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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; 73:1509-1528. [PMID: 38821858 PMCID: PMC11347226 DOI: 10.1136/gutjnl-2023-331519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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2
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Hushmandi K, Saadat SH, Raei M, Daneshi S, Aref AR, Nabavi N, Taheriazam A, Hashemi M. Implications of c-Myc in the pathogenesis and treatment efficacy of urological cancers. Pathol Res Pract 2024; 259:155381. [PMID: 38833803 DOI: 10.1016/j.prp.2024.155381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
Urological cancers, including prostate, bladder, and renal cancers, are significant causes of death and negatively impact the quality of life for patients. The development and progression of these cancers are linked to the dysregulation of molecular pathways. c-Myc, recognized as an oncogene, exhibits abnormal levels in various types of tumors, and current evidence supports the therapeutic targeting of c-Myc in cancer treatment. This review aims to elucidate the role of c-Myc in driving the progression of urological cancers. c-Myc functions to enhance tumorigenesis and has been documented to increase growth and metastasis in prostate, bladder, and renal cancers. Furthermore, the dysregulation of c-Myc can result in a diminished response to therapy in these cancers. Non-coding RNAs, β-catenin, and XIAP are among the regulators of c-Myc in urological cancers. Targeting and suppressing c-Myc therapeutically for the treatment of these cancers has been explored. Additionally, the expression level of c-Myc may serve as a prognostic factor in clinical settings.
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Affiliation(s)
- Kiavash Hushmandi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Seyed Hassan Saadat
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Raei
- Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran; Department of Epidemiology and Biostatistics, School of Health, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Salman Daneshi
- Department of Public Health,School of Health,Jiroft University Of Medical Sciences, Jiroft, Iran
| | - Amir Reza Aref
- Department of Translational Sciences, Xsphera Biosciences Inc. Boston, MA, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6, Vancouver, BC, Canada
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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3
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Woodworth AM, Hardy K, Taberlay PC, Dickinson JL, Holloway AF. RUNX1 regulates promoter activity in the absence of cognate DNA binding motifs. J Cell Biochem 2024; 125:e30570. [PMID: 38616697 DOI: 10.1002/jcb.30570] [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: 12/21/2023] [Revised: 03/29/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
Runt-related transcription factor 1 (RUNX1) plays an important role in normal haematopoietic cell development and function, and its function is frequently disrupted in leukaemia. RUNX1 is widely recognised as a sequence-specific DNA binding factor that recognises the motif 5'-TG(T/C)GGT-3' in promoter and enhancer regions of its target genes. Moreover, RUNX1 fusion proteins, such as RUNX1-ETO formed by the t(8;21) translocation, retain the ability to recognise and bind to this sequence to elicit atypical gene regulatory effects on bona fide RUNX1 targets. However, our analysis of publicly available RUNX1 chromatin immunoprecipitation sequencing (ChIP-Seq) data has provided evidence challenging this dogma, revealing that this motif-specific model of RUNX1 recruitment and function is incomplete. Our analyses revealed that the majority of RUNX1 genomic localisation occurs outside of promoters, that 20% of RUNX1 binding sites lack consensus RUNX motifs, and that binding in the absence of a cognate binding site is more common in promoter regions compared to distal sites. Reporter assays demonstrate that RUNX1 can drive promoter activity in the absence of a recognised DNA binding motif, in contrast to RUNX1-ETO. RUNX1-ETO supresses activity when it is recruited to promoters containing a sequence specific motif, while interestingly, it binds but does not repress promoters devoid of a RUNX1 recognition site. These data suggest that RUNX1 regulation of target genes occurs through multiple mechanisms depending on genomic location, the type of regulatory element and mode of recruitment.
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Affiliation(s)
- Alex M Woodworth
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology and Mathematics, Discipline of Biomedical Science, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Adele F Holloway
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Tasmania, Australia
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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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Freie B, Carroll PA, Varnum-Finney BJ, Ramsey EL, Ramani V, Bernstein I, Eisenman RN. A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies. Genes Dev 2024; 38:253-272. [PMID: 38565249 PMCID: PMC11065175 DOI: 10.1101/gad.351292.123] [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: 10/23/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently acquire point mutations in the MYC phosphodegron, including at threonine 58 (T58), where phosphorylation permits binding via the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenous c-Myc locus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60% of adult homozygous T58A mice. We found that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and up-regulate a subset of MYC target genes important in maintaining stem/progenitor cell balance. In lymphocytes, genomic occupancy by MYC-T58A was increased at all promoters compared with WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation stabilizing MYC is sufficient to skew target gene expression, producing a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
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Affiliation(s)
- Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
| | - Patrick A Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | | | - Erin L Ramsey
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, University of California, San Francisco, San Francisco, California 94158, USA
| | - Irwin Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA;
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6
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Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, Ade CP, Gallant P, Wolf E, Larsen DH, Munschauer M, Burger K. Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts. Nucleic Acids Res 2024; 52:3050-3068. [PMID: 38224452 PMCID: PMC11014278 DOI: 10.1093/nar/gkae022] [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: 07/13/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA-RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
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Affiliation(s)
- Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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7
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Jakobsen ST, Jensen RAM, Madsen MS, Ravnsborg T, Vaagenso CS, Siersbæk MS, Einarsson H, Andersson R, Jensen ON, Siersbæk R. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch. Nat Genet 2024; 56:663-674. [PMID: 38454021 DOI: 10.1038/s41588-024-01676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.
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Affiliation(s)
- Simon T Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rikke A M Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria S Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Majken S Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hjorleifur Einarsson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Rasmus Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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8
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Murillo-González FE, García-Aguilar R, Limón-Pacheco J, Cabañas-Cortés MA, Elizondo G. 2,3,7,8-Tetrachlorodibenzo-p-dioxin and kynurenine induce Parkin expression in neuroblastoma cells through different signaling pathways mediated by the aryl hydrocarbon receptor. Toxicol Lett 2024; 394:114-127. [PMID: 38437907 DOI: 10.1016/j.toxlet.2024.02.015] [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: 10/02/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Parkin regulates protein degradation and mitophagy in dopaminergic neurons. Deficiencies in Parkin expression or function lead to cellular stress, cell degeneration, and the death of dopaminergic neurons, which promotes Parkinson's disease. In contrast, Parkin overexpression promotes neuronal survival. Therefore, the mechanisms of Parkin upregulation are crucial to understand. We describe here the molecular mechanism of AHR-mediated Parkin regulation in human SH-SY5Y neuroblastoma cells. Specifically, we report that the human Parkin gene (PRKN) is transcriptionally upregulated by the aryl hydrocarbon receptor (AHR) through two different selective ligand-dependent pathways. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a stress-inducing AHR ligand, indirectly promotes PRKN transcription by inducing ATF4 expression via TCDD-mediated endoplasmic reticulum (ER) stress. In contrast, kynurenine, a nontoxic AHR agonist, induces PRKN transcription by promoting AHR binding to the PRKN promoter without activating ER stress. Our results demonstrate that AHR activation may be a potential pharmacological pathway to induce human Parkin, but such a strategy must carefully consider the choice of AHR ligand to avoid neurotoxic side effects.
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Affiliation(s)
| | - Rosario García-Aguilar
- Departamento de Toxicología, CINVESTAV-IPN, Av. IPN 2508, Ciudad de México C.P. 07360, Mexico
| | - Jorge Limón-Pacheco
- Departamento de Biología Celular, CINVESTAV-IPN, Av. IPN 2508, Ciudad de México C.P. 07360, Mexico
| | | | - Guillermo Elizondo
- Departamento de Biología Celular, CINVESTAV-IPN, Av. IPN 2508, Ciudad de México C.P. 07360, Mexico.
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9
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Chan KI, Zhang S, Li G, Xu Y, Cui L, Wang Y, Su H, Tan W, Zhong Z. MYC Oncogene: A Druggable Target for Treating Cancers with Natural Products. Aging Dis 2024; 15:640-697. [PMID: 37450923 PMCID: PMC10917530 DOI: 10.14336/ad.2023.0520] [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: 04/24/2023] [Accepted: 05/20/2023] [Indexed: 07/18/2023] Open
Abstract
Various diseases, including cancers, age-associated disorders, and acute liver failure, have been linked to the oncogene, MYC. Animal testing and clinical trials have shown that sustained tumor volume reduction can be achieved when MYC is inactivated, and different combinations of therapeutic agents including MYC inhibitors are currently being developed. In this review, we first provide a summary of the multiple biological functions of the MYC oncoprotein in cancer treatment, highlighting that the equilibrium points of the MYC/MAX, MIZ1/MYC/MAX, and MAD (MNT)/MAX complexes have further potential in cancer treatment that could be used to restrain MYC oncogene expression and its functions in tumorigenesis. We also discuss the multifunctional capacity of MYC in various cellular cancer processes, including its influences on immune response, metabolism, cell cycle, apoptosis, autophagy, pyroptosis, metastasis, angiogenesis, multidrug resistance, and intestinal flora. Moreover, we summarize the MYC therapy patent landscape and emphasize the potential of MYC as a druggable target, using herbal medicine modulators. Finally, we describe pending challenges and future perspectives in biomedical research, involving the development of therapeutic approaches to modulate MYC or its targeted genes. Patients with cancers driven by MYC signaling may benefit from therapies targeting these pathways, which could delay cancerous growth and recover antitumor immune responses.
