Song B, Liu D, Dai W, McMyn N, Wang Q, Yang D, Krejci A, Vasilyev A, Untermoser N, Loregger A, Song D, Williams B, Rosen B, Cheng X, Chao L, Kale HT, Zhang H, Diao Y, Bürckstümmer T, Siliciano JM, Li JJ, Siliciano R, Huangfu D, Li W. Decoding Heterogenous Single-cell Perturbation Responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564796. [PMID: 37961332 PMCID: PMC10635009 DOI: 10.1101/2023.10.30.564796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Understanding diverse responses of individual cells to the same perturbation is central to many biological and biomedical problems. Current methods, however, do not precisely quantify the strength of perturbation responses and, more importantly, reveal new biological insights from heterogeneity in responses. Here we introduce the perturbation-response score (PS), based on constrained quadratic optimization, to quantify diverse perturbation responses at a single-cell level. Applied to single-cell transcriptomes of large-scale genetic perturbation datasets (e.g., Perturb-seq), PS outperforms existing methods for quantifying partial gene perturbation responses. In addition, PS presents two major advances. First, PS enables large-scale, single-cell-resolution dosage analysis of perturbation, without the need to titrate perturbation strength. By analyzing the dose-response patterns of over 2,000 essential genes in Perturb-seq, we identify two distinct patterns, depending on whether a moderate reduction in their expression induces strong downstream expression alterations. Second, PS identifies intrinsic and extrinsic biological determinants of perturbation responses. We demonstrate the application of PS in contexts such as T cell stimulation, latent HIV-1 expression, and pancreatic cell differentiation. Notably, PS unveiled a previously unrecognized, cell-type-specific role of coiled-coil domain containing 6 (CCDC6) in guiding liver and pancreatic lineage decisions, where CCDC6 knockouts drive the endoderm cell differentiation towards liver lineage, rather than pancreatic lineage. The PS approach provides an innovative method for dose-to-function analysis and will enable new biological discoveries from single-cell perturbation datasets. One sentence summary We present a method to quantify diverse perturbation responses and discover novel biological insights in single-cell perturbation datasets.
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8
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Liu H, Jian Y, Hou J, Zeng C, Zhao Y. RNet: a network strategy to predict RNA binding preferences. Brief Bioinform 2023; 25:bbad482. [PMID: 38145947 PMCID: PMC10749790 DOI: 10.1093/bib/bbad482] [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: 09/05/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 12/27/2023] Open
Abstract
Determining the RNA binding preferences remains challenging because of the bottleneck of the binding interactions accompanied by subtle RNA flexibility. Typically, designing RNA inhibitors involves screening thousands of potential candidates for binding. Accurate binding site information can increase the number of successful hits even with few candidates. There are two main issues regarding RNA binding preference: binding site prediction and binding dynamical behavior prediction. Here, we propose one interpretable network-based approach, RNet, to acquire precise binding site and binding dynamical behavior information. RNetsite employs a machine learning-based network decomposition algorithm to predict RNA binding sites by analyzing the local and global network properties. Our research focuses on large RNAs with 3D structures without considering smaller regulatory RNAs, which are too small and dynamic. Our study shows that RNetsite outperforms existing methods, achieving precision values as high as 0.701 on TE18 and 0.788 on RB9 tests. In addition, RNetsite demonstrates remarkable robustness regarding perturbations in RNA structures. We also developed RNetdyn, a distance-based dynamical graph algorithm, to characterize the interface dynamical behavior consequences upon inhibitor binding. The simulation testing of competitive inhibitors indicates that RNetdyn outperforms the traditional method by 30%. The benchmark testing results demonstrate that RNet is highly accurate and robust. Our interpretable network algorithms can assist in predicting RNA binding preferences and accelerating RNA inhibitor design, providing valuable insights to the RNA research community.
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Affiliation(s)
- Haoquan Liu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Yiren Jian
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | - Jinxuan Hou
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
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9
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Langenbacher AD, Lu F, Tsang L, Huang ZYS, Keer B, Tian Z, Eide A, Pellegrini M, Nakano H, Nakano A, Chen JN. Rtf1-dependent transcriptional pausing regulates cardiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562296. [PMID: 37873297 PMCID: PMC10592831 DOI: 10.1101/2023.10.13.562296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
During heart development, a well-characterized network of transcription factors initiates cardiac gene expression and defines the precise timing and location of cardiac progenitor specification. However, our understanding of the post-initiation transcriptional events that regulate cardiac gene expression is still incomplete. The PAF1C component Rtf1 is a transcription regulatory protein that modulates pausing and elongation of RNA Pol II, as well as cotranscriptional histone modifications. Here we report that Rtf1 is essential for cardiogenesis in fish and mammals, and that in the absence of Rtf1 activity, cardiac progenitors arrest in an immature state. We found that Rtf1's Plus3 domain, which confers interaction with the transcriptional pausing and elongation regulator Spt5, was necessary for cardiac progenitor formation. ChIP-seq analysis further revealed changes in the occupancy of RNA Pol II around the transcription start site (TSS) of cardiac genes in rtf1 morphants reflecting a reduction in transcriptional pausing. Intriguingly, inhibition of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal gene expression levels in a cardiac developmental context.
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Affiliation(s)
- Adam D. Langenbacher
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Fei Lu
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Luna Tsang
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Zi Yi Stephanie Huang
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benjamin Keer
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Zhiyu Tian
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Alette Eide
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Haruko Nakano
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Atsushi Nakano
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jau-Nian Chen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
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10
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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11
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Hafer TL, Felton A, Delgado Y, Srinivasan H, Emerman M. A CRISPR Screen of HIV Dependency Factors Reveals That CCNT1 Is Non-Essential in T Cells but Required for HIV-1 Reactivation from Latency. Viruses 2023; 15:1863. [PMID: 37766271 PMCID: PMC10535513 DOI: 10.3390/v15091863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. The knockout of Cyclin T1 (CCNT1), a component of the P-TEFb complex that is important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting the activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is non-essential in T cells but is absolutely required for HIV latency reversal.
