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Schwartz I, Vunjak M, Budroni V, Cantoran García A, Mastrovito M, Soderholm A, Hinterndorfer M, de Almeida M, Hacker K, Wang J, Froussios K, Jude J, Decker T, Zuber J, Versteeg GA. SPOP targets the immune transcription factor IRF1 for proteasomal degradation. eLife 2023; 12:e89951. [PMID: 37622993 PMCID: PMC10491434 DOI: 10.7554/elife.89951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Adaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon regulatory factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a 'Goldilocks' zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor speckle type BTB/POZ protein (SPOP) to mediate IRF1 proteasomal turnover in human and mouse cells. We identified S/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, elevated IRF1 protein levels functionally increased IRF1-dependent cellular responses, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.
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Affiliation(s)
- Irene Schwartz
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Milica Vunjak
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Adriana Cantoran García
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Marialaura Mastrovito
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Adrian Soderholm
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Matthias Hinterndorfer
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Melanie de Almeida
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Kathrin Hacker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Jingkui Wang
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Kimon Froussios
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
- Medical University of Vienna, Vienna BioCenterViennaAustria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
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2
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Pinter T, Fischer M, Schäfer M, Fellner M, Jude J, Zuber J, Busslinger M, Wöhner M. Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development. Front Immunol 2022; 13:979606. [PMID: 36189249 PMCID: PMC9521597 DOI: 10.3389/fimmu.2022.979606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Plasma cells (PCs) and their progenitors plasmablasts (PBs) are essential for the acute and long-term protection of the host against infections by providing vast levels of highly specific antibodies. Several transcription factors, like Blimp1 and Irf4, are already known to be essential for PC and PB differentiation and survival. We set out to identify additional genes, that are essential for PB development by CRISPR-Cas9 screening of 3,000 genes for the loss of PBs by employing the in vitro-inducible germinal center B cell (iGB) culture system and Rosa26Cas9/+ mice. Identified hits in the screen were Mau2 and Nipbl, which are known to contribute to the loop extrusion function of the cohesin complex. Other examples of promising hits were Taf6, Stat3, Ppp6c and Pgs1. We thus provide a new set of genes, which are important for PB development.
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3
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Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nat Genet 2022; 54:1702-1710. [PMID: 36333500 PMCID: PMC9649441 DOI: 10.1038/s41588-022-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
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Affiliation(s)
- Stefan Butz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Nina Schmolka
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D. Karemaker
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rodrigo Villaseñor
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.5252.00000 0004 1936 973XPresent Address: Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Isabel Schwarz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Silvia Domcke
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland ,grid.34477.330000000122986657Present Address: Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Esther C. H. Uijttewaal
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Lienert
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R. Krebs
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.4709.a0000 0004 0495 846XPresent Address: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nathalie P. de Wagenaar
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Johannes Zuber
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. .,Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands.
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Umkehrer C, Holstein F, Formenti L, Jude J, Froussios K, Neumann T, Cronin SM, Haas L, Lipp JJ, Burkard TR, Fellner M, Wiesner T, Zuber J, Obenauf AC. Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters. Nat Biotechnol 2021; 39:174-178. [PMID: 32719478 DOI: 10.1038/s41587-020-0614-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
Abstract
We developed a functional lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise clonal tracing of millions of cells with the ability to retrospectively isolate founding clones alive before and during selection, allowing functional experiments. Using CaTCH, we captured rare clones representing as little as 0.001% of a population and investigated the emergence of resistance to targeted melanoma therapy in vivo.
