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Hess L, Moos V, Lauber AA, Reiter W, Schuster M, Hartl N, Lackner D, Boenke T, Koren A, Guzzardo PM, Gundacker B, Riegler A, Vician P, Miccolo C, Leiter S, Chandrasekharan MB, Vcelkova T, Tanzer A, Jun JQ, Bradner J, Brosch G, Hartl M, Bock C, Bürckstümmer T, Kubicek S, Chiocca S, Bhaskara S, Seiser C. A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation. PLoS Genet 2022; 18:e1010376. [PMID: 35994477 PMCID: PMC9436093 DOI: 10.1371/journal.pgen.1010376] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/01/2022] [Accepted: 08/06/2022] [Indexed: 02/07/2023] Open
Abstract
The class I histone deacetylases are essential regulators of cell fate decisions in health and disease. While pan- and class-specific HDAC inhibitors are available, these drugs do not allow a comprehensive understanding of individual HDAC function, or the therapeutic potential of isoform-specific targeting. To systematically compare the impact of individual catalytic functions of HDAC1, HDAC2 and HDAC3, we generated human HAP1 cell lines expressing catalytically inactive HDAC enzymes. Using this genetic toolbox we compare the effect of individual HDAC inhibition with the effects of class I specific inhibitors on cell viability, protein acetylation and gene expression. Individual inactivation of HDAC1 or HDAC2 has only mild effects on cell viability, while HDAC3 inactivation or loss results in DNA damage and apoptosis. Inactivation of HDAC1/HDAC2 led to increased acetylation of components of the COREST co-repressor complex, reduced deacetylase activity associated with this complex and derepression of neuronal genes. HDAC3 controls the acetylation of nuclear hormone receptor associated proteins and the expression of nuclear hormone receptor regulated genes. Acetylation of specific histone acetyltransferases and HDACs is sensitive to inactivation of HDAC1/HDAC2. Over a wide range of assays, we determined that in particular HDAC1 or HDAC2 catalytic inactivation mimics class I specific HDAC inhibitors. Importantly, we further demonstrate that catalytic inactivation of HDAC1 or HDAC2 sensitizes cells to specific cancer drugs. In summary, our systematic study revealed isoform-specific roles of HDAC1/2/3 catalytic functions. We suggest that targeted genetic inactivation of particular isoforms effectively mimics pharmacological HDAC inhibition allowing the identification of relevant HDACs as targets for therapeutic intervention.
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Affiliation(s)
- Lena Hess
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Verena Moos
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Arnel A. Lauber
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Natascha Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
| | | | - Thorina Boenke
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Brigitte Gundacker
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Anna Riegler
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Petra Vician
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Claudia Miccolo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Susanna Leiter
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Mahesh B. Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Terezia Vcelkova
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Andrea Tanzer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Jun Qi Jun
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - James Bradner
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gerald Brosch
- Institute of Molecular Biology, Innsbruck Medical University, Innsbruck, Austria
| | - Markus Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Susanna Chiocca
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Srividya Bhaskara
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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Datlinger P, Rendeiro AF, Boenke T, Senekowitsch M, Krausgruber T, Barreca D, Bock C. Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing. Nat Methods 2021; 18:635-642. [PMID: 34059827 PMCID: PMC7612019 DOI: 10.1038/s41592-021-01153-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/08/2021] [Indexed: 02/02/2023]
Abstract
Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed 'single-cell combinatorial fluidic indexing' (scifi). The scifi-RNA-seq assay combines one-step combinatorial preindexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. Preindexing allows us to load several cells per droplet and computationally demultiplex their individual expression profiles. Thereby, scifi-RNA-seq massively increases the throughput of droplet-based single-cell RNA-seq, and provides a straightforward way of multiplexing thousands of samples in a single experiment. Compared with multiround combinatorial indexing, scifi-RNA-seq provides an easy and efficient workflow. Compared to cell hashing methods, which flag and discard droplets containing more than one cell, scifi-RNA-seq resolves and retains individual transcriptomes from overloaded droplets. We benchmarked scifi-RNA-seq on various human and mouse cell lines, validated it for primary human T cells and applied it in a highly multiplexed CRISPR screen with single-cell transcriptome readout of T cell receptor activation.
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Affiliation(s)
- Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thorina Boenke
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria.
