1
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Donnio LM, Giglia-Mari G. Keep calm and reboot - how cells restart transcription after DNA damage and DNA repair. FEBS Lett 2024. [PMID: 38991979 DOI: 10.1002/1873-3468.14964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/12/2024] [Accepted: 04/21/2024] [Indexed: 07/13/2024]
Abstract
The effects of genotoxic agents on DNA and the processes involved in their removal have been thoroughly studied; however, very little is known about the mechanisms governing the reinstatement of cellular activities after DNA repair, despite restoration of the damage-induced block of transcription being essential for cell survival. In addition to impeding transcription, DNA lesions have the potential to disrupt the precise positioning of chromatin domains within the nucleus and alter the meticulously organized architecture of the nucleolus. Alongside the necessity of resuming transcription mediated by RNA polymerase 1 and 2 transcription, it is crucial to restore the structure of the nucleolus to facilitate optimal ribosome biogenesis and ensure efficient and error-free translation. Here, we examine the current understanding of how transcriptional activity from RNA polymerase 2 is reinstated following DNA repair completion and explore the mechanisms involved in reassembling the nucleolus to safeguard the correct progression of cellular functions. Given the lack of information on this vital function, this Review seeks to inspire researchers to explore deeper into this specific subject and offers essential suggestions on how to investigate this complex and nearly unexplored process further.
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Affiliation(s)
- Lise-Marie Donnio
- Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG_PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, 69008, France
| | - Giuseppina Giglia-Mari
- Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle (INMG_PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, 69008, France
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2
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Min S, Ji JH, Heo Y, Cho H. Transcriptional regulation and chromatin dynamics at DNA double-strand breaks. Exp Mol Med 2022; 54:1705-1712. [PMID: 36229590 PMCID: PMC9636152 DOI: 10.1038/s12276-022-00862-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic cells, DNA damage can occur at any time and at any chromatin locus, including loci at which active transcription is taking place. DNA double-strand breaks affect chromatin integrity and elicit a DNA damage response to facilitate repair of the DNA lesion. Actively transcribed genes near DNA lesions are transiently suppressed by crosstalk between DNA damage response factors and polycomb repressive complexes. Epigenetic modulation of the chromatin environment also contributes to efficient DNA damage response signaling and transcriptional repression. On the other hand, RNA transcripts produced in the G1 phase, as well as the active chromatin context of the lesion, appear to drive homologous recombination repair. Here, we discuss how the ISWI family of chromatin remodeling factors coordinates the DNA damage response and transcriptional repression, especially in transcriptionally active regions, highlighting the direct modulation of the epigenetic environment.
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Affiliation(s)
- Sunwoo Min
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Jae-Hoon Ji
- grid.267309.90000 0001 0629 5880Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, Texas, 78229-3000 USA
| | - Yungyeong Heo
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Hyeseong Cho
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
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3
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Fludarabine increases nuclease-free AAV- and CRISPR/Cas9-mediated homologous recombination in mice. Nat Biotechnol 2022; 40:1285-1294. [PMID: 35393561 DOI: 10.1038/s41587-022-01240-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Homologous recombination (HR)-based gene therapy using adeno-associated viruses (AAV-HR) without nucleases has several advantages over classic gene therapy, especially the potential for permanent transgene expression. However, the low efficiency of AAV-HR remains a major limitation. Here, we tested a series of small-molecule compounds and found that ribonucleotide reductase (RNR) inhibitors substantially enhance AAV-HR efficiency in mouse and human liver cell lines approximately threefold. Short-term administration of the RNR inhibitor fludarabine increased the in vivo efficiency of both non-nuclease- and CRISPR/Cas9-mediated AAV-HR two- to sevenfold in the murine liver, without causing overt toxicity. Fludarabine administration induced transient DNA damage signaling in both proliferating and quiescent hepatocytes. Notably, the majority of AAV-HR events occurred in non-proliferating hepatocytes in both fludarabine-treated and control mice, suggesting that the induction of transient DNA repair signaling in non-dividing hepatocytes was responsible for enhancing AAV-HR efficiency in mice. These results suggest that use of a clinically approved RNR inhibitor can potentiate AAV-HR-based genome-editing therapeutics.
