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Bogacheva MS, Kuivanen S, Potdar S, Hassinen A, Huuskonen S, Pöhner I, Luck TJ, Turunen L, Feodoroff M, Szirovicza L, Savijoki K, Saarela J, Tammela P, Paavolainen L, Poso A, Varjosalo M, Kallioniemi O, Pietiäinen V, Vapalahti O. Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome. Antiviral Res 2024; 223:105813. [PMID: 38272320 DOI: 10.1016/j.antiviral.2024.105813] [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] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and for discovery of therapeutic agents against the virus. Here, we took advantage of drug repurposing to identify if existing drugs could inhibit SARS-CoV-2 infection. We established an open high throughput platform for in vitro screening of drugs against SARS-CoV-2 infection. We screened ∼1000 drugs for their ability to inhibit SARS-CoV-2-induced cell death in the African green monkey kidney cell line (Vero-E6), analyzed how the hit compounds affect the viral N (nucleocapsid) protein expression in human cell lines using high-content microscopic imaging and analysis, determined the hit drug targets in silico, and assessed their ability to cause phospholipidosis, which can interfere with the viral replication. Duvelisib was found by in silico interaction assay as a potential drug targeting virus-host protein interactions. The predicted interaction between PARP1 and S protein, affected by Duvelisib, was further validated by immunoprecipitation. Our results represent a rapidly applicable platform for drug repurposing and evaluation of the new emerging viruses' responses to the drugs. Further in silico studies help us to discover the druggable host pathways involved in the infectious cycle of SARS-CoV-2.
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Affiliation(s)
- Mariia S Bogacheva
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Suvi Kuivanen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sini Huuskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ina Pöhner
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tamara J Luck
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Michaela Feodoroff
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Leonora Szirovicza
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Kirsi Savijoki
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Poso
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Department of Internal Medicine VIII, University Hospital Tubingen, Tubingen, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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2
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Rizzo A, Maresca C, D'Angelo C, Porru M, Di Vito S, Salvati E, Sacconi A, Berardinelli F, Sgura A, Kuznetsov S, Potdar S, Hassinen A, Stoppacciaro A, Zizza P, Biroccio A. Drug repositioning strategy for the identification of novel telomere-damaging agents: A role for NAMPT inhibitors. Aging Cell 2023; 22:e13944. [PMID: 37858982 PMCID: PMC10652301 DOI: 10.1111/acel.13944] [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: 01/13/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/21/2023] Open
Abstract
Drug repositioning strategy represents a valid tool to accelerate the pharmacological development through the identification of new applications for already existing compounds. In this view, we aimed at discovering molecules able to trigger telomere-localized DNA damage and tumor cell death. By applying an automated high-content spinning-disk microscopy, we performed a screening aimed at identifying, on a library of 527 drugs, molecules able to negatively affect the expression of TRF2, a key protein in telomere maintenance. FK866, resulting from the screening as the best candidate hit, was then validated at biochemical and molecular levels and the mechanism underlying its activity in telomere deprotection was elucidated both in vitro and in vivo. The results of this study allow us to discover a novel role of FK866 in promoting, through the production of reactive oxygen species, telomere loss and deprotection, two events leading to an accumulation of DNA damage and tumor cell death. The ability of FK866 to induce telomere damage and apoptosis was also demonstrated in advanced preclinical models evidencing the antitumoral activity of FK866 in triple-negative breast cancer-a particularly aggressive breast cancer subtype still orphan of targeted therapies and characterized by high expression levels of both NAMPT and TRF2. Overall, our findings pave the way to the development of novel anticancer strategies to counteract triple-negative breast cancer, based on the use of telomere deprotecting agents, including NAMPT inhibitors, that would rapidly progress from bench to bedside.
