1
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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2
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Vogt M, Dudvarski Stankovic N, Cruz Garcia Y, Hofstetter J, Schneider K, Kuybu F, Hauck T, Adhikari B, Hamann A, Rocca Y, Grysczyk L, Martin B, Gebhardt-Wolf A, Wiegering A, Diefenbacher M, Gasteiger G, Knapp S, Saur D, Eilers M, Rosenfeldt M, Erhard F, Vos SM, Wolf E. Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2. Gut 2024:gutjnl-2023-331519. [PMID: 38821858 DOI: 10.1136/gutjnl-2023-331519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/15/2024] [Indexed: 06/02/2024]
Abstract
OBJECTIVE The hallmark oncogene MYC drives the progression of most tumours, but direct inhibition of MYC by a small-molecule drug has not reached clinical testing. MYC is a transcription factor that depends on several binding partners to function. We therefore explored the possibility of targeting MYC via its interactome in pancreatic ductal adenocarcinoma (PDAC). DESIGN To identify the most suitable targets among all MYC binding partners, we constructed a targeted shRNA library and performed screens in cultured PDAC cells and tumours in mice. RESULTS Unexpectedly, many MYC binding partners were found to be important for cultured PDAC cells but dispensable in vivo. However, some were also essential for tumours in their natural environment and, among these, the ATPases RUVBL1 and RUVBL2 ranked first. Degradation of RUVBL1 by the auxin-degron system led to the arrest of cultured PDAC cells but not untransformed cells and to complete tumour regression in mice, which was preceded by immune cell infiltration. Mechanistically, RUVBL1 was required for MYC to establish oncogenic and immunoevasive gene expression identifying the RUVBL1/2 complex as a druggable vulnerability in MYC-driven cancer. CONCLUSION One implication of our study is that PDAC cell dependencies are strongly influenced by the environment, so genetic screens should be performed in vitro and in vivo. Moreover, the auxin-degron system can be applied in a PDAC model, allowing target validation in living mice. Finally, by revealing the nuclear functions of the RUVBL1/2 complex, our study presents a pharmaceutical strategy to render pancreatic cancers potentially susceptible to immunotherapy.
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Affiliation(s)
- Markus Vogt
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Nevenka Dudvarski Stankovic
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Yiliam Cruz Garcia
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Katharina Schneider
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Filiz Kuybu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Theresa Hauck
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bikash Adhikari
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Anton Hamann
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Yamila Rocca
- Max Planck Research Group and Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Lara Grysczyk
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Benedikt Martin
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Anneli Gebhardt-Wolf
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Armin Wiegering
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery, University Hospital Würzburg, Würzburg, Germany
| | - Markus Diefenbacher
- Comprehensive Pneumology Center (CPC)/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL/CPC-M), Munich, Germany
- Ludwig-Maximilian-Universität München (LMU), Munich, Germany
| | - Georg Gasteiger
- Max Planck Research Group and Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Dieter Saur
- Institute of Translational Cancer Research, TUM School of Medicine and Health, Munich, Germany
| | - Martin Eilers
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | | | - Florian Erhard
- Computational Systems Virology and Bioinformatics, Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Elmar Wolf
- Cancer Systems Biology Group, Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
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3
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Thatikonda V, Supper V, Wachter J, Kaya O, Kombara A, Bilgilier C, Ravichandran MC, Lipp JJ, Sharma R, Badertscher L, Boghossian AS, Rees MG, Ronan MM, Roth JA, Grosche S, Neumüller RA, Mair B, Mauri F, Popa A. Genetic dependencies associated with transcription factor activities in human cancer cell lines. Cell Rep 2024; 43:114175. [PMID: 38691456 DOI: 10.1016/j.celrep.2024.114175] [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: 03/14/2023] [Revised: 02/02/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024] Open
Abstract
Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focus on TF activity (TFa) as a biomarker for cell-line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss of function of a given gene (i.e., genetic dependencies [GDs]). Our linear-regression-based framework identifies 3,047 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which are then cross-examined for impact on survival in patient cohorts. One of the most prominent biomarkers is TEAD1 activity, whose associations with its predicted GDs are validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology.
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Affiliation(s)
- Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
| | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Johannes Wachter
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Onur Kaya
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ceren Bilgilier
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | | | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Rahul Sharma
- Myllia Biotechnology GmbH, Am Kanal 27, Vienna 1110, Austria
| | | | | | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Melissa M Ronan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Grosche
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Federico Mauri
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
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4
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Dong J, Scott TG, Mukherjee R, Guertin MJ. ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594008. [PMID: 38798607 PMCID: PMC11118474 DOI: 10.1101/2024.05.13.594008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. ZNF143 binds the promoter of nearly all its activated target genes. ZNF143 also binds near the site of genic transcription initiation to directly repress a subset of genes. Although ZNF143 stimulates initiation at ZNF143-repressed genes (i.e. those that increase expression upon ZNF143 depletion), the molecular context of binding leads to cis repression. ZNF143 competes with other more efficient activators for promoter access, physically occludes transcription initiation sites and promoter-proximal sequence elements, and acts as a molecular roadblock to RNA Polymerases during early elongation. The term context specific is often invoked to describe transcription factors that have both activation and repression functions. We define the context and molecular mechanisms of ZNF143-mediated cis activation and repression.
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Affiliation(s)
- Jinhong Dong
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
| | - Thomas G Scott
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rudradeep Mukherjee
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
| | - Michael J Guertin
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America
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5
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Li M, Yang Y, Wang P, Que W, Zhong L, Cai Z, Liu Y, Yang L, Liu Y. Transcriptome dynamics of the BHK21 cell line in response to human coronavirus OC43 infection. Microbiol Res 2024; 285:127750. [PMID: 38761489 DOI: 10.1016/j.micres.2024.127750] [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: 03/19/2024] [Revised: 04/16/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024]
Abstract
The progress of viral infection involves numerous transcriptional regulatory events. The identification of the newly synthesized transcripts helps us to understand the replication mechanisms and pathogenesis of the virus. Here, we utilized a time-resolved technique called metabolic RNA labeling approach called thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) to differentially elucidate the levels of steady-state and newly synthesized RNAs of BHK21 cell line in response to human coronavirus OC43 (HCoV-OC43) infection. Our results showed that the Wnt/β-catenin signaling pathway was significantly enriched with the newly synthesized transcripts of BHK21 cell line in response to HCoV-OC43 infection. Moreover, inhibition of the Wnt pathway promoted viral replication in the early stage of infection, but inhibited it in the later stage of infection. Furthermore, remdesivir inhibits the upregulation of the Wnt/β-catenin signaling pathway induced by early infection with HCoV-OC43. Collectively, our study showed the diverse roles of Wnt/β-catenin pathway at different stages of HCoV-OC43 infection, suggesting a potential target for the antiviral treatment. In addition, although infection with HCoV-OC43 induces cytopathic effects in BHK21 cells, inhibiting apoptosis does not affect the intracellular replication of the virus. Monitoring newly synthesized RNA based on such time-resolved approach is a highly promising method for studying the mechanism of viral infections.
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Affiliation(s)
- Mianhuan Li
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China; Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China
| | - Yang Yang
- Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China
| | - Pusen Wang
- Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China
| | - Weitao Que
- Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China
| | - Lin Zhong
- Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China
| | - Zhao Cai
- Shenzhen Mindray Bio-Medical Electronics Co.,Ltd, Shenzhen 518057, People's Republic of China
| | - Yang Liu
- Southern University of Science and Technology Hospital, Shenzhen 518055, People's Republic of China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China; Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China.
| | - Yingxia Liu
- Shenzhen Third People's Hospital, National Clinical Research Centre for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, People's Republic of China.
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6
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Müller JM, Moos K, Baar T, Maier KC, Zumer K, Tresch A. Nuclear export is a limiting factor in eukaryotic mRNA metabolism. PLoS Comput Biol 2024; 20:e1012059. [PMID: 38753883 PMCID: PMC11135743 DOI: 10.1371/journal.pcbi.1012059] [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: 10/20/2023] [Revised: 05/29/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments of human cancer cells. We develop a model that reliably quantifies mRNA-specific synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3'UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.