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Affiliation(s)
- Terry L. Hafer
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA;
| | - Abby Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yennifer Delgado
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Harini Srinivasan
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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12
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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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13
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Hafer TL, Felton A, Delgado Y, Srinivasan H, Emerman M. A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551016. [PMID: 37546973 PMCID: PMC10402164 DOI: 10.1101/2023.07.28.551016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL , UBE2M , TBL1XR1 , HDAC3 , AMBRA1 , and ALYREF . Knockout of Cyclin T1 ( CCNT1 ), a component of the P-TEFb complex important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is redundant in T cells but is absolutely required for HIV latency reversal.
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Affiliation(s)
- Terry L Hafer
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Abby Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yennifer Delgado
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Harini Srinivasan
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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14
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Ocker M, Neureiter D. Gene expression inhibitors for the treatment of liver fibrosis: drugs under preclinical and early clinical investigation. Expert Opin Investig Drugs 2023; 32:1133-1141. [PMID: 37997755 DOI: 10.1080/13543784.2023.2288075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023]
Abstract
INTRODUCTION Liver fibrosis represents an unmet medical condition with growing incidence and only limited therapeutic options. Interfering with dysregulated gene expression was considered a specific treatment approach, and we are here reviewing the current options to modulate transcription and translation with small molecule inhibitors of involved enzymes, transcription factors or by using non-coding RNA molecules (RNA interference) or DNA antisense oligonucleotides. Despite promising results in preclinical models, only limited data are available from studies in humans. AREAS COVERED This expert opinion provides a general overview of how to interfere with gene expression (transcription and translation) and highlighting recent achievements in liver fibrosis. EXPERT OPINION Many compounds that were explored to modulate gene expression in liver fibrosis (models) were developed as anti-cancer agents. Their use in humans with impaired liver function is often impaired by the lack of specificity to inhibit only fibrosis-related genes in the liver and by associated general toxicity and narrow therapeutic windows. RNAi approaches show a higher degree of specificity and potentially less systemic toxicity. Clinical development in liver fibrosis requires close interaction between pharmaceutical companies and regulatory authorities to address topics like relevant (surrogate) endpoints to achieve meaningful readouts faster.
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Affiliation(s)
- Matthias Ocker
- Medical Department, Division of Hematology, Oncology, and Cancer Immunology, Campus Charité Mitte, Charité University Medicine Berlin, Berlin, Germany
- EO Translational Insights Consulting GmbH, Berlin, Germany
- Tacalyx GmbH, Berlin, Germany
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/University Hospital Salzburg (SALK), Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
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15
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Chinnapaiyan S, Santiago MJ, Panda K, Rahman MS, Alluin J, Rossi J, Unwalla HJ. A conditional RNA Pol II mono-promoter drives HIV-inducible, CRISPR-mediated cyclin T1 suppression and HIV inhibition. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:553-565. [PMID: 37215150 PMCID: PMC10192333 DOI: 10.1016/j.omtn.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023]
Abstract
Gene editing using clustered regularly interspaced short palindromic repeats (CRISPR) targeted to HIV proviral DNA has shown excision of HIV from infected cells. However, CRISPR-based HIV excision is vulnerable to viral escape. Targeting cellular co-factors provides an attractive yet risky alternative to render viral escape irrelevant. Cyclin T1 is a critical modulator of HIV transcription and mediates recruitment of positive transcription elongation factor-b (P-TEFb) kinase for transcriptional elongation. Hence, a CRISPR-mediated cyclin T1 inactivation will silence HIV transcription, locking it in an inactive form in the cell and thereby serving as an effective antiviral and possibly effecting a functional cure. However, cellular genes play important roles, and their uncontrolled inhibition can promote undesirable effects. Here, we demonstrate a conditional inducible RNA polymerase II (RNA Pol II) mono-promoter-based co-expression of a CRISPR system targeting cyclin T1 from a single transcription unit. Co-expression of guide RNA (gRNA) and CRISPR-associated protein (Cas9) is observed only in HIV-infected cells and leads to sustained HIV suppression in stringent chronically infected cell lines as well as in T cell lines. We further show that incorporation of cis-acting ribozymes immediately upstream of the gRNA further enhances HIV silencing.
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Affiliation(s)
- Srinivasan Chinnapaiyan
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Maria-Jose Santiago
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Kingshuk Panda
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Md. Sohanur Rahman
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Jessica Alluin
- Beckman Research Institute of the City of Hope National Medical Center, Monrovia Biomedical Research Center MBRC, 1218 S. Fifth Av., Monrovia, CA 91008, USA
| | - John Rossi
- Beckman Research Institute of the City of Hope National Medical Center, Monrovia Biomedical Research Center MBRC, 1218 S. Fifth Av., Monrovia, CA 91008, USA
| | - Hoshang J. Unwalla
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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16
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Guo C, Zhang Y, Shuai S, Sigbessia A, Hao S, Xie P, Jiang X, Luo Z, Lin C. The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release. EMBO Rep 2023; 24:e55699. [PMID: 36629390 PMCID: PMC9986819 DOI: 10.15252/embr.202255699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.
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Affiliation(s)
- Chenghao Guo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
| | - Yadi Zhang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shimin Shuai
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Abire Sigbessia
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shaohua Hao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Peng Xie
- Southeast University‐Allen Institute Joint Center, Institute for Brain and IntelligenceSoutheast UniversityNanjingChina
| | - Xu Jiang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Key Laboratory of Technical Evaluation of Fertility Regulation of Non‐human primate, Fujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
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17
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Fujinaga K, Huang F, Peterlin BM. P-TEFb: The master regulator of transcription elongation. Mol Cell 2023; 83:393-403. [PMID: 36599353 PMCID: PMC9898187 DOI: 10.1016/j.molcel.2022.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/10/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023]
Abstract
The positive transcription elongation factor b (P-TEFb) is composed of cyclins T1 or T2 and cyclin-dependent kinase 9 that regulate the elongation phase of transcription by RNA polymerase II. By antagonizing negative elongation factors and phosphorylating the C-terminal domain of RNA polymerase II, P-TEFb facilitates the elongation and co-transcriptional processing of nascent transcripts. This step is critical for the expression of most eukaryotic genes. In growing cells, P-TEFb is regulated negatively by its reversible associations with HEXIM1/2 in the 7SK snRNP and positively by a number of transcription factors, as well as the super elongation complex. In resting cells, P-TEFb falls apart, and cyclin T1 is degraded by the proteasome. This complex regulation of P-TEFb has evolved for the precise temporal and spatial regulation of gene expression in the organism. Its dysregulation contributes to inflammatory and neoplastic conditions.