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Affiliation(s)
- Ka Iong Chan
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Siyuan Zhang
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Guodong Li
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Yida Xu
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Liao Cui
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang 524000, China
| | - Yitao Wang
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Huanxing Su
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Wen Tan
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Zhangfeng Zhong
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
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10
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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11
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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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12
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Hofstetter J, Ogunleye A, Kutschke A, Buchholz LM, Wolf E, Raabe T, Gallant P. Spt5 interacts genetically with Myc and is limiting for brain tumor growth in Drosophila. Life Sci Alliance 2024; 7:e202302130. [PMID: 37935464 PMCID: PMC10629571 DOI: 10.26508/lsa.202302130] [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: 05/03/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
The transcription factor SPT5 physically interacts with MYC oncoproteins and is essential for efficient transcriptional activation of MYC targets in cultured cells. Here, we use Drosophila to address the relevance of this interaction in a living organism. Spt5 displays moderate synergy with Myc in fast proliferating young imaginal disc cells. During later development, Spt5-knockdown has no detectable consequences on its own, but strongly enhances eye defects caused by Myc overexpression. Similarly, Spt5-knockdown in larval type 2 neuroblasts has only mild effects on brain development and survival of control flies, but dramatically shrinks the volumes of experimentally induced neuroblast tumors and significantly extends the lifespan of tumor-bearing animals. This beneficial effect is still observed when Spt5 is knocked down systemically and after tumor initiation, highlighting SPT5 as a potential drug target in human oncology.
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Affiliation(s)
- Julia Hofstetter
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ayoola Ogunleye
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - André Kutschke
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Lisa Marie Buchholz
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Elmar Wolf
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Raabe
- https://ror.org/00fbnyb24 Molecular Genetics, Biocenter, Am Hubland, University of Würzburg, Würzburg, Germany
| | - Peter Gallant
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
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13
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Bumpous LA, Moe KC, Wang J, Carver LA, Williams AG, Romer AS, Scobee JD, Maxwell JN, Jones CA, Chung DH, Tansey WP, Liu Q, Weissmiller AM. WDR5 facilitates recruitment of N-MYC to conserved WDR5 gene targets in neuroblastoma cell lines. Oncogenesis 2023; 12:32. [PMID: 37336886 PMCID: PMC10279693 DOI: 10.1038/s41389-023-00477-z] [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: 01/20/2023] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023] Open
Abstract
Collectively, the MYC family of oncoprotein transcription factors is overexpressed in more than half of all malignancies. The ability of MYC proteins to access chromatin is fundamental to their role in promoting oncogenic gene expression programs in cancer and this function depends on MYC-cofactor interactions. One such cofactor is the chromatin regulator WDR5, which in models of Burkitt lymphoma facilitates recruitment of the c-MYC protein to chromatin at genes associated with protein synthesis, allowing for tumor progression and maintenance. However, beyond Burkitt lymphoma, it is unknown whether these observations extend to other cancers or MYC family members, and whether WDR5 can be deemed as a "universal" MYC recruiter. Here, we focus on N-MYC amplified neuroblastoma to determine the extent of colocalization between N-MYC and WDR5 on chromatin while also demonstrating that like c-MYC, WDR5 can facilitate the recruitment of N-MYC to conserved WDR5-bound genes. We conclude based on this analysis that N-MYC and WDR5 colocalize invariantly across cell lines at predicted sites of facilitated recruitment associated with protein synthesis genes. Surprisingly, we also identify N-MYC-WDR5 cobound genes that are associated with DNA repair and cell cycle processes. Dissection of chromatin binding characteristics for N-MYC and WDR5 at all cobound genes reveals that sites of facilitated recruitment are inherently different than most N-MYC-WDR5 cobound sites. Our data reveals that WDR5 acts as a universal MYC recruiter at a small cohort of previously identified genes and highlights novel biological functions that may be coregulated by N-MYC and WDR5 to sustain the neuroblastoma state.
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Affiliation(s)
- Leigh A Bumpous
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Kylie C Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - Logan A Carver
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Alexandria G Williams
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Alexander S Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jesse D Scobee
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jack N Maxwell
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Cheyenne A Jones
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Dai H Chung
- Department of Pediatric Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, 75234, USA
| | - William P Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37240, USA
| | - April M Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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14
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Li M, Yang L, Chan AKN, Pokharel SP, Liu Q, Mattson N, Xu X, Chang W, Miyashita K, Singh P, Zhang L, Li M, Wu J, Wang J, Chen B, Chan LN, Lee J, Zhang XH, Rosen ST, Müschen M, Qi J, Chen J, Hiom K, Bishop AJR, Chen C. Epigenetic Control of Translation Checkpoint and Tumor Progression via RUVBL1-EEF1A1 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206584. [PMID: 37075745 PMCID: PMC10265057 DOI: 10.1002/advs.202206584] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Epigenetic dysregulation is reported in multiple cancers including Ewing sarcoma (EwS). However, the epigenetic networks underlying the maintenance of oncogenic signaling and therapeutic response remain unclear. Using a series of epigenetics- and complex-focused CRISPR screens, RUVBL1, the ATPase component of NuA4 histone acetyltransferase complex, is identified to be essential for EwS tumor progression. Suppression of RUVBL1 leads to attenuated tumor growth, loss of histone H4 acetylation, and ablated MYC signaling. Mechanistically, RUVBL1 controls MYC chromatin binding and modulates the MYC-driven EEF1A1 expression and thus protein synthesis. High-density CRISPR gene body scan pinpoints the critical MYC interacting residue in RUVBL1. Finally, this study reveals the synergism between RUVBL1 suppression and pharmacological inhibition of MYC in EwS xenografts and patient-derived samples. These results indicate that the dynamic interplay between chromatin remodelers, oncogenic transcription factors, and protein translation machinery can provide novel opportunities for combination cancer therapy.
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Affiliation(s)
- Mingli Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lu Yang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Anthony K. N. Chan
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Sheela Pangeni Pokharel
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Qiao Liu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Nicole Mattson
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Xiaobao Xu
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Wen‐Han Chang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kazuya Miyashita
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Priyanka Singh
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Leisi Zhang
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Maggie Li
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jun Wu
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Jinhui Wang
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Bryan Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Lai N. Chan
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOH44195USA
| | - Jaewoong Lee
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
- School of Biosystems and Biomedical SciencesCollege of Health ScienceKorea UniversitySeoul02841South Korea
- Interdisciplinary Program in Precision Public HealthKorea UniversitySeoul02841South Korea
| | | | | | - Markus Müschen
- Center of Molecular and Cellular OncologyYale Cancer CenterYale School of MedicineNew HavenCT06510USA
| | - Jun Qi
- Department of Cancer BiologyDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMA02215USA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Kevin Hiom
- Division of Cellular MedicineSchool of MedicineUniversity of DundeeNethergateDundeeDD1 4HNUK
| | - Alexander J. R. Bishop
- Department of Cellular Systems and AnatomyUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Chun‐Wei Chen
- Department of Systems BiologyBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- Division of Epigenetic and Transcriptional EngineeringBeckman Research InstituteCity of Hope Comprehensive Cancer CenterDuarteCA91010USA
- City of Hope Comprehensive Cancer CenterDuarteCA91010USA
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15
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Liu C, Kudo T, Ye X, Gascoigne K. Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells. Cell Rep 2023; 42:112401. [PMID: 37060565 DOI: 10.1016/j.celrep.2023.112401] [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: 10/14/2022] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Cell-to-cell heterogeneity is vital for tumor evolution and survival. How cancer cells achieve and exploit this heterogeneity remains an active area of research. Here, we identify c-Myc as a highly heterogeneously expressed transcription factor and an orchestrator of transcriptional and phenotypic diversity in cancer cells. By monitoring endogenous c-Myc protein in individual living cells, we report the surprising pulsatile nature of c-Myc expression and the extensive cell-to-cell variability in its dynamics. We further show that heterogeneity in c-Myc dynamics leads to variable target gene transcription and that timing of c-Myc expression predicts cell-cycle progression rates and drug sensitivities. Together, our data advocate for a model in which cancer cells increase the heterogeneity of functionally diverse transcription factors such as c-Myc to rapidly survey transcriptional landscapes and survive stress.
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Affiliation(s)
- Chad Liu
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Takamasa Kudo
- Department of Cellular and Tissue Genomics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Karen Gascoigne
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.
