1
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Miniere HJM, Lima EABF, Lorenzo G, Hormuth II DA, Ty S, Brock A, Yankeelov TE. A mathematical model for predicting the spatiotemporal response of breast cancer cells treated with doxorubicin. Cancer Biol Ther 2024; 25:2321769. [PMID: 38411436 PMCID: PMC11057790 DOI: 10.1080/15384047.2024.2321769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
Tumor heterogeneity contributes significantly to chemoresistance, a leading cause of treatment failure. To better personalize therapies, it is essential to develop tools capable of identifying and predicting intra- and inter-tumor heterogeneities. Biology-inspired mathematical models are capable of attacking this problem, but tumor heterogeneity is often overlooked in in-vivo modeling studies, while phenotypic considerations capturing spatial dynamics are not typically included in in-vitro modeling studies. We present a data assimilation-prediction pipeline with a two-phenotype model that includes a spatiotemporal component to characterize and predict the evolution of in-vitro breast cancer cells and their heterogeneous response to chemotherapy. Our model assumes that the cells can be divided into two subpopulations: surviving cells unaffected by the treatment, and irreversibly damaged cells undergoing treatment-induced death. MCF7 breast cancer cells were previously cultivated in wells for up to 1000 hours, treated with various concentrations of doxorubicin and imaged with time-resolved microscopy to record spatiotemporally-resolved cell count data. Images were used to generate cell density maps. Treatment response predictions were initialized by a training set and updated by weekly measurements. Our mathematical model successfully calibrated the spatiotemporal cell growth dynamics, achieving median [range] concordance correlation coefficients of > .99 [.88, >.99] and .73 [.58, .85] across the whole well and individual pixels, respectively. Our proposed data assimilation-prediction approach achieved values of .97 [.44, >.99] and .69 [.35, .79] for the whole well and individual pixels, respectively. Thus, our model can capture and predict the spatiotemporal dynamics of MCF7 cells treated with doxorubicin in an in-vitro setting.
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Affiliation(s)
- Hugo J. M. Miniere
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
| | - Ernesto A. B. F. Lima
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Guillermo Lorenzo
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Department of Civil Engineering and Architecture, University of Pavia, Lombardy, Italy
| | - David A. Hormuth II
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Sophia Ty
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, USA
- Department of Oncology, The University of Texas at Austin, Austin, USA
- Division of Diagnostic Imaging, The University of Texas M.D. Anderson Cancer Center, Houston, USA
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2
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Roesmann F, Sertznig H, Klaassen K, Wilhelm A, Heininger D, Heß S, Elsner C, Marschalek R, Santiago ML, Esser S, Sutter K, Dittmer U, Widera M. The interferon-regulated host factor hnRNPA0 modulates HIV-1 production by interference with LTR activity, mRNA trafficking, and programmed ribosomal frameshifting. J Virol 2024; 98:e0053424. [PMID: 38899932 PMCID: PMC11265465 DOI: 10.1128/jvi.00534-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The interplay between host factors and viral components impacts viral replication efficiency profoundly. Members of the cellular heterogeneous nuclear ribonucleoprotein family (hnRNPs) have been extensively studied as HIV-1 host dependency factors, but whether they play a role in innate immunity is currently unknown. This study aimed to identify hnRNPA0 as a type I interferon (IFN)-repressed host factor in HIV-1-infected cells. Knockdown of hnRNPA0, a situation that mirrors conditions under IFN stimulation, increased LTR activity, export of unspliced HIV-1 mRNA, viral particle production, and thus, increased infectivity. Conversely, hnRNPA0 overexpression primarily reduced plasmid-driven and integrated HIV-1 long terminal repeat (LTR) activity, significantly decreasing total viral mRNA and protein levels. In addition, high levels of hnRNPA0 significantly reduced the HIV-1 programmed ribosomal frameshifting efficiency, resulting in a shift in the HIV-1 p55/p15 ratio. The HIV-1 alternative splice site usage remained largely unaffected by altered hnRNPA0 levels suggesting that the synergistic inhibition of the LTR activity and viral mRNA transcription, as well as impaired ribosomal frameshifting efficiency, are critical factors for efficient HIV-1 replication regulated by hnRNPA0. The pleiotropic dose-dependent effects under high or low hnRNPA0 levels were further confirmed in HIV-1-infected Jurkat cells. Finally, our study revealed that hnRNPA0 levels in PBMCs were lower in therapy-naive HIV-1-infected individuals compared to healthy controls. Our findings highlight a significant role for hnRNPA0 in HIV-1 replication and suggest that its IFN-I-regulated expression levels are critical for viral fitness allowing replication in an antiviral environment.IMPORTANCERNA-binding proteins, in particular, heterogeneous nuclear ribonucleoproteins (hnRNPs), have been extensively studied. Some act as host dependency factors for HIV-1 since they are involved in multiple cellular gene expression processes. Our study revealed hnRNPA0 as an IFN-regulated host factor, that is differently expressed after IFN-I treatment in HIV-1 target cells and lower expressed in therapy-naïve HIV-1-infected individuals. Our findings demonstrate the significant pleiotropic role of hnRNPA0 in viral replication: In high concentrations, hnRNPA0 limits viral replication by negatively regulating Tat-LTR transcription, retaining unspliced mRNA in the nucleus, and significantly impairing programmed ribosomal frameshifting. Low hnRNPA0 levels as observed in IFN-treated THP-1 cells, particularly facilitate HIV LTR activity and unspliced mRNA export, suggesting a role in innate immunity in favor of HIV replication. Understanding the mode of action between hnRNPA0 and HIV-1 gene expression might help to identify novel therapeutically strategies against HIV-1 and other viruses.
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Affiliation(s)
- Fabian Roesmann
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katleen Klaassen
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Delia Heininger
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Stefanie Heß
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Mario L. Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Stefan Esser
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Dermatology, HPSTD Outpatient Clinic, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
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3
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Rodríguez TC, Yurkovetskiy L, Nagalekshmi K, Lam CHO, Jazbec E, Maitland SA, Wolfe SA, Sontheimer EJ, Luban J. PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603173. [PMID: 39026796 PMCID: PMC11257501 DOI: 10.1101/2024.07.12.603173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
An obligate step in the life cycle of HIV-1 and other retroviruses is the establishment of the provirus in target cell chromosomes. Transcriptional regulation of proviruses is complex, and understanding the mechanisms underlying this regulation has ramifications for fundamental biology, human health, and gene therapy implementation. The three core components of the Human Silencing Hub (HUSH) complex, TASOR, MPHOSPH8 (MPP8), and PPHLN1 (Periphilin 1), were identified in forward genetic screens for host genes that repress provirus expression. Subsequent loss-of-function screens revealed accessory proteins that collaborate with the HUSH complex to silence proviruses in particular contexts. To identify proteins associated with a HUSH complex-repressed provirus in human cells, we developed a technique, Provirus Proximal Proteomics, based on proximity labeling with C-BERST (dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging). Our screen exploited a lentiviral reporter that is silenced by the HUSH complex in a manner that is independent of the integration site in chromatin. Our data reveal that proviruses silenced by the HUSH complex are associated with DNA repair, mRNA processing, and transcriptional silencing proteins, including L3MBTL2, a member of the non-canonical polycomb repressive complex 1.6 (PRC1.6). A forward genetic screen confirmed that PRC1.6 components L3MBTL2 and MGA contribute to HUSH complex-mediated silencing. PRC1.6 was then shown to silence HUSH-sensitive proviruses in a promoter-specific manner. Genome wide profiling showed striking colocalization of the PRC1.6 and HUSH complexes on chromatin, primarily at sites of active promoters. Finally, PRC1.6 binding at a subset of genes that are silenced by the HUSH complex was dependent on the core HUSH complex component MPP8. These studies offer new tools with great potential for studying the transcriptional regulation of proviruses and reveal crosstalk between the HUSH complex and PRC1.6.
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Affiliation(s)
- Tomás C. Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karthika Nagalekshmi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Chin Hung Oscar Lam
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Eva Jazbec
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jeremy Luban
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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4
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Lin TY, Kleemann L, Jeżowski J, Dobosz D, Rawski M, Indyka P, Ważny G, Mehta R, Chramiec-Głąbik A, Koziej Ł, Ranff T, Fufezan C, Wawro M, Kochan J, Bereta J, Leidel SA, Glatt S. The molecular basis of tRNA selectivity by human pseudouridine synthase 3. Mol Cell 2024; 84:2472-2489.e8. [PMID: 38996458 PMCID: PMC11258540 DOI: 10.1016/j.molcel.2024.06.013] [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: 04/25/2023] [Revised: 03/14/2024] [Accepted: 06/13/2024] [Indexed: 07/14/2024]
Abstract
Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. However, the molecular mechanisms by which it recognizes its RNA targets and achieves site specificity remain elusive. Here, we determine single-particle cryo-EM structures of PUS3 in its apo form and bound to three tRNAs, showing how the symmetric PUS3 homodimer recognizes tRNAs and positions the target uridine next to its active site. Structure-guided and patient-derived mutations validate our structural findings in complementary biochemical assays. Furthermore, we deleted PUS1 and PUS3 in HEK293 cells and mapped transcriptome-wide Ψ sites by Pseudo-seq. Although PUS1-dependent sites were detectable in tRNA and mRNA, we found no evidence that human PUS3 modifies mRNAs. Our work provides the molecular basis for PUS3-mediated tRNA modification in humans and explains how its tRNA modification activity is linked to intellectual disabilities.
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Affiliation(s)
- Ting-Yu Lin
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
| | - Leon Kleemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Jakub Jeżowski
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Dominika Dobosz
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - Grzegorz Ważny
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | - Rahul Mehta
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | | | - Łukasz Koziej
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Tristan Ranff
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Christian Fufezan
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland.
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5
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Hernandez-Olmos V, Heering J, Marinescu B, Schermeng T, Ivanov VV, Moroz YS, Nevermann S, Mathes M, Ehrler JHM, Alnouri MW, Wolf M, Haydo AS, Schmachtel T, Zaliani A, Höfner G, Kaiser A, Schubert-Zsilavecz M, Beck-Sickinger AG, Offermanns S, Gribbon P, Rieger MA, Merk D, Sisignano M, Steinhilber D, Proschak E. Development of a Potent and Selective G2A (GPR132) Agonist. J Med Chem 2024; 67:10567-10588. [PMID: 38917049 PMCID: PMC11249017 DOI: 10.1021/acs.jmedchem.3c02164] [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: 11/18/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
G protein-coupled receptor G2A was postulated to be a promising target for the development of new therapeutics in neuropathic pain, acute myeloid leukemia, and inflammation. However, there is still a lack of potent, selective, and drug-like G2A agonists to be used as a chemical tool or as the starting matter for the development of drugs. In this work, we present the discovery and structure-activity relationship elucidation of a new potent and selective G2A agonist scaffold. Systematic optimization resulted in (3-(pyridin-3-ylmethoxy)benzoyl)-d-phenylalanine (T-10418) exhibiting higher potency than the reference and natural ligand 9-HODE and high selectivity among G protein-coupled receptors. With its favorable activity, a clean selectivity profile, excellent solubility, and high metabolic stability, T-10418 qualifies as a pharmacological tool to investigate the effects of G2A activation.