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Affiliation(s)
- Jason M. Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Katharina Moos
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Till Baar
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kerstin C. Maier
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kristina Zumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne, Germany
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7
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Huang QX, Fan DM, Zheng ZZ, Ran T, Bai A, Xiao RQ, Hu GS, Liu W. Peptide Inhibitor Targeting the Extraterminal Domain in BRD4 Potently Suppresses Breast Cancer Both In Vitro and In Vivo. J Med Chem 2024; 67:6658-6672. [PMID: 38569135 PMCID: PMC11056977 DOI: 10.1021/acs.jmedchem.4c00141] [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: 01/17/2024] [Revised: 02/27/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
BRD4 is associated with a variety of human diseases, including breast cancer. The crucial roles of amino-terminal bromodomains (BDs) of BRD4 in binding with acetylated histones to regulate oncogene expression make them promising drug targets. However, adverse events impede the development of the BD inhibitors. BRD4 adopts an extraterminal (ET) domain, which recruits proteins to drive oncogene expression. We discovered a peptide inhibitor PiET targeting the ET domain to disrupt BRD4/JMJD6 interaction, a protein complex critical in oncogene expression and breast cancer. The cell-permeable form of PiET, TAT-PiET, and PROTAC-modified TAT-PiET, TAT-PiET-PROTAC, potently inhibits the expression of BRD4/JMJD6 target genes and breast cancer cell growth. Combination therapy with TAT-PiET/TAT-PiET-PROTAC and JQ1, iJMJD6, or Fulvestrant exhibits synergistic effects. TAT-PiET or TAT-PiET-PROTAC treatment overcomes endocrine therapy resistance in ERα-positive breast cancer cells. Taken together, we demonstrated that targeting the ET domain is effective in suppressing breast cancer, providing a therapeutic avenue in the clinic.
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Affiliation(s)
- Qi-xuan Huang
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Da-meng Fan
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zao-zao Zheng
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ting Ran
- Bioland
Laboratory (Guangzhou Regenerative Medicine and Health—Guangdong
Laboratory), KaiYuan
Road, Guangzhou, Guangdong 510530, China
| | - Ao Bai
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Rong-quan Xiao
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Guo-sheng Hu
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
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8
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Jin C, Einig E, Xu W, Kollampally RB, Schlosser A, Flentje M, Popov N. The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage. Nucleic Acids Res 2024; 52:3011-3030. [PMID: 38227944 PMCID: PMC11024517 DOI: 10.1093/nar/gkae004] [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: 04/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
DNA replication is a major source of endogenous DNA damage in tumor cells and a key target of cellular response to genotoxic stress. DNA replication can be deregulated by oncoproteins, such as transcription factor MYC, aberrantly activated in many human cancers. MYC is stringently regulated by the ubiquitin system - for example, ubiquitination controls recruitment of the elongation factor PAF1c, instrumental in MYC activity. Curiously, a key MYC-targeting deubiquitinase USP28 also controls cellular response to DNA damage via the mediator protein 53BP1. USP28 forms stable dimers, but the biological role of USP28 dimerization is unknown. We show here that dimerization limits USP28 activity and restricts recruitment of PAF1c by MYC. Expression of monomeric USP28 stabilizes MYC and promotes PAF1c recruitment, leading to ectopic DNA synthesis and replication-associated DNA damage. USP28 dimerization is stimulated by 53BP1, which selectively binds USP28 dimers. Genotoxic stress diminishes 53BP1-USP28 interaction, promotes disassembly of USP28 dimers and stimulates PAF1c recruitment by MYC. This triggers firing of DNA replication origins during early response to genotoxins and exacerbates DNA damage. We propose that dimerization of USP28 prevents ectopic DNA replication at transcriptionally active chromatin to maintain genome stability.
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Affiliation(s)
- Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Wenshan Xu
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Ravi Babu Kollampally
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str 2, 97080 Würzburg, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
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9
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Layden HM, Ellis JD, Bomber ML, Bartlett LN, Hiebert SW, Stengel KR. Mutant FOXO1 controls an oncogenic network via enhancer accessibility. CELL GENOMICS 2024; 4:100537. [PMID: 38604128 PMCID: PMC11019358 DOI: 10.1016/j.xgen.2024.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/21/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Transcriptional dysregulation is a hallmark of diffuse large B cell lymphoma (DLBCL), as transcriptional regulators are frequently mutated. However, our mechanistic understanding of how normal transcriptional programs are co-opted in DLBCL has been hindered by a lack of methodologies that provide the temporal resolution required to separate direct and indirect effects on transcriptional control. We applied a chemical-genetic approach to engineer the inducible degradation of the transcription factor FOXO1, which is recurrently mutated (mFOXO1) in DLBCL. The combination of rapid degradation of mFOXO1, nascent transcript detection, and assessment of chromatin accessibility allowed us to identify the direct targets of mFOXO1. mFOXO1 was required to maintain accessibility at specific enhancers associated with multiple oncogenes, and mFOXO1 degradation impaired RNA polymerase pause-release at some targets. Wild-type FOXO1 appeared to weakly regulate many of the same targets as mFOXO1 and was able to complement the degradation of mFOXO1 in the context of AKT inhibition.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jacob D Ellis
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Luke N Bartlett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA.
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY, USA.
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10
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Tan VWT, Salmi TM, Karamalakis AP, Gillespie A, Ong AJS, Balic JJ, Chan YC, Bladen CE, Brown KK, Dawson MA, Cox AG. SLAM-ITseq identifies that Nrf2 induces liver regeneration through the pentose phosphate pathway. Dev Cell 2024; 59:898-910.e6. [PMID: 38366599 DOI: 10.1016/j.devcel.2024.01.024] [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: 04/28/2023] [Revised: 12/07/2023] [Accepted: 01/24/2024] [Indexed: 02/18/2024]
Abstract
The liver exhibits a remarkable capacity to regenerate following injury. Despite this unique attribute, toxic injury is a leading cause of liver failure. The temporal processes by which the liver senses injury and initiates regeneration remain unclear. Here, we developed a transgenic zebrafish model wherein hepatocyte-specific expression of uracil phosphoribosyltransferase (UPRT) enabled the implementation of SLAM-ITseq to investigate the nascent transcriptome during initiation of liver injury and regeneration. Using this approach, we identified a rapid metabolic transition from the fed to the fasted state that was followed by induction of the nuclear erythroid 2-related factor (Nrf2) antioxidant program. We find that activation of Nrf2 in hepatocytes is required to induce the pentose phosphate pathway (PPP) and improve survival following liver injury. Mechanistically, we demonstrate that inhibition of the PPP disrupts nucleotide biosynthesis to prevent liver regeneration. Together, these studies provide fundamental insights into the mechanism by which early metabolic adaptation to injury facilitates tissue regeneration.
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Affiliation(s)
- Vicky W T Tan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Talhah M Salmi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Anthony P Karamalakis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Andrea Gillespie
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Athena Jessica S Ong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jesse J Balic
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Cerys E Bladen
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kristin K Brown
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Andrew G Cox
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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11
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Su BG, Vos SM. Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing. Mol Cell 2024; 84:1243-1256.e5. [PMID: 38401543 PMCID: PMC10997474 DOI: 10.1016/j.molcel.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.
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Affiliation(s)
- Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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12
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Gold S, Shilatifard A. Therapeutic targeting of BET bromodomain and other epigenetic acetylrecognition domain-containing factors. Curr Opin Genet Dev 2024; 86:102181. [PMID: 38564841 DOI: 10.1016/j.gde.2024.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
Development of cancer therapies targeting chromatin modifiers and transcriptional regulatory factors is rapidly expanding to include new targets and novel targeting strategies. At the same time, basic molecular research continues to refine our understanding of the epigenetic mechanisms regulating transcription, gene expression, and oncogenesis. This mini-review focuses on cancer therapies targeting the chromatin-associated factors that recognize histone lysine acetylation. Recently reported safety and efficacy are discussed for inhibitors targeting the bromodomains of bromodomain and extraterminal domain (BET) family proteins. In light of recent results indicating that the transcriptional regulator BRD4-PTEFb can function independently of BRD4's bromodomains, the clinical trial performance of these BET inhibitors is placed in a broader context of existing and potential strategies for targeting BRD4-PTEFb. Recently developed therapies targeting bromodomain-containing factors within the SWI/SNF (BAF) family of chromatin remodeling complexes are discussed, as is the potential for targeting the bromodomain-containing transcription factor TAF1 and the YEATS acetylrecognition domain-containing factor GAS41. Recent findings regarding the selectivity and combinatorial specificity of acetylrecognition are highlighted. In conclusion, the potential for further development is discussed with a focus on proximity-based therapies targeting this class of epigenetic factors.