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Affiliation(s)
- Christian Umkehrer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Felix Holstein
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Laura Formenti
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Kimon Froussios
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Shona M Cronin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Lisa Haas
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jesse J Lipp
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - Thomas R Burkard
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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5
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Umkehrer C, Holstein F, Formenti L, Jude J, Froussios K, Neumann T, Cronin SM, Haas L, Lipp J, Burkard TR, Fellner M, Wiesner T, Zuber J, Obenauf AC. Abstract PO-132: CaTCH - A barcode-guided CRISPRa-inducible reporter to isolate clones from heterogeneous populations. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The emergence of resistant cell clones to targeted therapies poses a significant issue in the treatment of metastatic melanoma. While these founding clones are often extremely rare in a starting population, their isolation and characterization holds unique potential for understanding disease processes, uncovering novel biomarkers and developing therapeutic concepts. The functional characterization of such founder clones and comprehensive comparisons to their post-selection counterparts requires live cells. To achieve this, we developed a novel lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise mapping of the lineage history of millions of cells with the ability to isolate any given clone alive from a complex population based on genetic barcodes. CaTCH thereby enables the retrospective isolation and analysis of founding clones from heterogeneous cell populations prior to evolutionary selection. In first applications, we use CaTCH to provide insights into the development of resistance to targeted cancer therapies. We demonstrate that CaTCH can be used to trace and isolate a single pre-existing therapy-resistant clone from a complex cancer cell population in vitro. Furthermore, we validate the utility of CaTCH for applications in vivo by investigating the origins of resistance to clinically relevant RAF/MEK inhibition in an immunocompetent melanoma mouse model. Here we find that most clones have the capacity to acquire resistance to combined RAF/MEK inhibitor therapy, indicating that resistance to this clinically relevant regimen is a universally achievable state in this model. We envision that CaTCH will address fundamental questions in basic and translational research (e.g., how cell identity states and trajectories are determined in therapy resistance, metastasis formation, tissue development and somatic cell re-programming), potentially revealing new vulnerabilities that can serve as targets for therapies.
Citation Format: Christian Umkehrer, Felix Holstein, Laura Formenti, Julian Jude, Kimon Froussios, Tobias Neumann, Shona M. Cronin, Lisa Haas, Jesse Lipp, Thomas R. Burkard, Michaela Fellner, Thomas Wiesner, Johannes Zuber, Anna C. Obenauf. CaTCH - A barcode-guided CRISPRa-inducible reporter to isolate clones from heterogeneous populations [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-132.
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Affiliation(s)
| | - Felix Holstein
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Laura Formenti
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Julian Jude
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Kimon Froussios
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Tobias Neumann
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Shona M. Cronin
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Lisa Haas
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Jesse Lipp
- 2Boehringer Ingelheim RCV GmbH & Co KG, Austria, Vienna, Austria,
| | | | - Michaela Fellner
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Thomas Wiesner
- 3Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Zuber
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Anna C. Obenauf
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
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Aichinger M, Santoro V, Slavic-Obradovic K, Ruhland S, Wernitznig A, Neudolt A, Schaefer M, Kallenda S, Zach D, Olt S, Salomon C, Rieser S, Weissenboeck M, Ebner F, Schlattl A, De Almeida MT, Langlois R, Sykora M, Reschke M, Zichner T, Gerlach D, Jude J, Fellner M, Scharn D, Kraut N, Moll J, Zuber J, Carotta S, Impagnatiello MA, Tontsch-Grunt U. Abstract 6221: Targeting IAP in cancer: BI 891065 a potent small molecule SMAC mimetic that synergizes with immune checkpoint inhibition. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Engagement of Tumor Necrosis Factor-α (TNF-α) with its receptor can lead to dramatically different cellular outcomes ranging from regulating cell survival and inflammation to induction of programmed forms of cell death. A critical proximal checkpoint determining the nature of TNF-α signaling is put in place by the cellular inhibitor of apoptosis proteins (cIAPs). In the context of cancer therapy these constitute an attractive target as they (1) block the TNF-α induced activation of apoptotic/necroptotic cues and (2) are negatively regulated by a highly selective endogenous ligand (i.e. SMAC), which served as a blueprint for the development of small molecule inhibitors of IAP (so called SMAC mimetics).
Methods: Here we investigated the efficacy of SMAC mimetic BI891065 in enhancing targeted and chemotherapeutic approaches in preclinical mouse cancer models and describe immune-modulatory effects in syngeneic settings. To identify responding indications, a large pan-cancer cell line panel screening comprising 246 cell lines was performed (Eurofins). Proliferation of cells treated with increasing concentrations of BI 891065 combined with a fixed concentration of TNF-α was assessed by high-content screening. Furthermore, to gain a better understanding of the molecular determinants associated with sensitivity to SMAC mimetic treatment, genome-wide CRISPR/Cas9 drug modifier screens were performed.