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Affiliation(s)
- Victor Hernandez-Olmos
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer
Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Jan Heering
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer
Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Beatrice Marinescu
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Tina Schermeng
- Institute
of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | | | - Yurii S. Moroz
- Taras Shevchenko
National University of Kyiv, 64 Volodymyrska Street, Kyiv 01601, Ukraine
- Chemspace
LLC, 85 Chervonotkatska
Street, Kyiv 02094, Ukraine
| | - Sheila Nevermann
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Marius Mathes
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Johanna H. M. Ehrler
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Mohamad Wessam Alnouri
- Department
of Pharmacology, Max Planck Institute for
Heart and Lung Research, Ludwigstr. 43, 61231Bad Nauheim, Germany
| | - Markus Wolf
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Discovery
Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Alicia S. Haydo
- Department
of Medicine, Hematology/Oncology, Goethe
University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Tessa Schmachtel
- Department
of Medicine, Hematology/Oncology, Goethe
University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Discovery
Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Georg Höfner
- Department of Pharmacy, Ludwig-Maximilians-Universität
München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Astrid Kaiser
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Annette G. Beck-Sickinger
- Institute
of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Stefan Offermanns
- Department
of Pharmacology, Max Planck Institute for
Heart and Lung Research, Ludwigstr. 43, 61231Bad Nauheim, Germany
- Center for Molecular Medicine, Goethe University
Frankfurt, Theodor-Stern-Kai
7, 60590 Frankfurt, Germany
| | - Philipp Gribbon
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Discovery
Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Michael A. Rieger
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Discovery
Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
- Frankfurt Cancer Institute, 60590 Frankfurt
am Main, Germany
- Cardio-Pulmonary Institute (CPI), 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German
Cancer Research Institute
(DKFZ), Im Neuenheimer
Feld 280, 69120 Heidelberg, Germany
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität
München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Marco Sisignano
- Pharmazentrum
Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai
7, 60590 Frankfurt
am Main, Germany
| | - Dieter Steinhilber
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer
Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
| | - Ewgenij Proschak
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Fraunhofer
Cluster of Excellence Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Street
9, 60438 Frankfurt
am Main, Germany
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6
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024; 7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [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: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of the CEBPA transcript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescent reporter coupled with CRISPRi screening. Our screen uncovered a role of the ribosome rescue factor PELOTA (PELO) in promoting the expression of the longer C/EBPα isoform by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin kinase. Our work uncovers further links between ribosome recycling and translation reinitiation that regulate a key transcription factor, with implications for normal hematopoiesis and leukemogenesis.
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Affiliation(s)
- Samantha G Fernandez
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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7
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Kim JW, Yong AJH, Aisenberg EE, Lobel JH, Wang W, Dawson TM, Dawson VL, Gao R, Jan YN, Bateup HS, Ingolia NT. Molecular recording of calcium signals via calcium-dependent proximity labeling. Nat Chem Biol 2024; 20:894-905. [PMID: 38658655 DOI: 10.1038/s41589-024-01603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that generates permanent molecular traces in a calcium-dependent manner. The enzyme, calcium-dependent BioID (Cal-ID), biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity labeling in the brain. In summary, Cal-ID produces a biochemical record of calcium signals and neuronal activity with high spatial resolution and molecular specificity.
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Affiliation(s)
- J Wren Kim
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Adeline J H Yong
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Erin E Aisenberg
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
| | - Joseph H Lobel
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Wei Wang
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruixuan Gao
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Yuh Nung Jan
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA.
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8
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Li Z, Di Vagno L, Chawla H, Ni Cheallaigh A, Critcher M, Sammon D, Briggs DC, Chung N, Chang V, Mahoney KE, Cioce A, Murphy LD, Chen YH, Narimatsu Y, Miller RL, Willems LI, Malaker SA, Huang ML, Miller GJ, Hohenester E, Schumann B. Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.572522. [PMID: 38979271 PMCID: PMC11230170 DOI: 10.1101/2023.12.20.572522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mammalian cells orchestrate signalling through interaction events on their surfaces. Proteoglycans are an intricate part of these interactions, carrying large glycosaminoglycan polysaccharides that recruit signalling molecules. Despite their importance in development, cancer and neurobiology, a relatively small number of proteoglycans have been identified. In addition to the complexity of glycan extension, biosynthetic redundancy in the first protein glycosylation step by two xylosyltransferase isoenzymes XT1 and XT2 complicates annotation of proteoglycans. Here, we develop a chemical genetic strategy that manipulates the glycan attachment site of cellular proteoglycans. By employing a tactic termed bump- and-hole engineering, we engineer the two isoenzymes XT1 and XT2 to specifically transfer a chemically modified xylose analogue to target proteins. The chemical modification contains a bioorthogonal tag, allowing the ability to visualise and profile target proteins modified by both transferases in mammalian cells. The versatility of our approach allows pinpointing glycosylation sites by tandem mass spectrometry, and exploiting the chemical handle to manufacture proteoglycans with defined GAG chains for cellular applications. Engineered XT enzymes permit a view into proteoglycan biology that is orthogonal to conventional techniques in biochemistry.
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9
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Gerke C, Bauersfeld L, Schirmeister I, Mireisz CNM, Oberhardt V, Mery L, Wu D, Jürges CS, Spaapen RM, Mussolino C, Le-Trilling VTK, Trilling M, Dölken L, Paster W, Erhard F, Hofmann M, Schlosser A, Hengel H, Momburg F, Halenius A. Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning. eLife 2024; 13:e85560. [PMID: 38900146 PMCID: PMC11189632 DOI: 10.7554/elife.85560] [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: 12/13/2022] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Human leucocyte antigen class I (HLA-I) molecules play a central role for both NK and T-cell responses that prevent serious human cytomegalovirus (HCMV) disease. To create opportunities for viral spread, several HCMV-encoded immunoevasins employ diverse strategies to target HLA-I. Among these, the glycoprotein US10 is so far insufficiently studied. While it was reported that US10 interferes with HLA-G expression, its ability to manipulate classical HLA-I antigen presentation remains unknown. In this study, we demonstrate that US10 recognizes and binds to all HLA-I (HLA-A, -B, -C, -E, -G) heavy chains. Additionally, impaired recruitment of HLA-I to the peptide loading complex was observed. Notably, the associated effects varied significantly dependending on HLA-I genotype and allotype: (i) HLA-A molecules evaded downregulation by US10, (ii) tapasin-dependent HLA-B molecules showed impaired maturation and cell surface expression, and (iii) β2m-assembled HLA-C, in particular HLA-C*05:01 and -C*12:03, and HLA-G were strongly retained in complex with US10 in the endoplasmic reticulum. These genotype-specific effects on HLA-I were confirmed through unbiased HLA-I ligandome analyses. Furthermore, in HCMV-infected fibroblasts inhibition of overlapping US10 and US11 transcription had little effect on HLA-A, but induced HLA-B antigen presentation. Thus, the US10-mediated impact on HLA-I results in multiple geno- and allotypic effects in a so far unparalleled and multimodal manner.
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Affiliation(s)
- Carolin Gerke
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Spemann Graduate School of Biology and Medicine (SGBM), University of FreiburgFreiburgGermany
- Faculty of Biology, University of FreiburgFreiburgGermany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Ivo Schirmeister
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Chiara Noemi-Marie Mireisz
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Valerie Oberhardt
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Lea Mery
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Di Wu
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | | | - Robbert M Spaapen
- Department of Immunopathology, Sanquin ResearchAmsterdamNetherlands
- Landsteiner Laboratory, Amsterdam UMC, University of AmsterdamAmsterdamNetherlands
| | - Claudio Mussolino
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center University of FreiburgFreiburgGermany
- Center for Chronic Immunodeficiency, Medical Center University of FreiburgFreiburgGermany
| | | | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-EssenEssenGermany
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital EssenEssenGermany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
- Institute of Virology, Hannover Medical SchoolHannoverGermany
| | - Wolfgang Paster
- St. Anna Children’s Cancer Research Institute (CCRI)ViennaAustria
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of WürzburgWürzburgGermany
| | - Maike Hofmann
- Faculty of Medicine, University of FreiburgFreiburgGermany
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Medical Center University of FreiburgFreiburgGermany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of WürzburgWürzburgGermany
| | - Hartmut Hengel
- Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Frank Momburg
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, National Center for Tumor Diseases (NCT), Heidelberg University HospitalHeidelbergGermany
| | - Anne Halenius
- Institute of Virology, Medical Center University of FreiburgFreiburgGermany
- Faculty of Medicine, University of FreiburgFreiburgGermany
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10
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Chojnacka W, Teng J, Kim JJ, Jensen AA, Hibbs RE. Structural insights into GABA A receptor potentiation by Quaalude. Nat Commun 2024; 15:5244. [PMID: 38898000 PMCID: PMC11187190 DOI: 10.1038/s41467-024-49471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Methaqualone, a quinazolinone marketed commercially as Quaalude, is a central nervous system depressant that was used clinically as a sedative-hypnotic, then became a notorious recreational drug in the 1960s-80s. Due to its high abuse potential, medical use of methaqualone was eventually prohibited, yet it persists as a globally abused substance. Methaqualone principally targets GABAA receptors, which are the major inhibitory neurotransmitter-gated ion channels in the brain. The restricted status and limited accessibility of methaqualone have contributed to its pharmacology being understudied. Here, we use cryo-EM to localize the GABAA receptor binding sites of methaqualone and its more potent derivative, PPTQ, to the same intersubunit transmembrane sites targeted by the general anesthetics propofol and etomidate. Both methaqualone and PPTQ insert more deeply into subunit interfaces than the previously-characterized modulators. Binding of quinazolinones to this site results in widening of the extracellular half of the ion-conducting pore, following a trend among positive allosteric modulators in destabilizing the hydrophobic activation gate in the pore as a mechanism for receptor potentiation. These insights shed light on the underexplored pharmacology of quinazolinones and further elucidate the molecular mechanisms of allosteric GABAA receptor modulation through transmembrane binding sites.
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Affiliation(s)
- Weronika Chojnacka
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jinfeng Teng
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jeong Joo Kim
- Protein Structure and Function, Loxo@Lilly, Louisville, CO, USA
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ryan E Hibbs
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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11
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Chudy P, Kochan J, Wawro M, Nguyen P, Gorczyca M, Varanko A, Retka A, Ghadei SS, Napieralska E, Grochot-Przęczek A, Szade K, Berendes LS, Park J, Sokołowski G, Yu Q, Józkowicz A, Nowak WN, Krzeptowski W. Heme oxygenase-1 protects cells from replication stress. Redox Biol 2024; 75:103247. [PMID: 39047636 DOI: 10.1016/j.redox.2024.103247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Heme oxygenase-1 (HO-1, HMOX1) degrades heme protecting cells from heme-induced oxidative damage. Beyond its well-established cellular functions, heme has emerged as a stabilizer of G-quadruplexes. These secondary DNA structures interfere with DNA replication. We recently revealed that nuclear HO-1 colocalizes with DNA G-quadruplexes and promotes their removal. Here, we investigate whether HO-1 safeguards cells against replication stress. Experiments were conducted in control and HMOX1-deficient HEK293T cell lines. Immunostaining unveiled that DNA G-quadruplexes accumulated in the absence of HO-1, the effect that was further enhanced in response to δ-aminolevulinic acid (ALA), a substrate in heme synthesis. This was associated with replication stress, as evidenced by an elevated proportion of stalled forks analyzed by fiber assay. We observed the same effects in hematopoietic stem cells isolated from Hmox1 knockout mice and in a lymphoblastoid cell line from an HMOX1-deficient patient. Interestingly, in the absence of HO-1, the speed of fork progression was higher, and the response to DNA conformational hindrance less stringent, indicating dysfunction of the PARP1-p53-p21 axis. PARP1 activity was not decreased in the absence of HO-1. Instead, we observed that HO-1 deficiency impairs the nuclear import and accumulation of p53, an effect dependent on the removal of excess heme. We also demonstrated that administering ALA is a more specific method for increasing intracellular free heme compared to treatment with hemin, which in turn induces strong lipid peroxidation. Our results indicate that protection against replication stress is a universal feature of HO-1, presumably contributing to its widely recognized cytoprotective activity.
