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Su M, Fleischer T, Grosheva I, Horev MB, Olszewska M, Mattioli CC, Barr H, Plotnikov A, Carvalho S, Moskovich Y, Minden MD, Chapal-Ilani N, Wainstein A, Papapetrou EP, Dezorella N, Cheng T, Kaushansky N, Geiger B, Shlush LI. Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure. iScience 2024; 27:109443. [PMID: 38558935 PMCID: PMC10981050 DOI: 10.1016/j.isci.2024.109443] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Spliceosome machinery mutations are common early mutations in myeloid malignancies; however, effective targeted therapies against them are still lacking. In the current study, we used an in vitro high-throughput drug screen among four different isogenic cell lines and identified RKI-1447, a Rho-associated protein kinase inhibitor, as selective cytotoxic effector of SRSF2 mutant cells. RKI-1447 targeted SRSF2 mutated primary human samples in xenografts models. RKI-1447 induced mitotic catastrophe and induced major reorganization of the microtubule system and severe nuclear deformation. Transmission electron microscopy and 3D light microscopy revealed that SRSF2 mutations induce deep nuclear indentation and segmentation that are apparently driven by microtubule-rich cytoplasmic intrusions, which are exacerbated by RKI-1447. The severe nuclear deformation in RKI-1447-treated SRSF2 mutant cells prevents cells from completing mitosis. These findings shed new light on the interplay between microtubules and the nucleus and offers new ways for targeting pre-leukemic SRSF2 mutant cells.
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Affiliation(s)
- Minhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Fleischer
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Grosheva
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Melanie Bokstad Horev
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Malgorzata Olszewska
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Plotnikov
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Carvalho
- Wohl Institute for Drug Discovery, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovich
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON Canada
| | - Noa Chapal-Ilani
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Wainstein
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nili Dezorella
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Nathali Kaushansky
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I. Shlush
- Department of Molecular and Cellular Biology, Weizmann Institute of Science, Rehovot, Israel
- Molecular Hematology Clinic, Maccabi Healthcare, Tel Aviv, Israel
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel
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2
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Ciolli Mattioli C, Avraham R. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria. Methods Mol Biol 2024; 2784:3-23. [PMID: 38502475 DOI: 10.1007/978-1-0716-3766-1_1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this chapter, we describe in detail how to perform a successful smFISH experiment and how to quantify mRNA transcripts in bacterial cells. The flexibility of the method allows for straightforward adaptation to different bacterial species and experimental conditions. Thanks to the feasibility of the approach, the method can easily be adapted by other laboratories. Finally, we believe that this method has a great potential to generate insights into the complicated life of bacteria.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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3
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Ciolli Mattioli C, Eisner K, Rosenbaum A, Wang M, Rivalta A, Amir A, Golding I, Avraham R. Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation. Curr Biol 2023; 33:4880-4892.e14. [PMID: 37879333 PMCID: PMC10843543 DOI: 10.1016/j.cub.2023.09.064] [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: 06/08/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Bacteria undergo cycles of growth and starvation to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. Although high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individual Salmonella cells by using fluorescence in situ hybridization (rRNA-FISH) and measured a dramatic decrease in rRNA numbers only in a subpopulation during nutrient limitation, resulting in a bimodal distribution of cells with high and low rRNA content. During nutritional upshifts, the two subpopulations were associated with distinct phenotypes. Using a transposon screen coupled with rRNA-FISH, we identified two mutants, DksA and RNase I, acting on rRNA transcription shutdown and degradation, which abolished the formation of the subpopulation with low rRNA content. Our work identifies a bacterial mechanism for regulation of ribosomal bimodality that may be beneficial for population survival during starvation.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kfir Eisner
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aviel Rosenbaum
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mengyu Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andre' Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ariel Amir
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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4
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Heyman O, Yehezkel D, Ciolli Mattioli C, Blumberger N, Rosenberg G, Solomon A, Hoffman D, Bossel Ben-Moshe N, Avraham R. Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks. Proc Natl Acad Sci U S A 2023; 120:e2218812120. [PMID: 37399397 PMCID: PMC10334762 DOI: 10.1073/pnas.2218812120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/07/2022] [Accepted: 05/24/2023] [Indexed: 07/05/2023] Open
Abstract
Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA sequencing (scRNA-seq) is increasingly used to study the host factors underlying diverse cellular phenotypes but has limited capacity to analyze the role of bacterial factors. Here, we developed scPAIR-seq, a single-cell approach to analyze infection with a pooled library of multiplex-tagged, barcoded bacterial mutants. Infected host cells and barcodes of intracellular bacterial mutants are both captured by scRNA-seq to functionally analyze mutant-dependent changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We analyzed redundancy between effectors and mutant-specific unique fingerprints and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.