Results: Here we present key data demonstrating antitumor activity of BI891065 in preclinical models, our efforts towards understanding of genetic determinants of SMAC sensitivity and of potential responsive indications. By using genome-wide CRISPR/Cas9 drug modifier screens we not only demonstrated the feasibility of such unbiased approaches, as we identified many known (e.g. TNF Receptor 1, RIPK1, Caspase 8 and members of the NFκB signaling pathways) - but also potentially novel - regulators of TNF-α/SMAC mimetic induced cell death. In addition, to identify potential responsive indications to BI891065, extensive profiling of in vitro drug sensitivity across a large set of cancer cell types was performed. As a result of this, colorectal cancer (n=56) was identified as a promising indication: 5% of cell lines were found to be sensitive to BI 891065 single treatment. This could be further extended by the exogenous supply of TNF-α to BI 891065, increasing the number of sensitive cells to 21%.
Conclusion: The presented data demonstrate the potential of BI 891065 to facilitate tumor cell death and to enhance anti-tumor immune responses, and nominate the compound as an attractive combination partner in cancer therapy. Our results led to the identification of potentially novel modulators of SMAC mimetic sensitivity via genome-wide CRISPR/Cas9 drug sensitizer screens and suggest colorectal cancer as a promising indication for clinical positioning.
Citation Format: Martin Aichinger, Valeria Santoro, Ksenija Slavic-Obradovic, Stefanie Ruhland, Andreas Wernitznig, Andrea Neudolt, Markus Schaefer, Sabine Kallenda, Daniel Zach, Sabine Olt, Carina Salomon, Sarah Rieser, Martina Weissenboeck, Florian Ebner, Andreas Schlattl, Melanie Talata De Almeida, Rebecca Langlois, Martina Sykora, Markus Reschke, Thomas Zichner, Daniel Gerlach, Julian Jude, Michaela Fellner, Dirk Scharn, Norbert Kraut, Juergen Moll, Johannes Zuber, Sebastian Carotta, Maria Antonietta Impagnatiello, Ulrike Tontsch-Grunt. Targeting IAP in cancer: BI 891065 a potent small molecule SMAC mimetic that synergizes with immune checkpoint inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6221.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sarah Rieser
- 2Research Institute of Molecular Pathology, IMP, Austria
| | | | | | | | | | | | | | | | | | | | - Julian Jude
- 2Research Institute of Molecular Pathology, IMP, Austria
| | | | | | | | | | - Johannes Zuber
- 2Research Institute of Molecular Pathology, IMP, Austria
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7
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Michlits G, Jude J, Hinterndorfer M, de Almeida M, Vainorius G, Hubmann M, Neumann T, Schleiffer A, Burkard TR, Fellner M, Gijsbertsen M, Traunbauer A, Zuber J, Elling U. Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles. Nat Methods 2020; 17:708-716. [PMID: 32514112 DOI: 10.1038/s41592-020-0850-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
CRISPR-Cas9 screens have emerged as a transformative approach to systematically probe gene functions. The quality and success of these screens depends on the frequencies of loss-of-function alleles, particularly in negative-selection screens widely applied for probing essential genes. Using optimized screening workflows, we performed essentialome screens in cancer cell lines and embryonic stem cells and achieved dropout efficiencies that could not be explained by common frameshift frequencies. We find that these superior effect sizes are mainly determined by the impact of in-frame mutations on protein function, which can be predicted based on amino acid composition and conservation. We integrate protein features into a 'Bioscore' and fuse it with improved predictors of single-guide RNA activity and indel formation to establish a score that captures all relevant processes in CRISPR-Cas9 mutagenesis. This Vienna Bioactivity CRISPR score (www.vbc-score.org) outperforms previous prediction tools and enables the selection of sgRNAs that effectively produce loss-of-function alleles.