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16
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Lim TY, Wilde BR, Thomas ML, Murphy KE, Vahrenkamp JM, Conway ME, Varley KE, Gertz J, Ayer DE. TXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic binding. PLoS Biol 2023; 21:e3001778. [PMID: 36930677 PMCID: PMC10058090 DOI: 10.1371/journal.pbio.3001778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 03/29/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
The c-Myc protooncogene places a demand on glucose uptake to drive glucose-dependent biosynthetic pathways. To meet this demand, c-Myc protein (Myc henceforth) drives the expression of glucose transporters, glycolytic enzymes, and represses the expression of thioredoxin interacting protein (TXNIP), which is a potent negative regulator of glucose uptake. A Mychigh/TXNIPlow gene signature is clinically significant as it correlates with poor clinical prognosis in triple-negative breast cancer (TNBC) but not in other subtypes of breast cancer, suggesting a functional relationship between Myc and TXNIP. To better understand how TXNIP contributes to the aggressive behavior of TNBC, we generated TXNIP null MDA-MB-231 (231:TKO) cells for our study. We show that TXNIP loss drives a transcriptional program that resembles those driven by Myc and increases global Myc genome occupancy. TXNIP loss allows Myc to invade the promoters and enhancers of target genes that are potentially relevant to cell transformation. Together, these findings suggest that TXNIP is a broad repressor of Myc genomic binding. The increase in Myc genomic binding in the 231:TKO cells expands the Myc-dependent transcriptome we identified in parental MDA-MB-231 cells. This expansion of Myc-dependent transcription following TXNIP loss occurs without an apparent increase in Myc's intrinsic capacity to activate transcription and without increasing Myc levels. Together, our findings suggest that TXNIP loss mimics Myc overexpression, connecting Myc genomic binding and transcriptional programs to the nutrient and progrowth signals that control TXNIP expression.
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Affiliation(s)
- Tian-Yeh Lim
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Blake R Wilde
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Mallory L Thomas
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Kristin E Murphy
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Megan E Conway
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Donald E Ayer
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
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17
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Das SK, Lewis BA, Levens D. MYC: a complex problem. Trends Cell Biol 2023; 33:235-246. [PMID: 35963793 PMCID: PMC9911561 DOI: 10.1016/j.tcb.2022.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/22/2022]
Abstract
The MYC protooncogene functions as a universal amplifier of transcription through interaction with numerous factors and complexes that regulate almost every cellular process. However, a comprehensive model that explains MYC's actions and the interplay governing the complicated dynamics of components of the transcription and replication machinery is still lacking. Here, we review the potency of MYC as an oncogenic driver and how it regulates the broad spectrum of complexes (effectors and regulators). We propose a 'hand-over model' for differential partitioning and trafficking of unstructured MYC via a loose interaction network between various gene-regulatory complexes and factors. Additionally, the article discusses how unstructured-MYC energetically favors efficient modulation of the energy landscape of the transcription cycle.
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Affiliation(s)
- Subhendu K Das
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - Brian A Lewis
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA.
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18
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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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19
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Karadkhelkar NM, Lin M, Eubanks LM, Janda KD. Demystifying the Druggability of the MYC Family of Oncogenes. J Am Chem Soc 2023; 145:3259-3269. [PMID: 36734615 PMCID: PMC10182829 DOI: 10.1021/jacs.2c12732] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The MYC family of oncogenes (MYC, MYCN, and MYCL) encodes a basic helix-loop-helix leucine zipper (bHLHLZ) transcriptional regulator that is responsible for moving the cell through the restriction point. Through the HLHZIP domain, MYC heterodimerizes with the bHLHLZ protein MAX, which enables this MYC-MAX complex to bind to E-box regulatory DNA elements thereby controlling transcription of a large group of genes and their proteins. Translationally, MYC is one of the foremost oncogenic targets, and deregulation of expression of the MYC family gene/proteins occurs in over half of all human tumors and is recognized as a hallmark of cancer initiation and maintenance. Additionally, unexpected roles for this oncoprotein have been found in cancers that nominally have a non-MYC etiology. Although MYC is rarely mutated, its gain of function in cancer results from overexpression or from amplification. Moreover, MYC is a pleiotropic transcription factor possessing broad pathogenic prominence making it a coveted cancer target. A widely held notion within the biomedical research community is that the reliable modulation of MYC represents a tremendous therapeutic opportunity given its role in directly potentiating oncogenesis. However, the MYC-MAX heterodimer interaction contains a large surface area with a lack of well-defined binding sites creating the perception that targeting of MYC-MAX is forbidding. Here, we discuss the biochemistry behind MYC and MYC-MAX as it relates to cancer progression associated with these transcription factors. We also discuss the notion that MYC should no longer be regarded as undruggable, providing examples that a therapeutic window is achievable despite global MYC inhibition.
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Affiliation(s)
- Nishant M. Karadkhelkar
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Mingliang Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Lisa M. Eubanks
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
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20
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Scagnoli F, Palma A, Favia A, Scuoppo C, Illi B, Nasi S. A New Insight into MYC Action: Control of RNA Polymerase II Methylation and Transcription Termination. Biomedicines 2023; 11:biomedicines11020412. [PMID: 36830948 PMCID: PMC9952900 DOI: 10.3390/biomedicines11020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
MYC oncoprotein deregulation is a common catastrophic event in human cancer and limiting its activity restrains tumor development and maintenance, as clearly shown via Omomyc, an MYC-interfering 90 amino acid mini-protein. MYC is a multifunctional transcription factor that regulates many aspects of transcription by RNA polymerase II (RNAPII), such as transcription activation, pause release, and elongation. MYC directly associates with Protein Arginine Methyltransferase 5 (PRMT5), a protein that methylates a variety of targets, including RNAPII at the arginine residue R1810 (R1810me2s), crucial for proper transcription termination and splicing of transcripts. Therefore, we asked whether MYC controls termination as well, by affecting R1810me2S. We show that MYC overexpression strongly increases R1810me2s, while Omomyc, an MYC shRNA, or a PRMT5 inhibitor and siRNA counteract this phenomenon. Omomyc also impairs Serine 2 phosphorylation in the RNAPII carboxyterminal domain, a modification that sustains transcription elongation. ChIP-seq experiments show that Omomyc replaces MYC and reshapes RNAPII distribution, increasing occupancy at promoter and termination sites. It is unclear how this may affect gene expression. Transcriptomic analysis shows that transcripts pivotal to key signaling pathways are both up- or down-regulated by Omomyc, whereas genes directly controlled by MYC and belonging to a specific signature are strongly down-regulated. Overall, our data point to an MYC/PRMT5/RNAPII axis that controls termination via RNAPII symmetrical dimethylation and contributes to rewiring the expression of genes altered by MYC overexpression in cancer cells. It remains to be clarified which role this may have in tumor development.
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Affiliation(s)
- Fiorella Scagnoli
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Alessandro Palma
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
| | - Annarita Favia
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
| | - Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Barbara Illi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
| | - Sergio Nasi
- IBPM—CNR, Biology and Biotechnology Department, Sapienza University, 00185 Rome, Italy
- Correspondence: (F.S.); (B.I.); (S.N.)
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21
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MYC multimers shield stalled replication forks from RNA polymerase. Nature 2022; 612:148-155. [PMID: 36424410 DOI: 10.1038/s41586-022-05469-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022]
Abstract
Oncoproteins of the MYC family drive the development of numerous human tumours1. In unperturbed cells, MYC proteins bind to nearly all active promoters and control transcription by RNA polymerase II2,3. MYC proteins can also coordinate transcription with DNA replication4,5 and promote the repair of transcription-associated DNA damage6, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from many of its binding sites in active promoters and forms multimeric, often sphere-like structures in response to perturbation of transcription elongation, mRNA splicing or inhibition of the proteasome. Multimerization is accompanied by a global change in the MYC interactome towards proteins involved in transcription termination and RNA processing. MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround FANCD2, ATR and BRCA1 proteins, which are located at stalled forks7,8. MYC multimerization is triggered in a HUWE16 and ubiquitylation-dependent manner. At active promoters, MYC multimers block antisense transcription and stabilize FANCD2 association with chromatin. This limits DNA double strand break formation during S-phase, suggesting that the multimerization of MYC enables tumour cells to proliferate under stressful conditions.
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22
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Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol 2022; 40:1624-1633. [PMID: 35697807 PMCID: PMC9646498 DOI: 10.1038/s41587-022-01342-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 04/29/2022] [Indexed: 12/30/2022]
Abstract
Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
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Grants
- U01 CA196403 NCI NIH HHS
- P30 CA016672 NCI NIH HHS
- U01 CA224044 NCI NIH HHS
- R01 CA268380 NCI NIH HHS
- Department of Health
- FC001169 Cancer Research UK
- C416/A21999 Cancer Research UK
- MR/L016311/1 Medical Research Council
- R01 CA231465 NCI NIH HHS
- U01 CA256780 NCI NIH HHS
- R01 CA183793 NCI NIH HHS
- FC001202 Medical Research Council
- U01 CA200468 NCI NIH HHS
- FC001202 Wellcome Trust
- R01 CA234629 NCI NIH HHS
- U01 CA214194 NCI NIH HHS
- FC001202 Cancer Research UK
- P50 CA221707 NCI NIH HHS
- C11496/A17786 Cancer Research UK
- L30 CA171000 NCI NIH HHS
- FC001169 Wellcome Trust
- FC001169 Medical Research Council
- U24 CA248265 NCI NIH HHS
- K22 CA234406 NCI NIH HHS
- P30 CA016042 NCI NIH HHS
- C11496/A30025 Cancer Research UK
- U24 CA224020 NCI NIH HHS
- Norman Jaffe Professorship in Pediatrics Endowment Fund, MD Anderson Colorectal Cancer Moon Shot Program, and NIH R01CA183793
- American Thyroid Association (American Thyroid Association, lnc.)