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4
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Kang D, Liu Y, Song Y, Fang B, Zhang Q, Hu L. Triptolide Shows High Sensitivity and Low Toxicity Against Acute Myeloid Leukemia Cell Lines Through Inhibiting WSTF-RNAPII Complex. Front Oncol 2022; 12:811850. [PMID: 35251980 PMCID: PMC8888427 DOI: 10.3389/fonc.2022.811850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
Triptolide exhibits superior and broad-spectrum antitumor activity. However, the narrow safety window caused by the toxicity of triptolide limits its clinical applications. Although several characterized targets for triptolide are reported, the association between triptolide and its targets in cancer therapy is not fully understood. Here, we show that acute myeloid leukemia (AML) cell lines are sensitive to triptolide by constructing an in vitro cell and in vivo xenograft models. Meanwhile, the triptolide-induced hepatotoxicity increases with increasing dosages within the xenograft models. Additionally, the expression levels of WSTF-RPB1 are strongly associated with the sensitivity to triptolide in hematological cancer cells and can be downregulated in a dose and time-dependent manner. Finally, we show that optimizing dosing regimens can achieve the same pharmaceutical effect and reduce toxicity. In summary, this study aims to search for triptolide-sensitive cell lines as well as the underlying molecular mechanisms in order to broaden the safety window of triptolide; thus, increasing its clinical utility.
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Affiliation(s)
- Di Kang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Liu
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Song
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bingqian Fang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qichun Zhang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lihong Hu
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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5
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Rafiq A, Aashaq S, Jan I, Beigh MA. SIX1 transcription factor: A review of cellular functions and regulatory dynamics. Int J Biol Macromol 2021; 193:1151-1164. [PMID: 34742853 DOI: 10.1016/j.ijbiomac.2021.10.133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
Sine Oculis Homeobox 1 (SIX1) is a member of homeobox transcription factor family having pivotal roles in organismal development and differentiation. This protein functionally acts to regulate the expression of different proteins that are involved in organ development during embryogenesis and in disorders like cancer. Aberrant expression of this homeoprotein has therefore been reported in multiple pathological complexities like hearing impairment and renal anomalies during development and tumorigenesis in adult life. Most of the cellular effects mediated by it are mostly due to its role as a transcription factor. This review presents a concise narrative of its structure, interaction partners and cellular functions vis a vis its role in cancer. We thoroughly discuss the reported molecular mechanisms that govern its function in cellular milieu. Its post-translational regulation by phosphorylation and ubiquitination are also discussed with an emphasis on yet to be explored mechanistic insights regulating its molecular dynamics to fully comprehend its role in development and disease.
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Affiliation(s)
- Asma Rafiq
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India
| | - Sabreena Aashaq
- Department of Immunology and Molecular Medicine, Sher-i-Kashmir Institute of Medical Sciences, Soura, Srinagar JK-190011, India
| | - Iqra Jan
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India
| | - Mushtaq A Beigh
- Department of Nanotechnology, University of Kashmir, Hazratbal Campus, Srinagar JK-190006, India.
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6
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Min S, Lee HS, Ji JH, Heo Y, Kim Y, Chae S, Choi YW, Kang HC, Nakanishi M, Cho H. The chromatin remodeler RSF1 coordinates epigenetic marks for transcriptional repression and DSB repair. Nucleic Acids Res 2021; 49:12268-12283. [PMID: 34850117 PMCID: PMC8643642 DOI: 10.1093/nar/gkab1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
DNA lesions impact on local transcription and the damage-induced transcriptional repression facilitates efficient DNA repair. However, how chromatin dynamics cooperates with these two events remained largely unknown. We here show that histone H2A acetylation at K118 is enriched in transcriptionally active regions. Under DNA damage, the RSF1 chromatin remodeling factor recruits HDAC1 to DSB sites. The RSF1-HDAC1 complex induces the deacetylation of H2A(X)-K118 and its deacetylation is indispensable for the ubiquitination of histone H2A at K119. Accordingly, the acetylation mimetic H2A-K118Q suppressed the H2A-K119ub level, perturbing the transcriptional repression at DNA lesions. Intriguingly, deacetylation of H2AX at K118 also licenses the propagation of γH2AX and recruitment of MDC1. Consequently, the H2AX-K118Q limits DNA repair. Together, the RSF1-HDAC1 complex controls the traffic of the DNA damage response and transcription simultaneously in transcriptionally active chromatins. The interplay between chromatin remodelers and histone modifiers highlights the importance of chromatin versatility in the maintenance of genome integrity.