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Affiliation(s)
- Patryk Chudy
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Phu Nguyen
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gorczyca
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aliaksandra Varanko
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Retka
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Swati Sweta Ghadei
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Emilija Napieralska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Lea-Sophie Berendes
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Julien Park
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Grzegorz Sokołowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Qiuliyang Yu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Witold N Nowak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; August Chełkowski Institute of Physics, Faculty of Science and Technology, University of Silesia, Chorzów, Poland.
| | - Wojciech Krzeptowski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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12
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Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Daniel ZA, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. Genome Med 2024; 16:73. [PMID: 38816749 PMCID: PMC11138074 DOI: 10.1186/s13073-024-01340-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/26/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND KCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility. METHODS In this study, we leveraged the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein-coding KCNE1 variants. RESULTS We comprehensively assayed KCNE1 variant cell surface expression (2554/2709 possible single-amino-acid variants) and function (2534 variants). Our study identified 470 loss- or partial loss-of-surface expression and 574 loss- or partial loss-of-function variants. Of the 574 loss- or partial loss-of-function variants, 152 (26.5%) had reduced cell surface expression, indicating that most functionally deleterious variants affect channel gating. Nonsense variants at residues 56-104 generally had WT-like trafficking scores but decreased functional scores, indicating that the latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation (with > 70% loss-of-function variants) were in predicted close contact with binding partners KCNQ1 or calmodulin. Our functional assay data were consistent with gold standard electrophysiological data (ρ = - 0.64), population and patient cohorts (32/38 presumed benign or pathogenic variants with consistent scores), and computational predictors (ρ = - 0.62). Our data provide moderate-strength evidence for the American College of Medical Genetics/Association of Molecular Pathology functional criteria for benign and pathogenic variants. CONCLUSIONS Comprehensive variant effect maps of KCNE1 can both provide insight into I Ks channel biology and help reclassify variants of uncertain significance.
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Affiliation(s)
- Ayesha Muhammad
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, 37232, USA
| | - Maria E Calandranis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bian Li
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - M Lorena Harvey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jeremy E Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zerubabell A Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ashli E Chew
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94143, USA
| | - Kenneth A Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Dan M Roden
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrew M Glazer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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13
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Mygind KJ, Nikodemus D, Gnosa S, Kweder R, Albrechtsen NJW, Kveiborg M, Erler JT, Albrechtsen R. ADAM12-Generated Basigin Ectodomain Binds β1 Integrin and Enhances the Expression of Cancer-Related Extracellular Matrix Proteins. Int J Mol Sci 2024; 25:5871. [PMID: 38892056 PMCID: PMC11172339 DOI: 10.3390/ijms25115871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Desmoplasia is a common feature of aggressive cancers, driven by a complex interplay of protein production and degradation. Basigin is a type 1 integral membrane receptor secreted in exosomes or released by ectodomain shedding from the cell surface. Given that soluble basigin is increased in the circulation of patients with a poor cancer prognosis, we explored the putative role of the ADAM12-generated basigin ectodomain in cancer progression. We show that recombinant basigin ectodomain binds β1 integrin and stimulates gelatin degradation and the migration of cancer cells in a matrix metalloproteinase (MMP)- and β1-integrin-dependent manner. Subsequent in vitro and in vivo experiments demonstrated the altered expression of extracellular matrix proteins, including fibronectin and collagen type 5. Thus, we found increased deposits of collagen type 5 in the stroma of nude mice tumors of the human tumor cell line MCF7 expressing ADAM12-mimicking the desmoplastic response seen in human cancer. Our findings indicate a feedback loop between ADAM12 expression, basigin shedding, TGFβ signaling, and extracellular matrix (ECM) remodeling, which could be a mechanism by which ADAM12-generated basigin ectodomain contributes to the regulation of desmoplasia, a key feature in human cancer progression.
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Affiliation(s)
- Kasper J. Mygind
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | - Denise Nikodemus
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | - Sebastian Gnosa
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | - Ramya Kweder
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | | | - Marie Kveiborg
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | - Janine T. Erler
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
| | - Reidar Albrechtsen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (K.J.M.); (D.N.); (S.G.); (R.K.); (M.K.); (J.T.E.)
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14
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Ishaqat A, Hahmann J, Lin C, Zhang X, He C, Rath WH, Habib P, Sahnoun SEM, Rahimi K, Vinokur R, Mottaghy FM, Göstl R, Bartneck M, Herrmann A. In Vivo Polymer Mechanochemistry with Polynucleotides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2403752. [PMID: 38804595 DOI: 10.1002/adma.202403752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Polymer mechanochemistry utilizes mechanical force to activate latent functionalities in macromolecules and widely relies on ultrasonication techniques. Fundamental constraints of frequency and power intensity have prohibited the application of the polymer mechanochemistry principles in a biomedical context up to now, although medical ultrasound is a clinically established modality. Here, a universal polynucleotide framework is presented that allows the binding and release of therapeutic oligonucleotides, both DNA- and RNA-based, as cargo by biocompatible medical imaging ultrasound. It is shown that the high molar mass, colloidal assembly, and a distinct mechanochemical mechanism enable the force-induced release of cargo and subsequent activation of biological function in vitro and in vivo. Thereby, this work introduces a platform for the exploration of biological questions and therapeutics development steered by mechanical force.
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Affiliation(s)
- Aman Ishaqat
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Johannes Hahmann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Max Planck School Matter to Life, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Cheng Lin
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
- Department of Rheumatology and Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 1630 Dongfang Road, Shanghai, 200127, China
| | - Xiaofeng Zhang
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Chuanjiang He
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Wolfgang H Rath
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Pardes Habib
- Department of Neurosurgery and Stanford Stroke Center, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA, 94304, USA
| | - Sabri E M Sahnoun
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Khosrow Rahimi
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Rostislav Vinokur
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Felix M Mottaghy
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center (MUMC+), P. Debyelaan 25, Maastricht, 6229 HX, The Netherlands
| | - Robert Göstl
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Department of Chemistry and Biology, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Matthias Bartneck
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Andreas Herrmann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Max Planck School Matter to Life, Jahnstr. 29, 69120, Heidelberg, Germany
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15
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Nevue AA, Sairavi A, Huang SJ, Nakai H, Mello CV. Genomic loss of GPR108 disrupts AAV transduction in birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.589954. [PMID: 38798475 PMCID: PMC11118497 DOI: 10.1101/2024.05.16.589954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The G protein-coupled receptor 108 (GPR108) gene encodes a protein factor identified as critical for adeno-associated virus (AAV) entry into mammalian cells, but whether it is universally involved in AAV transduction is unknown. Remarkably, we have discovered that GPR108 is absent in the genomes of birds and in most other sauropsids, providing a likely explanation for the overall lower AAV transduction efficacy of common AAV serotypes in birds compared to mammals. Importantly, transgenic expression of human GPR108 and manipulation of related glycan binding sites in the viral capsid significantly boost AAV transduction in zebra finch cells. These findings contribute to a more in depth understanding of the mechanisms and evolution of AAV transduction, with potential implications for the design of efficient tools for gene manipulation in experimental animal models, and a range of gene therapy applications in humans.
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Affiliation(s)
- Alexander A Nevue
- Department of Behavioral Neuroscience, Oregon Health & Science University, Oregon, USA
| | - Anusha Sairavi
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Oregon, USA
| | - Samuel J Huang
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Oregon, USA
| | - Hiroyuki Nakai
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Oregon, USA
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Oregon, USA
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16
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Wang F, Huang Y, Li J, Zhou W, Wang W. Targeted gene delivery systems for T-cell engineering. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00954-6. [PMID: 38753155 DOI: 10.1007/s13402-024-00954-6] [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] [Accepted: 04/28/2024] [Indexed: 06/27/2024] Open
Abstract
T lymphocytes are indispensable for the host systems of defense against pathogens, tumors, and environmental threats. The therapeutic potential of harnessing the cytotoxic properties of T lymphocytes for antigen-specific cell elimination is both evident and efficacious. Genetically engineered T-cells, such as those employed in CAR-T and TCR-T cell therapies, have demonstrated significant clinical benefits in treating cancer and autoimmune disorders. However, the current landscape of T-cell genetic engineering is dominated by strategies that necessitate in vitro T-cell isolation and modification, which introduce complexity and prolong the development timeline of T-cell based immunotherapies. This review explores the complexities of gene delivery systems designed for T cells, covering both viral and nonviral vectors. Viral vectors are known for their high transduction efficiency, yet they face significant limitations, such as potential immunogenicity and the complexities involved in large-scale production. Nonviral vectors, conversely, offer a safer profile and the potential for scalable manufacturing, yet they often struggle with lower transduction efficiency. The pursuit of gene delivery systems that can achieve targeted gene transfer to T cell without the need for isolation represents a significant advancement in the field. This review assesses the design principles and current research progress of such systems, highlighting the potential for in vivo gene modification therapies that could revolutionize T-cell based treatments. By providing a comprehensive analysis of these systems, we aim to contribute valuable insights into the future development of T-cell immunotherapy.
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Affiliation(s)
- Fengling Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yong Huang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - JiaQian Li
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Weilin Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Wei Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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17
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Lange S, Kuntze A, Wüstmann N, Reckers T, Humberg V, Dirks WG, Huss S, Vieler J, Schrader AJ, Bögemann M, Schlack K, Bernemann C. Establishment of primary prostate epithelial and tumorigenic cell lines using a non-viral immortalization approach. Biol Res 2024; 57:21. [PMID: 38704600 PMCID: PMC11069155 DOI: 10.1186/s40659-024-00507-z] [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: 10/17/2023] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Research on prostate cancer is mostly performed using cell lines derived from metastatic disease, not reflecting stages of tumor initiation or early progression. Establishment of cancer cell lines derived from the primary tumor site has not been described so far. By definition, cancer cells are able to be cultured indefinitely, whereas normal epithelial cells undergo senescence in vitro. Epithelial cells can be immortalized, accomplished by using viral integration of immortalization factors. Viral approaches, however, might be impaired by regulatory and safety issues as well as random integration into regulatory genetic elements, modifying precise gene expression. We intend to use surgical specimen of prostate cancer patients to (i) prove for establishment of cancer cell lines, and (ii) perform non-viral, Sleeping Beauty (SB) transposase-based immortalization of prostate epithelial cells. METHODS Radical prostatectomy samples of prostate cancer patients (n = 4) were dissociated and cultured in vitro. Cells were cultivated either without or after non-viral, Sleeping-Beauty transposase-based stable transfection with immortalization factors SV40LT and hTERT. Established cell lines were analyzed in vitro and in vivo for characteristics of prostate (cancer) cells. RESULTS Initial cell cultures without genetic manipulation underwent senescence within ≤ 15 passages, demonstrating inability to successfully derive primary prostate cancer cell lines. By using SB transposase-based integration of immortalization factors, we were able to establish primary prostate cell lines. Three out of four cell lines displayed epithelial characteristics, however without expression of prostate (cancer) characteristics, e.g., androgen receptor. In vivo, one cell line exhibited tumorigenic potential, yet characteristics of prostate adenocarcinoma were absent. CONCLUSION Whereas no primary prostate cancer cell line could be established, we provide for the first-time immortalization of primary prostate cells using the SB transposase system, thereby preventing regulatory and molecular issues based on viral immortalization approaches. Although, none of the newly derived cell lines demonstrated prostate cancer characteristics, tumor formation was observed in one cell line. Given the non-prostate adenocarcinoma properties of the tumor, cells have presumably undergone oncogenic transformation rather than prostate cancer differentiation. Still, these cell lines might be used as a tool for research on prostate cancer initiation and early cancer progression.