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Affiliation(s)
- Sarah Gold
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. https://twitter.com/@rwx_life
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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13
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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14
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Behrens K, Brajanovski N, Xu Z, Viney EM, DiRago L, Hediyeh-Zadeh S, Davis MJ, Pearson RB, Sanij E, Alexander WS, Ng AP. ERG and c-MYC regulate a critical gene network in BCR::ABL1-driven B cell acute lymphoblastic leukemia. SCIENCE ADVANCES 2024; 10:eadj8803. [PMID: 38457494 PMCID: PMC10923517 DOI: 10.1126/sciadv.adj8803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/31/2024] [Indexed: 03/10/2024]
Abstract
Philadelphia chromosome-positive B cell acute lymphoblastic leukemia (B-ALL), characterized by the BCR::ABL1 fusion gene, remains a poor prognosis cancer needing new therapeutic approaches. Transcriptomic profiling identified up-regulation of oncogenic transcription factors ERG and c-MYC in BCR::ABL1 B-ALL with ERG and c-MYC required for BCR::ABL1 B-ALL in murine and human models. Profiling of ERG- and c-MYC-dependent gene expression and analysis of ChIP-seq data established ERG and c-MYC coordinate a regulatory network in BCR::ABL1 B-ALL that controls expression of genes involved in several biological processes. Prominent was control of ribosome biogenesis, including expression of RNA polymerase I (POL I) subunits, the importance of which was validated by inhibition of BCR::ABL1 cells by POL I inhibitors, including CX-5461, that prevents promoter recruitment and transcription initiation by POL I. Our results reveal an essential ERG- and c-MYC-dependent transcriptional network involved in regulation of metabolic and ribosome biogenesis pathways in BCR::ABL1 B-ALL, from which previously unidentified vulnerabilities and therapeutic targets may emerge.
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Affiliation(s)
- Kira Behrens
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Natalie Brajanovski
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Zhen Xu
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Elizabeth M. Viney
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ladina DiRago
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Melissa J. Davis
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Australia
- The Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Richard B. Pearson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia
| | - Elaine Sanij
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia
- St. Vincent’s Institute of Medical Research, Fitzroy, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Warren S. Alexander
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Ashley P. Ng
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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15
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Venkadakrishnan VB, Presser AG, Singh R, Booker MA, Traphagen NA, Weng K, Voss NC, Mahadevan NR, Mizuno K, Puca L, Idahor O, Ku SY, Bakht MK, Borah AA, Herbert ZT, Tolstorukov MY, Barbie DA, Rickman DS, Brown M, Beltran H. Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes. RESEARCH SQUARE 2024:rs.3.rs-3935288. [PMID: 38405800 PMCID: PMC10889062 DOI: 10.21203/rs.3.rs-3935288/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase and emerging therapeutic target that is overexpressed in most castration-resistant prostate cancers and implicated as a driver of disease progression and resistance to hormonal therapies. Here we define the lineage-specific action and differential activity of EZH2 in both prostate adenocarcinoma (PRAD) and neuroendocrine prostate cancer (NEPC) subtypes of advanced prostate cancer to better understand the role of EZH2 in modulating differentiation, lineage plasticity, and to identify mediators of response and resistance to EZH2 inhibitor therapy. Mechanistically, EZH2 modulates bivalent genes that results in upregulation of NEPC-associated transcriptional drivers (e.g., ASCL1) and neuronal gene programs, and leads to forward differentiation after targeting EZH2 in NEPC. Subtype-specific downstream effects of EZH2 inhibition on cell cycle genes support the potential rationale for co-targeting cyclin/CDK to overcome resistance to EZH2 inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Loredana Puca
- Division of Medical Oncology, Weill Cornell Medicine
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16
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Chen M, Guo X, Guo J, Shi C, Wu Y, Chen L, Mao R, Fan Y. Cytoplasmic Accumulation of Histones Induced by BET Inhibition Protects Cells from C9orf72 Poly(PR)-Induced Cell Death. Adv Biol (Weinh) 2024; 8:e2300334. [PMID: 38213020 DOI: 10.1002/adbi.202300334] [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: 07/14/2023] [Revised: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Repeat dipeptides such as poly(proline-arginine) (polyPR) are generated from the hexanucleotide GGGGCC repeat expansions in the C9orf72 gene. These dipeptides are often considered as the genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In the study, fluorescein isothiocyanate (FITC) labeled PR20 is used to investigate PR20-induced cell death. The findings reveal that the cell death induced by PR20 is dependent on its nuclear distribution and can be blocked by a nuclear import inhibitor called importazole. Further investigation reveals that BRD4 inhibitors, such as JQ-1 and I-BET762, restrict cytoplasmic localization of PR20, thereby reducing its cytotoxic effect. Mechanistically, the inhibition of BRD4 leads to an increase in the expression of numerous histones, resulting in the accumulation of histones in the cytoplasm. These cytoplasmic histones associate with PR20 and limit its distribution within the nucleus. Notably, the ectopic expression of histones alone is enough to confer protection to cells treated with PR20. In addition, phenylephrine (PE) induces cellular hypertrophy and cytoplasmic distribution of histone, which also helps protect cells from PR20-induced cell death. The research suggests that temporarily inducing the presence of cytoplasmic histones may alleviate the neurotoxic effects of dipeptide repeat proteins.
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Affiliation(s)
- Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xiaohong Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Jinjing Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Conglin Shi
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yuanyuan Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
| | - Liuting Chen
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, 226001, China
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, 226001, China
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17
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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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18
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Li S, Wang Y, van der Stoel M, Zhou X, Madhusudan S, Kanerva K, Nguyen VD, Eskici N, Olkkonen VM, Zhou Y, Raivio T, Ikonen E. HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells. Genome Biol 2024; 25:58. [PMID: 38409044 PMCID: PMC10895734 DOI: 10.1186/s13059-024-03187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in human embryonic stem cells (hESCs). Here, we develop HiHo-AID2, a streamlined procedure for rapid, one-step generation of human cancer and hESC lines with high homozygous degron-tagging efficiency based on an optimized AID2 system and homology-directed repair enhancers. We demonstrate its application for rapid and inducible functional inactivation of twelve endogenous target proteins in five cell lines, including targets with diverse expression levels and functions in hESCs and cells differentiated from hESCs.
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Affiliation(s)
- Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
| | - Yafei Wang
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Miesje van der Stoel
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Xin Zhou
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Shrinidhi Madhusudan
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kristiina Kanerva
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Van Dien Nguyen
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nazli Eskici
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Vesa M Olkkonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - You Zhou
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
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19
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Sepulveda GP, Gushchanskaia ES, Mora-Martin A, Esse R, Nikorich I, Ceballos A, Kwan J, Blum BC, Dholiya P, Emili A, Perissi V, Cardamone MD, Grishok A. DOT1L stimulates MYC/Mondo transcription factor activity by promoting its degradation cycle on chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579191. [PMID: 38370658 PMCID: PMC10871221 DOI: 10.1101/2024.02.06.579191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The proto-oncogene c-MYC is a key representative of the MYC transcription factor network regulating growth and metabolism. MML-1 (Myc- and Mondo-like) is its homolog in C. elegans. The functional and molecular cooperation between c-MYC and H3 lysine 79 methyltransferase DOT1L was demonstrated in several human cancer types, and we have earlier discovered the connection between C. elegans MML-1 and DOT-1.1. Here, we demonstrate the critical role of DOT1L/DOT-1.1 in regulating c-MYC/MML-1 target genes genome-wide by ensuring the removal of "spent" transcription factors from chromatin by the nuclear proteasome. Moreover, we uncover a previously unrecognized proteolytic activity of DOT1L, which may facilitate c-MYC turnover. This new mechanism of c-MYC regulation by DOT1L may lead to the development of new approaches for cancer treatment.