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Affiliation(s)
- Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
| | - Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
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18
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Chen R, Hassankhani R, Long Y, Basnet SKC, Teo T, Yang Y, Mekonnen L, Yu M, Wang S. Discovery of Potent Inhibitors of Cyclin-Dependent Kinases 7 and 9: Design, Synthesis, Structure-Activity Relationship Analysis and Biological Evaluation. ChemMedChem 2023; 18:e202200582. [PMID: 36400715 DOI: 10.1002/cmdc.202200582] [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: 10/31/2022] [Revised: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Cyclin-dependent kinases (CDKs) 7 and 9 are deregulated in various types of human cancer and are thus viewed as therapeutic targets. Accordingly, small-molecule inhibitors of both CDKs are highly sought-after. Capitalising on our previous discovery of CDKI-73, a potent CDK9 inhibitor, medicinal chemistry optimisation was pursued. A number of N-pyridinylpyrimidin-2-amines were rationally designed, chemically synthesised and biologically assessed. Among them, N-(6-(4-cyclopentylpiperazin-1-yl)pyridin-3-yl)-4-(imidazo[1,2-a]pyrimidin-3-yl)pyrimidin-2-amine was found to be one of the most potent inhibitors of CDKs 7 and 9 as well as the most effective anti-proliferative agent towards multiple human cancer cell lines. The cellular mode of action of this compound was investigated in MV4-11 acute myeloid leukaemia cells, revealing that the compound dampened the kinase activity of cellular CDKs 7 and 9, arrested the cell cycle at sub-G1 phase and induced apoptosis.
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Affiliation(s)
- Renjie Chen
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Ramin Hassankhani
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Yi Long
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Sunita K C Basnet
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Theodosia Teo
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Yuchao Yang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Laychiluh Mekonnen
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
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19
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Asamitsu K, Hirokawa T, Okamoto T. Identification of a novel CDK9 inhibitor targeting the intramolecular hidden cavity of CDK9 induced by Tat binding. PLoS One 2022; 17:e0277024. [PMCID: PMC9665388 DOI: 10.1371/journal.pone.0277024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 transcription is specifically augmented by a transcriptional activator complex composed of Tat, an HIV-1-encoded activator, and the host transcription elongation factor P-TEFb, which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. Several observations suggest that P-TEFb is an attractive anti-HIV-1 drug target. However, the long-term cytotoxicity of CDK9 inhibitors hinders their widespread use in HIV-1 therapy. Thus, novel and safe inhibitors are sorely needed. By performing molecular dynamics simulations of the 3D structure of Tat/P-TEFb, we previously identified a unique cavity structure of CDK9, the CDK9 hidden cavity, that is specifically induced by Tat binding. Here, we attempted to identify compounds that fit this cavity and inhibit CDK9 activity by in silico screening. We identified compounds that could inhibit CDK9 activity. One of such compound, 127, showed the strongest inhibitory activity against CDK9. Interestingly, it also inhibited CDK6 to a similar extent. We inspected the amino acid sequence and structural properties of the CDK9 hidden cavity to determine whether it is conserved in other CDKs, such as CDK6. The Ile61, comprising the center of the CDK9 hidden cavity, appears to be crucial for its kinase activity, thus indicating that the identification of the CDK9 hidden cavity may provide vital information for the development of novel CDK9 inhibitors.
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Affiliation(s)
- Kaori Asamitsu
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
- * E-mail: (KA); (TH)
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaragi, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaragi, Japan
- * E-mail: (KA); (TH)
| | - Takashi Okamoto
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
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20
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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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21
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Dai W, Wu F, McMyn N, Song B, Walker-Sperling VE, Varriale J, Zhang H, Barouch DH, Siliciano JD, Li W, Siliciano RF. Genome-wide CRISPR screens identify combinations of candidate latency reversing agents for targeting the latent HIV-1 reservoir. Sci Transl Med 2022; 14:eabh3351. [PMID: 36260688 PMCID: PMC9705157 DOI: 10.1126/scitranslmed.abh3351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Reversing HIV-1 latency promotes killing of infected cells and is essential for cure strategies; however, no single latency reversing agent (LRA) or LRA combination have been shown to reduce HIV-1 latent reservoir size in persons living with HIV-1 (PLWH). Here, we describe an approach to systematically identify LRA combinations to reactivate latent HIV-1 using genome-wide CRISPR screens. Screens on cells treated with suboptimal concentrations of an LRA can identify host genes whose knockout enhances viral gene expression. Therefore, inhibitors of these genes should synergize with the LRA. We tested this approach using AZD5582, an activator of the noncanonical nuclear factor κB (ncNF-κB) pathway, as an LRA and identified histone deacetylase 2 (HDAC2) and bromodomain-containing protein 2 (BRD2), part of the bromodomain and extra-terminal motif (BET) protein family targeted by BET inhibitors, as potential targets. Using CD4+ T cells from PLWH, we confirmed synergy between AZD5582 and several HDAC inhibitors and between AZD5582 and the BET inhibitor, JQ1. A reciprocal screen using suboptimal concentrations of an HDAC inhibitor as an LRA identified BRD2 and ncNF-κB regulators, especially BIRC2, as synergistic candidates for use in combination with HDAC inhibition. Moreover, we identified and validated additional synergistic drug candidates in latency cell line cells and primary lymphocytes isolated from PLWH. Specifically, the knockout of genes encoding CYLD or YPEL5 displayed synergy with existing LRAs in inducing HIV mRNAs. Our study provides insights into the roles of host factors in HIV-1 reactivation and validates a system for identifying drug combinations for HIV-1 latency reversal.