- Mark Foundation for Cancer Research ASPIRE award
- Human Cell Atlas Seed Network - Breast, Chan Zuckerberg Institute, MD Anderson Colorectal Cancer Moon Shot Program, NIH R01CA183793
- NIH R01CA239342
- Cancer Prevention and Research Institute of Texas as a CPRIT Scholar in Cancer Research and by National Institutes of Health (K22CA234406)
- NIH R01CA158113
- NIH (T32CA009599)
- MD Anderson Pancreatic Cancer Moon Shot Program, the Khalifa Bin Zayed Al-Nahyan Foundation, and the National Institutes of Health (NIH U01CA196403, U01CA200468, U24CA224020, P50CA221707)
- Norwegian Cancer Society (grant number 198016-2018)
- Norman Jaffe Professorship in Pediatrics Endowment Fund
- the Welch Foundation, MEI Pharma, Inc., Cancer Research United Kingdom (CRUK), Kadoorie Charitable Foundation, NIH/NCI (U01 CA224044-01A1, 1R01CA231465-01A1)
- Career Development Award by the American Society of Clinical Oncology, a Research Award by KCCure, the MD Anderson Khalifa Scholar Award, and the MD Anderson Physician-Scientist Award
- NIH/NCI under awards number P30CA016042, 1U01CA214194-01 and 1U24CA248265-01
- the Medical Research Council (grant number MR/L016311/1), the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie Grant Agreement No. 703594-DECODE) and the Research Foundation – Flanders (FWO, Grant No. 12J6916N)
- the Medical Research Council (grant number MR/L016311/1), Winton Charitable Foundation
- NIH R01CA183793
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Affiliation(s)
- Shaolong Cao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer R Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shuangxi Ji
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Yang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Statistics, Rice University, Houston, TX, USA
| | - Yaoyi Dai
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Shuai Guo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew D Montierth
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiao Zhao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jingxiao Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaewon James Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola A Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas Spetsieris
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nikolai Engedal
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Kaixian Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julie Livingstone
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Vinayak Bhandari
- Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Shawna M Hubert
- Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Najat C Daw
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eleni Efstathiou
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic Head Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Bogdan A Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Powel H Brown
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Pavlos Msaouel
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VC, Australia
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medical Biophysics, University of Toronto, Toronto ON, Canada
| | - Hongtu Zhu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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23
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Vollmuth N, Schlicker L, Guo Y, Hovhannisyan P, Janaki-Raman S, Kurmasheva N, Schmitz W, Schulze A, Stelzner K, Rajeeve K, Rudel T. c-Myc plays a key role in IFN-γ-induced persistence of Chlamydia trachomatis. eLife 2022; 11:76721. [PMID: 36155135 PMCID: PMC9512400 DOI: 10.7554/elife.76721] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia trachomatis (Ctr) can persist over extended times within their host cell and thereby establish chronic infections. One of the major inducers of chlamydial persistence is interferon-gamma (IFN-γ) released by immune cells as a mechanism of immune defence. IFN-γ activates the catabolic depletion of L-tryptophan (Trp) via indoleamine-2,3-dioxygenase (IDO), resulting in persistent Ctr. Here, we show that IFN-γ induces the downregulation of c-Myc, the key regulator of host cell metabolism, in a STAT1-dependent manner. Expression of c-Myc rescued Ctr from IFN-γ-induced persistence in cell lines and human fallopian tube organoids. Trp concentrations control c-Myc levels most likely via the PI3K-GSK3β axis. Unbiased metabolic analysis revealed that Ctr infection reprograms the host cell tricarboxylic acid (TCA) cycle to support pyrimidine biosynthesis. Addition of TCA cycle intermediates or pyrimidine/purine nucleosides to infected cells rescued Ctr from IFN-γ-induced persistence. Thus, our results challenge the longstanding hypothesis of Trp depletion through IDO as the major mechanism of IFN-γ-induced metabolic immune defence and significantly extends the understanding of the role of IFN-γ as a broad modulator of host cell metabolism.
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Affiliation(s)
- Nadine Vollmuth
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Lisa Schlicker
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yongxia Guo
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Pargev Hovhannisyan
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | - Naziia Kurmasheva
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Wuerzburg, Würzburg, Germany
| | - Almut Schulze
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Biochemistry and Molecular Biology, University of Wuerzburg, Würzburg, Germany
| | - Kathrin Stelzner
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Karthika Rajeeve
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
| | - Thomas Rudel
- Department of Microbiology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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24
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Bangalore DM, Tessmer I. Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress. Nucleic Acids Res 2022; 50:10385-10398. [PMID: 36156093 PMCID: PMC9561264 DOI: 10.1093/nar/gkac796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The base excision repair (BER) glycosylase hOGG1 (human oxoguanine glycosylase 1) is responsible for repairing oxidative lesions in the genome, in particular oxidised guanine bases (oxoG). In addition, a role of hOGG1 in transcription regulation by recruitment of various transcription factors has been reported. Here, we demonstrate direct interactions between hOGG1 and the medically important oncogene transcription factor Myc that is involved in transcription initiation of a large number of genes including inflammatory genes. Using single molecule atomic force microscopy (AFM), we reveal recruitment of Myc to its E-box promoter recognition sequence by hOGG1 specifically under oxidative stress conditions, and conformational changes in hOGG1-Myc complexes at oxoG lesions that suggest loading of Myc at oxoG lesions by hOGG1. Importantly, our data show suppression of hOGG1 catalytic activity in oxoG repair by Myc. Furthermore, mutational analyses implicate the C28 residue in hOGG1 in oxidation induced protein dimerisation and suggest a role of hOGG1 dimerisation under oxidising conditions in hOGG1-Myc interactions. From our data we develop a mechanistic model for Myc recruitment by hOGG1 under oxidising, inflammatory conditions, which may be responsible for the observed enhanced gene expression of Myc target genes.
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Affiliation(s)
- Disha M Bangalore
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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25
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Schwarz JD, Lukassen S, Bhandare P, Eing L, Snaebjörnsson MT, García YC, Kisker JP, Schulze A, Wolf E. The glycolytic enzyme ALDOA and the exon junction complex protein RBM8A are regulators of ribosomal biogenesis. Front Cell Dev Biol 2022; 10:954358. [PMID: 36187487 PMCID: PMC9515781 DOI: 10.3389/fcell.2022.954358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
Cellular growth is a fundamental process of life and must be precisely controlled in multicellular organisms. Growth is crucially controlled by the number of functional ribosomes available in cells. The production of new ribosomes depends critically on the activity of RNA polymerase (RNAP) II in addition to the activity of RNAP I and III, which produce ribosomal RNAs. Indeed, the expression of both, ribosomal proteins and proteins required for ribosome assembly (ribosomal biogenesis factors), is considered rate-limiting for ribosome synthesis. Here, we used genetic screening to identify novel transcriptional regulators of cell growth genes by fusing promoters from a ribosomal protein gene (Rpl18) and from a ribosomal biogenesis factor (Fbl) with fluorescent protein genes (RFP, GFP) as reporters. Subsequently, both reporters were stably integrated into immortalized mouse fibroblasts, which were then transduced with a genome-wide sgRNA-CRISPR knockout library. Subsequently, cells with altered reporter activity were isolated by FACS and the causative sgRNAs were identified. Interestingly, we identified two novel regulators of growth genes. Firstly, the exon junction complex protein RBM8A controls transcript levels of the intronless reporters used here. By acute depletion of RBM8A protein using the auxin degron system combined with the genome-wide analysis of nascent transcription, we showed that RBM8A is an important global regulator of ribosomal protein transcripts. Secondly, we unexpectedly observed that the glycolytic enzyme aldolase A (ALDOA) regulates the expression of ribosomal biogenesis factors. Consistent with published observations that a fraction of this protein is located in the nucleus, this may be a mechanism linking transcription of growth genes to metabolic processes and possibly to metabolite availability.