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Affiliation(s)
- Angela Rizzo
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Carmen Maresca
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Carmen D'Angelo
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Manuela Porru
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Serena Di Vito
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Erica Salvati
- Institute of Molecular Biology and PathologyNational Research CouncilRomeItaly
| | - Andrea Sacconi
- IRCCS—Regina Elena National Cancer InstituteClinical Trial Center, Biostatistics and Bioinformatics UnitRomeItaly
| | | | | | - Sergey Kuznetsov
- Institute for Molecular Medicine Finland (FIMM), University of HelsinkiHelsinkiFinland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), University of HelsinkiHelsinkiFinland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), University of HelsinkiHelsinkiFinland
| | - Antonella Stoppacciaro
- Department of Clinical and Molecular Medicine, Sant'Andrea HospitalSapienza University of RomeRomeItaly
| | - Pasquale Zizza
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
| | - Annamaria Biroccio
- IRCCS—Regina Elena National Cancer InstituteTranslational Oncology Research UnitRomeItaly
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3
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Pietiäinen V, Polso M, Migh E, Guckelsberger C, Harmati M, Diosdi A, Turunen L, Hassinen A, Potdar S, Koponen A, Sebestyen EG, Kovacs F, Kriston A, Hollandi R, Burian K, Terhes G, Visnyovszki A, Fodor E, Lacza Z, Kantele A, Kolehmainen P, Kakkola L, Strandin T, Levanov L, Kallioniemi O, Kemeny L, Julkunen I, Vapalahti O, Buzas K, Paavolainen L, Horvath P, Hepojoki J. Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2. Cell Rep Methods 2023; 3:100565. [PMID: 37671026 PMCID: PMC10475844 DOI: 10.1016/j.crmeth.2023.100565] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
We present a miniaturized immunofluorescence assay (mini-IFA) for measuring antibody response in patient blood samples. The method utilizes machine learning-guided image analysis and enables simultaneous measurement of immunoglobulin M (IgM), IgA, and IgG responses against different viral antigens in an automated and high-throughput manner. The assay relies on antigens expressed through transfection, enabling use at a low biosafety level and fast adaptation to emerging pathogens. Using severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the model pathogen, we demonstrate that this method allows differentiation between vaccine-induced and infection-induced antibody responses. Additionally, we established a dedicated web page for quantitative visualization of sample-specific results and their distribution, comparing them with controls and other samples. Our results provide a proof of concept for the approach, demonstrating fast and accurate measurement of antibody responses in a research setup with prospects for clinical diagnostics.
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Affiliation(s)
- Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Minttu Polso
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ede Migh
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Christian Guckelsberger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
- Finnish Center for Artificial Intelligence, Espoo, Finland
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London, UK
| | - Maria Harmati
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Akos Diosdi
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Annika Koponen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Edina Gyukity Sebestyen
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Ferenc Kovacs
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Single-Cell Technologies Ltd., Szeged, Hungary
| | - Andras Kriston
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Single-Cell Technologies Ltd., Szeged, Hungary
| | - Reka Hollandi
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Katalin Burian
- Department of Medical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gabriella Terhes
- Department of Medical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Adam Visnyovszki
- 1 Department of Internal Medicine, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Eszter Fodor
- Department of Sports Physiology, Institute of Sports and Health Sciences, University of Physical Education, Budapest, Hungary
| | - Zsombor Lacza
- Department of Sports Physiology, Institute of Sports and Health Sciences, University of Physical Education, Budapest, Hungary
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | | | - Laura Kakkola
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Lev Levanov
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Lajos Kemeny
- HCEMM-USZ Skin Research Group, Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Ilkka Julkunen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Turku University Hospital, Turku, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Krisztina Buzas