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Affiliation(s)
- Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010
| | - Victoria E. Walker-Sperling
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital. 111 Michigan Ave NW, Washington, DC 20010,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010,To whom correspondence should be addressed; ;
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205,To whom correspondence should be addressed; ;
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22
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Clopper KC, Taatjes DJ. Chemical inhibitors of transcription-associated kinases. Curr Opin Chem Biol 2022; 70:102186. [PMID: 35926294 PMCID: PMC10676000 DOI: 10.1016/j.cbpa.2022.102186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function in mammalian cells. Here, we focus on chemical inhibitors of the transcription-associated kinases CDK7, CDK8, CDK9, CDK12, CDK13, and CDK19. We provide a brief overview of the function of these kinases and common activation mechanisms. We then highlight the advantages of kinase inhibitors compared with other basic research methods, and describe the caveats associated with non-selective compounds (e.g. flavopiridol). We conclude with strategies and recommendations for implementation of chemical inhibitors for experimental analysis of transcription-associated kinases.
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Affiliation(s)
- Kevin C Clopper
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA.
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23
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Ji C, Deng C, Antor K, Bischler T, Schneider C, Fischer U, Sendtner M, Briese M. hnRNP
R negatively regulates transcription by modulating the association of
P‐TEFb
with
7SK
and
BRD4. EMBO Rep 2022; 23:e55432. [PMID: 35856391 PMCID: PMC9442301 DOI: 10.15252/embr.202255432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Changhe Ji
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Chunchu Deng
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Katharina Antor
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine University of Wuerzburg Wuerzburg Germany
| | - Cornelius Schneider
- Department of Biochemistry, Theodor Boveri Institute University of Wuerzburg Wuerzburg Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute University of Wuerzburg Wuerzburg Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
| | - Michael Briese
- Institute of Clinical Neurobiology University Hospital Wuerzburg Wuerzburg Germany
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24
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Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM. A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Commun Biol 2022; 5:819. [PMID: 35970937 PMCID: PMC9378691 DOI: 10.1038/s42003-022-03734-w] [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: 02/09/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Productive transcriptional elongation of many cellular and viral mRNAs requires transcriptional factors to extract pTEFb from the 7SK snRNP by modulating the association between HEXIM and 7SK snRNA. In HIV-1, Tat binds to 7SK by displacing HEXIM. However, without the structure of the 7SK-HEXIM complex, the constraints that must be overcome for displacement remain unknown. Furthermore, while structure details of the TatNL4-3-7SK complex have been elucidated, it is unclear how subtypes with more HEXIM-like Tat sequences accomplish displacement. Here we report the structures of HEXIM, TatG, and TatFin arginine rich motifs in complex with the apical stemloop-1 of 7SK. While most interactions between 7SK with HEXIM and Tat are similar, critical differences exist that guide function. First, the conformational plasticity of 7SK enables the formation of three different base pair configurations at a critical remodeling site, which allows for the modulation required for HEXIM binding and its subsequent displacement by Tat. Furthermore, the specific sequence variations observed in various Tat subtypes all converge on remodeling 7SK at this region. Second, we show that HEXIM primes its own displacement by causing specific local destabilization upon binding - a feature that is then exploited by Tat to bind 7SK more efficiently.
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Affiliation(s)
- Vincent V Pham
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Michael Gao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Victoria M D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
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25
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Li J, Liu T, Song Y, Wang M, Liu L, Zhu H, Li Q, Lin J, Jiang H, Chen K, Zhao K, Wang M, Zhou H, Lin H, Luo C. Discovery of Small-Molecule Degraders of the CDK9-Cyclin T1 Complex for Targeting Transcriptional Addiction in Prostate Cancer. J Med Chem 2022; 65:11034-11057. [PMID: 35925880 DOI: 10.1021/acs.jmedchem.2c00257] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aberrant hyperactivation of cyclins results in carcinogenesis and therapy resistance in cancers. Direct degradation of the specific cyclin or cyclin-dependent kinase (CDK)-cyclin complex by small-molecule degraders remains a great challenge. Here, we applied the first application of hydrophobic tagging to induce degradation of CDK9-cyclin T1 heterodimer, which is required to keep productive transcription of oncogenes in cancers. LL-K9-3 was identified as a potent small-molecule degrader of CDK9-cyclin T1. Quantitative and time-resolved proteome profiling exhibited LL-K9-3 induced selective and synchronous degradation of CDK9 and cyclin T1. The expressions of androgen receptor (AR) and cMyc were reduced by LL-K9-3 in 22RV1 cells. LL-K9-3 exhibited enhanced anti-proliferative and pro-apoptotic effects compared with its parental CDK9 inhibitor SNS032 and suppressed downstream signaling of CDK9 and AR more effectively than SNS032. Moreover, LL-K9-3 inhibited AR and Myc-driven oncogenic transcriptional programs and exerted stronger inhibitory effects on several intrinsic target genes of AR than the monomeric CDK9 PROTAC (Thal-SNS032).