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Affiliation(s)
- Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, TX 78229-3000, USA
| | - Yungyeong Heo
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Yonghyeon Kim
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon 16499, Korea
| | - Yong Won Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
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7
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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8
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Hegde RS, Roychoudhury K, Pandey RN. The multi-functional eyes absent proteins. Crit Rev Biochem Mol Biol 2020; 55:372-385. [PMID: 32727223 PMCID: PMC7727457 DOI: 10.1080/10409238.2020.1796922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 07/14/2020] [Indexed: 12/13/2022]
Abstract
The Eyes Absent (EYA) proteins are the only known instance of a single polypeptide housing the following three separable biochemical activities: tyrosine phosphatase, threonine phosphatase, and transactivation. This uniquely positions the EYAs to participate in both transcriptional regulation and signal transduction pathways. But it also complicates the assignment of biological roles to individual biochemical activities through standard loss-of-function experiments. Nevertheless, there is an emerging literature linking developmental and pathological functions with the various EYA activities, and a growing list of disease states that might benefit from EYA-targeted therapeutics. There also remain multiple unresolved issues with significant implications for our understanding of how the EYAs might impact such ubiquitous signaling cascades as the MYC and Notch pathways. This review will describe the unique juxtaposition of biochemical activities in the EYAs, their interaction with signaling pathways and cellular processes, emerging evidence of roles in disease states, and the feasibility of therapeutic targeting of individual EYA activities. We will focus on the phosphatase activities of the vertebrate EYA proteins and will examine the current state of knowledge regarding: • substrates and signaling pathways affected by the EYA tyrosine phosphatase activity; • modes of regulation of the EYA tyrosine phosphatase activity; • signaling pathways that implicate the threonine phosphatase activity of the EYAs including a potential interaction with PP2A-B55α; • the interplay between the two phosphatase activities and the transactivation function of the EYAs; • disease states associated with the EYAs and the current state of development of EYA-targeted therapeutics.
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Affiliation(s)
- Rashmi S. Hegde
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
| | - Kaushik Roychoudhury
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
| | - Ram Naresh Pandey
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
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9
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Dong C, West KL, Tan XY, Li J, Ishibashi T, Yu CH, Sy SMH, Leung JWC, Huen MSY. Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin. Proc Natl Acad Sci U S A 2020; 117:17019-17030. [PMID: 32611815 PMCID: PMC7382216 DOI: 10.1073/pnas.2002193117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand breaks (DSBs) trigger transient pausing of nearby transcription, an emerging ATM-dependent response that suppresses chromosomal instability. We screened a chemical library designed to target the human kinome for new activities that mediate gene silencing on DSB-flanking chromatin, and have uncovered the DYRK1B kinase as an early respondent to DNA damage. We showed that DYRK1B is swiftly and transiently recruited to laser-microirradiated sites, and that genetic inactivation of DYRK1B or its kinase activity attenuated DSB-induced gene silencing and led to compromised DNA repair. Notably, global transcription shutdown alleviated DNA repair defects associated with DYRK1B loss, suggesting that DYRK1B is strictly required for DSB repair on active chromatin. We also found that DYRK1B mediates transcription silencing in part via phosphorylating and enforcing DSB accumulation of the histone methyltransferase EHMT2. Together, our findings unveil the DYRK1B signaling network as a key branch of mammalian DNA damage response circuitries, and establish the DYRK1B-EHMT2 axis as an effector that coordinates DSB repair on transcribed chromatin.