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Department of Immunology, Faculty of Medicine, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Peter Horvath
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
- Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Single-Cell Technologies Ltd., Szeged, Hungary
| | - Jussi Hepojoki
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
- University of Zurich, Vetsuisse Faculty, Institute of Veterinary Pathology, Zürich, Switzerland
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4
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Feodoroff M, Mikkonen P, Turunen L, Hassinen A, Paasonen L, Paavolainen L, Potdar S, Murumägi A, Kallioniemi O, Pietiäinen V. Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT). SLAS Discov 2023:S2472-5552(23)00025-4. [PMID: 36934951 DOI: 10.1016/j.slasd.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 03/21/2023]
Abstract
Central to the success of functional precision medicine of solid tumors is to perform drug testing of patient-derived cancer cells (PDCs) in tumor-mimicking ex vivo conditions. While high throughput (HT) drug screening methods have been well-established for cells cultured in two-dimensional (2D) format, this approach may have limited value in predicting clinical responses. Here, we describe the results of the optimization of drug sensitivity and resistance testing (DSRT) in three-dimensional (3D) growth supporting matrices in a HT mode (3D-DSRT) using the hepatocyte cell line (HepG2) as an example. Supporting matrices included widely used animal-derived Matrigel and cellulose-based hydrogel, GrowDex, which has earlier been shown to support 3D growth of cell lines and stem cells. Further, the sensitivity of ovarian cancer PDCs, from two patients included in the functional precision medicine study, was tested for 52 drugs in 5 different concentrations using 3D-DSRT. Shortly, in the optimized protocol, the PDCs are embedded with matrices and seeded to 384-well plates to allow the formation of the spheroids prior to the addition of drugs in nanoliter volumes with acoustic dispenser. The sensitivity of spheroids to drug treatments is measured with cell viability readout (here, 72 h after addition of drugs). The quality control and data analysis are performed with openly available Breeze software. We show the usability of both matrices in established 3D-DSRT, and report 2D vs 3D growth condition dependent differences in sensitivities of ovarian cancer PDCs to MEK-inhibitors and cytotoxic drugs. This study provides a proof-of-concept for robust and fast screening of drug sensitivities of PDCs in 3D-DSRT, which is important not only for drug discovery but also for personalized ex vivo drug testing in functional precision medicine studies. These findings suggest that comparing results of 2D- and 3D-DSRT is essential for understanding drug mechanisms and for selecting the most effective treatment for the patient.
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Affiliation(s)
- Michaela Feodoroff
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; Laboratory of Immunovirotherapy, Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Uusimaa, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Piia Mikkonen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; UPM-Kymmene Oyj, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | | | - Lassi Paavolainen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland; Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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5
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Wang Z, Mačáková M, Bugai A, Kuznetsov SG, Hassinen A, Lenasi T, Potdar S, Friedel CC, Barborič M. P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway. Nucleic Acids Res 2023; 51:1687-1706. [PMID: 36727434 PMCID: PMC9976905 DOI: 10.1093/nar/gkad001] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Positive transcription elongation factor b (P-TEFb) is the crucial player in RNA polymerase II (Pol II) pause release that has emerged as a promising target in cancer. Because single-agent therapy may fail to deliver durable clinical response, targeting of P-TEFb shall benefit when deployed as a combination therapy. We screened a comprehensive oncology library and identified clinically relevant antimetabolites and Mouse double minute 2 homolog (MDM2) inhibitors as top compounds eliciting p53-dependent death of colorectal cancer cells in synergy with selective inhibitors of P-TEFb. While the targeting of P-TEFb augments apoptosis by anti-metabolite 5-fluorouracil, it switches the fate of cancer cells by the non-genotoxic MDM2 inhibitor Nutlin-3a from cell-cycle arrest to apoptosis. Mechanistically, the fate switching is enabled by the induction of p53-dependent pro-apoptotic genes and repression of P-TEFb-dependent pro-survival genes of the PI3K-AKT signaling cascade, which stimulates caspase 9 and intrinsic apoptosis pathway in BAX/BAK-dependent manner. Finally, combination treatments trigger apoptosis of cancer cell spheroids. Together, co-targeting of P-TEFb and suppressors of intrinsic apoptosis could become a viable strategy to eliminate cancer cells.