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Affiliation(s)
- Simon Lange
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | - Anna Kuntze
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Neele Wüstmann
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | - Theresa Reckers
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | - Verena Humberg
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | - Wilhelm G Dirks
- Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures, GmbH), Braun-Schweig, Germany
| | - Sebastian Huss
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Julia Vieler
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | | | - Martin Bögemann
- Department of Urology, University Hospital Muenster, Muenster, Germany
| | - Katrin Schlack
- Department of Urology, University Hospital Muenster, Muenster, Germany
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Gulyas L, Glaunsinger BA. The general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575933. [PMID: 38746429 PMCID: PMC11092454 DOI: 10.1101/2024.01.16.575933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Many stressors, including viral infection, induce a widespread suppression of cellular RNA polymerase II (RNAPII) transcription, yet the mechanisms underlying transcriptional repression are not well understood. Here we find that a crucial component of the RNA polymerase II holoenzyme, general transcription factor IIB (TFIIB), is targeted for post-translational turnover by two pathways, each of which contribute to its depletion during stress. Upon DNA damage, translational stress, apoptosis, or replication of the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), TFIIB is cleaved by activated caspase-3, leading to preferential downregulation of pro-survival genes. TFIIB is further targeted for rapid proteasome-mediated turnover by the E3 ubiquitin ligase TRIM28. KSHV counteracts proteasome-mediated turnover of TFIIB, thereby preserving a sufficient pool of TFIIB for transcription of viral genes. Thus, TFIIB may be a lynchpin for transcriptional outcomes during stress and a key target for nuclear replicating DNA viruses that rely on host transcriptional machinery. Significance Statement Transcription by RNA polymerase II (RNAPII) synthesizes all cellular protein-coding mRNA. Many cellular stressors and viral infections dampen RNAPII activity, though the processes underlying this are not fully understood. Here we describe a two-pronged degradation strategy by which cells respond to stress by depleting the abundance of the key RNAPII general transcription factor, TFIIB. We further demonstrate that an oncogenic human gammaherpesvirus antagonizes this process, retaining enough TFIIB to support its own robust viral transcription. Thus, modulation of RNAPII machinery plays a crucial role in dictating the outcome of cellular perturbation.
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Moore WM, Brea RJ, Knittel C, Wrightsman E, Hui B, Lou J, Ancajas CF, Best MD, Devaraj NK, Budin I. Subcellular imaging of lipids and sugars using genetically encoded proximity sensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592120. [PMID: 38746395 PMCID: PMC11092643 DOI: 10.1101/2024.05.01.592120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Live cell imaging of lipids and other metabolites is a long-standing challenge in cell biology. Bioorthogonal labeling tools allow for the conjugation of fluorophores to several phospholipid classes, but cannot discern their trafficking between adjacent organelles or asymmetry across individual membrane leaflets. Here we present fluorogen-activating coincidence sensing (FACES), a chemogenetic tool capable of quantitatively imaging subcellular lipid pools and reporting their transbilayer orientation in living cells. FACES combines bioorthogonal chemistry with genetically encoded fluorogen-activating proteins (FAPs) for reversible proximity sensing of conjugated molecules. We first validate this approach for quantifying discrete phosphatidylcholine pools in the ER and mitochondria that are trafficked by lipid transfer proteins. We then show that transmembrane domain-containing FAPs can be used to reveal the membrane asymmetry of multiple lipid classes that are generated in the trans-Golgi network. Lastly, we demonstrate that FACES is a generalizable tool for subcellular bioorthogonal imaging by measuring changes in mitochondrial N -acetylhexosamine levels. These results demonstrate the use of fluorogenic tags for spatially-defined molecular imaging.
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20
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Zech TJ, Wolf A, Hector M, Bischoff-Kont I, Krishnathas GM, Kuntschar S, Schmid T, Bracher F, Langmann T, Fürst R. 2-Desaza-annomontine (C81) impedes angiogenesis through reduced VEGFR2 expression derived from inhibition of CDC2-like kinases. Angiogenesis 2024; 27:245-272. [PMID: 38403816 PMCID: PMC11021337 DOI: 10.1007/s10456-024-09906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024]
Abstract
Angiogenesis is a crucial process in the progression of various pathologies, like solid tumors, wet age-related macular degeneration, and chronic inflammation. Current anti-angiogenic treatments still have major drawbacks like limited efficacy in diseases that also rely on inflammation. Therefore, new anti-angiogenic approaches are sorely needed, and simultaneous inhibition of angiogenesis and inflammation is desirable. Here, we show that 2-desaza-annomontine (C81), a derivative of the plant alkaloid annomontine previously shown to inhibit endothelial inflammation, impedes angiogenesis by inhibiting CDC2-like kinases (CLKs) and WNT/β-catenin signaling. C81 reduced choroidal neovascularization in a laser-induced murine in vivo model, inhibited sprouting from vascular endothelial growth factor A (VEGF-A)-activated murine aortic rings ex vivo, and reduced angiogenesis-related activities of endothelial cells in multiple functional assays. This was largely phenocopied by CLK inhibitors and knockdowns, but not by inhibitors of the other known targets of C81. Mechanistically, CLK inhibition reduced VEGF receptor 2 (VEGFR2) mRNA and protein expression as well as downstream signaling. This was partly caused by a reduction of WNT/β-catenin pathway activity, as activating the pathway induced, while β-catenin knockdown impeded VEGFR2 expression. Surprisingly, alternative splicing of VEGFR2 was not detected. In summary, C81 and other CLK inhibitors could be promising compounds in the treatment of diseases that depend on angiogenesis and inflammation due to their impairment of both processes.
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Affiliation(s)
- T J Zech
- Faculty of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Biology, Goethe University Frankfurt, Frankfurt, Germany.
| | - A Wolf
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - M Hector
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - I Bischoff-Kont
- Faculty of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - G M Krishnathas
- Faculty of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - S Kuntschar
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
| | - T Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
| | - F Bracher
- Pharmaceutical Chemistry, Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - T Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - R Fürst
- Faculty of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Biology, Goethe University Frankfurt, Frankfurt, Germany
- Pharmaceutical Biology, Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
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21
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Albert MC, Uranga-Murillo I, Arias M, De Miguel D, Peña N, Montinaro A, Varanda AB, Theobald SJ, Areso I, Saggau J, Koch M, Liccardi G, Peltzer N, Rybniker J, Hurtado-Guerrero R, Merino P, Monzón M, Badiola JJ, Reindl-Schwaighofer R, Sanz-Pamplona R, Cebollada-Solanas A, Megyesfalvi Z, Dome B, Secrier M, Hartmann B, Bergmann M, Pardo J, Walczak H. Identification of FasL as a crucial host factor driving COVID-19 pathology and lethality. Cell Death Differ 2024; 31:544-557. [PMID: 38514848 PMCID: PMC11093991 DOI: 10.1038/s41418-024-01278-6] [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: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
The dysregulated immune response and inflammation resulting in severe COVID-19 are still incompletely understood. Having recently determined that aberrant death-ligand-induced cell death can cause lethal inflammation, we hypothesized that this process might also cause or contribute to inflammatory disease and lung failure following SARS-CoV-2 infection. To test this hypothesis, we developed a novel mouse-adapted SARS-CoV-2 model (MA20) that recapitulates key pathological features of COVID-19. Concomitantly with occurrence of cell death and inflammation, FasL expression was significantly increased on inflammatory monocytic macrophages and NK cells in the lungs of MA20-infected mice. Importantly, therapeutic FasL inhibition markedly increased survival of both, young and old MA20-infected mice coincident with substantially reduced cell death and inflammation in their lungs. Intriguingly, FasL was also increased in the bronchoalveolar lavage fluid of critically-ill COVID-19 patients. Together, these results identify FasL as a crucial host factor driving the immuno-pathology that underlies COVID-19 severity and lethality, and imply that patients with severe COVID-19 may significantly benefit from therapeutic inhibition of FasL.
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Affiliation(s)
- Marie-Christine Albert
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Iratxe Uranga-Murillo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Maykel Arias
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Diego De Miguel
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Natacha Peña
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Antonella Montinaro
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Ana Beatriz Varanda
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Itziar Areso
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Julia Saggau
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Manuel Koch
- Institue for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, Cologne, 50931, Germany
| | - Gianmaria Liccardi
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Nieves Peltzer
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- Department of Translational Genomics, University of Cologne, Cologne, 50931, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark
- Fundación ARAID, Zaragoza, 50018, Spain
| | - Pedro Merino
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
| | - Marta Monzón
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
- Department of Human Anatomy and Histology, University of Zaragoza, Zaragoza, 50009, Spain
| | - Juan J Badiola
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
| | | | - Rebeca Sanz-Pamplona
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Fundación ARAID, Zaragoza, 50018, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Alberto Cebollada-Solanas
- Aragon Biomedical Research Center (CIBA), Instituto Aragonés de Ciencias de la Salud (IACS), Unidad de Biocomputación, Zaragoza, 50018, Spain
| | - Zsolt Megyesfalvi
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
| | - Balazs Dome
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
- Department of Translational Medicine, Lund University, Lund, SE-22100, Sweden
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Boris Hartmann
- Virology Group, Institute for Veterinary Disease Control at AGES, Moedling, 2340, Austria
| | - Michael Bergmann
- Div. of Visceral Surgery, Dept. of General Surgery, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, 1090, Austria
| | - Julián Pardo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Henning Walczak
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany.
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany.
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
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Quiros-Fernandez I, Libório-Ramos S, Leifert L, Schönfelder B, Vlodavsky I, Cid-Arregui A. Dual T cell receptor/chimeric antigen receptor engineered NK-92 cells targeting the HPV16 E6 oncoprotein and the tumor-associated antigen L1CAM exhibit enhanced cytotoxicity and specificity against tumor cells. J Med Virol 2024; 96:e29630. [PMID: 38659368 DOI: 10.1002/jmv.29630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
The human papillomavirus type 16 (HPV16) causes a large fraction of genital and oropharyngeal carcinomas. To maintain the transformed state, the tumor cells must continuously synthesize the E6 and E7 viral oncoproteins, which makes them tumor-specific antigens. Indeed, specific T cell responses against them have been well documented and CD8+ T cells engineered to express T cell receptors (TCRs) that recognize epitopes of E6 or E7 have been tested in clinical studies with promising results, yet with limited clinical success. Using CD8+ T cells from peripheral blood of healthy donors, we have identified two novel TCRs reactive to an unexplored E618-26 epitope. These TCRs showed limited standalone cytotoxicity against E618-26-HLA-A*02:01-presenting tumor cells. However, a single-signaling domain chimeric antigen receptor (ssdCAR) targeting L1CAM, a cell adhesion protein frequently overexpressed in HPV16-induced cancer, prompted a synergistic effect that significantly enhanced the cytotoxic capacity of NK-92/CD3/CD8 cells armored with both TCR and ssdCAR when both receptors simultaneously engaged their respective targets, as shown by live microscopy of 2-D and 3-D co-cultures. Thus, virus-specific TCRs from the CD8+ T cell repertoire of healthy donors can be combined with a suitable ssdCAR to enhance the cytotoxic capacity of the effector cells and, indirectly, their specificity.
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MESH Headings
- Humans
- Oncogene Proteins, Viral/immunology
- Oncogene Proteins, Viral/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Repressor Proteins/immunology
- Repressor Proteins/genetics
- CD8-Positive T-Lymphocytes/immunology
- Killer Cells, Natural/immunology
- Human papillomavirus 16/immunology
- Human papillomavirus 16/genetics
- Cytotoxicity, Immunologic
- Cell Line, Tumor
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Affiliation(s)
- Isaac Quiros-Fernandez
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Research Center on Tropical Diseases (CIET)/Research Center on Surgery and Cancer (CICICA), Faculty of Microbiology, Universidad de Costa Rica, San Jose, Costa Rica
| | - Sofia Libório-Ramos
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Leifert
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bruno Schönfelder
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Angel Cid-Arregui
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Khaniya A, Rad SMAH, Halpin J, Tawinwung S, McLellan A, Suppipat K, Hirankarn N. Development of a compact bidirectional promoter-driven dual chimeric antigen receptor (CAR) construct targeting CD19 and CD20 in the Sleeping Beauty (SB) transposon system. J Immunother Cancer 2024; 12:e008555. [PMID: 38677881 PMCID: PMC11057265 DOI: 10.1136/jitc-2023-008555] [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] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND A bidirectional promoter-driven chimeric antigen receptor (CAR) cassette provides the simultaneous expression of two CARs, which significantly enhances dual antigen-targeted CAR T-cell therapy. METHODS We developed a second-generation CAR directing CD19 and CD20 antigens, incorporating them in a head-to-head orientation from a bidirectional promoter using a single Sleeping Beauty transposon system. The efficacy of bidirectional promoter-driven dual CD19 and CD20 CAR T cells was determined in vitro against cell lines expressing either, or both, CD19 and CD20 antigens. In vivo antitumor activity was tested in Raji lymphoma-bearing immunodeficient NOD-scid IL2Rgammanull (NSG) mice. RESULTS Of all tested promoters, the bidirectional EF-1α promoter optimally expressed transcripts from both sense (CD19-CAR) and antisense (GFP.CD20-CAR) directions. Superior cytotoxicity, cytokine production and antigen-specific activation were observed in vitro in the bidirectional EF-1α promoter-driven CD19/CD20 CAR T cells. In contrast, a unidirectional construct driven by the EF-1α promoter, but using self-cleaving peptide-linked CD19 and CD20 CARs, showed inferior expression and in vitro function. Treatment of mice bearing advanced Raji lymphomas with bidirectional EF-1α promoter-driven CD19/CD20 CAR T cells effectively controlled tumor growth and extended the survival of mice compared with group treated with single antigen targeted CAR T cells. CONCLUSION The use of bidirectional promoters in a single vector offers advantages of size and robust CAR expression with the potential to expand use in other forms of gene therapies like CAR T cells.