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Affiliation(s)
- Gian P. Sepulveda
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ekaterina S. Gushchanskaia
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Tessera Therapeutics, Somerville, MA, 02143, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Ruben Esse
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Cell and Gene Therapy Catapult, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iana Nikorich
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Present address: Research Unit, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Benjamin C. Blum
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Prakruti Dholiya
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
- Division of Computational Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: OHSU Knight Cancer Institute, School of Medicine, Portland, OR, 97239, USA
| | - Valentina Perissi
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Maria D. Cardamone
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Korro Bio Inc., Cambridge, MA, 02139, USA
| | - Alla Grishok
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Genome Science Institute, Boston University, Boston, MA, 02118, USA
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20
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Dansu DK, Sauma S, Huang D, Li M, Moyon S, Casaccia P. The epigenetic landscape of oligodendrocyte progenitors changes with time. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579145. [PMID: 38501119 PMCID: PMC10946295 DOI: 10.1101/2024.02.06.579145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
SUMMARY Dansu et al. identify distinct histone H4 modifications as potential mechanism underlying the functional differences between adult and neonatal progenitors. While H4K8ac favors the expression of differentiation genes, their expression is halted by H4K20me3. Adult oligodendrocyte progenitors (aOPCs) generate myelinating oligodendrocytes, like neonatal progenitors (nOPCs), but they also display unique functional features. Here, using RNA-sequencing, unbiased histone proteomics analysis and ChIP-sequencing, we define the transcripts and histone marks underlying the unique properties of aOPCs. We describe the lower proliferative capacity and higher levels of expression of oligodendrocyte specific genes in aOPCs compared to nOPCs, as well as the greater levels of H4 histone marks. We also report increased occupancy of the H4K8ac mark at chromatin locations corresponding to oligodendrocyte-specific transcription factors and lipid metabolism genes. Pharmacological inhibition of H4K8ac deposition reduces the levels of these transcripts in aOPCs, rendering their transcriptome more similar to nOPCs. The repressive H4K20me3 mark is also higher in aOPCs compared to nOPCs and pharmacological inhibition of its deposition results in increased levels of genes related to the mature oligodendrocyte state. Overall, this study identifies two histone marks which are important for the unique transcriptional and functional identity of aOPCs.
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21
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Zhang X, Zhang M, Sun H, Wang X, Wang X, Sheng W, Xu M. The role of transcription factors in the crosstalk between cancer-associated fibroblasts and tumor cells. J Adv Res 2024:S2090-1232(24)00046-8. [PMID: 38309692 DOI: 10.1016/j.jare.2024.01.033] [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: 11/29/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Transcription factors (TFs) fulfill a critical role in the formation and maintenance of different cell types during the developmental process as well as disease. It is believed that cancer-associated fibroblasts (CAFs) are activation status of tissue-resident fibroblasts or derived from form other cell types via transdifferentiation or dedifferentiation. Despite a subgroup of CAFs exhibit anti-cancer effects, most of them are reported to exert effects on tumor progression, further indicating their heterogeneous origin. AIM OF REVIEW This review aimed to summarize and review the roles of TFs in the reciprocal crosstalk between CAFs and tumor cells, discuss the emerging mechanisms, and their roles in cell-fate decision, cellular reprogramming and advancing our understanding of the gene regulatory networks over the period of cancer initiation and progression. KEY SCIENTIFIC CONCEPTS OF REVIEW This manuscript delves into the key contributory factors of TFs that are involved in activating CAFs and maintaining their unique states. Additionally, it explores how TFs play a pivotal and multifaceted role in the reciprocal crosstalk between CAFs and tumor cells. This includes their involvement in processes such as epithelial-mesenchymal transition (EMT), proliferation, invasion, and metastasis, as well as metabolic reprogramming. TFs also have a role in constructing an immunosuppressive microenvironment, inducing resistance to radiation and chemotherapy, facilitating angiogenesis, and even 'educating' CAFs to support the malignancies of tumor cells. Furthermore, this manuscript delves into the current status of TF-targeted therapy and considers the future directions of TFs in conjunction with anti-CAFs therapies to address the challenges in clinical cancer treatment.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Meng Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Hui Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xu Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Xin Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China
| | - Weiqi Sheng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Institute of Pathology, Fudan University, Shanghai 200032, China.
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22
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Li Z, Huang Y, Hung TI, Sun J, Aispuro D, Chen B, Guevara N, Ji F, Cong X, Zhu L, Wang S, Guo Z, Chang CE, Xue M. MYC-Targeting Inhibitors Generated from a Stereodiversified Bicyclic Peptide Library. J Am Chem Soc 2024; 146:1356-1363. [PMID: 38170904 PMCID: PMC10797614 DOI: 10.1021/jacs.3c09615] [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: 09/02/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
Here, we present the second generation of our bicyclic peptide library (NTB), featuring a stereodiversified structure and a simplified construction strategy. We utilized a tandem ring-opening metathesis and ring-closing metathesis reaction (ROM-RCM) to cyclize the linear peptide library in a single step, representing the first reported instance of this reaction being applied to the preparation of macrocyclic peptides. Moreover, the resulting bicyclic peptide can be easily linearized for MS/MS sequencing with a one-step deallylation process. We employed this library to screen against the E363-R378 epitope of MYC and identified several MYC-targeting bicyclic peptides. Subsequent in vitro cell studies demonstrated that one candidate, NT-B2R, effectively suppressed MYC transcription activities and cell proliferation.
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Affiliation(s)
- Zhonghan Li
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Yi Huang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Ta I Hung
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Jianan Sun
- Environmental
Toxicology Graduate Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Desiree Aispuro
- Environmental
Toxicology Graduate Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Boxi Chen
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Nathan Guevara
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Fei Ji
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Xu Cong
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Lingchao Zhu
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Siwen Wang
- Environmental
Toxicology Graduate Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Zhili Guo
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Chia-en Chang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
- Environmental
Toxicology Graduate Program, University
of California, Riverside, Riverside, California 92521, United States
| | - Min Xue
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
- Environmental
Toxicology Graduate Program, University
of California, Riverside, Riverside, California 92521, United States
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23
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Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I, Chambers C, Loeza Cabrera M, Hoffman D, Parchem RJ, Wang W, Nencka R, Barbieri E, Hodges HC. Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF. Nucleic Acids Res 2024; 52:4-21. [PMID: 37993417 PMCID: PMC10783513 DOI: 10.1093/nar/gkad1081] [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: 08/23/2023] [Revised: 09/29/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023] Open
Abstract
Several cancer core regulatory circuitries (CRCs) depend on the sustained generation of DNA accessibility by SWI/SNF chromatin remodelers. However, the window when SWI/SNF is acutely essential in these settings has not been identified. Here we used neuroblastoma (NB) cells to model and dissect the relationship between cell-cycle progression and SWI/SNF ATPase activity. We find that SWI/SNF inactivation impairs coordinated occupancy of non-pioneer CRC members at enhancers within 1 hour, rapidly breaking their autoregulation. By precisely timing inhibitor treatment following synchronization, we show that SWI/SNF is dispensable for survival in S and G2/M, but becomes acutely essential only during G1 phase. We furthermore developed a new approach to analyze the oscillating patterns of genome-wide DNA accessibility across the cell cycle, which revealed that SWI/SNF-dependent CRC binding sites are enriched at enhancers with peak accessibility during G1 phase, where they activate genes involved in cell-cycle progression. SWI/SNF inhibition strongly impairs G1-S transition and potentiates the ability of retinoids used clinically to induce cell-cycle exit. Similar cell-cycle effects in diverse SWI/SNF-addicted settings highlight G1-S transition as a common cause of SWI/SNF dependency. Our results illustrate that deeper knowledge of the temporal patterns of enhancer-related dependencies may aid the rational targeting of addicted cancers.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Ling Tao
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew D Montierth
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Yuen San Chan
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Ivanshi Patel
- Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Courtney Chambers
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Translational Biology and Molecular Medicine Graduate Program, Houston, TX, USA
| | - Mario Loeza Cabrera
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Dane Hoffman
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Ronald J Parchem
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eveline Barbieri
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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24
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Layden HM, Johnson AE, Hiebert SW. Chemical-genetics refines transcription factor regulatory circuits. Trends Cancer 2024; 10:65-75. [PMID: 37722945 PMCID: PMC10840957 DOI: 10.1016/j.trecan.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023]
Abstract
Transcriptional dysregulation is a key step in oncogenesis, but our understanding of transcriptional control has relied on genetic approaches that are slow and allow for compensation. Chemical-genetic approaches have shortened the time frame for the analysis of transcription factors from days or weeks to minutes. These studies show that while DNA-binding proteins bind to thousands of sites, they are directly required to regulate only a small cadre of genes. Moreover, these transcriptional control networks are far more distinct, with much less overlap and interconnectivity than predicted from DNA binding. The identified direct targets can then be used to dissect the mechanism of action of these factors, which could identify ways to therapeutically manipulate these oncogenic transcriptional control networks.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA.
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25
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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26
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Pascual‐Reguant L, Serra‐Camprubí Q, Datta D, Cianferoni D, Kourtis S, Gañez‐Zapater A, Cannatá C, Espinar L, Querol J, García‐López L, Musa‐Afaneh S, Guirola M, Gkanogiannis A, Miró Canturri A, Guzman M, Rodríguez O, Herencia‐Ropero A, Arribas J, Serra V, Serrano L, Tian TV, Peiró S, Sdelci S. Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. EMBO Mol Med 2023; 15:e18459. [PMID: 37937685 PMCID: PMC10701626 DOI: 10.15252/emmm.202318459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Triple-negative breast cancer (TNBC) often develops resistance to single-agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B-MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co-inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4-MED1 colocalization, and the transcription of cell cycle genes, thus suppressing TNBC cell proliferation. Targeting the interaction between BRD4S and LOXL2 could be a starting point for the development of new anticancer strategies for the treatment of TNBC.