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Affiliation(s)
- Zhijia Wang
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Monika Mačáková
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Andrii Bugai
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland.,Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Sergey G Kuznetsov
- High-Throughput Biomedicine Unit (HTB), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Antti Hassinen
- High Content Imaging and Analysis Unit (HCA), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Tina Lenasi
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Swapnil Potdar
- High-Throughput Biomedicine Unit (HTB), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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6
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Liu X, Huuskonen S, Laitinen T, Redchuk T, Bogacheva M, Salokas K, Pöhner I, Öhman T, Tonduru AK, Hassinen A, Gawriyski L, Keskitalo S, Vartiainen MK, Pietiäinen V, Poso A, Varjosalo M. SARS-CoV-2-host proteome interactions for antiviral drug discovery. Mol Syst Biol 2021; 17:e10396. [PMID: 34709727 PMCID: PMC8552907 DOI: 10.15252/msb.202110396] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/20/2022] Open
Abstract
Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great resources for understanding viral replication. However, host proteins that functionally associate with SARS-CoV-2 are localized in the corresponding subnetwork within the comprehensive human interactome. Therefore, constructing a downstream network including all potential viral receptors, host cell proteases, and cofactors is necessary and should be used as an additional criterion for the validation of critical host machineries used for viral processing. This study applied both affinity purification mass spectrometry (AP-MS) and the complementary proximity-based labeling MS method (BioID-MS) on 29 viral ORFs and 18 host proteins with potential roles in viral replication to map the interactions relevant to viral processing. The analysis yields a list of 693 hub proteins sharing interactions with both viral baits and host baits and revealed their biological significance for SARS-CoV-2. Those hub proteins then served as a rational resource for drug repurposing via a virtual screening approach. The overall process resulted in the suggested repurposing of 59 compounds for 15 protein targets. Furthermore, antiviral effects of some candidate drugs were observed in vitro validation using image-based drug screen with infectious SARS-CoV-2. In addition, our results suggest that the antiviral activity of methotrexate could be associated with its inhibitory effect on specific protein-protein interactions.
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Affiliation(s)
- Xiaonan Liu
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Sini Huuskonen
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Tuomo Laitinen
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
| | - Taras Redchuk
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Mariia Bogacheva
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
- Department of VirologyUniversity of HelsinkiHelsinkiFinland
| | - Kari Salokas
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Ina Pöhner
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
| | - Tiina Öhman
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | | | - Antti Hassinen
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Lisa Gawriyski
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Salla Keskitalo
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Maria K Vartiainen
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Vilja Pietiäinen
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Antti Poso
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
- Department of Internal Medicine VIIIUniversity Hospital TübingenTübingenGermany
| | - Markku Varjosalo
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
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7
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Kuisma H, Bramante S, Rajamäki K, Sipilä LJ, Kaasinen E, Kaukomaa J, Palin K, Mäkinen N, Sjöberg J, Sarvilinna N, Taipale J, Kauppi L, Tumiati M, Hassinen A, Pitkäniemi J, Jalkanen J, Heikkinen S, Pasanen A, Heikinheimo O, Bützow R, Välimäki N, Aaltonen LA. Parity associates with chromosomal damage in uterine leiomyomas. Nat Commun 2021; 12:5448. [PMID: 34521855 PMCID: PMC8440576 DOI: 10.1038/s41467-021-25806-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/27/2020] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Mechanical forces in a constrained cellular environment were recently established as a facilitator of chromosomal damage. Whether this could contribute to tumorigenesis is not known. Uterine leiomyomas are common neoplasms that display relatively few chromosomal aberrations. We hypothesized that if mechanical forces contribute to chromosomal damage, signs of this could be seen in uterine leiomyomas from parous women. We examined the karyotypes of 1946 tumors, and found a striking overrepresentation of chromosomal damage associated with parity. We then subjected myometrial cells to physiological forces similar to those encountered during pregnancy, and found this to cause DNA breaks and a DNA repair response. While mechanical forces acting in constrained cellular environments may thus contribute to neoplastic degeneration, and genesis of uterine leiomyoma, further studies are needed to prove possible causality of the observed association. No evidence for progression to malignancy was found.
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Affiliation(s)
- Heli Kuisma
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Simona Bramante
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Lauri J Sipilä
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Eevi Kaasinen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Jaana Kaukomaa
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Netta Mäkinen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Jari Sjöberg
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nanna Sarvilinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Liisa Kauppi
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Manuela Tumiati
- Systems Oncology Research Program, University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- FIMM-HCA, Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Janne Pitkäniemi
- Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Helsinki, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jyrki Jalkanen
- Department of Obstetrics and Gynecology, Central Finland Central Hospital, Jyväskylä, Finland
| | - Sanna Heikkinen
- Institute for Statistical and Epidemiological Cancer Research, Finnish Cancer Registry, Helsinki, Finland
| | - Annukka Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ralf Bützow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics and Applied Tumor Genomics Research Program University of Helsinki, Helsinki, Finland.