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MESH Headings
- Antigens, CD19/immunology
- Antigens, CD19/genetics
- Humans
- Animals
- Antigens, CD20/genetics
- Antigens, CD20/metabolism
- Antigens, CD20/immunology
- Mice
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/immunology
- DNA Transposable Elements
- Promoter Regions, Genetic
- Immunotherapy, Adoptive/methods
- Mice, Inbred NOD
- Cell Line, Tumor
- Mice, SCID
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Asmita Khaniya
- Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
- Cellular Immunotherapy Research Unit, Chulalongkorn University, Bangkok, Thailand
| | | | - Josh Halpin
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Supannikar Tawinwung
- Cellular Immunotherapy Research Unit, Chulalongkorn University, Bangkok, Thailand
- Pharmacology and Physiology, Chulalongkorn University Faculty of Pharmaceutical Sciences, Bangkok, Thailand
| | - Alexander McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Koramit Suppipat
- Cellular Immunotherapy Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Research Affairs, Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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24
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024:10.1038/s41596-024-00979-z. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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25
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Hickson SE, Hyde JL. RNA structures within Venezuelan equine encephalitis virus E1 alter macrophage replication fitness and contribute to viral emergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588743. [PMID: 38645187 PMCID: PMC11030350 DOI: 10.1101/2024.04.09.588743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne +ssRNA virus belonging to the Togaviridae . VEEV is found throughout Central and South America and is responsible for periodic epidemic/epizootic outbreaks of febrile and encephalitic disease in equines and humans. Endemic/enzootic VEEV is transmitted between Culex mosquitoes and sylvatic rodents, whereas epidemic/epizootic VEEV is transmitted between mosquitoes and equids, which serve as amplification hosts during outbreaks. Epizootic VEEV emergence has been shown to arise from mutation of enzootic VEEV strains. Specifically, epizootic VEEV has been shown to acquire amino acid mutations in the E2 viral glycoprotein that facilitate viral entry and equine amplification. However, the abundance of synonymous mutations which accumulate across the epizootic VEEV genome suggests that other viral determinants such as RNA secondary structure may also play a role in VEEV emergence. In this study we identify novel RNA structures in the E1 gene which specifically alter replication fitness of epizootic VEEV in macrophages but not other cell types. We show that SNPs are conserved within epizootic lineages and that RNA structures are conserved across different lineages. We also identified several novel RNA-binding proteins that are necessary for altered macrophage replication. These results suggest that emergence of VEEV in nature requires multiple mutations across the viral genome, some of which alter cell-type specific replication fitness in an RNA structure-dependent manner. AUTHOR SUMMARY Understanding how viral pathogens emerge is critical for ongoing surveillance and outbreak preparedness. However, our understanding of the molecular mechanisms that drive viral emergence are still not completely understood. Emergence of the mosquito-borne virus Venezuelan equine encephalitis virus (VEEV) is known to require mutations in the viral attachment protein (E2), which drive viremia and transmission. We have observed that emergent strains (epizootic VEEV) also accumulate many silent mutations, suggesting that other determinants independent of protein sequence also contributes to emergence. In this study we identify novel RNA secondary structures associated with epizootic VEEV that alters viral replication in a cell-type dependent manner. We show that these RNA structures are conserved across epizootic viruses and identify host proteins that specifically bind these RNAs. These findings imply that viral emergence requires multiple mutations, a number of which likely alter viral structure in a manner that benefits viral replication and transmission.
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26
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Pearson GJ, Mears HV, Broncel M, Snijders AP, Bauer DLV, Carlton JG. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. SCIENCE ADVANCES 2024; 10:eadl5012. [PMID: 38569033 PMCID: PMC10990277 DOI: 10.1126/sciadv.adl5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release, and pathogenesis. We developed a nondisruptive tagging strategy for SARS-CoV-2 E and find that, at steady state, it localizes to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for endoplasmic reticulum-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP ribosylation factor 1/adaptor protein-1 (ARFRP1/AP-1)-dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses, and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and, by developing a trans-complementation assay for SARS-CoV-2 structural proteins, that lysosomal delivery of E and its viroporin activity is necessary for efficient viral replication and release.
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Affiliation(s)
- Guy J. Pearson
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
| | - Harriet V. Mears
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Malgorzata Broncel
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy G. Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
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27
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Ito T, Saito A, Kamikawa Y, Nakazawa N, Imaizumi K. AIbZIP/CREB3L4 Promotes Cell Proliferation via the SKP2-p27 Axis in Luminal Androgen Receptor Subtype Triple-Negative Breast Cancer. Mol Cancer Res 2024; 22:373-385. [PMID: 38236913 PMCID: PMC10985479 DOI: 10.1158/1541-7786.mcr-23-0629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer ranks first in incidence and fifth in cancer-related deaths among all types of cancer globally. Among breast cancer, triple-negative breast cancer (TNBC) has few known therapeutic targets and a poor prognosis. Therefore, new therapeutic targets and strategies against TNBC are required. We found that androgen-induced basic leucine zipper (AIbZIP), also known as cyclic AMP-responsive element-binding protein 3-like protein 4 (CREB3L4), which is encoded by Creb3l4, is highly upregulated in a particular subtype of TNBC, luminal androgen receptor (LAR) subtype. We analyzed the function of AIbZIP through depletion of AIbZIP by siRNA knockdown in LAR subtype TNBC cell lines, MFM223 and MDAMB453. In AIbZIP-depleted cells, the proliferation ratios of cells were greatly suppressed. Moreover, G1-S transition was inhibited in AIbZIP-depleted cells. We comprehensively analyzed the expression levels of proteins that regulate G1-S transition and found that p27 was specifically upregulated in AIbZIP-depleted cells. Furthermore, we identified that this p27 downregulation was caused by protein degradation modulated by the ubiquitin-proteasome system via F-box protein S-phase kinase-associated protein 2 (SKP2) upregulation. Our findings demonstrate that AIbZIP is a novel p27-SKP2 pathway-regulating factor and a potential molecule that contributes to LAR subtype TNBC progression. IMPLICATIONS This research shows a new mechanism for the proliferation of LAR subtype TNBC regulated by AIbZIP, that may provide novel insight into the LAR subtype TNBC progression and the molecular mechanisms involved in cell proliferation.
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Affiliation(s)
- Taichi Ito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunao Kamikawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Nayuta Nakazawa
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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28
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Rak M, Menge A, Tesch R, Berger LM, Balourdas DI, Shevchenko E, Krämer A, Elson L, Berger BT, Abdi I, Wahl LM, Poso A, Kaiser A, Hanke T, Kronenberger T, Joerger AC, Müller S, Knapp S. Development of Selective Pyrido[2,3- d]pyrimidin-7(8 H)-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. J Med Chem 2024; 67:3813-3842. [PMID: 38422480 DOI: 10.1021/acs.jmedchem.3c02217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Mammalian STE20-like (MST) kinases 1-4 play key roles in regulating the Hippo and autophagy pathways, and their dysregulation has been implicated in cancer development. In contrast to the well-studied MST1/2, the roles of MST3/4 are less clear, in part due to the lack of potent and selective inhibitors. Here, we re-evaluated literature compounds, and used structure-guided design to optimize the p21-activated kinase (PAK) inhibitor G-5555 (8) to selectively target MST3/4. These efforts resulted in the development of MR24 (24) and MR30 (27) with good kinome-wide selectivity and high cellular potency. The distinct cellular functions of closely related MST kinases can now be elucidated with subfamily-selective chemical tool compounds using a combination of the MST1/2 inhibitor PF-06447475 (2) and the two MST3/4 inhibitors developed. We found that MST3/4-selective inhibition caused a cell-cycle arrest in the G1 phase, whereas MST1/2 inhibition resulted in accumulation of cells in the G2/M phase.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ismahan Abdi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laurenz M Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
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29
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Fallahee I, Hawiger D. Episomal Vectors for Stable Production of Recombinant Proteins and Engineered Antibodies. Antibodies (Basel) 2024; 13:18. [PMID: 38534208 PMCID: PMC10967652 DOI: 10.3390/antib13010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
There is tremendous interest in the production of recombinant proteins, particularly bispecific antibodies and antibody-drug conjugates for research and therapeutic use. Here, we demonstrate a highly versatile plasmid system that allows the rapid generation of stable Expi293 cell pools by episomal retention of transfected DNA. By linking protein expression to puromycin resistance through an attenuated internal ribosome entry site, we achieve stable cell pools producing proteins of interest. In addition, split intein-split puromycin-mediated selection of two separate protein expression cassettes allows the stable production of bispecific antibody-like molecules or antibodies with distinct C-terminal heavy chain modifications, such as an antigen on one chain and a sortase tag on the other chain. We also use this novel expression system to generate stable Expi293 cell pools that secrete sortase A Δ59 variant Srt4M. Using these reagents, we prepared a site-specific drug-to-antibody ratio of 1 antibody-siRNA conjugate. We anticipate the simple, robust, and rapid stable protein expression systems described here being useful for a wide variety of applications.
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Affiliation(s)
| | - Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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30
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Kowald L, Roedig J, Karlowitz R, Wagner K, Smith S, Juretschke T, Beli P, Müller S, van Wijk SJL. USP22 regulates APL differentiation via PML-RARα stabilization and IFN repression. Cell Death Discov 2024; 10:128. [PMID: 38467608 PMCID: PMC10928094 DOI: 10.1038/s41420-024-01894-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Ubiquitin-specific peptidase 22 (USP22) is a deubiquitinating enzyme (DUB) that underlies tumorigenicity, proliferation, cell death and differentiation through deubiquitination of histone and non-histone targets. Ubiquitination determines stability, localization and functions of cell fate proteins and controls cell-protective signaling pathways to surveil cell cycle progression. In a variety of carcinomas, lymphomas and leukemias, ubiquitination regulates the tumor-suppressive functions of the promyelocytic leukemia protein (PML), but PML-specific DUBs, DUB-controlled PML ubiquitin sites and the functional consequences of PML (de)ubiquitination remain unclear. Here, we identify USP22 as regulator of PML and the oncogenic acute promyelocytic leukemia (APL) fusion PML-RARα protein stability and identify a destabilizing role of PML residue K394. Additionally, loss of USP22 upregulates interferon (IFN) and IFN-stimulated gene (ISG) expression in APL and induces PML-RARα stabilization and a potentiation of the cell-autonomous sensitivity towards all-trans retinoic acid (ATRA)-mediated differentiation. Our findings imply USP22-dependent surveillance of PML-RARα stability and IFN signaling as important regulator of APL pathogenesis, with implications for viral mimicry, differentiation and cell fate regulation in other leukemia subtypes.
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Affiliation(s)
- Lisa Kowald
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Jens Roedig
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Rebekka Karlowitz
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Kristina Wagner
- Institute of Biochemistry II (IBCII), Medical Faculty, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sonja Smith
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefan Müller
- Institute of Biochemistry II (IBCII), Medical Faculty, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Pediatric Hematology and Oncology, Medical Faculty, Goethe-University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- University Cancer Centre Frankfurt (UCT), University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany.