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Affiliation(s)
- Jessica Denise Schwarz
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Sören Lukassen
- Center for Digital Health, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Lorenz Eing
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | | | - Yiliam Cruz García
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Jan Philipp Kisker
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - Almut Schulze
- Tumor Metabolism and Microenvironment, German Cancer Research Center, Heidelberg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- *Correspondence: Elmar Wolf,
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26
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Winkler R, Mägdefrau AS, Piskor EM, Kleemann M, Beyer M, Linke K, Hansen L, Schaffer AM, Hoffmann ME, Poepsel S, Heyd F, Beli P, Möröy T, Mahboobi S, Krämer OH, Kosan C. Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition. Oncogene 2022; 41:4560-4572. [PMID: 36068335 PMCID: PMC9525236 DOI: 10.1038/s41388-022-02450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022]
Abstract
Overexpression of MYC is a genuine cancer driver in lymphomas and related to poor prognosis. However, therapeutic targeting of the transcription factor MYC remains challenging. Here, we show that inhibition of the histone deacetylase 6 (HDAC6) using the HDAC6 inhibitor Marbostat-100 (M-100) reduces oncogenic MYC levels and prevents lymphomagenesis in a mouse model of MYC-induced aggressive B-cell lymphoma. M-100 specifically alters protein-protein interactions by switching the acetylation state of HDAC6 substrates, such as tubulin. Tubulin facilitates nuclear import of MYC, and MYC-dependent B-cell lymphoma cells rely on continuous import of MYC due to its high turn-over. Acetylation of tubulin impairs this mechanism and enables proteasomal degradation of MYC. M-100 targets almost exclusively B-cell lymphoma cells with high levels of MYC whereas non-tumor cells are not affected. M-100 induces massive apoptosis in human and murine MYC-overexpressing B-cell lymphoma cells. We identified the heat-shock protein DNAJA3 as an interactor of tubulin in an acetylation-dependent manner and overexpression of DNAJA3 resulted in a pronounced degradation of MYC. We propose a mechanism by which DNAJA3 associates with hyperacetylated tubulin in the cytoplasm to control MYC turnover. Taken together, our data demonstrate a beneficial role of HDAC6 inhibition in MYC-dependent B-cell lymphoma.
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Affiliation(s)
- René Winkler
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany.,Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, 08916, Spain
| | - Ann-Sophie Mägdefrau
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Eva-Maria Piskor
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Markus Kleemann
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Mandy Beyer
- Institute of Toxicology, University Medical Center Mainz, Mainz, 55131, Germany
| | - Kevin Linke
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Lisa Hansen
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | - Anna-Maria Schaffer
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany
| | | | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, Cologne, 50931, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany
| | - Florian Heyd
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, 14195, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, H2W 1R7, Canada
| | - Siavosh Mahboobi
- Department of Pharmaceutical/Medicinal Chemistry I, Institute of Pharmacy, University of Regensburg, Regensburg, 93040, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center Mainz, Mainz, 55131, Germany
| | - Christian Kosan
- Department of Biochemistry, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Jena, 07745, Germany.
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27
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Liang X, Brooks MJ, Swaroop A. Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina. Hum Mol Genet 2022; 31:3914-3933. [PMID: 35776116 DOI: 10.1093/hmg/ddac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein CRX and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. We predicted that NRL gradually establishes rod cell identity and function by temporal and dynamic regulation of stage-specific transcriptional targets. Therefore, we mapped the genomic occupancy of NRL at four stages of mouse photoreceptor differentiation by CUT&RUN analysis. Dynamics of NRL-binding revealed concordance with the corresponding changes in transcriptome of the developing rods. Notably, we identified c-Jun proto-oncogene as one of the targets of NRL, which could bind to specific cis-elements in the c-Jun promoter and modulate its activity in HEK293 cells. Coimmunoprecipitation studies showed association of NRL with c-Jun, also a bZIP protein, in transfected cells as well as in developing mouse retina. Additionally, shRNA-mediated knockdown of c-Jun in the mouse retina in vivo resulted in altered expression of almost 1000 genes, with reduced expression of phototransduction genes and many direct targets of NRL in rod photoreceptors. We propose that c-Jun-NRL heterodimers prime the NRL-directed transcriptional program in neonatal rod photoreceptors before high NRL expression suppresses c-Jun at later stages. Our study highlights a broader cooperation among cell-type restricted and widely expressed bZIP proteins, such as c-Jun, in specific spatiotemporal contexts during cellular differentiation.
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Affiliation(s)
- Xulong Liang
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
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28
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Holmes AG, Parker JB, Sagar V, Truica MI, Soni PN, Han H, Schiltz GE, Abdulkadir SA, Chakravarti D. A MYC inhibitor selectively alters the MYC and MAX cistromes and modulates the epigenomic landscape to regulate target gene expression. SCIENCE ADVANCES 2022; 8:eabh3635. [PMID: 35476451 PMCID: PMC9045724 DOI: 10.1126/sciadv.abh3635] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
MYC regulates multiple gene programs, raising questions about the potential selectivity and downstream transcriptional consequences of MYC inhibitors as cancer therapeutics. Here, we examined the effect of a small-molecule MYC inhibitor, MYCi975, on the MYC/MAX cistromes, epigenome, transcriptome, and tumorigenesis. Integrating these data revealed three major classes of MYCi975-modulated gene targets: type 1 (down-regulated), type 2 (up-regulated), and type 3 (unaltered). While cell cycle and signal transduction pathways were heavily targeted by MYCi, RNA biogenesis and core transcriptional pathway genes were spared. MYCi975 altered chromatin binding of MYC and the MYC network family proteins, and chromatin accessibility and H3K27 acetylation alterations revealed MYCi975 suppression of MYC-regulated lineage factors AR/ARv7, FOXA1, and FOXM1. Consequently, MYCi975 synergistically sensitized resistant prostate cancer cells to enzalutamide and estrogen receptor-positive breast cancer cells to 4-hydroxytamoxifen. Our results demonstrate that MYCi975 selectively inhibits MYC target gene expression and provide a mechanistic rationale for potential combination therapies.
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Affiliation(s)
- Austin G. Holmes
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - J. Brandon Parker
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vinay Sagar
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mihai I. Truica
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Pritin N. Soni
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Huiying Han
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Gary E. Schiltz
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sarki A. Abdulkadir
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Debabrata Chakravarti
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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29
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Ruan H, Leibowitz BJ, Peng Y, Shen L, Chen L, Kuang C, Schoen RE, Lu X, Zhang L, Yu J. Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer. MOLECULAR BIOMEDICINE 2022; 3:10. [PMID: 35307764 PMCID: PMC8934835 DOI: 10.1186/s43556-022-00070-7] [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: 09/30/2021] [Accepted: 01/21/2022] [Indexed: 12/16/2022] Open
Abstract
Mutant KRAS is a key driver in colorectal cancer (CRC) and promotes Myc translation and Myc-dependent stress adaptation and proliferation. Here, we report that the combination of two FDA-approved drugs Bortezomib and Everolimus (RAD001) (BR) is highly efficacious against mutant KRAS CRC cells. Mechanistically, the combination, not single agent, rapidly depletes Myc protein, not mRNA, and leads to GCN2- and p-eIF2α-dependent cell death through the activation of extrinsic and intrinsic apoptotic pathways. Cell death is selectively induced in mutant KRAS CRC cells with elevated basal Myc and p-eIF2α and is characterized by CHOP induction and transcriptional signatures in proteotoxicity, oxidative stress, metabolic inhibition, and immune activation. BR-induced p-GCN2/p-eIF2α elevation and cell death are strongly attenuated by MYC knockdown and enhanced by MYC overexpression. The BR combination is efficacious against mutant KRAS patient derived organoids (PDO) and xenografts (PDX) by inducing p-eIF2α/CHOP and cell death. Interestingly, an elevated four-gene (DDIT3, GADD45B, CRYBA4 and HSPA1L) stress signature is linked to shortened overall survival in CRC patients. These data support that Myc-dependent stress adaptation drives the progression of mutant KRAS CRC and serves as a therapeutic vulnerability, which can be targeted using dual translational inhibitors.
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Affiliation(s)
- Hang Ruan
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Brian J. Leibowitz
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Yingpeng Peng
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Lin Shen
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.452223.00000 0004 1757 7615Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008 P.R. China
| | - Lujia Chen
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Medical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232 USA
| | - Charlie Kuang
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Robert E. Schoen
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Epidemiology, University of Pittsburgh School of Public Health Pittsburgh, Pittsburgh, PA 15213 USA
| | - Xinghua Lu
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Medical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232 USA
| | - Lin Zhang
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Jian Yu
- grid.412689.00000 0001 0650 7433UPMC Hillman Cancer Center Research Pavilion, Suite 2.26h, 5117 Centre Ave., Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
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30
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See YX, Chen K, Fullwood MJ. MYC overexpression leads to increased chromatin interactions at superenhancers and MYC binding sites. Genome Res 2022; 32:629-642. [PMID: 35115371 PMCID: PMC8997345 DOI: 10.1101/gr.276313.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022]
Abstract
The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Because super-enhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into super-enhancers and alters the cancer genome organization. To that end, we performed ChIP-seq, RNA-seq, circular chromosome conformation capture (4C-seq), and Spike-in Quantitative Hi-C (SIQHiC) on the U2OS osteosarcoma cell line with tetracycline-inducible MYC. MYC overexpression in U2OS cells modulated histone acetylation and increased MYC binding at super-enhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting MYC binding sites at promoters and enhancers. Immunofluorescence staining showed that MYC molecules formed punctate foci at these transcriptionally active domains after MYC overexpression. These results demonstrate the accumulation of overexpressed MYC at promoter–enhancer hubs and suggest that MYC invades into enhancers through spatial proximity. At the same time, the increased protein–protein interactions may strengthen these chromatin interactions to increase chromatin contact frequency. CTCF siRNA knockdown in MYC-overexpressed U2OS cells demonstrated that removal of architectural proteins can disperse MYC and abrogate the increase in chromatin contacts. By elucidating the chromatin landscape of MYC-driven cancers, we can potentially target MYC-associated chromatin interactions for cancer therapy.