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Affiliation(s)
- Ori Heyman
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Dror Yehezkel
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Neta Blumberger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Gili Rosenberg
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Aryeh Solomon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Dotan Hoffman
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Noa Bossel Ben-Moshe
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
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5
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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6
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Rosenberg G, Yehezkel D, Hoffman D, Mattioli CC, Fremder M, Ben-Arosh H, Vainman L, Nissani N, Hen-Avivi S, Brenner S, Itkin M, Malitsky S, Ohana E, Ben-Moshe NB, Avraham R. Host succinate is an activation signal for
Salmonella
virulence during intracellular infection. Science 2021; 371:400-405. [DOI: 10.1126/science.aba8026] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/06/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dror Yehezkel
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dotan Hoffman
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Moran Fremder
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Hadar Ben-Arosh
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Leia Vainman
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Noa Nissani
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shelly Hen-Avivi
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shirley Brenner
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ehud Ohana
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Noa Bossel Ben-Moshe
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, 7610001 Rehovot, Israel
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7
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Imbastari F, Dahlmann M, Sporbert A, Mattioli CC, Mari T, Scholz F, Timm L, Twamley S, Migotti R, Walther W, Dittmar G, Rehm A, Stein U. MACC1 regulates clathrin-mediated endocytosis and receptor recycling of transferrin receptor and EGFR in colorectal cancer. Cell Mol Life Sci 2021; 78:3525-3542. [PMID: 33469705 PMCID: PMC8038998 DOI: 10.1007/s00018-020-03734-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 02/12/2020] [Revised: 11/16/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Metastasis Associated in Colon Cancer 1 (MACC1) is a novel prognostic, predictive and causal biomarker for tumor progression and metastasis in many cancer types, including colorectal cancer. Besides its clinical value, little is known about its molecular function. Its similarity to SH3BP4, involved in regulating uptake and recycling of transmembrane receptors, suggests a role of MACC1 in endocytosis. By exploring the MACC1 interactome, we identified the clathrin-mediated endocytosis (CME)-associated proteins CLTC, DNM2 and AP-2 as MACC1 binding partners. We unveiled a MACC1-dependent routing of internalized transferrin receptor towards recycling. Elevated MACC1 expression caused also the activation and internalization of EGFR, a higher rate of receptor recycling, as well as earlier and stronger receptor activation and downstream signaling. These effects are limited by deletion of CME-related protein interaction sites in MACC1. Thus, MACC1 regulates CME and receptor recycling, causing increased growth factor-mediated downstream signaling and cell proliferation. This novel mechanism unveils potential therapeutic intervention points restricting MACC1-driven metastasis.