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Affiliation(s)
- Jiacheng Li
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Ting Liu
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Yuanli Song
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyu Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Liping Liu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Hongwen Zhu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qi Li
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jin Lin
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Mingliang Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hua Lin
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Cheng Luo
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.,The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
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26
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Pyrazole-Curcumin Suppresses Cardiomyocyte Hypertrophy by Disrupting the CDK9/CyclinT1 Complex. Pharmaceutics 2022; 14:pharmaceutics14061269. [PMID: 35745840 PMCID: PMC9227296 DOI: 10.3390/pharmaceutics14061269] [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: 04/11/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
The intrinsic histone acetyltransferase (HAT), p300, has an important role in the development and progression of heart failure. Curcumin (CUR), a natural p300-specific HAT inhibitor, suppresses hypertrophic responses and prevents deterioration of left-ventricular systolic function in heart-failure models. However, few structure–activity relationship studies on cardiomyocyte hypertrophy using CUR have been conducted. To evaluate if prenylated pyrazolo curcumin (PPC) and curcumin pyrazole (PyrC) can suppress cardiomyocyte hypertrophy, cultured cardiomyocytes were treated with CUR, PPC, or PyrC and then stimulated with phenylephrine (PE). PE-induced cardiomyocyte hypertrophy was inhibited by PyrC but not PPC at a lower concentration than CUR. Western blotting showed that PyrC suppressed PE-induced histone acetylation. However, an in vitro HAT assay showed that PyrC did not directly inhibit p300-HAT activity. As Cdk9 phosphorylates both RNA polymerase II and p300 and increases p300-HAT activity, the effects of CUR and PyrC on the kinase activity of Cdk9 were examined. Phosphorylation of p300 by Cdk9 was suppressed by PyrC. Immunoprecipitation-WB showed that PyrC inhibits Cdk9 binding to CyclinT1 in cultured cardiomyocytes. PyrC may prevent cardiomyocyte hypertrophic responses by indirectly suppressing both p300-HAT activity and RNA polymerase II transcription elongation activity via inhibition of Cdk9 kinase activity.
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27
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Huang F, Feng Y, Peterlin BM, Fujinaga K. P-TEFb is degraded by Siah1/2 in quiescent cells. Nucleic Acids Res 2022; 50:5000-5013. [PMID: 35524561 PMCID: PMC9122529 DOI: 10.1093/nar/gkac291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
P-TEFb, composed of CycT1 and CDK9, regulates the elongation of transcription by RNA polymerase II. In proliferating cells, it is regulated by 7SK snRNA in the 7SK snRNP complex. In resting cells, P-TEFb is absent, because CycT1 is dephosphorylated, released from CDK9 and rapidly degraded. In this study, we identified the mechanism of this degradation. We mapped the ubiquitination and degradation of free CycT1 to its N-terminal region from positions 1 to 280. This region is ubiquitinated at six lysines, where E3 ligases Siah1 and Siah2 bind and degrade these sequences. Importantly, the inhibition of Siah1/2 rescued the expression of free CycT1 in proliferating as well as resting primary cells. We conclude that Siah1/2 are the E3 ligases that bind and degrade the dissociated CycT1 in resting, terminally differentiated, anergic and/or exhausted cells.
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Affiliation(s)
- Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
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28
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Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. eLife 2021; 10:68473. [PMID: 34821217 PMCID: PMC8648303 DOI: 10.7554/elife.68473] [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: 03/17/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is a critical coactivator for transcription of most cellular and viral genes, including those of HIV. While P-TEFb is regulated by 7SK snRNA in proliferating cells, P-TEFb is absent due to diminished levels of CycT1 in quiescent and terminally differentiated cells, which has remained unexplored. In these cells, we found that CycT1 not bound to CDK9 is rapidly degraded. Moreover, productive CycT1:CDK9 interactions are increased by PKC-mediated phosphorylation of CycT1 in human cells. Conversely, dephosphorylation of CycT1 by PP1 reverses this process. Thus, PKC inhibitors or removal of PKC by chronic activation results in P-TEFb disassembly and CycT1 degradation. This finding not only recapitulates P-TEFb depletion in resting CD4+ T cells but also in anergic T cells. Importantly, our studies reveal mechanisms of P-TEFb inactivation underlying T cell quiescence, anergy, and exhaustion as well as proviral latency and terminally differentiated cells.
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Affiliation(s)
- Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Trang Tt Nguyen
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Ramachandran Rakesh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Daniele C Cary
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Hana Paculova
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QBI), San Francisco, United States
| | - Arthur Weiss
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Boris Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
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29
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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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30
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BET Proteins as Attractive Targets for Cancer Therapeutics. Int J Mol Sci 2021; 22:ijms222011102. [PMID: 34681760 PMCID: PMC8538173 DOI: 10.3390/ijms222011102] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be an essential driver of cancer initiation and progression. Loss of transcriptional control can cause cancer cells to become dependent on certain regulators of gene expression. Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate the expression of multiple genes involved in carcinogenesis. BET inhibitors (BETis) disrupt BET protein binding to acetylated lysine residues of chromatin and suppress the transcription of various genes, including oncogenic transcription factors. Phase I and II clinical trials demonstrated BETis’ potential as anticancer drugs against solid tumours and haematological malignancies; however, their clinical success was limited as monotherapies. Emerging treatment-associated toxicities, drug resistance and a lack of predictive biomarkers limited BETis’ clinical progress. The preclinical evaluation demonstrated that BETis synergised with different classes of compounds, including DNA repair inhibitors, thus supporting further clinical development of BETis. The combination of BET and PARP inhibitors triggered synthetic lethality in cells with proficient homologous recombination. Mechanistic studies revealed that BETis targeted multiple essential homologous recombination pathway proteins, including RAD51, BRCA1 and CtIP. The exact mechanism of BETis’ anticancer action remains poorly understood; nevertheless, these agents provide a novel approach to epigenome and transcriptome anticancer therapy.