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Affiliation(s)
- Yi Xiang See
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore
| | - Kaijing Chen
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore
| | - Melissa J Fullwood
- Nanyang Technological University, Cancer Science Institute of Singapore, National University of Singapore, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR)
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31
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Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR. MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Rep 2022; 38:110292. [PMID: 35081348 DOI: 10.1016/j.celrep.2021.110292] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022] Open
Abstract
The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. Here, we seek to answer these questions with an in vivo readout of discrete events of gene expression in single cells. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the immediate consequence of MYC overexpression is an increase in the duration rather than in the frequency of bursts, a functional role that is different from the majority of human transcription factors. We further propose that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA polymerase II complex assembly and productive elongation.
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Affiliation(s)
- Simona Patange
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yihan Wan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michelle Girvan
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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32
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Das SK, Kuzin V, Cameron DP, Sanford S, Jha RK, Nie Z, Rosello MT, Holewinski R, Andresson T, Wisniewski J, Natsume T, Price DH, Lewis BA, Kouzine F, Levens D, Baranello L. MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". Mol Cell 2021; 82:140-158.e12. [PMID: 34890565 DOI: 10.1016/j.molcel.2021.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 08/11/2021] [Accepted: 11/13/2021] [Indexed: 12/25/2022]
Abstract
High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must manage this interfering torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with topoisomerase 1 (TOP1) and TOP2 that was confirmed in vitro and in cells. Beyond recruiting topoisomerases, MYC directly stimulates their activities. We identify a MYC-nucleated "topoisome" complex that unites TOP1 and TOP2 and increases their levels and activities at promoters, gene bodies, and enhancers. Whether TOP2A or TOP2B is included in the topoisome is dictated by the presence of MYC versus MYCN, respectively. Thus, in vitro and in cells, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions.
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Affiliation(s)
- Subhendu K Das
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Donald P Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Suzanne Sanford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Rajiv Kumar Jha
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Zuqin Nie
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Marta Trullols Rosello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ronald Holewinski
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Thorkell Andresson
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD 21701, USA
| | - Jan Wisniewski
- Confocal Microscopy and Digital Imaging Facility, National Cancer Institute, Bethesda, MD 20892, USA
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Shizuoka 411-8540, Japan; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Brian A Lewis
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - Fedor Kouzine
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20814, USA.
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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33
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Differential Transcriptional Reprogramming by Wild Type and Lymphoma-Associated Mutant MYC Proteins as B-Cells Convert to a Lymphoma Phenotype. Cancers (Basel) 2021; 13:cancers13236093. [PMID: 34885204 PMCID: PMC8657136 DOI: 10.3390/cancers13236093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
The MYC transcription factor regulates a vast number of genes and is implicated in many human malignancies. In some hematological malignancies, MYC is frequently subject to missense mutations that enhance its transformation activity. Here, we use a novel murine cell system to (i) characterize the transcriptional effects of progressively increasing MYC levels as normal primary B-cells transform to lymphoma cells and (ii) determine how this gene regulation program is modified by lymphoma-associated MYC mutations (T58A and T58I) that enhance its transformation activity. Unlike many previous studies, the cell system exploits primary B-cells that are transduced to allow regulated MYC expression under circumstances where apoptosis and senescence pathways are abrogated by the over-expression of the Bcl-xL and BMI1 proteins. In such cells, transition from a normal to a lymphoma phenotype is directly dependent on the MYC expression level, without a requirement for secondary events that are normally required during MYC-driven oncogenic transformation. A generalized linear model approach allowed an integrated analysis of RNA sequencing data to identify regulated genes in relation to both progressively increasing MYC level and wild type or mutant status. Using this design, a total of 7569 regulated genes were identified, of which the majority (n = 7263) were regulated in response to progressively increased levels of wild type MYC, while a smaller number of genes (n = 917) were differentially regulated, compared to wild type MYC, in T58A MYC- and/or T58I MYC-expressing cells. Unlike most genes that are similarly regulated by both wild type and mutant MYC genes, the set of 917 genes did not significantly overlap with known lipopolysaccharide regulated genes, which represent genes regulated by MYC in normal B cells. The genes that were differently regulated in cells expressing mutant MYC proteins were significantly enriched in DNA replication and G2 phase to mitosis transition genes. Thus, mutants affecting MYC proteins may augment quantitative oncogenic effects on the expression of normal MYC-target genes with qualitative oncogenic effects, by which sets of cell cycle genes are abnormally targeted by MYC as B cells transition into lymphoma cells. The T58A and T58I mutations augment MYC-driven transformation by distinct mechanisms.
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34
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Ji A, Qian L, Tian Z, Cui J. WDR5 promotes the proliferation of lung adenocarcinoma by inducing SOX9 expression. Biomark Med 2021; 15:1599-1609. [PMID: 34743548 DOI: 10.2217/bmm-2021-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: WDR5 is a coactivator of transcription factor which promotes the progression of several cancer types, but its function in lung adenocarcinoma (AC) is unknown. Materials & methods: We detected WDR5 expression in lung AC with quantitative real-time polymerase chain reaction and immunohistochemistry. Results: WDR5 was significantly overexpressed in ACs compared with normal lung tissues. Moreover, WDR5 was an independent prognostic biomarker of lung AC. With clinical analyzation and in vitro experiments, we proved that SOX9 was a downstream effector of WDR5 in promoting A549 proliferation, and that SOX9 was also an unfavorable prognostic biomarker of lung AC. Conclusion: WDR5 and SOX9 are both prognostic biomarkers predicting poor outcome of lung AC. WDR5 could promote proliferation of lung AC by elevating SOX9 expression.
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Affiliation(s)
- Aihua Ji
- Department of Gastrointestinal Surgery, Yidu Central Hospital, Weifang, Shandong, 262500, China
| | - Lei Qian
- Department of Cardiothoracic Surgery, Yidu Central Hospital, Weifang, Shandong, 262500, China
| | - Zhenmin Tian
- Department of Clinical Laboratory, Yidu Central Hospital, Weifang, Shandong, 262500, China
| | - Jie Cui
- Department of Oncology, Central Hospital of Ankang City, Ankang, Shaanxi, 725000, China
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35
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Zhou Y, Gao X, Yuan M, Yang B, He Q, Cao J. Targeting Myc Interacting Proteins as a Winding Path in Cancer Therapy. Front Pharmacol 2021; 12:748852. [PMID: 34658888 PMCID: PMC8511624 DOI: 10.3389/fphar.2021.748852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
MYC, as a well-known oncogene, plays essential roles in promoting tumor occurrence, development, invasion and metastasis in many kinds of solid tumors and hematologic neoplasms. In tumors, the low expression and the short half-life of Myc are reversed, cause tumorigenesis. And proteins that directly interact with different Myc domains have exerted a significant impact in the process of Myc-driven carcinogenesis. Apart from affecting the transcription of Myc target genes, Myc interaction proteins also regulate the stability of Myc through acetylation, methylation, phosphorylation and other post-translational modifications, as well as competitive combination with Myc. In this review, we summarize a series of Myc interacting proteins and recent advances in the related inhibitors, hoping that can provide new opportunities for Myc-driven cancer treatment.
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Affiliation(s)
- Yihui Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomeng Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meng Yuan
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
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36
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p53-Dependent Repression: DREAM or Reality? Cancers (Basel) 2021; 13:cancers13194850. [PMID: 34638334 PMCID: PMC8508069 DOI: 10.3390/cancers13194850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary The tumor suppressor p53 is a complex cell signaling hub encompassing multiple transcription programs and governs a vast repertoire of biological responses. However, despite several decades of research, how p53 selects one program over another is still elusive. Recent attempts have used meta-analyses of p53 ChIP-seq data to determine the core p53 transcriptional program, conserved across different models and stimuli. This review highlights the complexity of the multiple layers of p53 regulation and the context specificity of p53 target genes. More specifically, we discuss the controversy over the mechanisms of p53-dependent transcriptional repression and its potential role in the flexibility of p53 response. Abstract p53 is a major tumor suppressor that integrates diverse types of signaling in mammalian cells. In response to a broad range of intra- or extra-cellular stimuli, p53 controls the expression of multiple target genes and elicits a vast repertoire of biological responses. The exact code by which p53 integrates the various stresses and translates them into an appropriate transcriptional response is still obscure. p53 is tightly regulated at multiple levels, leading to a wide diversity in p53 complexes on its target promoters and providing adaptability to its transcriptional program. As p53-targeted therapies are making their way into clinics, we need to understand how to direct p53 towards the desired outcome (i.e., cell death, senescence or other) selectively in cancer cells without affecting normal tissues or the immune system. While the core p53 transcriptional program has been proposed, the mechanisms conferring a cell type- and stimuli-dependent transcriptional outcome by p53 require further investigations. The mechanism by which p53 localizes to repressed promoters and manages its co-repressor interactions is controversial and remains an important gap in our understanding of the p53 cistrome. We hope that our review of the recent literature will help to stimulate the appreciation and investigation of largely unexplored p53-mediated repression.