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8
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Vangeti S, Strandin T, Liu S, Tauriainen J, Räisänen-Sokolowski A, Cabrera LE, Hassinen A, Mäkelä S, Mustonen J, Vaheri A, Vapalahti O, Klingström J, Smed-Sörensen A. Correction: Monocyte subset redistribution from blood to kidneys in patients with Puumala virus caused hemorrhagic fever with renal syndrome. PLoS Pathog 2021; 17:e1009876. [PMID: 34432861 PMCID: PMC8386823 DOI: 10.1371/journal.ppat.1009876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Kaustio M, Nayebzadeh N, Hinttala R, Tapiainen T, Åström P, Mamia K, Pernaa N, Lehtonen J, Glumoff V, Rahikkala E, Honkila M, Olsén P, Hassinen A, Polso M, Al Sukaiti N, Al Shekaili J, Al Kindi M, Al Hashmi N, Almusa H, Bulanova D, Haapaniemi E, Chen P, Suo-Palosaari M, Vieira P, Tuominen H, Kokkonen H, Al Macki N, Al Habsi H, Löppönen T, Rantala H, Pietiäinen V, Zhang SY, Renko M, Hautala T, Al Farsi T, Uusimaa J, Saarela J. Loss of DIAPH1 causes SCBMS, combined immunodeficiency, and mitochondrial dysfunction. J Allergy Clin Immunol 2021; 148:599-611. [PMID: 33662367 DOI: 10.1016/j.jaci.2020.12.656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/15/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Homozygous loss of DIAPH1 results in seizures, cortical blindness, and microcephaly syndrome (SCBMS). We studied 5 Finnish and 2 Omani patients with loss of DIAPH1 presenting with SCBMS, mitochondrial dysfunction, and immunodeficiency. OBJECTIVE We sought to further characterize phenotypes and disease mechanisms associated with loss of DIAPH1. METHODS Exome sequencing, genotyping and haplotype analysis, B- and T-cell phenotyping, in vitro lymphocyte stimulation assays, analyses of mitochondrial function, immunofluorescence staining for cytoskeletal proteins and mitochondria, and CRISPR-Cas9 DIAPH1 knockout in heathy donor PBMCs were used. RESULTS Genetic analyses found all Finnish patients homozygous for a rare DIAPH1 splice-variant (NM_005219:c.684+1G>A) enriched in the Finnish population, and Omani patients homozygous for a previously described pathogenic DIAPH1 frameshift-variant (NM_005219:c.2769delT;p.F923fs). In addition to microcephaly, epilepsy, and cortical blindness characteristic to SCBMS, the patients presented with infection susceptibility due to defective lymphocyte maturation and 3 patients developed B-cell lymphoma. Patients' immunophenotype was characterized by poor lymphocyte activation and proliferation, defective B-cell maturation, and lack of naive T cells. CRISPR-Cas9 knockout of DIAPH1 in PBMCs from healthy donors replicated the T-cell activation defect. Patient-derived peripheral blood T cells exhibited impaired adhesion and inefficient microtubule-organizing center repositioning to the immunologic synapse. The clinical symptoms and laboratory tests also suggested mitochondrial dysfunction. Experiments with immortalized, patient-derived fibroblasts indicated that DIAPH1 affects the amount of complex IV of the mitochondrial respiratory chain. CONCLUSIONS Our data demonstrate that individuals with SCBMS can have combined immune deficiency and implicate defective cytoskeletal organization and mitochondrial dysfunction in SCBMS pathogenesis.