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31
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Sanchez L, Lensen A, Connor MG, Hamon M, Enninga J, Valenzuela C. Shigella generates distinct IAM subpopulations during epithelial cell invasion to promote efficient intracellular niche formation. Eur J Cell Biol 2024; 103:151381. [PMID: 38183814 DOI: 10.1016/j.ejcb.2023.151381] [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: 05/22/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/08/2024] Open
Abstract
The facultative intracellular pathogen Shigella flexneri invades non-phagocytic epithelial gut cells. Through a syringe-like apparatus called type 3 secretion system, it injects effector proteins into the host cell triggering actin rearrangements leading to its uptake within a tight vacuole, termed the bacterial-containing vacuole (BCV). Simultaneously, Shigella induces the formation of large vesicles around the entry site, which we refer to as infection-associated macropinosomes (IAMs). After entry, Shigella ruptures the BCV and escapes into the host cytosol by disassembling the BCV remnants. Previously, IAM formation has been shown to be required for efficient BCV escape, but the molecular events associated with BCV disassembly have remained unclear. To identify host components required for BCV disassembly, we performed a microscopy-based screen to monitor the recruitment of BAR domain-containing proteins, which are a family of host proteins involved in membrane shaping and sensing (e.g. endocytosis and recycling) during Shigella epithelial cell invasion. We identified endosomal recycling BAR protein Sorting Nexin-8 (SNX8) localized to IAMs in a PI(3)P-dependent manner before BCV disassembly. At least two distinct IAM subpopulations around the BCV were found, either being recycled back to cellular compartments such as the plasma membrane or transitioning to become RAB11A positive "contact-IAMs" involved in promoting BCV rupture. The IAM subpopulation duality was marked by the exclusive recruitment of either SNX8 or RAB11A. Hindering PI(3)P production at the IAMs led to an inhibition of SNX8 recruitment at these compartments and delayed both, the step of BCV rupture time and successful BCV disassembly. Finally, siRNA depletion of SNX8 accelerated BCV rupture and unpeeling of BCV remnants, indicating that SNX8 is involved in controlling the timing of the cytosolic release. Overall, our work sheds light on how Shigella establishes its intracellular niche through the subversion of a specific set of IAMs.
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Affiliation(s)
- Lisa Sanchez
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France
| | - Arthur Lensen
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France
| | - Michael G Connor
- Institut Pasteur, Université Paris Cité, Chromatin and Infection Unit, 75015 Paris, France
| | - Mélanie Hamon
- Institut Pasteur, Université Paris Cité, Chromatin and Infection Unit, 75015 Paris, France
| | - Jost Enninga
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France.
| | - Camila Valenzuela
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France.
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Burke SM, Avstrikova M, Noviello CM, Mukhtasimova N, Changeux JP, Thakur GA, Sine SM, Cecchini M, Hibbs RE. Structural mechanisms of α7 nicotinic receptor allosteric modulation and activation. Cell 2024; 187:1160-1176.e21. [PMID: 38382524 PMCID: PMC10950261 DOI: 10.1016/j.cell.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that plays an important role in cholinergic signaling throughout the nervous system. Its unique physiological characteristics and implications in neurological disorders and inflammation make it a promising but challenging therapeutic target. Positive allosteric modulators overcome limitations of traditional α7 agonists, but their potentiation mechanisms remain unclear. Here, we present high-resolution structures of α7-modulator complexes, revealing partially overlapping binding sites but varying conformational states. Structure-guided functional and computational tests suggest that differences in modulator activity arise from the stable rotation of a channel gating residue out of the pore. We extend the study using a time-resolved cryoelectron microscopy (cryo-EM) approach to reveal asymmetric state transitions for this homomeric channel and also find that a modulator with allosteric agonist activity exploits a distinct channel-gating mechanism. These results define mechanisms of α7 allosteric modulation and activation with implications across the pentameric receptor superfamily.
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Affiliation(s)
- Sean M Burke
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariia Avstrikova
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France
| | - Colleen M Noviello
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nuriya Mukhtasimova
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Jean-Pierre Changeux
- Neuroscience Department, Institut Pasteur, Collège de France, 75015 Paris, France
| | - Ganesh A Thakur
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France.
| | - Ryan E Hibbs
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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33
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Weinelt N, Wächtershäuser KN, Celik G, Jeiler B, Gollin I, Zein L, Smith S, Andrieux G, Das T, Roedig J, Feist L, Rotter B, Boerries M, Pampaloni F, van Wijk SJL. LUBAC-mediated M1 Ub regulates necroptosis by segregating the cellular distribution of active MLKL. Cell Death Dis 2024; 15:77. [PMID: 38245534 PMCID: PMC10799905 DOI: 10.1038/s41419-024-06447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
Plasma membrane accumulation of phosphorylated mixed lineage kinase domain-like (MLKL) is a hallmark of necroptosis, leading to membrane rupture and inflammatory cell death. Pro-death functions of MLKL are tightly controlled by several checkpoints, including phosphorylation. Endo- and exocytosis limit MLKL membrane accumulation and counteract necroptosis, but the exact mechanisms remain poorly understood. Here, we identify linear ubiquitin chain assembly complex (LUBAC)-mediated M1 poly-ubiquitination (poly-Ub) as novel checkpoint for necroptosis regulation downstream of activated MLKL in cells of human origin. Loss of LUBAC activity inhibits tumor necrosis factor α (TNFα)-mediated necroptosis, not by affecting necroptotic signaling, but by preventing membrane accumulation of activated MLKL. Finally, we confirm LUBAC-dependent activation of necroptosis in primary human pancreatic organoids. Our findings identify LUBAC as novel regulator of necroptosis which promotes MLKL membrane accumulation in human cells and pioneer primary human organoids to model necroptosis in near-physiological settings.
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Affiliation(s)
- Nadine Weinelt
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Kaja Nicole Wächtershäuser
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Biological Sciences (IZN), Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Gulustan Celik
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Birte Jeiler
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Isabelle Gollin
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Laura Zein
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Sonja Smith
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
| | - Tonmoy Das
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
| | - Jens Roedig
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Biological Sciences (IZN), Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- University Cancer Centre Frankfurt (UCT), University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany.
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34
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Sowinska W, Wawro M, Kochan J, Solecka A, Polak J, Kwinta B, Kasza A. Regnase-2 inhibits glioblastoma cell proliferation. Sci Rep 2024; 14:1574. [PMID: 38238463 PMCID: PMC10796923 DOI: 10.1038/s41598-024-51809-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
Regnase-2 (Reg-2/MCPIP2/ZC3H12B) is uniquely expressed at a high level in the healthy brain and down-regulated in samples from patients with glioma, reaching the lowest level in high-grade glioblastoma multiforme (GBM). This RNase is involved in the regulation of neuroinflammation through the degradation of IL-6 and IL-1 mRNAs, key pro-inflammatory cytokines for GBM pathology. Reg-2 is a strong inhibitor of the proliferation of human glioblastoma cell lines and blocks their potential to form colonies. Here, we describe that overexpression of Reg-2 stalls glioblastoma cells in the G1 phase of the cell cycle and reduces the level of transcripts implicated in cell cycle progression. These newly identified targets include CCND1, CCNE1, CCNE2, CCNA2, CCNB1, and CCNB2, encoding the cyclins as well as AURKA and PLK1, encoding two important mitosis regulators. By RNA immunoprecipitation we confirmed the direct interaction of Reg-2 with the investigated transcripts. We also tested mRNA regions involved in their interaction with Reg-2 on the example of CCNE2. Reg-2 interacts with the 3'UTR of CCNE2 in a dose-dependent manner. In conclusion, our results indicate that Reg-2 controls key elements in GBM biology by restricting neuroinflammation and inhibiting cancer cell proliferation.
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Affiliation(s)
- Weronika Sowinska
- Department of Cell Biochemistry, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Krakow, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Krakow, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Krakow, Poland
| | - Aleksandra Solecka
- Department of Cell Biochemistry, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Krakow, Poland
| | - Jarosław Polak
- Department of Neurosurgery and Neurotraumatology, Jagiellonian University Medical College, Kraków, Poland
| | - Borys Kwinta
- Department of Neurosurgery and Neurotraumatology, Jagiellonian University Medical College, Kraków, Poland
| | - Aneta Kasza
- Department of Cell Biochemistry, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Krakow, Poland.
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35
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Amrhein JA, Berger LM, Balourdas DI, Joerger AC, Menge A, Krämer A, Frischkorn JM, Berger BT, Elson L, Kaiser A, Schubert-Zsilavecz M, Müller S, Knapp S, Hanke T. Synthesis of Pyrazole-Based Macrocycles Leads to a Highly Selective Inhibitor for MST3. J Med Chem 2024; 67:674-690. [PMID: 38126712 DOI: 10.1021/acs.jmedchem.3c01980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
MST1, MST2, MST3, MST4, and YSK1 are conserved members of the mammalian sterile 20-like serine/threonine (MST) family that regulate cellular functions such as proliferation and migration. The MST3 isozyme plays a role in regulating cell growth and apoptosis, and its dysregulation has been linked to high-grade tumors. To date, there are no isoform-selective inhibitors that could be used for validating the role of MST3 in tumorigenesis. We designed a series of 3-aminopyrazole-based macrocycles based on the structure of a promiscuous inhibitor. By varying the moieties targeting the solvent-exposed region and optimizing the linker, macrocycle JA310 (21c) was synthesized. JA310 exhibited high cellular potency for MST3 (EC50 = 106 nM) and excellent kinome-wide selectivity. The crystal structure of the MST3-JA310 complex provided intriguing insights into the binding mode, which is associated with large-scale structural rearrangements. In summary, JA310 demonstrates the utility of macrocyclization for the design of highly selective inhibitors and presents the first chemical probe for MST3.
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Affiliation(s)
- Jennifer Alisa Amrhein
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena Marie Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz 69120 Heidelberg, Germany
| | - Julia Marie Frischkorn
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz 69120 Heidelberg, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
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36
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Fallahee I, Hawiger D. EPISOMAL VECTORS FOR STABLE PRODUCTION OF RECOMBINANT PROTEINS AND ENGINEERED ANTIBODIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574076. [PMID: 38260603 PMCID: PMC10802304 DOI: 10.1101/2024.01.03.574076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
There is tremendous interest in the production of recombinant proteins, particularly bispecific antibodies and antibody-drug conjugates for research and therapeutic use. Here, we demonstrate a highly versatile plasmid system that allows rapid generation of stable Expi293 cell pools by episomal retention of transfected DNA. By linking protein expression to puromycin resistance though an attenuated internal ribosome entry site, we achieve stable cell pools producing proteins of interest. In addition, split intein-split puromycin-mediated selection of two separate protein expression cassettes allows the stable production of bispecific antibody-like molecules or antibodies with distinct C-terminal heavy chain modifications, such as an antigen on one chain and a sortase tag on the other chain. We also use this novel expression system to generate stable Expi293 cell pools that secrete sortase A Δ59 variant Srt4M. Using these reagents, we prepared a site-specific drug-to-antibody ratio of 1 antibody-siRNA conjugate. We anticipate the simple, robust, and rapid stable protein expression systems described here being useful for a wide variety of applications.