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Affiliation(s)
- Chao Dong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kirk L West
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Xin Yi Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Junshi Li
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China
| | - Cheng-Han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Shirley M H Sy
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205;
| | - Michael S Y Huen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China;
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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10
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Ta HQ, Dworak N, Ivey ML, Roller DG, Gioeli D. AR phosphorylation and CHK2 kinase activity regulates IR-stabilized AR-CHK2 interaction and prostate cancer survival. eLife 2020; 9:51378. [PMID: 32579110 PMCID: PMC7338052 DOI: 10.7554/elife.51378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
We have previously demonstrated that checkpoint kinase 2 (CHK2) is a critical negative regulator of androgen receptor (AR) transcriptional activity, prostate cancer (PCa) cell growth, and androgen sensitivity. We have now uncovered that the AR directly interacts with CHK2 and ionizing radiation (IR) increases this interaction. This IR-induced increase in AR-CHK2 interactions requires AR phosphorylation and CHK2 kinase activity. PCa associated CHK2 mutants with impaired kinase activity reduced IR-induced AR-CHK2 interactions. The destabilization of AR - CHK2 interactions induced by CHK2 variants impairs CHK2 negative regulation of cell growth. CHK2 depletion increases transcription of DNAPK and RAD54, increases clonogenic survival, and increases resolution of DNA double strand breaks. The data support a model where CHK2 sequesters the AR through direct binding decreasing AR transcription and suppressing PCa cell growth. CHK2 mutation or loss of expression thereby leads to increased AR transcriptional activity and survival in response to DNA damage.
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Affiliation(s)
- Huy Q Ta
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, United States
| | - Natalia Dworak
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, United States
| | - Melissa L Ivey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, United States
| | - Devin G Roller
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, United States
| | - Daniel Gioeli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, United States.,Cancer Center Member, University of Virginia, Charlottesville, United States
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11
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Kaplan N, Wang J, Wray B, Patel P, Yang W, Peng H, Lavker RM. Single-Cell RNA Transcriptome Helps Define the Limbal/Corneal Epithelial Stem/Early Transit Amplifying Cells and How Autophagy Affects This Population. Invest Ophthalmol Vis Sci 2019; 60:3570-3583. [PMID: 31419300 PMCID: PMC6701873 DOI: 10.1167/iovs.19-27656] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Single-cell RNA-sequencing (scRNA-seq) was used to interrogate the relatively rare stem (SC) and early transit amplifying (TA) cell populations in limbal/corneal epithelia from wild-type and autophagy-compromised mice. Methods We conducted scRNA-seq on ocular anterior segmental tissue from wild-type and beclin 1–deficient (beclin1+/−) mice, using a 10X Gemomics pipeline. Cell populations were distinguished by t-distributed stochastic neighbor embedding. Seurat analysis was conducted to compare gene expression profiles between these two groups of mice. Differential protein expression patterns were validated by immunofluorescence staining and immunoblotting. Results Unbiased clustering detected 10 distinct populations: three clusters of mesenchymal and seven clusters of epithelial cells, based on their unique molecular signatures. A discrete group of mesenchymal cells expressed genes associated with corneal stromal SCs. We identified three limbal/corneal epithelial cell subpopulations designated as stem/early TA, mature TA, and differentiated corneal epithelial cells. Thioredoxin-interacting protein and PDZ-binding kinase (PBK) were identified as novel regulators of stem/early TA cell quiescence. PBK arrested corneal epithelial cells in G2/M phase of the cell cycle. Beclin1+/− mice displayed a decrease in proliferation-associated (Ki67, Lrig1) and stress-response (H2ax) genes. The most increased gene in beclin1+/− mice was transcription factor ATF3, which negatively regulates limbal epithelial cell proliferation. Conclusions Establishment of a comprehensive atlas of genes expressed by stromal and epithelial cells from limbus and cornea forms the foundation for unraveling regulatory networks among these distinct tissues. Similarly, scRNA-seq profiling of the anterior segmental epithelia from wild-type and autophagy-deficient mice provides new insights into how autophagy influences proliferation in these tissues.
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Affiliation(s)
- Nihal Kaplan
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Junyi Wang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States.,Department of Ophthalmology, Ophthalmology and Visual Science Key Lab of PLA, Chinese PLA General Hospital, Beijing, China
| | - Brian Wray
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Priyam Patel
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Wending Yang
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Han Peng
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Robert M Lavker
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
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