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Affiliation(s)
- Meri Kaustio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Naemeh Nayebzadeh
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Biocenter Oulu, Oulu, Finland
| | - Reetta Hinttala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Biocenter Oulu, Oulu, Finland
| | - Terhi Tapiainen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Biocenter Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Pirjo Åström
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway
| | - Nora Pernaa
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Johanna Lehtonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway; Folkhälsan Research Center, Helsinki, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Elisa Rahikkala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Minna Honkila
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Päivi Olsén
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Minttu Polso
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nashat Al Sukaiti
- Department of Pediatric Allergy and Clinical Immunology, The Royal Hospital, Muscat, Oman
| | - Jalila Al Shekaili
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Mahmood Al Kindi
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nadia Al Hashmi
- Department of Clinical and Biochemical Genetics, The Royal Hospital, Muscat, Oman
| | - Henrikki Almusa
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Daria Bulanova
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Emma Haapaniemi
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway; Department of Pediatric Research, Oslo University Hospital, Oslo, Norway; Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pu Chen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Suo-Palosaari
- Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Diagnostic Radiology, Oulu University Hospital and University of Oulu, Oulu, Finland; Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Päivi Vieira
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Hannu Tuominen
- Department of Pathology, Oulu University Hospital, Oulu, Finland
| | - Hannaleena Kokkonen
- Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Clinical Genetics, Northern Finland Laboratory Centre, Oulu University Hospital, Oulu, Finland
| | - Nabil Al Macki
- Department of Pediatric Neurology, The Royal Hospital, Muscat, Oman
| | - Huda Al Habsi
- Department of General Pediatrics, The Royal Hospital, Muscat, Oman
| | - Tuija Löppönen
- Department of Pediatrics, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Paris Descartes University, Imagine Institute, Paris, France; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, Paris, France
| | - Marjo Renko
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Department of Pediatrics, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo Hautala
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland; Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Tariq Al Farsi
- Department of Pediatric Allergy and Clinical Immunology, The Royal Hospital, Muscat, Oman
| | - Johanna Uusimaa
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
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10
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Kozlova N, Mennerich D, Samoylenko A, Dimova EY, Koivunen P, Biterova E, Richter K, Hassinen A, Kellokumpu S, Manninen A, Miinalainen I, Glumoff V, Ruddock L, Drobot LB, Kietzmann T. The Pro-Oncogenic Adaptor CIN85 Acts as an Inhibitory Binding Partner of Hypoxia-Inducible Factor Prolyl Hydroxylase 2. Cancer Res 2019; 79:4042-4056. [PMID: 31142511 DOI: 10.1158/0008-5472.can-18-3852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/17/2019] [Accepted: 05/24/2019] [Indexed: 11/16/2022]
Abstract
The EGFR adaptor protein, CIN85, has been shown to promote breast cancer malignancy and hypoxia-inducible factor (HIF) stability. However, the mechanisms underlying cancer promotion remain ill defined. Here we show that CIN85 is a novel binding partner of the main HIF-prolyl hydroxylase, PHD2, but not of PHD1 or PHD3. Mechanistically, the N-terminal SRC homology 3 domains of CIN85 interacted with the proline-arginine-rich region within the N-terminus of PHD2, thereby inhibiting PHD2 activity and HIF degradation. This activity is essential in vivo, as specific loss of the CIN85-PHD2 interaction in CRISPR/Cas9-edited cells affected growth and migration properties, as well as tumor growth in mice. Overall, we discovered a previously unrecognized tumor growth checkpoint that is regulated by CIN85-PHD2 and uncovered an essential survival function in tumor cells by linking growth factor adaptors with hypoxia signaling. SIGNIFICANCE: This study provides unprecedented evidence for an oxygen-independent mechanism of PHD2 regulation that has important implications in cancer cell survival. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/16/4042/F1.large.jpg.