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Affiliation(s)
- Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Debayan Datta
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez‐Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Cannatá
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Lorena Espinar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Laura García‐López
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sara Musa‐Afaneh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Guirola
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Anestis Gkanogiannis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andrea Miró Canturri
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Marta Guzman
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Olga Rodríguez
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Joaquin Arribas
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de CáncerMonforte de LemosMadridSpain
- Department of Biochemistry and Molecular BiologyUniversitat Autónoma de BarcelonaBellaterraSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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27
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Krawic C, Luczak MW, Valiente S, Zhitkovich A. Atypical genotoxicity of carcinogenic nickel(II): Linkage to dNTP biosynthesis, DNA-incorporated rNMPs, and impaired repair of TOP1-DNA crosslinks. J Biol Chem 2023; 299:105385. [PMID: 37890780 PMCID: PMC10692736 DOI: 10.1016/j.jbc.2023.105385] [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: 05/15/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is a genetic disease requiring multiple mutations for its development. However, many carcinogens are DNA-unreactive and nonmutagenic and consequently described as nongenotoxic. One of such carcinogens is nickel, a global environmental pollutant abundantly emitted by burning of coal. We investigated activation of DNA damage responses by Ni and identified this metal as a replication stressor. Genotoxic stress markers indicated the accumulation of ssDNA and stalled replication forks, and Ni-treated cells were dependent on ATR for suppression of DNA damage and long-term survival. Replication stress by Ni resulted from destabilization of RRM1 and RRM2 subunits of ribonucleotide reductase and the resulting deficiency in dNTPs. Ni also increased DNA incorporation of rNMPs (detected by a specific fluorescent assay) and strongly enhanced their genotoxicity as a result of repressed repair of TOP1-DNA protein crosslinks (TOP1-DPC). The DPC-trap assay found severely impaired SUMOylation and K48-polyubiquitination of DNA-crosslinked TOP1 due to downregulation of specific enzymes. Our findings identified Ni as the human carcinogen inducing genome instability via DNA-embedded ribonucleotides and accumulation of TOP1-DPC which are carcinogenic abnormalities with poor detectability by the standard mutagenicity tests. The discovered mechanisms for Ni could also play a role in genotoxicity of other protein-reactive carcinogens.
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Affiliation(s)
- Casey Krawic
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Sophia Valiente
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA.
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28
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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29
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Behrens RT, Rajashekar JK, Bruce JW, Evans EL, Hansen AM, Salazar-Quiroz N, Simons LM, Ahlquist P, Hultquist JF, Kumar P, Sherer NM. Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells. mBio 2023; 14:e0042023. [PMID: 37676006 PMCID: PMC10653828 DOI: 10.1128/mbio.00420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 gene editing to engineer a "mousified" version of one such host protein, cyclin T1 (CCNT1), in human T cells. CCNT1 is essential for efficient HIV-1 transcription, making it an intriguing target for gene-based inactivation of virus replication. We show that isogenic cell lines engineered to encode CCNT1 bearing a single mouse-informed amino acid change (tyrosine in place of cysteine at position 261) exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cell biology. These results provide proof of concept for targeting CCNT1 in the context of one or more functional HIV-1 cure strategies.
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Affiliation(s)
- Ryan T. Behrens
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James W. Bruce
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward L. Evans
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amelia M. Hansen
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Salazar-Quiroz
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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30
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Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
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Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
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31
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Rao A, Ni Z, Suresh D, Mohanty C, Wang AR, Lee DL, Nickel KP, Varambally SRJ, Lambert PF, Kendziorski C, Iyer G. Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560587. [PMID: 37873389 PMCID: PMC10592929 DOI: 10.1101/2023.10.02.560587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.
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Affiliation(s)
- Aakarsha Rao
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dhruthi Suresh
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Albert R. Wang
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Denis L Lee
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Kwangok P. Nickel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Sooryanarayana Randall J. Varambally
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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32
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Papadopoulos D, Uhl L, Ha SA, Eilers M. Beyond gene expression: how MYC relieves transcription stress. Trends Cancer 2023; 9:805-816. [PMID: 37422352 DOI: 10.1016/j.trecan.2023.06.008] [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: 04/23/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
MYC oncoproteins are key drivers of tumorigenesis. As transcription factors, MYC proteins regulate transcription by all three nuclear polymerases and gene expression. Accumulating evidence shows that MYC proteins are also crucial for enhancing the stress resilience of transcription. MYC proteins relieve torsional stress caused by active transcription, prevent collisions between the transcription and replication machineries, resolve R-loops, and repair DNA damage by participating in a range of protein complexes and forming multimeric structures at sites of genomic instability. We review the key complexes and multimerization properties of MYC proteins that allow them to mitigate transcription-associated DNA damage, and propose that the oncogenic functions of MYC extend beyond the modulation of gene expression.
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Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University Hospital Würzburg, Würzburg, Germany
| | - Leonie Uhl
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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33
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Schmitt A, Grimm M, Kreienkamp N, Junge H, Labisch J, Schuhknecht L, Schönfeld C, Görsch E, Tibello A, Menck K, Bleckmann A, Lengerke C, Rosenbauer F, Grau M, Zampieri M, Schulze-Osthoff K, Klener P, Dolnikova A, Lenz G, Hailfinger S. BRD4 inhibition sensitizes diffuse large B-cell lymphoma cells to ferroptosis. Blood 2023; 142:1143-1155. [PMID: 37294920 DOI: 10.1182/blood.2022019274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/11/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL), the most common form of non-Hodgkin lymphoma, is characterized by an aggressive clinical course. In approximately one-third of patients with DLBCL, first-line multiagent immunochemotherapy fails to produce a durable response. Molecular heterogeneity and apoptosis resistance pose major therapeutic challenges in DLBCL treatment. To circumvent apoptosis resistance, the induction of ferroptosis might represent a promising strategy for lymphoma therapy. In this study, a compound library, targeting epigenetic modulators, was screened to identify ferroptosis-sensitizing drugs. Strikingly, bromodomain and extra-terminal domain (BET) inhibitors sensitized cells of the germinal center B-cell-like (GCB) subtype of DLBCL to ferroptosis induction and the combination of BET inhibitors with ferroptosis inducers, such as dimethyl fumarate or RSL3, synergized in the killing of DLBCL cells in vitro and in vivo. On the molecular level, the BET protein BRD4 was found to be an essential regulator of ferroptosis suppressor protein 1 expression and thus to protect GCB-DLBCL cells from ferroptosis. Collectively, we identified and characterized BRD4 as an important player in ferroptosis suppression in GCB-DLBCL and provide a rationale for the combination of BET inhibitors with ferroptosis-inducing agents as a novel therapeutic approach for DLBCL treatment.
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Affiliation(s)
- Anja Schmitt
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Melanie Grimm
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Nina Kreienkamp
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Hannah Junge
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Jan Labisch
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Caroline Schönfeld
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Elsa Görsch
- Department for Internal Medicine, Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Alessia Tibello
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Kerstin Menck
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Annalen Bleckmann
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Claudia Lengerke
- Department for Internal Medicine, Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Michael Grau
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Mattia Zampieri
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Klaus Schulze-Osthoff
- Department of Molecular Medicine, Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung) and German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
- First Department of Medicine, Hematology, University General Hospital and First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - Alexandra Dolnikova
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Hailfinger
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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34
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Cortázar MA, Fong N, Bentley DL. Genome-wide Mapping of 5'-monophosphorylated Ends of Mammalian Nascent RNA Transcripts. Bio Protoc 2023; 13:e4828. [PMID: 37753464 PMCID: PMC10518774 DOI: 10.21769/bioprotoc.4828] [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: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 09/28/2023] Open
Abstract
In eukaryotic cells, RNA biogenesis generally requires processing of the nascent transcript as it is being synthesized by RNA polymerase. These processing events include endonucleolytic cleavage, exonucleolytic trimming, and splicing of the growing nascent transcript. Endonucleolytic cleavage events that generate an exposed 5'-monophosphorylated (5'-PO4) end on the growing nascent transcript occur in the maturation of rRNAs, tRNAs, and mRNAs. These 5'-PO4 ends can be a target of further processing or be subjected to 5'-3' exonucleolytic digestion that may result in termination of transcription. Here, we describe how to identify 5'-PO4 ends of intermediates in nascent RNA metabolism. We capture these species via metabolic labeling with bromouridine followed by immunoprecipitation and specific ligation of 5'-PO4 RNA ends with the 3'-hydroxyl group of a 5' adaptor (5'-PO4 Bru-Seq) using RNA ligase I. These ligation events are localized at single nucleotide resolution via highthroughput sequencing, which identifies the position of 5'-PO4 groups precisely. This protocol successfully detects the 5'monophosphorylated ends of RNA processing intermediates during production of mature ribosomal, transfer, and micro RNAs. When combined with inhibition of the nuclear 5'-3' exonuclease Xrn2, 5'-PO4 Bru-Seq maps the 5' splice sites of debranched introns and mRNA and tRNA 3' end processing sites cleaved by CPSF73 and RNaseZ, respectively. Key features • Metabolic labeling for brief periods with bromouridine focuses the analysis of 5'-PO4 RNA ends on the population of nascent transcripts that are actively transcribed. • Detects 5'-PO4 RNA ends on nascent transcripts produced by all RNA polymerases. • Detects 5'-PO4 RNA ends at single nucleotide resolution.