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37
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Meyer M, Parpoulas C, Barthélémy T, Becker JP, Charoentong P, Lyu Y, Börsig S, Bulbuc N, Tessmer C, Weinacht L, Ibberson D, Schmidt P, Pipkorn R, Eichmüller SB, Steinberger P, Lindner K, Poschke I, Platten M, Fröhling S, Riemer AB, Hassel JC, Roberti MP, Jäger D, Zörnig I, Momburg F. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front Immunol 2024; 14:1294565. [PMID: 38239352 PMCID: PMC10794645 DOI: 10.3389/fimmu.2023.1294565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Peptide-loaded MHC class I (pMHC-I) multimers have revolutionized our capabilities to monitor disease-associated T cell responses with high sensitivity and specificity. To improve the discovery of T cell receptors (TCR) targeting neoantigens of individual tumor patients with recombinant MHC molecules, we developed a peptide-loadable MHC class I platform termed MediMer. MediMers are based on soluble disulfide-stabilized β2-microglobulin/heavy chain ectodomain single-chain dimers (dsSCD) that can be easily produced in large quantities in eukaryotic cells and tailored to individual patients' HLA allotypes with only little hands-on time. Upon transient expression in CHO-S cells together with ER-targeted BirA biotin ligase, biotinylated dsSCD are purified from the cell supernatant and are ready to use. We show that CHO-produced dsSCD are free of endogenous peptide ligands. Empty dsSCD from more than 30 different HLA-A,B,C allotypes, that were produced and validated so far, can be loaded with synthetic peptides matching the known binding criteria of the respective allotypes, and stored at low temperature without loss of binding activity. We demonstrate the usability of peptide-loaded dsSCD multimers for the detection of human antigen-specific T cells with comparable sensitivities as multimers generated with peptide-tethered β2m-HLA heavy chain single-chain trimers (SCT) and wild-type peptide-MHC-I complexes prior formed in small-scale refolding reactions. Using allotype-specific, fluorophore-labeled competitor peptides, we present a novel dsSCD-based peptide binding assay capable of interrogating large libraries of in silico predicted neoepitope peptides by flow cytometry in a high-throughput and rapid format. We discovered rare T cell populations with specificity for tumor neoepitopes and epitopes from shared tumor-associated antigens in peripheral blood of a melanoma patient including a so far unreported HLA-C*08:02-restricted NY-ESO-1-specific CD8+ T cell population. Two representative TCR of this T cell population, which could be of potential value for a broader spectrum of patients, were identified by dsSCD-guided single-cell sequencing and were validated by cognate pMHC-I multimer staining and functional responses to autologous peptide-pulsed antigen presenting cells. By deploying the technically accessible dsSCD MHC-I MediMer platform, we hope to significantly improve success rates for the discovery of personalized neoepitope-specific TCR in the future by being able to also cover rare HLA allotypes.
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Affiliation(s)
- Marten Meyer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Christina Parpoulas
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titouan Barthélémy
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas P. Becker
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Pornpimol Charoentong
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Yanhong Lyu
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Selina Börsig
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadja Bulbuc
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Tessmer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Lisa Weinacht
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Heidelberg University, Heidelberg, Germany
| | - Patrick Schmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- GMP and T Cell Therapy, DKFZ, Heidelberg, Germany
| | | | | | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology, Medical University of Vienna, Vienna, Austria
| | - Katharina Lindner
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center, Mannheim, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz), Mainz, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika B. Riemer
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Jessica C. Hassel
- Section of DermatoOncology, Department of Dermatology and NCT, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria Paula Roberti
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Inka Zörnig
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
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38
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Slyp B, Darby JM, Flies AS. Conversion of Mouse-Derived Hybridomas to Tasmanian Devil Recombinant IgG Antibodies. Methods Mol Biol 2024; 2826:231-249. [PMID: 39017897 DOI: 10.1007/978-1-0716-3950-4_17] [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] [Indexed: 07/18/2024]
Abstract
The hybridoma method for production of monoclonal antibodies has been a cornerstone of biomedical research for several decades. Here we convert the monoclonal antibody sequence from mouse-derived hybridomas into a "devilized" recombinant antibody with devil IgG heavy chain and IgK light chain. The chimeric recombinant antibody can be used in functional assays, immunotherapy, and to improve understanding of antibodies and Fc receptors in Tasmanian devils. The process can be readily modified for other species.
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Affiliation(s)
- Bailey Slyp
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Jocelyn M Darby
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.
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39
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Ursic-Bedoya J, Gregoire D. Hydrodynamic Transfection of Hepatocytes for the Study of Hepatocellular Carcinogenesis. Methods Mol Biol 2024; 2769:77-85. [PMID: 38315390 DOI: 10.1007/978-1-0716-3694-7_6] [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] [Indexed: 02/07/2024]
Abstract
Hydrodynamic tail vein injection (HTVi), also called hydrodynamic gene transfer (HGT), is attracting increasing interest for modeling hepatic carcinogenesis. This highly versatile approach reproducibly provides efficient in vivo transfection of hepatocytes with naked DNA. Here, we give an in-depth description of the injection procedure, which is key for the success of the method. HTVi requires the injection of a large volume of a solution containing plasmids into the tail vein of the mouse. The transient right heart overload created by the injection forces the blood to flow back into the hepatic veins, enlarging the endothelial fenestrae and permeabilizing a fraction of hepatocytes for a few seconds. This results in the uptake of plasmids by the permeabilized hepatocytes, giving rise to their in vivo transfection. Including the Sleeping Beauty transposon system among the injected plasmids leads to the stable transfection of a subset of hepatocytes. HTVi is a powerful technique which enables numerous applications in liver cancer biology, such as a study of oncogene cooperation, of tumor heterogeneity, and interaction with the tumor microenvironment.
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Affiliation(s)
- José Ursic-Bedoya
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Damien Gregoire
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
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Dixon CL, Martin NR, Niphakis MJ, Cravatt BF, Fairn GD. Attenuating ABHD17 enhances S- palmitoylation, membrane localization and signal transduction of NOD2 and Crohn's disease-associated variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572362. [PMID: 38187608 PMCID: PMC10769251 DOI: 10.1101/2023.12.20.572362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
NOD2 is an intracellular innate immune receptor that senses bacterial peptidoglycans. Although soluble in the cytosol, a portion of the protein is associated with the plasma membrane and endosomal compartments for microbial surveillance. Palmitoylation of NOD2 by zDHHC5 promotes its membrane recruitment to drive proinflammatory and antimicrobial responses to pathogenic invasion. A depalmitoylation step by an unknown protein, thioesterase, releases NOD2 from membranes into the cytosol, where the protein can then enter a new cycle of palmitoylation-depalmitoylation. Here, we identify α/β -hydrolase domain-containing protein 17 isoforms (ABHD17A, 17B, 17C) as the thioesterases responsible for depalmitoylation of NOD2. Inhibiting ABHD17 increased the plasmalemmal localization of both wild-type NOD2 and a subset of hypo-palmitoylated Crohn's disease-associated variants, resulting in increased NF-κB activation and production of pro-inflammatory cytokines in epithelial cells. These results suggest that targeted inhibition of ABHD17 may rescue some Crohn's disease-associated NOD2 variants.
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Puig-Blasco L, Piotrowski KB, Michaelsen SR, Bager NS, Areškevičiūtiė A, Thorseth ML, Sun XF, Keller UAD, Kristensen BW, Madsen DH, Gnosa SP, Kveiborg M. Loss of cancer cell-derived ADAM15 alters the tumor microenvironment in colorectal tumors. Int J Cancer 2023; 153:2068-2081. [PMID: 37602921 DOI: 10.1002/ijc.34695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/18/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023]
Abstract
Tumor progression and response to treatment are highly affected by interactions between cancer cells and the tumor microenvironment (TME). Many of the soluble factors and signaling receptors involved in this crosstalk are shed by a disintegrin and metalloproteinases (ADAMs). Upregulation of ADAM15 has been linked to worse survival in cancer patients and a tumor-promoting function both in vitro and in murine cancer models. Although ADAM15 has been involved in cell-cell and cell-extracellular matrix interactions, its role in the crosstalk between cancer cells and the TME in vivo remains unexplored. Therefore, we aimed to understand how ADAM15 regulates the cell composition of the TME and how it affects tumor progression. Here, we showed an upregulation of ADAM15 in tumor tissues from rectal cancer patients. Subcutaneous injection of wildtype and ADAM15-knockout CT26 colon cancer cells in syngeneic mice confirmed the protumorigenic role of ADAM15. Profiling of tumors revealed higher immune cell infiltration and cancer cell apoptosis in the ADAM15-deficient tumors. Specifically, loss of ADAM15 led to a reduced number of granulocytes and higher infiltration of antigen-presenting cells, including dendritic cells and macrophages, as well as more T cells. Using in vitro assays, we confirmed the regulatory effect of ADAM15 on macrophage migration and identified ADAM15-derived CYR61 as a potential molecular mediator of this effect. Based on these findings, we speculate that targeting ADAM15 could increase the infiltration of immune cells in colorectal tumors, which is a prerequisite for effective immunotherapy.
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Affiliation(s)
- Laia Puig-Blasco
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof B Piotrowski
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Signe R Michaelsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nicolai S Bager
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Aušrinė Areškevičiūtiė
- Danish Reference Center for Prion Diseases, Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marie-Louise Thorseth
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, Copenhagen, Denmark
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bjarne W Kristensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel H Madsen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, Copenhagen, Denmark
| | - Sebastian P Gnosa
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Minerva Imaging, Ølstykke, Denmark
| | - Marie Kveiborg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
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Korenkov M, Zehner M, Cohen-Dvashi H, Borenstein-Katz A, Kottege L, Janicki H, Vanshylla K, Weber T, Gruell H, Koch M, Diskin R, Kreer C, Klein F. Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Immunity 2023; 56:2803-2815.e6. [PMID: 38035879 DOI: 10.1016/j.immuni.2023.11.004] [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: 04/21/2023] [Revised: 07/19/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Somatic hypermutation (SHM) drives affinity maturation and continues over months in SARS-CoV-2-neutralizing antibodies (nAbs). However, several potent SARS-CoV-2 antibodies carry no or only a few mutations, leaving the question of how ongoing SHM affects neutralization unclear. Here, we reverted variable region mutations of 92 antibodies and tested their impact on SARS-CoV-2 binding and neutralization. Reverting higher numbers of mutations correlated with decreasing antibody functionality. However, for some antibodies, including antibodies of the public clonotype VH1-58, neutralization of Wu01 remained unaffected. Although mutations were dispensable for Wu01-induced VH1-58 antibodies to neutralize Alpha, Beta, and Delta variants, they were critical for Omicron BA.1/BA.2 neutralization. We exploited this knowledge to convert the clinical antibody tixagevimab into a BA.1/BA.2 neutralizer. These findings broaden our understanding of SHM as a mechanism that not only improves antibody responses during affinity maturation but also contributes to antibody diversification, thus increasing the chances of neutralizing viral escape variants.
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Affiliation(s)
- Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hadas Cohen-Dvashi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Aliza Borenstein-Katz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lisa Kottege
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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43
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Aleksashin NA, Chang STL, Cate JHD. A highly efficient human cell-free translation system. RNA (NEW YORK, N.Y.) 2023; 29:1960-1972. [PMID: 37793791 PMCID: PMC10653386 DOI: 10.1261/rna.079825.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells before cell lysate preparation significantly simplifies lysate preparation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. During in vitro translation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
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Affiliation(s)
- Nikolay A Aleksashin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Stacey Tsai-Lan Chang
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, USA
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44
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Weber T, Dähling S, Rose S, Affeldt P, Vanshylla K, Ullrich L, Gieselmann L, Teipel F, Gruell H, Di Cristanziano V, Kim DS, Georgiou G, Koch M, Kreer C, Klein F. Enhanced SARS-CoV-2 humoral immunity following breakthrough infection builds upon the preexisting memory B cell pool. Sci Immunol 2023; 8:eadk5845. [PMID: 37976348 DOI: 10.1126/sciimmunol.adk5845] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
The human immune response must continuously adapt to newly emerging SARS-CoV-2 variants. To investigate how B cells respond to repeated SARS-CoV-2 antigen exposure by Wu01 booster vaccination and Omicron breakthrough infection, we performed a molecular longitudinal analysis of the memory B cell pool. We demonstrate that a subsequent breakthrough infection substantially increases the frequency of B cells encoding SARS-CoV-2-neutralizing antibodies. However, this is not primarily attributable to maturation, but to selection of preexisting B cell clones. Moreover, broadly reactive memory B cells arose early and even neutralized highly mutated variants like XBB.1.5 that the individuals had not encountered. Together, our data show that SARS-CoV-2 immunity is largely imprinted on Wu01 over the course of multiple antigen contacts but can respond to new variants through preexisting diversity.