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Affiliation(s)
- Nina Kozlova
- Cancer Center at Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts.,Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anatoly Samoylenko
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.,Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kati Richter
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aki Manninen
- Center for Cell-Matrix Research, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Virpi Glumoff
- The Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Lloyd Ruddock
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lyudmyla Borysivna Drobot
- Laboratory of Cell Signaling, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland. .,Biocenter Oulu, University of Oulu, Oulu, Finland
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11
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Hassinen A, Khoder-Agha F, Khosrowabadi E, Mennerich D, Harrus D, Noel M, Dimova EY, Glumoff T, Harduin-Lepers A, Kietzmann T, Kellokumpu S. A Golgi-associated redox switch regulates catalytic activation and cooperative functioning of ST6Gal-I with B4GalT-I. Redox Biol 2019; 24:101182. [PMID: 30959459 PMCID: PMC6454061 DOI: 10.1016/j.redox.2019.101182] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 02/11/2019] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 01/10/2023] Open
Abstract
Glycosylation, a common modification of cellular proteins and lipids, is often altered in diseases and pathophysiological states such as hypoxia, yet the underlying molecular causes remain poorly understood. By utilizing lectin microarray glycan profiling, Golgi pH and redox screens, we show here that hypoxia inhibits terminal sialylation of N- and O-linked glycans in a HIF- independent manner by lowering Golgi oxidative potential. This redox state change was accompanied by loss of two surface-exposed disulfide bonds in the catalytic domain of the α-2,6-sialyltransferase (ST6Gal-I) and its ability to functionally interact with B4GalT-I, an enzyme adding the preceding galactose to complex N-glycans. Mutagenesis of selected cysteine residues in ST6Gal-I mimicked these effects, and also rendered the enzyme inactive. Cells expressing the inactive mutant, but not those expressing the wild type ST6Gal-I, were able to proliferate and migrate normally, supporting the view that inactivation of the ST6Gal-I help cells to adapt to hypoxic environment. Structure comparisons revealed similar disulfide bonds also in ST3Gal-I, suggesting that this O-glycan and glycolipid modifying sialyltransferase is also sensitive to hypoxia and thereby contribute to attenuated sialylation of O-linked glycans in hypoxic cells. Collectively, these findings unveil a previously unknown redox switch in the Golgi apparatus that is responsible for the catalytic activation and cooperative functioning of ST6Gal-I with B4GalT-I.
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Affiliation(s)
- Antti Hassinen
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Fawzi Khoder-Agha
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Elham Khosrowabadi
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Daniela Mennerich
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Deborah Harrus
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Maxence Noel
- Université de Lille, CNRS, UMR 8576, UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Elitsa Y Dimova
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Tuomo Glumoff
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Anne Harduin-Lepers
- Université de Lille, CNRS, UMR 8576, UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Thomas Kietzmann
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland
| | - Sakari Kellokumpu
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu, Finland.
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12
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Khoder-Agha F, Sosicka P, Escriva Conde M, Hassinen A, Glumoff T, Olczak M, Kellokumpu S. N-acetylglucosaminyltransferases and nucleotide sugar transporters form multi-enzyme-multi-transporter assemblies in golgi membranes in vivo. Cell Mol Life Sci 2019; 76:1821-1832. [PMID: 30737517 PMCID: PMC6453868 DOI: 10.1007/s00018-019-03032-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/07/2019] [Accepted: 01/28/2019] [Indexed: 01/05/2023]
Abstract
Branching and processing of N-glycans in the medial-Golgi rely both on the transport of the donor UDP-N-acetylglucosamine (UDP-GlcNAc) to the Golgi lumen by the SLC35A3 nucleotide sugar transporter (NST) as well as on the addition of the GlcNAc residue to terminal mannoses in nascent N-glycans by several linkage-specific N-acetyl-glucosaminyltransferases (MGAT1-MGAT5). Previous data indicate that the MGATs and NSTs both form higher order assemblies in the Golgi membranes. Here, we investigate their specific and mutual interactions using high-throughput FRET- and BiFC-based interaction screens. We show that MGAT1, MGAT2, MGAT3, MGAT4B (but not MGAT5) and Golgi alpha-mannosidase IIX (MAN2A2) form several distinct molecular assemblies with each other and that the MAN2A2 acts as a central hub for the interactions. Similar assemblies were also detected between the NSTs SLC35A2, SLC35A3, and SLC35A4. Using in vivo BiFC-based FRET interaction screens, we also identified novel ternary complexes between the MGATs themselves or between the MGATs and the NSTs. These findings suggest that the MGATs and the NSTs self-assemble into multi-enzyme/multi-transporter complexes in the Golgi membranes in vivo to facilitate efficient synthesis of complex N-glycans.