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Affiliation(s)
- Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Melanie de Almeida
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Rainer Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Max Gijsbertsen
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Anna Traunbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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8
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van der Lelij P, Newman JA, Lieb S, Jude J, Katis V, Hoffmann T, Hinterndorfer M, Bader G, Kraut N, Pearson MA, Peters JM, Zuber J, Gileadi O, Petronczki M. STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers. Life Sci Alliance 2020; 3:e202000725. [PMID: 32467316 PMCID: PMC7266993 DOI: 10.26508/lsa.202000725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/31/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The cohesin subunit STAG2 has emerged as a recurrently inactivated tumor suppressor in human cancers. Using candidate approaches, recent studies have revealed a synthetic lethal interaction between STAG2 and its paralog STAG1 To systematically probe genetic vulnerabilities in the absence of STAG2, we have performed genome-wide CRISPR screens in isogenic cell lines and identified STAG1 as the most prominent and selective dependency of STAG2-deficient cells. Using an inducible degron system, we show that chemical genetic degradation of STAG1 protein results in the loss of sister chromatid cohesion and rapid cell death in STAG2-deficient cells, while sparing STAG2-wild-type cells. Biochemical assays and X-ray crystallography identify STAG1 regions that interact with the RAD21 subunit of the cohesin complex. STAG1 mutations that abrogate this interaction selectively compromise the viability of STAG2-deficient cells. Our work highlights the degradation of STAG1 and inhibition of its interaction with RAD21 as promising therapeutic strategies. These findings lay the groundwork for the development of STAG1-directed small molecules to exploit synthetic lethality in STAG2-mutated tumors.
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Grants
- Wellcome Trust
- 106169/ZZ14/Z Wellcome Trust
- European Research Council
- Human Frontier Science Program
- Wellcome
- Innovative Medicines Initiative (European Union-EU/European Federation of Pharmaceutical Industries and Associations-EFPIA)
- European Community’s Seventh Framework Programme
- Austrian Science Fund, FWF
- AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada
- Janssen, Merck KGaA Darmstadt Germany, MSD, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph A Newman
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Simone Lieb
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Vittorio Katis
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Mark A Pearson
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, VBC, Vienna, Austria
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Mark Petronczki
- Boehringer Ingelheim Regional Center Vienna (RCV) GmbH & Co KG, Vienna, Austria
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9
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Zepeda-Martinez JA, Pribitzer C, Wang J, Bsteh D, Golumbeanu S, Zhao Q, Burkard TR, Reichholf B, Rhie SK, Jude J, Moussa HF, Zuber J, Bell O. Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells. Sci Adv 2020; 6:eaax5692. [PMID: 32270030 PMCID: PMC7112768 DOI: 10.1126/sciadv.aax5692] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/09/2020] [Indexed: 05/29/2023]
Abstract
The transcriptional repressors Polycomb repressive complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyze distinct histone modifications, establishing repressive chromatin at shared targets. How PRC1, which consists of canonical PRC1 (cPRC1) and variant PRC1 (vPRC1) complexes, and PRC2 cooperate to silence genes and support mouse embryonic stem cell (mESC) self-renewal is unclear. Using combinatorial genetic perturbations, we show that independent pathways of cPRC1 and vPRC1 are responsible for maintenance of H2A monoubiquitylation and silencing of shared target genes. Individual loss of PRC2-dependent cPRC1 or PRC2-independent vPRC1 disrupts only one pathway and does not impair mESC self-renewal capacity. However, loss of both pathways leads to mESC differentiation and activation of a subset of lineage-specific genes co-occupied by relatively high levels of PRC1/PRC2. Thus, parallel pathways explain the differential requirements for PRC1 and PRC2 and provide robust silencing of lineage-specific genes.
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Affiliation(s)
- J. A. Zepeda-Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - C. Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - D. Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - S. Golumbeanu
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Q. Zhao
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - T. R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - B. Reichholf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - S. K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J. Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - H. F. Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - O. Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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10
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Schlager S, Salomon C, Olt S, Albrecht C, Ebert A, Bergner O, Wachter J, Trapani F, Gerlach D, Voss T, Traunbauer A, Jude J, Hinterndorfer M, Minnich M, Schweifer N, Blake SM, Zinzalla V, Drobits B, McConnell DB, Kraut N, Pearson M, Zuber J, Koegl M. Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis. Oncotarget 2020; 11:875-890. [PMID: 32180900 PMCID: PMC7061739 DOI: 10.18632/oncotarget.27506] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/08/2020] [Indexed: 02/06/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas worldwide and is characterized by a high diversity of genetic and molecular alterations. Chromosomal translocations and mutations leading to deregulated expression of the transcriptional repressor BCL6 occur in a significant fraction of DLBCL patients. An oncogenic role of BCL6 in the initiation of DLBCL has been shown as the constitutive expression of BCL6 in mice recapitulates the pathogenesis of human DLBCL. However, the role of BCL6 in tumor maintenance remains poorly investigated due to the absence of suitable genetic models and limitations of pharmacological inhibitors. Here, we have utilized tetracycline-inducible CRISPR/Cas9 mutagenesis to study the consequences of BCL6 deletion in established DLBCL models in culture and in vivo. We show that BCL6 knock-out in SU-DHL-4 cells in vitro results in an anti-proliferative response 4–7 days after Cas9 induction that was characterized by cell cycle (G1) arrest. Conditional BCL6 deletion in established DLBCL tumors in vivo induced a significant tumor growth inhibition with initial tumor stasis followed by slow tumor growth kinetics. Our findings support a role of BCL6 in the maintenance of lymphoma growth and showcase the utility of inducible CRISPR/Cas9 systems for probing oncogene addiction.