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31
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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32
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Yamayoshi A, Fukumoto H, Hayashi R, Kishimoto K, Kobori A, Koyanagi Y, Komano JA, Murakami A. Development of 7SK snRNA Mimics That Inhibit HIV Transcription. ChemMedChem 2021; 16:3181-3184. [PMID: 34233081 DOI: 10.1002/cmdc.202100422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/11/2022]
Abstract
The 332-nucleotide small nuclear RNA (snRNA) 7SK is a highly conserved non-coding RNA that regulates transcriptional elongation. By binding with positive transcriptional elongation factor b (P-TEFb) via HEXIM1, 7SK snRNA decreases the kinase activity of P-TEFb and inhibits transcriptional elongation. Additionally, it is reported that 7SK inhibition results in the stimulation of human immunodeficiency virus (HIV)-specific transcription. These reports suggest that 7SK is a naturally occurring functional molecule as negative regulator of P-TEFb and HIV transcription. In this study, we developed functional oligonucleotides that mimic the function of 7SK (7SK mimics) as novel inhibitors of HIV replication. We defined the essential region of 7SK regarding its suppressive effects on transcriptional downregulation using an antisense strategy. Based on the results, we designed 7SK mimics containing the defined region. The inhibitory effects of 7SK mimics on HIV-1 long terminal repeat promoter specific transcription was drastic compared with those of the control mimic molecule. Notably, these effects were found to be more enhanced by co-transfection with Tat-expressing plasmids. From these results, it is indicated that 7SK mimics may have great therapeutic potential for HIV/AIDS treatment.
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Affiliation(s)
- Asako Yamayoshi
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi Nagasaki-shi, Nagasaki, 852-8521, Japan
| | - Hiroyuki Fukumoto
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, 606-8585, (Japan)
| | - Rie Hayashi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, 606-8585, (Japan)
| | - Kyosuke Kishimoto
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, 606-8585, (Japan)
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, 606-8585, (Japan)
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-kawaramachi 53 Sakyo-ku, Kyoto, 606-8507, Japan
| | - Jun A Komano
- Department of Microbiology and Infection Control, Faculty and Graduate School of Pharmaceutical Sciences, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1041, (Japan)
| | - Akira Murakami
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, 606-8585, (Japan)
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33
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Cleavage and Polyadenylation Specificity Factor 6 Is Required for Efficient HIV-1 Latency Reversal. mBio 2021; 12:e0109821. [PMID: 34154414 PMCID: PMC8262898 DOI: 10.1128/mbio.01098-21] [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] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 latent reservoir is the major barrier to an HIV cure. Due to low levels or lack of transcriptional activity, HIV-1 latent proviruses in vivo are not easily detectable and cannot be targeted by either natural immune mechanisms or molecular therapies based on protein expression. To target the latent reservoir, further understanding of HIV-1 proviral transcription is required. In this study, we demonstrate a novel role for cleavage and polyadenylation specificity factor 6 (CPSF6) in HIV-1 transcription. We show that knockout of CPSF6 hinders reactivation of latent HIV-1 proviruses by PMA in primary CD4+ cells. CPSF6 knockout reduced HIV-1 transcription, concomitant with a drastic reduction in the phosphorylation levels of Pol II and CDK9. Knockout of CPSF6 led to abnormal stabilization of protein phosphatase 2A (PP2A) subunit A, which then acted to dephosphorylate CDK9, downmodulating CDK9's ability to phosphorylate the Pol II carboxy-terminal domain. In agreement with this mechanism, incubation with the PP2A inhibitor, LB100, restored HIV-1 transcription in the CPSF6 knockout cells. Destabilization of PP2A subunit A occurs in the ubiquitin proteasome pathway, wherein CPSF6 acts as a substrate adaptor for the ITCH ubiquitin ligase. Our observations reveal a novel role of CPSF6 in HIV-1 transcription, which appears to be independent of its known roles in cleavage and polyadenylation and the targeting of preintegration complexes to the chromatin for viral DNA integration. IMPORTANCE CPSF6 is a cellular factor that regulates cleavage and polyadenylation of mRNAs and participates in HIV-1 infection by facilitating targeting of preintegration complexes to the chromatin. Our observations reveal a second role of CPSF6 in the HIV-1 life cycle that involves regulation of viral transcription through controlling the stability of protein phosphatase 2A, which in turn regulates the phosphorylation/dephosphorylation status of critical residues in CDK9 and Pol II.
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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: 37] [Impact Index Per Article: 12.3] [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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You KS, Yi YW, Cho J, Park JS, Seong YS. Potentiating Therapeutic Effects of Epidermal Growth Factor Receptor Inhibition in Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2021; 14:589. [PMID: 34207383 PMCID: PMC8233743 DOI: 10.3390/ph14060589] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subset of breast cancer with aggressive characteristics and few therapeutic options. The lack of an appropriate therapeutic target is a challenging issue in treating TNBC. Although a high level expression of epidermal growth factor receptor (EGFR) has been associated with a poor prognosis among patients with TNBC, targeted anti-EGFR therapies have demonstrated limited efficacy for TNBC treatment in both clinical and preclinical settings. However, with the advantage of a number of clinically approved EGFR inhibitors (EGFRis), combination strategies have been explored as a promising approach to overcome the intrinsic resistance of TNBC to EGFRis. In this review, we analyzed the literature on the combination of EGFRis with other molecularly targeted therapeutics or conventional chemotherapeutics to understand the current knowledge and to provide potential therapeutic options for TNBC treatment.
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Affiliation(s)
- Kyu Sic You
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 3116, Chungcheongnam-do, Korea
| | - Yong Weon Yi
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
| | - Jeonghee Cho
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
| | - Jeong-Soo Park
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
| | - Yeon-Sun Seong
- Department of Biochemistry, College of Medicine, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea;
- Graduate School of Convergence Medical Science, Dankook University, Cheonan 3116, Chungcheongnam-do, Korea
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Chungcheongnam-do, Korea; (Y.W.Y.); (J.C.)
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Anshabo AT, Milne R, Wang S, Albrecht H. CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents. Front Oncol 2021; 11:678559. [PMID: 34041038 PMCID: PMC8143439 DOI: 10.3389/fonc.2021.678559] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are proteins pivotal to a wide range of cellular functions, most importantly cell division and transcription, and their dysregulations have been implicated as prominent drivers of tumorigenesis. Besides the well-established role of cell cycle CDKs in cancer, the involvement of transcriptional CDKs has been confirmed more recently. Most cancers overtly employ CDKs that serve as key regulators of transcription (e.g., CDK9) for a continuous production of short-lived gene products that maintain their survival. As such, dysregulation of the CDK9 pathway has been observed in various hematological and solid malignancies, making it a valuable anticancer target. This therapeutic potential has been utilized for the discovery of CDK9 inhibitors, some of which have entered human clinical trials. This review provides a comprehensive discussion on the structure and biology of CDK9, its role in solid and hematological cancers, and an updated review of the available inhibitors currently being investigated in preclinical and clinical settings.