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Preglej T, Hamminger P, Luu M, Bulat T, Andersen L, Göschl L, Stolz V, Rica R, Sandner L, Waltenberger D, Tschismarov R, Faux T, Boenke T, Laiho A, Elo LL, Sakaguchi S, Steiner G, Decker T, Bohle B, Visekruna A, Bock C, Strobl B, Seiser C, Boucheron N, Ellmeier W. Histone deacetylases 1 and 2 restrain CD4+ cytotoxic T lymphocyte differentiation. JCI Insight 2020; 5:133393. [PMID: 32102981 PMCID: PMC7101144 DOI: 10.1172/jci.insight.133393] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/24/2020] [Indexed: 12/11/2022] Open
Abstract
Some effector CD4+ T cell subsets display cytotoxic activity, thus breaking the functional dichotomy of CD4+ helper and CD8+ cytotoxic T lymphocytes. However, molecular mechanisms regulating CD4+ cytotoxic T lymphocyte (CD4+ CTL) differentiation are poorly understood. Here we show that levels of histone deacetylases 1 and 2 (HDAC1-HDAC2) are key determinants of CD4+ CTL differentiation. Deletions of both Hdac1 and 1 Hdac2 alleles (HDAC1cKO-HDAC2HET) in CD4+ T cells induced a T helper cytotoxic program that was controlled by IFN-γ-JAK1/2-STAT1 signaling. In vitro, activated HDAC1cKO-HDAC2HET CD4+ T cells acquired cytolytic activity and displayed enrichment of gene signatures characteristic of effector CD8+ T cells and human CD4+ CTLs. In vivo, murine cytomegalovirus-infected HDAC1cKO-HDAC2HET mice displayed a stronger induction of CD4+ CTL features compared with infected WT mice. Finally, murine and human CD4+ T cells treated with short-chain fatty acids, which are commensal-produced metabolites acting as HDAC inhibitors, upregulated CTL genes. Our data demonstrate that HDAC1-HDAC2 restrain CD4+ CTL differentiation. Thus, HDAC1-HDAC2 might be targets for the therapeutic induction of CD4+ CTLs.
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Affiliation(s)
- Teresa Preglej
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Patricia Hamminger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Maik Luu
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Tanja Bulat
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Liisa Andersen
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lisa Göschl
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Valentina Stolz
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ramona Rica
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lisa Sandner
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Darina Waltenberger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Thomas Faux
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Thorina Boenke
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Asta Laiho
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L. Elo
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Shinya Sakaguchi
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Günter Steiner
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
| | - Thomas Decker
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Barbara Bohle
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, and
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christian Seiser
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Nicole Boucheron
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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Bohnert M, Zerbes RM, Davies KM, Mühleip AW, Rampelt H, Horvath SE, Boenke T, Kram A, Perschil I, Veenhuis M, Kühlbrandt W, van der Klei IJ, Pfanner N, van der Laan M. Central role of Mic10 in the mitochondrial contact site and cristae organizing system. Cell Metab 2015; 21:747-55. [PMID: 25955210 DOI: 10.1016/j.cmet.2015.04.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/09/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
The mitochondrial contact site and cristae organizing system (MICOS) is a conserved multi-subunit complex crucial for maintaining the characteristic architecture of mitochondria. Studies with deletion mutants identified Mic10 and Mic60 as core subunits of MICOS. Mic60 has been studied in detail; however, topogenesis and function of Mic10 are unknown. We report that targeting of Mic10 to the mitochondrial inner membrane requires a positively charged internal loop, but no cleavable presequence. Both transmembrane segments of Mic10 carry a characteristic four-glycine motif, which has been found in the ring-forming rotor subunit of F1Fo-ATP synthases. Overexpression of Mic10 profoundly alters the architecture of the inner membrane independently of other MICOS components. The four-glycine motifs are dispensable for interaction of Mic10 with other MICOS subunits but are crucial for the formation of large Mic10 oligomers. Our studies identify a unique role of Mic10 oligomers in promoting the formation of inner membrane crista junctions.
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Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Ralf M Zerbes
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Universität Freiburg, 79104 Freiburg, Germany
| | - Karen M Davies
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Alexander W Mühleip
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Heike Rampelt
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thorina Boenke
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Anita Kram
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Inge Perschil
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Marten Veenhuis
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ida J van der Klei
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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