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Affiliation(s)
- Michael A. Cortázar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - David L. Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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35
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Guo X, Olajuyin A, Tucker TA, Idell S, Qian G. BRD4 as a Therapeutic Target in Pulmonary Diseases. Int J Mol Sci 2023; 24:13231. [PMID: 37686037 PMCID: PMC10487829 DOI: 10.3390/ijms241713231] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) proteins are epigenetic modulators that regulate gene transcription through interacting with acetylated lysine residues of histone proteins. BET proteins have multiple roles in regulating key cellular functions such as cell proliferation, differentiation, inflammation, oxidative and redox balance, and immune responses. As a result, BET proteins have been found to be actively involved in a broad range of human lung diseases including acute lung inflammation, asthma, pulmonary arterial hypertension, pulmonary fibrosis, and chronic obstructive pulmonary disease (COPD). Due to the identification of specific small molecular inhibitors of BET proteins, targeting BET in these lung diseases has become an area of increasing interest. Emerging evidence has demonstrated the beneficial effects of BET inhibitors in preclinical models of various human lung diseases. This is, in general, largely related to the ability of BET proteins to bind to promoters of genes that are critical for inflammation, differentiation, and beyond. By modulating these critical genes, BET proteins are integrated into the pathogenesis of disease progression. The intrinsic histone acetyltransferase activity of bromodomain-containing protein 4 (BRD4) is of particular interest, seems to act independently of its bromodomain binding activity, and has implication in some contexts. In this review, we provide a brief overview of the research on BET proteins with a focus on BRD4 in several major human lung diseases, the underlying molecular mechanisms, as well as findings of targeting BET proteins using pharmaceutical inhibitors in different lung diseases preclinically.
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Affiliation(s)
| | | | | | | | - Guoqing Qian
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA; (X.G.); (A.O.); (T.A.T.); (S.I.)
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36
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Bressin A, Jasnovidova O, Arnold M, Altendorfer E, Trajkovski F, Kratz TA, Handzlik JE, Hnisz D, Mayer A. High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nat Commun 2023; 14:4971. [PMID: 37591883 PMCID: PMC10435483 DOI: 10.1038/s41467-023-40633-y] [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: 02/03/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Gene transcription by RNA polymerase II (Pol II) is under control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II correlating with their activity. How enhancer transcription is regulated and coordinated with transcription at target genes has remained unclear. Here, we developed a high-sensitive native elongating transcript sequencing approach, called HiS-NET-seq, to provide an extended high-resolution view on transcription, especially at lowly transcribed regions such as enhancers. HiS-NET-seq uncovers new transcribed enhancers in human cells. A multi-omics analysis shows that genome-wide enhancer transcription depends on the BET family protein BRD4. Specifically, BRD4 co-localizes to enhancer and promoter-proximal gene regions, and is required for elongation activation at enhancers and their genes. BRD4 keeps a set of enhancers and genes in proximity through long-range contacts. From these studies BRD4 emerges as a general regulator of enhancer transcription that may link transcription at enhancers and genes.
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Affiliation(s)
- Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Filip Trajkovski
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Thomas A Kratz
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Joanna E Handzlik
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
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Zheng B, Gold S, Iwanaszko M, Howard BC, Wang L, Shilatifard A. Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation. Mol Cell 2023; 83:2896-2910.e4. [PMID: 37442129 PMCID: PMC10527981 DOI: 10.1016/j.molcel.2023.06.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
The BET family protein BRD4, which forms the CDK9-containing BRD4-PTEFb complex, is considered to be a master regulator of RNA polymerase II (Pol II) pause release. Because its tandem bromodomains interact with acetylated histone lysine residues, it has long been thought that BRD4 requires these bromodomains for its recruitment to chromatin and transcriptional regulatory function. Here, using rapid depletion and genetic complementation with domain deletion mutants, we demonstrate that BRD4 bromodomains are dispensable for Pol II pause release. A minimal, bromodomain-less C-terminal BRD4 fragment containing the PTEFb-interacting C-terminal motif (CTM) is instead both necessary and sufficient to mediate Pol II pause release in the absence of full-length BRD4. Although BRD4-PTEFb can associate with chromatin through acetyl recognition, our results indicate that a distinct, active BRD4-PTEFb population functions to regulate transcription independently of bromodomain-mediated chromatin association. These findings may enable more effective pharmaceutical modulation of BRD4-PTEFb activity.
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Affiliation(s)
- Bin Zheng
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sarah Gold
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin Charles Howard
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lu Wang
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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Imai H, Utsumi D, Torihara H, Takahashi K, Kuroyanagi H, Yamashita A. Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification. Nucleic Acids Res 2023; 51:e76. [PMID: 37378452 PMCID: PMC10415123 DOI: 10.1093/nar/gkad545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires nascent RNA synthesis and translation. Analysis of the coordinated regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprogramming of nascent RNA synthesis and translation. Our nascent P-TRAP (nP-TRAP) method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.
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Affiliation(s)
- Hirotatsu Imai
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Daisuke Utsumi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidetsugu Torihara
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Kenzo Takahashi
- Department of Dermatology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Hidehito Kuroyanagi
- Department of Biochemistry, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0215, Japan
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Hoffmann T, Hörmann A, Corcokovic M, Zmajkovic J, Hinterndorfer M, Salkanovic J, Spreitzer F, Köferle A, Gitschtaler K, Popa A, Oberndorfer S, Andersch F, Schaefer M, Fellner M, Budano N, Ruppert JG, Chetta P, Wurm M, Zuber J, Neumüller RA. Precision RNAi using synthetic shRNAmir target sites. eLife 2023; 12:RP84792. [PMID: 37552050 PMCID: PMC10409502 DOI: 10.7554/elife.84792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.
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Affiliation(s)
- Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Jakub Zmajkovic
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | | | - Jasko Salkanovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Katrin Gitschtaler
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Florian Andersch
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Markus Schaefer
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
| | - Nicole Budano
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Jan G Ruppert
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Paolo Chetta
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Melanie Wurm
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1ViennaAustria
- Medical University of Vienna, Vienna BioCenterViennaAustria
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-GasseViennaAustria
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40
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Letson CT, Balasis ME, Newman H, Binder M, Vedder A, Kinose F, Ball M, Kruer T, Quintana A, Lasho TL, Finke CM, Almada LL, Grants JM, Zhang G, Fernandez-Zapico ME, Gaspar-Maia A, Lancet J, Komrokji R, Haura E, Sallman DA, Reuther GW, Karsan A, Rix U, Patnaik MM, Padron E. Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML. Clin Cancer Res 2023; 29:2919-2932. [PMID: 37223910 PMCID: PMC10524644 DOI: 10.1158/1078-0432.ccr-22-3929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/19/2023] [Accepted: 05/19/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE Preclinical studies in myeloid neoplasms have demonstrated efficacy of bromodomain and extra-terminal protein inhibitors (BETi). However, BETi demonstrates poor single-agent activity in clinical trials. Several studies suggest that combination with other anticancer inhibitors may enhance the efficacy of BETi. EXPERIMENTAL DESIGN To nominate BETi combination therapies for myeloid neoplasms, we used a chemical screen with therapies currently in clinical cancer development and validated this screen using a panel of myeloid cell line, heterotopic cell line models, and patient-derived xenograft models of disease. We used standard protein and RNA assays to determine the mechanism responsible for synergy in our disease models. RESULTS We identified PIM inhibitors (PIMi) as therapeutically synergistic with BETi in myeloid leukemia models. Mechanistically, we show that PIM kinase is increased after BETi treatment, and that PIM kinase upregulation is sufficient to induce persistence to BETi and sensitize cells to PIMi. Furthermore, we demonstrate that miR-33a downregulation is the underlying mechanism driving PIM1 upregulation. We also show that GM-CSF hypersensitivity, a hallmark of chronic myelomonocytic leukemia (CMML), represents a molecular signature for sensitivity to combination therapy. CONCLUSIONS Inhibition of PIM kinases is a potential novel strategy for overcoming BETi persistence in myeloid neoplasms. Our data support further clinical investigation of this combination.