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Affiliation(s)
- Francesca Imbastari
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Mathias Dahlmann
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Anje Sporbert
- Advanced Light Microscopy, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Tommaso Mari
- Proteome Dynamics, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Florian Scholz
- Tumor Immunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Lena Timm
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Shailey Twamley
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | | | - Wolfgang Walther
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Armin Rehm
- Tumor Immunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Ulrike Stein
- Translational Oncology of Solid Tumors, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine Berlin in the Helmholtz-Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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8
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Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M. Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res 2019; 47:2560-2573. [PMID: 30590745 PMCID: PMC6411841 DOI: 10.1093/nar/gky1270] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [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: 09/20/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3′UTRs. Therefore, processes that generate alternative 3′UTRs—alternative splicing and polyadenylation—have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3′UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3′UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3′UTR swapping experiments, we have identified the role of alternative 3′UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3′UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3′UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aviv Rom
- Weizmann Institute of Science, Rehovot, Israel
| | - Vedran Franke
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Gerard Arrey
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mandy Terne
- Developmental Biology / Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Andrew Woehler
- BIMSB Light Microscopy platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Altuna Akalin
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | | | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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9
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Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M. RNA localization is a key determinant of neurite-enriched proteome. Nat Commun 2017; 8:583. [PMID: 28928394 PMCID: PMC5605627 DOI: 10.1038/s41467-017-00690-6] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [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: 02/20/2017] [Accepted: 07/19/2017] [Indexed: 11/09/2022] Open
Abstract
Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes. Protein localization occurs through three mechanisms: protein transport, mRNA localization, and local translation. However, the relative contribution of each process to neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze protein and RNA expression and translation rates in isolated cell bodies and neurites genome-wide. We quantify 7323 proteins and the entire transcriptome, and identify hundreds of neurite-localized proteins and locally translated mRNAs. Our results demonstrate that mRNA localization is the primary mechanism for protein localization in neurites that may account for half of the neurite-localized proteome. Moreover, we identify multiple neurite-targeted non-coding RNAs and RNA-binding proteins with potential regulatory roles. These results provide further insight into the mechanisms underlying the establishment of neuronal polarity. Subcellular localization of RNAs and proteins is important for polarized cells such as neurons. Here the authors differentiate mouse embryonic stem cells into neurons, and analyze the local transcriptome, proteome, and translated transcriptome in their cell bodies and neurites, providing a unique resource for future studies on neuronal polarity.
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Affiliation(s)
- Alessandra Zappulo
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - David van den Bruck
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Vedran Franke
- BIMSB Bioinformatics Platform, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Erik McShane
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | | | - Lorenzo Calviello
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Andrei Filipchyk
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Esteban Peguero-Sanchez
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.,Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP, 62210, Mexico
| | - Thomas Müller
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Andrew Woehler
- BIMSB Light Microscopy Platform, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP, 62210, Mexico
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY, 10003-6688, USA
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Altuna Akalin
- BIMSB Bioinformatics Platform, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Marina Chekulaeva
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.
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10
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Costa DC, Mattioli CC, Silva WS, Takata R, Leme FOP, Oliveira AL, Luz RK. The effect of environmental colour on the growth, metabolism, physiology and skin pigmentation of the carnivorous freshwater catfish Lophiosilurus alexandri. J Fish Biol 2017; 90:922-935. [PMID: 27981570 DOI: 10.1111/jfb.13208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/12/2016] [Indexed: 05/20/2023]
Abstract
The growth, physiology and skin pigmentation of pacamã Lophiosilurus alexandri juveniles were evaluated in an experiment using different tank colours (white, yellow, green, blue, brown and black) over an 80 day period. The tank colours did not cause significant differences to final body mass, total length, survival rate, carcass composition (moisture, crude protein, ash, ether extract, calcium, phosphorus, energy), or to plasma protein, triglyceride and cholesterol values. Haematocrit values, however, were highest for fish kept in white tanks (ANOVA P < 0·05), while the greatest haemoglobin levels were recorded for fish kept in blue and brown tanks (P < 0·01). The concentrations of cortisol (P < 0·001) and glucose (P < 0·01) were the most in fish in the black tanks. Tank colour affected skin pigmentation significantly, with fish in white tanks having the highest values of L* (brightness) and the lowest values in blue and black tanks. L*, however, decreased in all treatments throughout the experiment. C*ab increased significantly over the course of the experiment in fish kept in white tanks. Similar increases of C*ab were recorded in the other treatments but to a lesser extent. The use of black tanks during the cultivation of L. alexandri caused stress and should be avoided. Cultivation in white and yellow tanks produced individuals with a pale skin colour, while cultivation in blue and black tanks resulted in juveniles with a darker and more pigmented skin.