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Affiliation(s)
| | | | - Sabine Olt
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Anja Ebert
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | | | | | | | - Tilman Voss
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Anna Traunbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Martina Minnich
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Sophia M Blake
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Current address: AstraZeneca AB, Gothenburg, Sweden
| | | | | | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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11
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Skucha A, Ebner J, Schmöllerl J, Roth M, Eder T, César-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Müller AC, Győrffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F. MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. Nat Commun 2018; 9:1983. [PMID: 29777171 PMCID: PMC5959866 DOI: 10.1038/s41467-018-04329-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 10/31/2017] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.
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Affiliation(s)
- Anna Skucha
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Jessica Ebner
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | | | - Mareike Roth
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Thomas Eder
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Sarah Vittori
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Bin Lu
- Cold Spring Harbor Larboratory, Cold Spring Harbor, 11724, NY, USA
| | - Martin Aichinger
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Second Department of Pediatrics, Semmelweis University, Budapest, 1094, Hungary
| | | | - Peter Valent
- Department of Internal Medicine I. Division of Hematology and Hemostaseology, Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, 1090, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria.
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, 1210, Austria.
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12
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Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science 2018; 360:800-805. [PMID: 29622725 PMCID: PMC6409205 DOI: 10.1126/science.aao2793] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [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: 07/05/2017] [Revised: 02/08/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Defining direct targets of transcription factors and regulatory pathways is key to understanding their roles in physiology and disease. We combined SLAM-seq [thiol(SH)-linked alkylation for the metabolic sequencing of RNA], a method for direct quantification of newly synthesized messenger RNAs (mRNAs), with pharmacological and chemical-genetic perturbation in order to define regulatory functions of two transcriptional hubs in cancer, BRD4 and MYC, and to interrogate direct responses to BET bromodomain inhibitors (BETis). We found that BRD4 acts as general coactivator of RNA polymerase II-dependent transcription, which is broadly repressed upon high-dose BETi treatment. At doses triggering selective effects in leukemia, BETis deregulate a small set of hypersensitive targets including MYC. In contrast to BRD4, MYC primarily acts as a selective transcriptional activator controlling metabolic processes such as ribosome biogenesis and de novo purine synthesis. Our study establishes a simple and scalable strategy to identify direct transcriptional targets of any gene or pathway.
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Affiliation(s)
- Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Anja Ebert
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Christian Umkehrer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim-Regional Center Vienna GmbH and Company KG, 1121 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Jesse J Lipp
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria
| | - Brian Reichholf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria
| | - David A Cisneros
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Moritz F Schlapansky
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Pooja Bhat
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Thomas Köcher
- Vienna Biocenter Core Facilities (VBCF), 1030 Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim-Regional Center Vienna GmbH and Company KG, 1121 Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), VBC, 1030 Vienna, Austria.
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
- Medical University of Vienna, VBC, 1030 Vienna, Austria
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13
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van der Lelij P, Lieb S, Jude J, Wutz G, Santos CP, Falkenberg K, Schlattl A, Ban J, Schwentner R, Hoffmann T, Kovar H, Real FX, Waldman T, Pearson MA, Kraut N, Peters JM, Zuber J, Petronczki M. Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts. eLife 2017; 6:e26980. [PMID: 28691904 PMCID: PMC5531830 DOI: 10.7554/elife.26980] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 03/19/2017] [Accepted: 07/03/2017] [Indexed: 11/13/2022] Open
Abstract
Recent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex, STAG2, displays a strong synthetic lethal interaction with its paralog STAG1. Mechanistically, STAG1 loss abrogates sister chromatid cohesion in STAG2 mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 support sister chromatid cohesion to redundantly ensure cell survival. STAG1 represents a vulnerability of cancer cells carrying mutations in the major emerging tumor suppressor STAG2 across different cancer contexts. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.