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Affiliation(s)
- Abel Tesfaye Anshabo
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Robert Milne
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shudong Wang
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Hugo Albrecht
- Drug Discovery and Development, Centre for Cancer Diagnostics and Therapeutics, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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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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Kaur R, Kumar K. Synthetic and medicinal perspective of quinolines as antiviral agents. Eur J Med Chem 2021; 215:113220. [PMID: 33609889 PMCID: PMC7995244 DOI: 10.1016/j.ejmech.2021.113220] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/17/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
In current scenario, various heterocycles have come up exhibiting crucial role in various medicinal agents which are valuable for mankind. Out of diverse range of heterocycle, quinoline scaffold have been proved to play an important role in broad range of biological activities. Several drug molecules bearing a quinoline molecule with useful anticancer, antibacterial activities etc have been marketed such as chloroquine, saquinavir etc. Owing to their broad spectrum biological role, various synthetic strategies such as Skraup reaction, Combes reaction etc. has been developed by the researchers all over the world. But still the synthetic methods are associated with various limitations as formation of side products, use of expensive metal catalysts. Thus, several efforts to develop an efficient and cost effective synthetic protocol are still carried out till date. Moreover, quinoline scaffold displays remarkable antiviral activity. Therefore, in this review we have made an attempt to describe recent synthetic protocols developed by various research groups along with giving a complete explanation about the role of quinoline derivatives as antiviral agent. Quinoline derivatives were found potent against various strains of viruses like zika virus, enterovirus, herpes virus, human immunodeficiency virus, ebola virus, hepatitis C virus, SARS virus and MERS virus etc.
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Affiliation(s)
- Ramandeep Kaur
- Department of Pharmaceutical Chemistry, Indo-Soviet Friendship College of Pharmacy (ISFCP), Moga, Punjab, 142001, India
| | - Kapil Kumar
- School of Pharmacy and Technology Management, SVKM's NMIMS, Hyderabad, Telangana, 509301, India.
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Dollinger R, Gilmour DS. Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans. J Mol Biol 2021; 433:166897. [PMID: 33640324 DOI: 10.1016/j.jmb.2021.166897] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Regulation of transcription is a tightly choreographed process. The establishment of RNA polymerase II promoter proximal pausing soon after transcription initiation and the release of Pol II into productive elongation are key regulatory processes that occur in early elongation. We describe the techniques and tools that have become available for the study of promoter proximal pausing and their utility for future experiments. We then provide an overview of the factors and interactions that govern a multipartite pausing process and address emerging questions surrounding the mechanism of RNA polymerase II's subsequent advancement into the gene body. Finally, we address remaining controversies and future areas of study.
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Affiliation(s)
- Roberta Dollinger
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 462 North Frear, University Park, PA 16802, USA.
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 465A North Frear, University Park, PA 16802, USA.
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Tatum NJ, Endicott JA. Chatterboxes: the structural and functional diversity of cyclins. Semin Cell Dev Biol 2020; 107:4-20. [PMID: 32414682 DOI: 10.1016/j.semcdb.2020.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Proteins of the cyclin family have divergent sequences and execute diverse roles within the cell while sharing a common fold: the cyclin box domain. Structural studies of cyclins have played a key role in our characterization and understanding of cellular processes that they control, though to date only ten of the 29 CDK-activating cyclins have been structurally characterized by X-ray crystallography or cryo-electron microscopy with or without their cognate kinases. In this review, we survey the available structures of human cyclins, highlighting their molecular features in the context of their cellular roles. We pay particular attention to how cyclin activity is regulated through fine control of degradation motif recognition and ubiquitination. Finally, we discuss the emergent roles of cyclins independent of their roles as cyclin-dependent protein kinase activators, demonstrating the cyclin box domain to be a versatile and generalized scaffolding domain for protein-protein interactions across the cellular machinery.
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Affiliation(s)
- Natalie J Tatum
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
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41
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Ventura JD. Human Immunodeficiency Virus 1 (HIV-1): Viral Latency, the Reservoir, and the Cure. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2020; 93:549-560. [PMID: 33005119 PMCID: PMC7513431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An estimated 37 million people globally suffer from Human Immunodeficiency Virus-1 (HIV-1) infection with 1.7 million newly acquired infections occurring on average each year. Although crucial advances in combined antiretroviral therapy (ART) over the last two decades have transformed an HIV-1 diagnosis into a tolerable and controlled condition, enabling over 20 million people living with HIV-1 to enjoy healthy and productive lives, no cure or vaccine yet exists. Developing a successful cure strategy will require a firm understanding of how viral latency is established and how a persistent and long-lived latent is generated. The latent reservoir remains the primary obstacle for cure development and most putative cure strategies proposed fundamentally address its eradication or permanent suppression.
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Affiliation(s)
- John D. Ventura
- To whom all correspondence should be addressed:
Dr. John D. Ventura, . ORCID iD:
https://orcid.org/0000-0002-4373-3242.
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Liang D, Yu Y, Ma Z. Novel strategies targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery. Eur J Med Chem 2020; 200:112426. [DOI: 10.1016/j.ejmech.2020.112426] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
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Loyer P, Trembley JH. Roles of CDK/Cyclin complexes in transcription and pre-mRNA splicing: Cyclins L and CDK11 at the cross-roads of cell cycle and regulation of gene expression. Semin Cell Dev Biol 2020; 107:36-45. [PMID: 32446654 DOI: 10.1016/j.semcdb.2020.04.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/18/2022]
Abstract
Cyclin Dependent Kinases (CDKs) represent a large family of serine/threonine protein kinases that become active upon binding to a Cyclin regulatory partner. CDK/cyclin complexes recently identified, as well as "canonical" CDK/Cyclin complexes regulating cell cycle, are implicated in the regulation of gene expression via the phosphorylation of key components of the transcription and pre-mRNA processing machineries. In this review, we summarize the role of CDK/cyclin-dependent phosphorylation in the regulation of transcription and RNA splicing and highlight recent findings that indicate the involvement of CDK11/cyclin L complexes at the cross-roads of cell cycle, transcription and RNA splicing. Finally, we discuss the potential of CDK11 and Cyclins L as therapeutic targets in cancer.