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Affiliation(s)
| | | | - Hannah Newman
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Moritz Binder
- Division of Hematology, Mayo Clinic, Rochester, MN
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexis Vedder
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Fumi Kinose
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Markus Ball
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Traci Kruer
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Ariel Quintana
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Terra L. Lasho
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Christy M. Finke
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Luciana L. Almada
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN
| | | | - Guolin Zhang
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | - Alexandre Gaspar-Maia
- Division of Hematology, Mayo Clinic, Rochester, MN
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jeffrey Lancet
- Malignant Hematology Department, Moffitt Cancer Center, Tampa, FL
| | - Rami Komrokji
- Malignant Hematology Department, Moffitt Cancer Center, Tampa, FL
| | - Eric Haura
- Department of Drug Discovery, H Lee Moffitt Cancer Center, Tampa, FL
| | - David A. Sallman
- Malignant Hematology Department, Moffitt Cancer Center, Tampa, FL
| | - Gary W. Reuther
- Department of Molecular Oncology, H Lee Moffitt Cancer Center, Tampa, FL
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
| | - Uwe Rix
- Department of Drug Discovery, H Lee Moffitt Cancer Center, Tampa, FL
| | - Mrinal M. Patnaik
- Division of Hematology, Mayo Clinic, Rochester, MN
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric Padron
- Malignant Hematology Department, Moffitt Cancer Center, Tampa, FL
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Coomar S, Mota P, Penson A, Schwaller J, Abdel-Wahab O, Gillingham D. Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation. Mol Cancer Res 2023; 21:768-778. [PMID: 37255411 PMCID: PMC10395616 DOI: 10.1158/1541-7786.mcr-22-0541] [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: 07/07/2022] [Revised: 03/16/2023] [Accepted: 05/09/2023] [Indexed: 05/14/2023]
Abstract
Certain arylsulfonamides (ArSulf) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. However, degradation of a splicing factor introduces complex pleiotropic effects that are difficult to untangle, since, aside from direct protein degradation, downstream transcriptional effects also influence the proteome. By overlaying transcriptional data and proteome datasets, we distinguish transcriptional from direct degradation effects, pinpointing those proteins most impacted by splicing changes. Using our workflow, we identify and validate the upregulation of the arginine-and-serine rich protein (RSRP1) and the downregulation of the key kinesin motor proteins KIF20A and KIF20B due to altered splicing in the absence of RBM39. We further show that kinesin downregulation is connected to the multinucleation phenotype observed upon RBM39 depletion by ArSulfs. Our approach should be helpful in the assessment of potential cancer drug candidates which target splicing factors. IMPLICATIONS Our approach provides a workflow for identifying and studying the most strongly modulated proteins when splicing is altered. The work also uncovers a splicing-based approach toward pharmacologic targeting of mitotic kinesins.
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Affiliation(s)
- Seemon Coomar
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Pedro Mota
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Alexander Penson
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital (UKBB), University of Basel, Basel, Switzerland
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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42
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Vock IW, Simon MD. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA (NEW YORK, N.Y.) 2023; 29:958-976. [PMID: 37028916 DOI: 10.1261/rna.079451.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortcoming and are widely used approaches to identify changes in RNA synthesis and degradation kinetics. While advanced statistical models implemented in user-friendly software (e.g., DESeq2) have ensured the statistical rigor of differential expression analyses, no such tools that facilitate differential kinetic analysis with NR-seq exist. Here, we report the development of Bayesian analysis of the kinetics of RNA (bakR; https:// github.com/simonlabcode/bakR), an R package to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Analyses of simulated data confirmed that bakR implementations of the hierarchical model outperform attempts to analyze differential kinetics with existing models. bakR also uncovers biological signals in real NR-seq data sets and provides improved analyses of existing data sets. This work establishes bakR as an important tool for identifying differential RNA synthesis and degradation kinetics.
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Affiliation(s)
- Isaac W Vock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
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43
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Schwanke H, Gonçalves Magalhães V, Schmelz S, Wyler E, Hennig T, Günther T, Grundhoff A, Dölken L, Landthaler M, van Ham M, Jänsch L, Büssow K, van den Heuvel J, Blankenfeldt W, Friedel CC, Erhard F, Brinkmann MM. The Cytomegalovirus M35 Protein Directly Binds to the Interferon-β Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes. J Virol 2023; 97:e0040023. [PMID: 37289084 PMCID: PMC10308904 DOI: 10.1128/jvi.00400-23] [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: 03/17/2023] [Accepted: 05/04/2023] [Indexed: 06/09/2023] Open
Abstract
Induction of type I interferon (IFN) gene expression is among the first lines of cellular defense a virus encounters during primary infection. We previously identified the tegument protein M35 of murine cytomegalovirus (MCMV) as an essential antagonist of this antiviral system, showing that M35 interferes with type I IFN induction downstream of pattern-recognition receptor (PRR) activation. Here, we report structural and mechanistic details of M35's function. Determination of M35's crystal structure combined with reverse genetics revealed that homodimerization is a key feature for M35's immunomodulatory activity. In electrophoretic mobility shift assays (EMSAs), purified M35 protein specifically bound to the regulatory DNA element that governs transcription of the first type I IFN gene induced in nonimmune cells, Ifnb1. DNA-binding sites of M35 overlapped with the recognition elements of interferon regulatory factor 3 (IRF3), a key transcription factor activated by PRR signaling. Chromatin immunoprecipitation (ChIP) showed reduced binding of IRF3 to the host Ifnb1 promoter in the presence of M35. We furthermore defined the IRF3-dependent and the type I IFN signaling-responsive genes in murine fibroblasts by RNA sequencing of metabolically labeled transcripts (SLAM-seq) and assessed M35's global effect on gene expression. Stable expression of M35 broadly influenced the transcriptome in untreated cells and specifically downregulated basal expression of IRF3-dependent genes. During MCMV infection, M35 impaired expression of IRF3-responsive genes aside of Ifnb1. Our results suggest that M35-DNA binding directly antagonizes gene induction mediated by IRF3 and impairs the antiviral response more broadly than formerly recognized. IMPORTANCE Replication of the ubiquitous human cytomegalovirus (HCMV) in healthy individuals mostly goes unnoticed but can impair fetal development or cause life-threatening symptoms in immunosuppressed or -deficient patients. Like other herpesviruses, CMV extensively manipulates its hosts and establishes lifelong latent infections. Murine CMV (MCMV) presents an important model system as it allows the study of CMV infection in the host organism. We previously showed that during entry into host cells, MCMV virions release the evolutionary conserved protein M35 protein to immediately dampen the antiviral type I interferon (IFN) response induced by pathogen detection. Here, we show that M35 dimers bind to regulatory DNA elements and interfere with recruitment of interferon regulatory factor 3 (IRF3), a key cellular factor for antiviral gene expression. Thereby, M35 interferes with expression of type I IFNs and other IRF3-dependent genes, reflecting the importance for herpesviruses to avoid IRF3-mediated gene induction.
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Affiliation(s)
- Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | | | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Konrad Büssow
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun 2023; 14:3559. [PMID: 37321987 PMCID: PMC10272207 DOI: 10.1038/s41467-023-39163-4] [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: 09/29/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
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Affiliation(s)
- Teresa Rummel
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany.
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstr. 4, 93053, Regensburg, Germany.