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Affiliation(s)
- Petra van der Lelij
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Catarina P Santos
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Katrina Falkenberg
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | | | - Jozef Ban
- Children’s Cancer Research Institute, Vienna, Austria
| | | | - Thomas Hoffmann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Heinrich Kovar
- Children’s Cancer Research Institute, Vienna, Austria
- Department for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Francisco X Real
- Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Department de Ciències Experimentals I de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington DC, United States
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
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14
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Lelij PVD, Lieb S, Jude J, Wutz G, Pereira C, Falkenberg K, Ban J, Kovar H, Waldman T, Real F, Pearson M, Kraut N, Peters JM, Zuber J, Petronczki MP. Abstract 3452: The cohesin subunit STAG1 is a hardwired genetic dependency of STAG2 mutant cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent genome analyses have identified recurrent mutations in subunits of the cohesin complex in human cancer. Cohesin is a chromosomal factor that is essential for sister chromatid cohesion and cell division and that contributes to gene regulation and DNA repair. Deleterious mutations in the cohesin subunit STAG2 have been detected in about 20% of bladder cancer, 15% of Ewing sarcoma and 6% of AML/MDS patients. The mechanistic involvement of cohesin mutations in the pathogenesis of human malignancies is currently under active investigation. We hypothesized that the loss of STAG2 could alter the properties and functionalities of the cohesin complex leading to unique vulnerabilities of STAG2 mutant cells. Using CRISPR/Cas9 and RNAi in isogenic solid cancer and leukemic models we identified STAG1, a STAG2 paralog, as a strong and clean genetic vulnerability of STAG2 mutant cells. Mechanistically, STAG1 loss abrogates sister chromatid cohesion specifically in STAG2 mutant but not wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of disease relevant STAG2 mutant but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutant bladder cancer model alleviates the dependence on STAG1. Our results demonstrate that the cohesin subunits STAG1 and STAG2 act redundantly to support sister chromatid cohesion and cell viability in human cells. We have identified STAG1 as a hardwired, context independent vulnerability of STAG2 mutant cancers. Specific synthetic lethalities elicited by recurrent cohesin mutations in human tumors hold the promise for the development of selective therapeutics.
Citation Format: Petra Van Der Lelij, Simone Lieb, Julian Jude, Gordana Wutz, Catarina Pereira, Katrina Falkenberg, Jozef Ban, Heinrich Kovar, Todd Waldman, Francisco Real, Mark Pearson, Norbert Kraut, Jan-Michael Peters, Johannes Zuber, Mark P. Petronczki. The cohesin subunit STAG1 is a hardwired genetic dependency of STAG2 mutant cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3452. doi:10.1158/1538-7445.AM2017-3452
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Affiliation(s)
| | | | - Julian Jude
- 1The Research Institute of Molecular Pathology, Vienna, Austria
| | - Gordana Wutz
- 1The Research Institute of Molecular Pathology, Vienna, Austria
| | | | | | - Jozef Ban
- 4CCRI- Children's Cancer Research Institute, Vienna, Austria
| | - Heinrich Kovar
- 4CCRI- Children's Cancer Research Institute, Vienna, Austria
| | | | - Francisco Real
- 3CNIO: Spanish National Cancer Research Centre, Madrid, Spain
| | | | | | | | - Johannes Zuber
- 1The Research Institute of Molecular Pathology, Vienna, Austria
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15
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Jude J, White CK, Cao G, Botelho D, Jester W, Panettieri R. Salicylic acid and toluene diisocyanate enhance carbachol-induced bronchoconstriction in human precision-cut lung slices (hPCLS). Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature 2016; 528:218-24. [PMID: 26659182 PMCID: PMC4866648 DOI: 10.1038/nature15749] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022]
Abstract
Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNAi screens targeting chromatin factors during transcription factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPSCs). Remarkably, subunits of the chromatin assembly factor-1 (CAF-1) complex emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPSC formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 as a novel regulator of somatic cell identity during transcription factor-induced cell fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.