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Affiliation(s)
- Pascal Loyer
- INSERM, INRAE, Univ Rennes, NuMeCan, Nutrition Metabolisms and Cancer, Rennes, France.
| | - Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN 55417, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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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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Multivalent Role of Human TFIID in Recruiting Elongation Components at the Promoter-Proximal Region for Transcriptional Control. Cell Rep 2020; 26:1303-1317.e7. [PMID: 30699356 DOI: 10.1016/j.celrep.2019.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/05/2018] [Accepted: 01/02/2019] [Indexed: 01/08/2023] Open
Abstract
Despite substantial progress in our understanding of the players involved and the regulatory mechanisms controlling the initiation and elongation steps of transcription, little is known about the recruitment of elongation factors at promoter-proximal regions for the initiation-to-elongation transition. Here, we show evidence that human TFIID, which initiates pre-initiation complex (PIC) assembly, contributes to regulating the recruitment of super-elongation complex (SEC) components at the promoter-proximal region through interactions among selective TAF and SEC components. In vitro direct interactions, coupled with cell-based assays, identified an important poly-Ser domain within SEC components that are involved in their interaction with TFIID. DNA template-based recruitment assays, using purified components, further show a direct role for poly-Ser domain-dependent TFIID interaction in recruiting SEC components on target DNA. Consistently, ChIP and RNA analyses have shown the importance of this mechanism in TFIID-dependent SEC recruitment and target gene expression within mammalian cells.
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Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A. Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy. Cancer Discov 2020; 10:351-370. [DOI: 10.1158/2159-8290.cd-19-0528] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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Wang Y, Qiu T. Positive transcription elongation factor b and its regulators in development. ALL LIFE 2020. [DOI: 10.1080/21553769.2019.1663277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Yan Wang
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
| | - Tong Qiu
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
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Wu J, Liang Y, Tan Y, Tang Y, Song H, Wang Z, Li Y, Lu M. CDK9 inhibitors reactivate p53 by downregulating iASPP. Cell Signal 2019; 67:109508. [PMID: 31866490 DOI: 10.1016/j.cellsig.2019.109508] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 12/24/2022]
Abstract
Loss of p53's tumor-suppressive function, either via TP53 mutation or hyperactive p53 inhibitory proteins, is one of the most frequent events in the development of human cancer. Here, we describe a strategy of pharmacologically inhibiting iASPP, a negative regulator of p53, to restore wild-type p53's tumor-suppressive function. iASPP knockdown in the colon cancer cell line HCT116 efficiently promoted p53's transcriptional activity and induced p53-dependent cell death, suggesting a key role for iASPP in silencing p53 in this cell line. Screening of a preclinical and clinical drug library using isogenic HCT116 cell models revealed that cyclin-dependent kinase 9 (CDK9) inhibitors preferentially inhibit p53+/+, rather than p53-/-, cells. Mechanistically, CDK9 inhibitors downregulated iASPP at the transcriptional level. This downregulation was dose- and time-dependent. CDK9 inhibitors further showed synergistic effects in killing p53+/+ HCT116 cells when combined with the MDM2 inhibitor Nutlin-3. In a large TCGA pan-cancer cohort, iASPP overexpression predicted poor overall survival (OS) in wild-type p53 patients, with worse OS observed when MDM2 was simultaneously overexpressed. Our study identifies CDK9 inhibitors as p53-reactivating agents, and proposes a strategy to treat cancer by efficiently reactivating p53 via the concurrent inhibition of iASPP and MDM2.
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Affiliation(s)
- Jiale Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Ying Liang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yun Tan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yigang Tang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Huaxin Song
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Zhengyuan Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yuntong Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Min Lu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Haematology, Rui Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China.
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Calvaruso M, Pucci G, Musso R, Bravatà V, Cammarata FP, Russo G, Forte GI, Minafra L. Nutraceutical Compounds as Sensitizers for Cancer Treatment in Radiation Therapy. Int J Mol Sci 2019; 20:ijms20215267. [PMID: 31652849 PMCID: PMC6861933 DOI: 10.3390/ijms20215267] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 02/05/2023] Open
Abstract
The improvement of diagnostic techniques and the efficacy of new therapies in clinical practice have allowed cancer patients to reach a higher chance to be cured together with a better quality of life. However, tumors still represent the second leading cause of death worldwide. On the contrary, chemotherapy and radiotherapy (RT) still lack treatment plans which take into account the biological features of tumors and depend on this for their response to treatment. Tumor cells' response to RT is strictly-connected to their radiosensitivity, namely, their ability to resist and to overcome cell damage induced by ionizing radiation (IR). For this reason, radiobiological research is focusing on the ability of chemical compounds to radiosensitize cancer cells so to make them more responsive to IR. In recent years, the interests of researchers have been focused on natural compounds that show antitumoral effects with limited collateral issues. Moreover, nutraceuticals are easy to recover and are thus less expensive. On these bases, several scientific projects have aimed to test also their ability to induce tumor radiosensitization both in vitro and in vivo. The goal of this review is to describe what is known about the role of nutraceuticals in radiotherapy, their use and their potential application.
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Affiliation(s)
- Marco Calvaruso
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Gaia Pucci
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Rosa Musso
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Valentina Bravatà
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Francesco P Cammarata
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Giorgio Russo
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Giusi I Forte
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
| | - Luigi Minafra
- Istituto di Bioimmagini e Fisiologia Molecolare-Consiglio Nazionale delle Ricerche (IBFM-CNR), 90015 Cefalù (PA), Italy.
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