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37
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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38
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Biophysical and Structural Methods to Study the bHLHZip Region of Human c-MYC. Methods Mol Biol 2021. [PMID: 34019285 DOI: 10.1007/978-1-0716-1476-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The C-terminal region of the c-MYC transcription factor consists of approximately 100 amino acids that in its native state does not adopt a stable structure. When this region binds to the obligatory partner MAX via a coupled folding-and-binding mechanism, it forms a basic-helix-loop-helix-leucine zipper (bHLHZip) heterodimeric complex. The C-terminal region of MYC is the target for numerous drug discovery programs for direct MYC inhibition via blocking the dimerization event and/or binding to DNA, and a proper understanding of the partially folded, dynamic nature of the heterodimeric complex is essential to these efforts. The bHLHZip motif also drives protein-protein interactions with cofactors that are crucial for both transcriptional repression and activation of MYC target genes. Targeting these interactions could potentially provide a means of developing alternative approaches to halt MYC functions; however, the molecular mechanism of these regulatory interactions is poorly understood. Herein we provide methods to produce high-quality human c-MYC C-terminal by itself and in complex MAX, and how to study them using Nuclear Magnetic Resonance spectroscopy and X-ray crystallography. Our protein expression and purification protocols have already been used to study interactions with cofactors.
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39
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Burchett JB, Knudsen-Clark AM, Altman BJ. MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer. Int J Mol Sci 2021; 22:7761. [PMID: 34299381 PMCID: PMC8305799 DOI: 10.3390/ijms22147761] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
The MYC oncoprotein and its family members N-MYC and L-MYC are known to drive a wide variety of human cancers. Emerging evidence suggests that MYC has a bi-directional relationship with the molecular clock in cancer. The molecular clock is responsible for circadian (~24 h) rhythms in most eukaryotic cells and organisms, as a mechanism to adapt to light/dark cycles. Disruption of human circadian rhythms, such as through shift work, may serve as a risk factor for cancer, but connections with oncogenic drivers such as MYC were previously not well understood. In this review, we examine recent evidence that MYC in cancer cells can disrupt the molecular clock; and conversely, that molecular clock disruption in cancer can deregulate and elevate MYC. Since MYC and the molecular clock control many of the same processes, we then consider competition between MYC and the molecular clock in several select aspects of tumor biology, including chromatin state, global transcriptional profile, metabolic rewiring, and immune infiltrate in the tumor. Finally, we discuss how the molecular clock can be monitored or diagnosed in human tumors, and how MYC inhibition could potentially restore molecular clock function. Further study of the relationship between the molecular clock and MYC in cancer may reveal previously unsuspected vulnerabilities which could lead to new treatment strategies.
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Affiliation(s)
- Jamison B. Burchett
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Amelia M. Knudsen-Clark
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Brian J. Altman
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA;
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
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40
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Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics 2021; 37:3702-3706. [PMID: 34179955 PMCID: PMC8570808 DOI: 10.1093/bioinformatics/btab229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Computational models of biological systems can exploit a broad range of rapidly developing approaches, including novel experimental approaches, bioinformatics data analysis, emerging modelling paradigms, data standards and algorithms. A discussion about the most recent advances among experts from various domains is crucial to foster data-driven computational modelling and its growing use in assessing and predicting the behaviour of biological systems. Intending to encourage the development of tools, approaches and predictive models, and to deepen our understanding of biological systems, the Community of Special Interest (COSI) was launched in Computational Modelling of Biological Systems (SysMod) in 2016. SysMod’s main activity is an annual meeting at the Intelligent Systems for Molecular Biology (ISMB) conference, which brings together computer scientists, biologists, mathematicians, engineers, computational and systems biologists. In the five years since its inception, SysMod has evolved into a dynamic and expanding community, as the increasing number of contributions and participants illustrate. SysMod maintains several online resources to facilitate interaction among the community members, including an online forum, a calendar of relevant meetings and a YouTube channel with talks and lectures of interest for the modelling community. For more than half a decade, the growing interest in computational systems modelling and multi-scale data integration has inspired and supported the SysMod community. Its members get progressively more involved and actively contribute to the annual COSI meeting and several related community workshops and meetings, focusing on specific topics, including particular techniques for computational modelling or standardisation efforts.
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Affiliation(s)
- Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, Surrey, UK.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford GU2 7XH, Surrey, UK.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Marc Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Laurence Calzone
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005 Paris, France
| | - Claudine Chaouiya
- Aix-Marseille Université, CNRS, Centrale Marseille, I2M, Marseille 2780-156, France.,Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Jan Hasenauer
- Interdisicplinary Research Unit Mathematics and Life Sciences, University of Bonn, Bonn 53115, Germany
| | - Jonathan R Karr
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Niarakis
- GenHotel, University of Evry, University of Paris-Saclay, Genopole, Évry 91025, France.,Lifeware Group, Inria Saclay-île de France, 91120 Palaiseau, France
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, 69120 Heidelberg, Germany
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.,Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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41
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Whitfield JR, Soucek L. The long journey to bring a Myc inhibitor to the clinic. J Cell Biol 2021; 220:212429. [PMID: 34160558 PMCID: PMC8240852 DOI: 10.1083/jcb.202103090] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
The oncogene Myc is deregulated in the majority of human tumors and drives numerous hallmarks of cancer. Despite its indisputable role in cancer development and maintenance, Myc is still undrugged. Developing a clinical inhibitor for Myc has been particularly challenging owing to its intrinsically disordered nature and lack of a binding pocket, coupled with concerns regarding potentially deleterious side effects in normal proliferating tissues. However, major breakthroughs in the development of Myc inhibitors have arisen in the last couple of years. Notably, the direct Myc inhibitor that we developed has just entered clinical trials. Celebrating this milestone, with this Perspective, we pay homage to the different strategies developed so far against Myc and all of the researchers focused on developing treatments for a target long deemed undruggable.
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Affiliation(s)
| | - Laura Soucek
- Vall d'Hebron Institute of Oncology, Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Peptomyc S.L., Barcelona, Spain
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42
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Sun XX, Li Y, Sears RC, Dai MS. Targeting the MYC Ubiquitination-Proteasome Degradation Pathway for Cancer Therapy. Front Oncol 2021; 11:679445. [PMID: 34178666 PMCID: PMC8226175 DOI: 10.3389/fonc.2021.679445] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/24/2021] [Indexed: 12/23/2022] Open
Abstract
Deregulated MYC overexpression and activation contributes to tumor growth and progression. Given the short half-life and unstable nature of the MYC protein, it is not surprising that the oncoprotein is highly regulated via diverse posttranslational mechanisms. Among them, ubiquitination dynamically controls the levels and activity of MYC during normal cell growth and homeostasis, whereas the disturbance of the ubiquitination/deubiquitination balance enables unwanted MYC stabilization and activation. In addition, MYC is also regulated by SUMOylation which crosstalks with the ubiquitination pathway and controls MYC protein stability and activity. In this mini-review, we will summarize current updates regarding MYC ubiquitination and provide perspectives about these MYC regulators as potential therapeutic targets in cancer.
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Affiliation(s)
- Xiao-Xin Sun
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Yanping Li
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
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Curti L, Campaner S. MYC-Induced Replicative Stress: A Double-Edged Sword for Cancer Development and Treatment. Int J Mol Sci 2021; 22:6168. [PMID: 34201047 PMCID: PMC8227504 DOI: 10.3390/ijms22126168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022] Open
Abstract
MYC is a transcription factor that controls the expression of a large fraction of cellular genes linked to cell cycle progression, metabolism and differentiation. MYC deregulation in tumors leads to its pervasive genome-wide binding of both promoters and distal regulatory regions, associated with selective transcriptional control of a large fraction of cellular genes. This pairs with alterations of cell cycle control which drive anticipated S-phase entry and reshape the DNA-replication landscape. Under these circumstances, the fine tuning of DNA replication and transcription becomes critical and may pose an intrinsic liability in MYC-overexpressing cancer cells. Here, we will review the current understanding of how MYC controls DNA and RNA synthesis, discuss evidence of replicative and transcriptional stress induced by MYC and summarize preclinical data supporting the therapeutic potential of triggering replicative stress in MYC-driven tumors.