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Affiliation(s)
- D C Costa
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
| | - C C Mattioli
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
| | - W S Silva
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
| | - R Takata
- Fundação Instituto de Pesca do Estado do Rio de Janeiro, Unidade de Pesquisa e Reprodução de Peixes, Av. Presidente Vargas, 197, Parque de Exposições, CEP 28540-000, Brazil
| | - F O P Leme
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
| | - A L Oliveira
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
| | - R K Luz
- Universidade Federal de Minas Gerais, Escola de Veterinária, Avenida Antônio Carlos, n° 6627, CEP 30161-970, Brazil
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11
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Sarmento N, Martins E, Costa DC, Silva WS, Mattioli CC, Luz MR, Luz RK. Effects of supplemental dietary vitamin C on quality of semen from Nile tilapia (Oreochromis niloticus) breeders. Reprod Domest Anim 2016; 52:144-152. [PMID: 27868249 DOI: 10.1111/rda.12870] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 09/17/2016] [Indexed: 12/01/2022]
Abstract
The objective of this study was to evaluate the effects of vitamin C on growth and quality of semen from Oreochromis niloticus breeders. One hundred and sixty males were fed with different levels of vitamin C (0, 261, 599 and 942 mg/kg diet). The higher weight values were recorded for 599 (166 g) and 942 (175 g) mg of vitamin C/kg diet. Sperm motility, vigour and concentration were higher with 599 and 942 mg of vitamin C/kg diet. The semen volume, gonadosomatic index and plasma protein data from the last week showed a direct relationship with increasing levels of vitamin C. No changes were observed in the hepatosomatic index and blood glucose. The haematocrit and erythrocyte showed higher values estimated by equations derived at 850 and 638 mg vitamin C/kg diet, respectively. The leucocytes were inversely proportional to the increasing levels of vitamin C. After 100 days of feeding, animals fed the diet containing 942 mg vitamin C/kg diet had higher sperm motility, linearity, curvilinear velocity, straight line velocity and average path velocity (p < .05). Higher values of beat cross-frequency were observed in broodfish fed diets containing 942 and 599 mg vitamin C/kg. The different vitamin C levels did not cause differences in straightness, lateral head displacement and sperm morphology. For Nile tilapia males on intensive rearing and handling conditions, vitamin C levels between 599 and 942 mg/kg may be used for a better performance and quality of semen.
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Affiliation(s)
- Nlaf Sarmento
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eff Martins
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - D C Costa
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - W S Silva
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - C C Mattioli
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - M R Luz
- Departamento de Clínica e Cirurgia Veterinárias da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - R K Luz
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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12
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Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M. Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution. Nucleic Acids Res 2016; 45:938-950. [PMID: 27604873 PMCID: PMC5314787 DOI: 10.1093/nar/gkw792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 06/16/2016] [Revised: 08/22/2016] [Accepted: 08/28/2016] [Indexed: 12/11/2022] Open
Abstract
Our current knowledge about the mechanisms of miRNA silencing is restricted to few lineages such as vertebrates, arthropods, nematodes and land plants. miRNA-mediated silencing in bilaterian animals is dependent on the proteins of the GW182 family. Here, we dissect the function of GW182 protein in the cnidarian Nematostella, separated by 600 million years from other Metazoa. Using cultured human cells, we show that Nematostella GW182 recruits the CCR4-NOT deadenylation complexes via its tryptophan-containing motifs, thereby inhibiting translation and promoting mRNA decay. Further, similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with Argonaute proteins, and functions downstream to repress mRNA. Thus, our work suggests that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria.
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Affiliation(s)
- Marta Mauri
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Marieluise Kirchner
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - David van den Bruck
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Nadya Gutkovitch
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Matthias Selbach
- Proteome dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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