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Affiliation(s)
- Sihem Cheloufi
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Barbara Hopfgartner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Aimee I Badeaux
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Cheen Euong Ang
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Danielle Tenen
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Daniel J Wesche
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nadezhda Abazova
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Max Hogue
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nilgun Tasdemir
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Justin Brumbaugh
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Andres Blanco
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Daniel Wenzel
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Marietta Zinner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Simon E Vidal
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Scott W Lowe
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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17
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Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryń ŁM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR, Zuber J. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature 2015; 525:543-547. [PMID: 26367798 DOI: 10.1038/nature14898] [Citation(s) in RCA: 378] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 07/07/2015] [Indexed: 12/18/2022]
Abstract
Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukaemia (AML), bromodomain and extra terminal protein (BET) inhibitors are being explored as a promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced haematological malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukaemia, here we perform a chromatin-focused RNAi screen in a sensitive MLL-AF9;Nras(G12D)-driven AML mouse model, and investigate dynamic transcriptional profiles in sensitive and resistant mouse and human leukaemias. Our screen shows that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET inhibitor resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodelling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukaemias regardless of their sensitivity, resistant leukaemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signalling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic chromatin immunoprecipitation sequencing and self-transcribing active regulatory region sequencing of enhancer profiles reveal that BET-resistant states are characterized by remodelled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signalling as a driver and candidate biomarker of primary and acquired BET resistance in leukaemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies.
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Affiliation(s)
- Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Mareike Roth
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Jae-Seok Roe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sumit Deswal
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sabine Cerny-Reiterer
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria
| | - Barbara Peter
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Łukasz M Boryń
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Elin Axelsson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Norbert Schweifer
- Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria
| | | | - Lukas E Dow
- Department of Medicine, Hematology & Medical Oncology, Weill Cornell Medical College, New York 10065, USA
| | - Davide Gianni
- Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim - Regional Center Vienna GmbH, 1121 Vienna, Austria
| | | | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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18
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Liu G, Cimmino L, Jude J, Hu Y, Kartal M, Witkowski M, McKenzie M, Best S, Tuohey L, Mullighan C, Farrar M, Nutt S, Smyth G, Zuber J, Dickins R. PAX5 loss imposes a reversible differentiation block in b-progenitor acute lymphoblastic leukemia. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Goel R, Mohan H, Kabeerdoss J, Jayaseelan V, Jude J, Joseph G, Danda D. SAT0289 Serum Soluble HLA E: A Biomarker of Disease Activity and Coronary Arteritis in Takayasu Arteritis. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2014-eular.4843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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20
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Rodrigues R, Neves J, Silva J, Almeida A, Belo C, Hamalainen T, Lummevaara T, Gratschew S, Jude J, Reddy K. Communication networks. Stud Health Technol Inform 2000; 78:311-28. [PMID: 11151603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Affiliation(s)
- R Rodrigues
- Instituto Superior Técnico, Lisbon, Portugal
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Ghahramani A, Iyengar R, Cunha D, Jude J, Sommer L. Myocardial infarction due to congenital coronary arterial aneurysm (with successful saphenous vein bypass graft). Am J Cardiol 1972; 29:863-7. [PMID: 4537523 DOI: 10.1016/0002-9149(72)90508-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Jude J. Clinical problems of defibrillation. J Assoc Adv Med Instrum 1969; 3:63-4. [PMID: 5293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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23
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24
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Smith PE, Mobin-Uddin K, Lombardo C, Jude J. Infusion of blood into the myocardium. Effect and flow studies. J Surg Res 1967; 7:549-55. [PMID: 6058549 DOI: 10.1016/0022-4804(67)90024-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Mobin-Uddin K, Smith PE, Lombardo C, Jude J. Percutaneous intracardiac pacing through the subclavian vein. J Thorac Cardiovasc Surg 1967; 54:545-8. [PMID: 6051441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Smith PE, Mobin-Uddin K, Lombardo C, Jude J. Metabolic studies of blood infused into the myocardium. J Thorac Cardiovasc Surg 1967; 53:566-71. [PMID: 6022413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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