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Affiliation(s)
- Timm Weber
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sabrina Dähling
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Svea Rose
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Patrick Affeldt
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kanika Vanshylla
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Leon Ullrich
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Finn Teipel
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dae Sung Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - George Georgiou
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
- Department of Chemical Engineering and Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, University of Texas Dell Medical School, Austin, Texas, USA
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty and University of Cologne, Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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45
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Zehner M, Alt M, Ashurov A, Goldsmith JA, Spies R, Weiler N, Lerma J, Gieselmann L, Stöhr D, Gruell H, Schultz EP, Kreer C, Schlachter L, Janicki H, Laib Sampaio K, Stegmann C, Nemetchek MD, Dähling S, Ullrich L, Dittmer U, Witzke O, Koch M, Ryckman BJ, Lotfi R, McLellan JS, Krawczyk A, Sinzger C, Klein F. Single-cell analysis of memory B cells from top neutralizers reveals multiple sites of vulnerability within HCMV Trimer and Pentamer. Immunity 2023; 56:2602-2620.e10. [PMID: 37967532 DOI: 10.1016/j.immuni.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/02/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Human cytomegalovirus (HCMV) can cause severe diseases in fetuses, newborns, and immunocompromised individuals. Currently, no vaccines are approved, and treatment options are limited. Here, we analyzed the human B cell response of four HCMV top neutralizers from a cohort of 9,000 individuals. By single-cell analyses of memory B cells targeting the pentameric and trimeric HCMV surface complexes, we identified vulnerable sites on the shared gH/gL subunits as well as complex-specific subunits UL128/130/131A and gO. Using high-resolution cryogenic electron microscopy, we revealed the structural basis of the neutralization mechanisms of antibodies targeting various binding sites. Moreover, we identified highly potent antibodies that neutralized a broad spectrum of HCMV strains, including primary clinical isolates, that outperform known antibodies used in clinical trials. Our study provides a deep understanding of the mechanisms of HCMV neutralization and identifies promising antibody candidates to prevent and treat HCMV infection.
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Affiliation(s)
- Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Mira Alt
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Artem Ashurov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rebecca Spies
- Institute for Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Nina Weiler
- Institute for Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Justin Lerma
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Dagmar Stöhr
- Institute for Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Eric P Schultz
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Linda Schlachter
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Cora Stegmann
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Michelle D Nemetchek
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Sabrina Dähling
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Leon Ullrich
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Brent J Ryckman
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Ramin Lotfi
- Institute for Transfusion Medicine, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Adalbert Krawczyk
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Christian Sinzger
- Institute for Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931 Cologne, Germany.
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Shaw TM, Maloney SM, Nennig K, Ramuta MD, Norton A, Ibarra R, Kuehnert P, Brinton M, Faaberg K, Kuhn JH, O'Connor DH, Warren CJ, Bailey AL. Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating virus 63 years after its discovery. J Virol 2023; 97:e0093023. [PMID: 37792000 PMCID: PMC10617578 DOI: 10.1128/jvi.00930-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mouse models of viral infection play an especially large role in virology. In 1960, a mouse virus, lactate dehydrogenase-elevating virus (LDV), was discovered and found to have the peculiar ability to evade clearance by the immune system, enabling it to persistently infect an individual mouse for its entire lifespan without causing overt disease. However, researchers were unable to grow LDV in culture, ultimately resulting in the demise of this system as a model of failed immunity. We solve this problem by identifying the cell-surface molecule CD163 as the critical missing component in cell-culture systems, enabling the growth of LDV in immortalized cell lines for the first time. This advance creates abundant opportunities for further characterizing LDV in order to study both failed immunity and the family of viruses to which LDV belongs, Arteriviridae (aka, arteriviruses).
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Affiliation(s)
- Teressa M Shaw
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Sara M Maloney
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Kylie Nennig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Mitchell D Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Andrew Norton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Rodrigo Ibarra
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Paul Kuehnert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Margo Brinton
- Department of Biology, Georgia State University , Atlanta, Georgia, USA
| | - Kay Faaberg
- Virus and Prion Research Unit, USA Department of Agriculture, National Animal Disease Center , Ames, Iowa, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick , Frederick, Maryland, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Cody J Warren
- Department of Veterinary Biosciences, The Ohio State University , Columbus, Ohio, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
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47
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Zak K, Antonescu CN. Doxycycline-inducible Expression of Proteins at Near-endogenous Levels in Mammalian Cells Using the Sleeping Beauty Transposon System. Bio Protoc 2023; 13:e4846. [PMID: 37900104 PMCID: PMC10603196 DOI: 10.21769/bioprotoc.4846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 10/31/2023] Open
Abstract
The function of a protein within a cell critically depends on its interaction with other proteins as well as its subcellular localization. The expression of mutants of a particular protein that have selective perturbation of specific protein interaction motifs is a very useful strategy for resolving a protein's mechanism of action in a cellular process. In addition, expression of fluorescent protein fusions is a key strategy for determining the subcellular localization of a protein. These strategies require tight regulation to avoid potential alterations in protein interactions or localizations that can result from protein overexpression. Previous work led to the development of a Sleeping Beauty transposon system that allows doxycycline-inducible expression of protein mutants or fusions; titration of doxycycline allows expression of protein fusions or mutants at near endogenous levels. When used in combination with siRNA gene silencing, this strategy allows for knockdown-rescue experiments to assess the function of specific protein mutants. In this protocol, we describe the use of this Sleeping Beauty strategy for expression of eGFP fusion or mutant proteins in ARPE-19 and MDA-MB-231 cells. This includes design of expression plasmids, transfection, and selection to obtain stable engineered cells, as well as doxycycline treatment for controlled induction of protein expression, either alone or in combination with siRNA silencing for knockdown-rescue experiments. This strategy is advantageous as it allows rapid generation of stable cells for controlled protein expression, suitable for functional studies that require knockdown-rescue as well as various forms of live cell fluorescence imaging. Key features • Highly versatile doxycycline-inducible expression system that can be used in various mammalian cell lines. • Stable integration of transgene allows for sustained and stable expression. • Titration of doxycycline levels allows expression of transgene at near endogenous levels.
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Affiliation(s)
- Karolina Zak
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
- Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Canada
| | - Costin N. Antonescu
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
- Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Canada
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48
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Sarparanta J, Jonson PH, Reimann J, Vihola A, Luque H, Penttilä S, Johari M, Savarese M, Hackman P, Kornblum C, Udd B. Extension of the DNAJB2a isoform in a dominant neuromyopathy family. Hum Mol Genet 2023; 32:3029-3039. [PMID: 37070754 PMCID: PMC10586202 DOI: 10.1093/hmg/ddad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Recessive mutations in the DNAJB2 gene, encoding the J-domain co-chaperones DNAJB2a and DNAJB2b, have previously been reported as the genetic cause of progressive peripheral neuropathies, rarely involving pyramidal signs, parkinsonism and myopathy. We describe here a family with the first dominantly acting DNAJB2 mutation resulting in a late-onset neuromyopathy phenotype. The c.832 T > G p.(*278Glyext*83) mutation abolishes the stop codon of the DNAJB2a isoform resulting in a C-terminal extension of the protein, with no direct effect predicted on the DNAJB2b isoform of the protein. Analysis of the muscle biopsy showed reduction of both protein isoforms. In functional studies, the mutant protein mislocalized to the endoplasmic reticulum due to a transmembrane helix in the C-terminal extension. The mutant protein underwent rapid proteasomal degradation and also increased the turnover of co-expressed wild-type DNAJB2a, potentially explaining the reduced protein amount in the patient muscle tissue. In line with this dominant negative effect, both wild-type and mutant DNAJB2a were shown to form polydisperse oligomers.
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Affiliation(s)
- Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Jens Reimann
- Klinik und Poliklinik für Neurologie, Sektion Neuromuskuläre Erkrankungen, Universitätsklinikum Bonn, D-53127 Bonn, Germany
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
| | - Helena Luque
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Sini Penttilä
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands WA, Australia
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
| | - Cornelia Kornblum
- Klinik und Poliklinik für Neurologie, Sektion Neuromuskuläre Erkrankungen, Universitätsklinikum Bonn, D-53127 Bonn, Germany
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland and Medicum, University of Helsinki, FI-00290 Helsinki, Finland
- Neuromuscular Research Center, Tampere University Hospital and Fimlab Laboratories, FI-33520 Tampere, Finland
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49
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Clark NK, Harris MT, Dahl WB, Knotts Z, Marr MT. The Insulin Receptor and Insulin like Growth Factor Receptor 5' UTRs Support Translation Initiation Independently of EIF4G1. Mol Cell Biol 2023; 43:485-499. [PMID: 37724583 PMCID: PMC10569357 DOI: 10.1080/10985549.2023.2255120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
IRES mediated translation initiation requires a different repertoire of factors than canonical cap-dependent translation. Treatments that inhibit the canonical translation factor EIF4G1 have little or no effect on the ability of the Insr and Igf1r cellular IRESes to promote translation. Transcripts for two cellular receptors contain RNA elements that facilitate translation initiation without intact EIF4G1. Cellular IRES mechanisms may resemble viral type III IRESes allowing them to promote translate with a limited number of initiation factors allowing them to work under stress conditions when canonical translation is repressed.
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Affiliation(s)
- Nicholas K. Clark
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- mRNA Center of Excellence, Sanofi, Waltham, Massachusetts, USA
| | - Meghan T. Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
- Myeloid Therapeutics, Cambridge, Massachusetts, USA
| | - William B. Dahl
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Zachary Knotts
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Michael T. Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, USA
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50
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Pereira RS, Kumar R, Cais A, Paulini L, Kahler A, Bravo J, Minciacchi VR, Krack T, Kowarz E, Zanetti C, Godavarthy PS, Hoeller F, Llavona P, Stark T, Tascher G, Nowak D, Meduri E, Huntly BJP, Münch C, Pampaloni F, Marschalek R, Krause DS. Distinct and targetable role of calcium-sensing receptor in leukaemia. Nat Commun 2023; 14:6242. [PMID: 37802982 PMCID: PMC10558580 DOI: 10.1038/s41467-023-41770-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 09/12/2023] [Indexed: 10/08/2023] Open
Abstract
Haematopoietic stem cells (HSC) reside in the bone marrow microenvironment (BMM), where they respond to extracellular calcium [eCa2+] via the G-protein coupled calcium-sensing receptor (CaSR). Here we show that a calcium gradient exists in this BMM, and that [eCa2+] and response to [eCa2+] differ between leukaemias. CaSR influences the location of MLL-AF9+ acute myeloid leukaemia (AML) cells within this niche and differentially impacts MLL-AF9+ AML versus BCR-ABL1+ leukaemias. Deficiency of CaSR reduces AML leukaemic stem cells (LSC) 6.5-fold. CaSR interacts with filamin A, a crosslinker of actin filaments, affects stemness-associated factors and modulates pERK, β-catenin and c-MYC signaling and intracellular levels of [Ca2+] in MLL-AF9+ AML cells. Combination treatment of cytarabine plus CaSR-inhibition in various models may be superior to cytarabine alone. Our studies suggest CaSR to be a differential and targetable factor in leukaemia progression influencing self-renewal of AML LSC via [eCa2+] cues from the BMM.
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Affiliation(s)
- Raquel S Pereira
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Rahul Kumar
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Alessia Cais
- Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara Paulini
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Alisa Kahler
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Jimena Bravo
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Valentina R Minciacchi
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Theresa Krack
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Costanza Zanetti
- University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Fabian Hoeller
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Pablo Llavona
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Tabea Stark
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eshwar Meduri
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Francesco Pampaloni
- Buchmann Institute for Molecular Life Sciences (BMLS, CEF-MC), Goethe University, Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.
- Institute of General Pharmacology and Toxicology, Goethe-University, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Frankfurt Cancer Institute, Frankfurt, Germany.
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