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Affiliation(s)
- Laura Curti
- Center for Genomic Science of IIT@CGS, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@CGS, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
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44
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Shostak A, Schermann G, Diernfellner A, Brunner M. MXD/MIZ1 transcription regulatory complexes activate the expression of MYC-repressed genes. FEBS Lett 2021; 595:1639-1655. [PMID: 33914337 DOI: 10.1002/1873-3468.14097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022]
Abstract
MXDs are transcription repressors that antagonize MYC-mediated gene activation. MYC, when associated with MIZ1, acts also as a repressor of a subset of genes, including p15 and p21. A role for MXDs in regulation of MYC-repressed genes is not known. We report that MXDs activate transcription of p15 and p21 in U2OS cells. This activation required DNA binding by MXDs and their interaction with MIZ1. MXD mutants deficient in MIZ1 binding interacted with the MYC-binding partner MAX and were active as repressors of MYC-activated genes but failed to activate MYC-repressed genes. Mutant MXDs with reduced DNA-binding affinity interacted with MAX and MIZ1 but neither repressed nor activated transcription. Our data show that MXDs and MYC have a reciprocally antagonistic potential to regulate transcription of target genes.
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45
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Ecker J, Thatikonda V, Sigismondo G, Selt F, Valinciute G, Oehme I, Müller C, Buhl JL, Ridinger J, Usta D, Qin N, van Tilburg CM, Herold-Mende C, Remke M, Sahm F, Westermann F, Kool M, Wechsler-Reya RJ, Chavez L, Krijgsveld J, Jäger N, Pfister SM, Witt O, Milde T. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma. Neuro Oncol 2021; 23:226-239. [PMID: 32822486 DOI: 10.1093/neuonc/noaa191] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The sensitivity of myelocytomatosis oncogene (MYC) amplified medulloblastoma to class I histone deacetylase (HDAC) inhibition has been shown previously; however, understanding the underlying molecular mechanism is crucial for selection of effective HDAC inhibitors for clinical use. The aim of this study was to investigate the direct molecular interaction of MYC and class I HDAC2, and the impact of class I HDAC inhibition on MYC function. METHODS Co-immunoprecipitation and mass spectrometry were used to determine the co-localization of MYC and HDAC2. Chromatin immunoprecipitation (ChIP) sequencing and gene expression profiling were used to analyze the co-localization of MYC and HDAC2 on DNA and the impact on transcriptional activity in primary tumors and a MYC amplified cell line treated with the class I HDAC inhibitor entinostat. The effect on MYC was investigated by quantitative real-time PCR, western blot, and immunofluorescence. RESULTS HDAC2 is a cofactor of MYC in MYC amplified medulloblastoma. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein, inducing a downregulation of MYC activated genes (MAGs) and upregulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and by distinct enhancer-box distribution. CONCLUSIONS Our data elucidate the molecular interaction of MYC and HDAC2 and support a model in which inhibition of class I HDACs directly targets MYC's transactivating and transrepressing functions.
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Affiliation(s)
- Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Gintvile Valinciute
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Carina Müller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Juliane L Buhl
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Johannes Ridinger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Diren Usta
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | | | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany.,Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natalie Jäger
- Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
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46
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Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, Sabò A. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. EMBO J 2021; 40:e105464. [PMID: 33792944 DOI: 10.15252/embj.2020105464] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor. Impairment of non-specific DNA backbone contacts caused pervasive loss of genome interactions and gene regulation, associated with increased intra-nuclear mobility of the Myc protein in murine cells. In contrast, a mutant lacking base-specific contacts retained DNA-binding and mobility profiles comparable to those of the wild-type protein, but failed to recognize its consensus binding motif (E-box) and could not activate Myc-target genes. Incidentally, this mutant gained weak affinity for an alternative motif, driving aberrant activation of different genes. Altogether, our data show that non-specific DNA binding is required to engage onto genomic regulatory regions; sequence recognition in turn contributes to transcriptional activation, acting at distinct levels: stabilization and positioning of Myc onto DNA, and-unexpectedly-promotion of its transcriptional activity. Hence, seemingly pervasive genome interaction profiles, as detected by ChIP-seq, actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
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Affiliation(s)
- Paola Pellanda
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Virginia Castillo Cano
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain
| | | | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Mapelli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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47
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Gene Transactivation and Transrepression in MYC-Driven Cancers. Int J Mol Sci 2021; 22:ijms22073458. [PMID: 33801599 PMCID: PMC8037706 DOI: 10.3390/ijms22073458] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
MYC is a proto-oncogene regulating a large number of genes involved in a plethora of cellular functions. Its deregulation results in activation of MYC gene expression and/or an increase in MYC protein stability. MYC overexpression is a hallmark of malignant growth, inducing self-renewal of stem cells and blocking senescence and cell differentiation. This review summarizes the latest advances in our understanding of MYC-mediated molecular mechanisms responsible for its oncogenic activity. Several recent findings indicate that MYC is a regulator of cancer genome and epigenome: MYC modulates expression of target genes in a site-specific manner, by recruiting chromatin remodeling co-factors at promoter regions, and at genome-wide level, by regulating the expression of several epigenetic modifiers that alter the entire chromatin structure. We also discuss novel emerging therapeutic strategies based on both direct modulation of MYC and its epigenetic cofactors.
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Reyes-González JM, Vivas-Mejía PE. c-MYC and Epithelial Ovarian Cancer. Front Oncol 2021; 11:601512. [PMID: 33718147 PMCID: PMC7952744 DOI: 10.3389/fonc.2021.601512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer is the deadliest of gynecological malignancies with approximately 49% of women surviving 5 years after initial diagnosis. The standard of care for ovarian cancer consists of cytoreductive surgery followed by platinum-based combination chemotherapy. Unfortunately, despite initial response, platinum resistance remains a major clinical challenge. Therefore, the identification of effective biomarkers and therapeutic targets is crucial to guide therapy regimen, maximize clinical benefit, and improve patient outcome. Given the pivotal role of c-MYC deregulation in most tumor types, including ovarian cancer, assessment of c-MYC biological and clinical relevance is essential. Here, we briefly describe the frequency of c-MYC deregulation in ovarian cancer and the consequences of its targeting.
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Affiliation(s)
- Jeyshka M Reyes-González
- Center for Collaborative Research in Health Disparities, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Pablo E Vivas-Mejía
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico.,Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
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Liu R, Shi P, Wang Z, Yuan C, Cui H. Molecular Mechanisms of MYCN Dysregulation in Cancers. Front Oncol 2021; 10:625332. [PMID: 33614505 PMCID: PMC7886978 DOI: 10.3389/fonc.2020.625332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
MYCN, a member of MYC proto-oncogene family, encodes a basic helix-loop-helix transcription factor N-MYC. Abnormal expression of N-MYC is correlated with high-risk cancers and poor prognosis. Initially identified as an amplified oncogene in neuroblastoma in 1983, the oncogenic effect of N-MYC is expanded to multiple neuronal and nonneuronal tumors. Direct targeting N-MYC remains challenge due to its "undruggable" features. Therefore, alternative therapeutic approaches for targeting MYCN-driven tumors have been focused on the disruption of transcription, translation, protein stability as well as synthetic lethality of MYCN. In this review, we summarize the latest advances in understanding the molecular mechanisms of MYCN dysregulation in cancers.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Pengfei Shi
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaoyu Yuan
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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Chen W, Mou KY, Solomon P, Aggarwal R, Leung KK, Wells JA. Large remodeling of the Myc-induced cell surface proteome in B cells and prostate cells creates new opportunities for immunotherapy. Proc Natl Acad Sci U S A 2021; 118:e2018861118. [PMID: 33483421 PMCID: PMC7848737 DOI: 10.1073/pnas.2018861118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
MYC is a powerful transcription factor overexpressed in many human cancers including B cell and prostate cancers. Antibody therapeutics are exciting opportunities to attack cancers but require knowledge of surface proteins that change due to oncogene expression. To identify how MYC overexpression remodels the cell surface proteome in a cell autologous fashion and in different cell types, we investigated the impact of MYC overexpression on 800 surface proteins in three isogenic model cell lines either of B cell or prostate cell origin engineered to have high or low MYC levels. We found that MYC overexpression resulted in dramatic remodeling (both up- and down-regulation) of the cell surfaceome in a cell type-dependent fashion. We found systematic and large increases in distinct sets of >80 transporters including nucleoside transporters and nutrient transporters making cells more sensitive to toxic nucleoside analogs like cytarabine, commonly used for treating hematological cancers. Paradoxically, MYC overexpression also increased expression of surface proteins driving cell turnover such as TNFRSF10B, also known as death receptor 5, and immune cell attacking signals such as the natural killer cell activating ligand NCR3LG1, also known as B7-H6. We generated recombinant antibodies to these two targets and verified their up-regulation in MYC overexpression cell lines and showed they were sensitive to bispecific T cell engagers (BiTEs). Our studies demonstrate how MYC overexpression leads to dramatic bidirectional remodeling of the surfaceome in a cell type-dependent but functionally convergent fashion and identify surface targets or combinations thereof as possible candidates for cytotoxic metabolite or immunotherapy.
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Affiliation(s)
- Wentao Chen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Department of Therapeutic Discovery, Amgen Research, Thousand Oaks, CA 91320
| | - Kurt Yun Mou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 11529
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Rahul Aggarwal
- Department of Medicine, University of California, San Francisco, CA 94158
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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