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45
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Yu H, Shi T, Yao L, Xu D, Ding Y, Xia Q, Liu W, Wang X. Elevated nuclear PIGL disrupts the cMyc/BRD4 axis and improves PD-1 blockade therapy by dampening tumor immune evasion. Cell Mol Immunol 2023:10.1038/s41423-023-01048-3. [PMID: 37280393 PMCID: PMC10387471 DOI: 10.1038/s41423-023-01048-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
To improve the efficacy of lenvatinib in combination with programmed death-1 (PD-1) blockade therapy for hepatocellular carcinoma (HCC), we screened the suppressive metabolic enzymes that sensitize HCC to lenvatinib and PD-1 blockade, thus impeding HCC progression. After analysis of the CRISPR‒Cas9 screen, phosphatidylinositol-glycan biosynthesis class L (PIGL) ranked first in the positive selection list. PIGL depletion had no effect on tumor cell growth in vitro but reprogrammed the tumor microenvironment (TME) in vivo to support tumor cell survival. Specifically, nuclear PIGL disrupted the interaction between cMyc/BRD4 on the distant promoter of target genes and thus decreased the expression of CCL2 and CCL20, which are involved in shaping the immunosuppressive TME by recruiting macrophages and regulatory T cells. PIGL phosphorylation at Y81 by FGFR2 abolished the interaction of PIGL with importin α/β1, thus retaining PIGL in the cytosol and facilitating tumor evasion by releasing CCL2 and CCL20. Clinically, elevated nuclear PIGL predicts a better prognosis for HCC patients and presents a positive correlation with CD8 + T-cell enrichment in tumors. Clinically, our findings highlight that the nuclear PIGL intensity or the change in PIGL-Y81 phosphorylation should be used as a biomarker to guide lenvatinib with PD-1 blockade therapy.
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Affiliation(s)
- Hua Yu
- Precise Genome Engineering Centre, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Tiezhu Shi
- Precise Genome Engineering Centre, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Linli Yao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200240, China
| | - Dongwei Xu
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Yufeng Ding
- Precise Genome Engineering Centre, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China.
| | - Xiongjun Wang
- Precise Genome Engineering Centre, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200240, China.
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Fischer J, Schulz MH. Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data. Bioinformatics 2023; 39:btad386. [PMID: 37326968 PMCID: PMC10310462 DOI: 10.1093/bioinformatics/btad386] [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: 01/04/2023] [Revised: 05/17/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
MOTIVATION DNA CpG methylation (CpGm) has proven to be a crucial epigenetic factor in the mammalian gene regulatory system. Assessment of DNA CpG methylation values via whole-genome bisulfite sequencing (WGBS) is, however, computationally extremely demanding. RESULTS We present FAst MEthylation calling (FAME), the first approach to quantify CpGm values directly from bulk or single-cell WGBS reads without intermediate output files. FAME is very fast but as accurate as standard methods, which first produce BS alignment files before computing CpGm values. We present experiments on bulk and single-cell bisulfite datasets in which we show that data analysis can be significantly sped-up and help addressing the current WGBS analysis bottleneck for large-scale datasets without compromising accuracy. AVAILABILITY AND IMPLEMENTATION An implementation of FAME is open source and licensed under GPL-3.0 at https://github.com/FischerJo/FAME.
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Affiliation(s)
- Jonas Fischer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Marcel H Schulz
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken 66123, Germany
- Institute of Cardiovascular Regeneration, Department of Medicine, Goethe University, Frankfurt am Main 60590, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhein-Main, Frankfurt am Main 60590, Germany
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47
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Shi Y, Liao Y, Liu Q, Ni Z, Zhang Z, Shi M, Li P, Li H, Rao Y. BRD4-targeting PROTAC as a unique tool to study biomolecular condensates. Cell Discov 2023; 9:47. [PMID: 37156794 PMCID: PMC10167318 DOI: 10.1038/s41421-023-00544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 05/10/2023] Open
Abstract
Biomolecular condensates play key roles in various biological processes. However, specific condensation modulators are currently lacking. PROTAC is a new technology that can use small molecules to degrade target proteins specifically. PROTAC molecules are expected to regulate biomolecular condensates dynamically by degrading/recovering key molecules in biomolecular condensates. In this study, we employed a BRD4-targeting PROTAC molecule to regulate the super-enhancer (SE) condensate and monitored the changes of SE condensate under PROTAC treatment using live-cell imaging and high-throughput sequencing technologies. As a result, we found that BRD4-targeting PROTACs can significantly reduce the BRD4 condensates, and we established a quantitative method for tracking BRD4 condensates by PROTAC and cellular imaging. Surprisingly and encouragingly, BRD4 condensates were observed to preferentially form and play specialized roles in biological process regulation for the first time. Additionally, BRD4 PROTAC makes it possible to observe the dynamics of other condensate components under the continued disruption of BRD4 condensates. Together, these results shed new light on research methods for liquid-liquid phase separation (LLPS), and specifically demonstrate that PROTAC presents a powerful and distinctive tool for the study of biomolecular condensates.
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Affiliation(s)
- Yi Shi
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuan Liao
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Beijing, China
| | - Qianlong Liu
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhihao Ni
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Zhenzhen Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
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48
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Hafner A, Park M, Berger SE, Murphy SE, Nora EP, Boettiger AN. Loop stacking organizes genome folding from TADs to chromosomes. Mol Cell 2023; 83:1377-1392.e6. [PMID: 37146570 PMCID: PMC10167645 DOI: 10.1016/j.molcel.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/17/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Although population-level analyses revealed significant roles for CTCF and cohesin in mammalian genome organization, their contributions at the single-cell level remain incompletely understood. Here, we used a super-resolution microscopy approach to measure the effects of removal of CTCF or cohesin in mouse embryonic stem cells. Single-chromosome traces revealed cohesin-dependent loops, frequently stacked at their loop anchors forming multi-way contacts (hubs), bridging across TAD boundaries. Despite these bridging interactions, chromatin in intervening TADs was not intermixed, remaining separated in distinct loops around the hub. At the multi-TAD scale, steric effects from loop stacking insulated local chromatin from ultra-long range (>4 Mb) contacts. Upon cohesin removal, the chromosomes were more disordered and increased cell-cell variability in gene expression. Our data revise the TAD-centric understanding of CTCF and cohesin and provide a multi-scale, structural picture of how they organize the genome on the single-cell level through distinct contributions to loop stacking.
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Affiliation(s)
- Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Minhee Park
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Scott E Berger
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Sedona E Murphy
- Department of Developmental Biology, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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49
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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50
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Quintela M, James DW, Pociute A, Powell L, Edwards K, Coombes Z, Garcia J, Garton N, Das N, Lutchman-Singh K, Margarit L, Beynon AL, Rioja I, Prinjha RK, Harker NR, Gonzalez D, Conlan RS, Francis LW. Bromodomain inhibitor i-BET858 triggers a unique transcriptional response coupled to enhanced DNA damage, cell cycle arrest and apoptosis in high-grade ovarian carcinoma cells. Clin Epigenetics 2023; 15:63. [PMID: 37060086 PMCID: PMC10105475 DOI: 10.1186/s13148-023-01477-x] [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: 06/08/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Ovarian cancer has a specific unmet clinical need, with a persistently poor 5-year survival rate observed in women with advanced stage disease warranting continued efforts to develop new treatment options. The amplification of BRD4 in a significant subset of high-grade serous ovarian carcinomas (HGSC) has led to the development of BET inhibitors (BETi) as promising antitumour agents that have subsequently been evaluated in phase I/II clinical trials. Here, we describe the molecular effects and ex vivo preclinical activities of i-BET858, a bivalent pan-BET inhibitor with proven in vivo BRD inhibitory activity. RESULTS i-BET858 demonstrates enhanced cytotoxic activity compared with earlier generation BETis both in cell lines and primary cells derived from clinical samples of HGSC. At molecular level, i-BET858 triggered a bipartite transcriptional response, comprised of a 'core' network of genes commonly associated with BET inhibition in solid tumours, together with a unique i-BET858 gene signature. Mechanistically, i-BET858 elicited enhanced DNA damage, cell cycle arrest and apoptotic cell death compared to its predecessor i-BET151. CONCLUSIONS Overall, our ex vivo and in vitro studies indicate that i-BET858 represents an optimal candidate to pursue further clinical validation for the treatment of HGSC.
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Affiliation(s)
- Marcos Quintela
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - David W James
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Agne Pociute
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Lydia Powell
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Kadie Edwards
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Zoe Coombes
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Jetzabel Garcia
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Neil Garton
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Nagindra Das
- Swansea Bay University Health Board, Swansea, SA12 7BR, UK
| | | | - Lavinia Margarit
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
- Cwm Taf Morgannwg University Health Board, Swansea, SA2 8QA, UK
| | | | - Inmaculada Rioja
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Rab K Prinjha
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Nicola R Harker
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Deyarina Gonzalez
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - R Steven Conlan
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Lewis W Francis
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
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