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Affiliation(s)
- Fawzi Khoder-Agha
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
| | - Paulina Sosicka
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland.,Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maria Escriva Conde
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland.,Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland.,Institute of Molecular Medicine, Helsinki, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, 90220, Oulu, Finland.
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13
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Kokkonen N, Khosrowabadi E, Hassinen A, Harrus D, Glumoff T, Kietzmann T, Kellokumpu S. Abnormal Golgi pH Homeostasis in Cancer Cells Impairs Apical Targeting of Carcinoembryonic Antigen by Inhibiting Its Glycosyl-Phosphatidylinositol Anchor-Mediated Association with Lipid Rafts. Antioxid Redox Signal 2019; 30:5-21. [PMID: 29304557 PMCID: PMC6276271 DOI: 10.1089/ars.2017.7389] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AIMS Carcinoembryonic antigen (CEACAM5, CEA) is a known tumor marker for colorectal cancer that localizes in a polarized manner to the apical surface in normal colon epithelial cells whereas in cancer cells it is present at both the apical and basolateral surfaces of the cells. Since the Golgi apparatus sorts and transports most proteins to these cell surface domains, we set out here to investigate whether any of the factors commonly associated with tumorigenesis, including hypoxia, generation of reactive oxygen species (ROS), altered redox homeostasis, or an altered Golgi pH, are responsible for mistargeting of CEA to the basolateral surface in cancer cells. RESULTS Using polarized nontumorigenic Madin-Darby canine kidney (MDCK) cells and CaCo-2 colorectal cancer cells as targets, we show that apical delivery of CEA is not affected by hypoxia, ROS, nor changes in the Golgi redox state. Instead, we find that an elevated Golgi pH induces basolateral targeting of CEA and increases its TX-100 solubility, indicating impaired association of CEA with lipid rafts. Moreover, disruption of lipid rafts by methyl-β-cyclodextrin induced accumulation of the CEA protein at the basolateral surface in MDCK cells. Experiments with the glycosylphosphatidylinositol (GPI)-anchorless CEA mutant and CEA-specific GPI-anchored enhanced green fluorescent protein (EGFP-GPI) fusion protein revealed that the GPI-anchor was critical for the pH-dependent apical delivery of the CEA in MDCK cells. Innovation and Conclusion: The findings indicate that an abnormal Golgi pH homeostasis in cancer cells is an important factor that causes mistargeting of CEA to the basolateral surface of cancer cells via inhibiting its GPI-anchor-mediated association with lipid rafts.
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Affiliation(s)
- Nina Kokkonen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Elham Khosrowabadi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Deborah Harrus
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Address correspondence to: Dr. Sakari Kellokumpu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu FI-90014, Finland
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14
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Harrus D, Khoder-Agha F, Peltoniemi M, Hassinen A, Ruddock L, Kellokumpu S, Glumoff T. The dimeric structure of wild-type human glycosyltransferase B4GalT1. PLoS One 2018; 13:e0205571. [PMID: 30352055 PMCID: PMC6198961 DOI: 10.1371/journal.pone.0205571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 05/24/2018] [Accepted: 09/27/2018] [Indexed: 11/26/2022] Open
Abstract
Most glycosyltransferases, including B4GalT1 (EC 2.4.1.38), are known to assemble into enzyme homomers and functionally relevant heteromers in vivo. However, it remains unclear why and how these enzymes interact at the molecular/atomic level. Here, we solved the crystal structure of the wild-type human B4GalT1 homodimer. We also show that B4GalT1 exists in a dynamic equilibrium between monomer and dimer, since a purified monomer reappears as a mixture of both and as we obtained crystal forms of the monomer and dimer assemblies in the same crystallization conditions. These two crystal forms revealed the unliganded B4GalT1 in both the open and the closed conformation of the Trp loop and the lid regions, responsible for donor and acceptor substrate binding, respectively. The present structures also show the lid region in full in an open conformation, as well as a new conformation for the GlcNAc acceptor loop (residues 272–288). The physiological relevance of the homodimer in the crystal was validated by targeted mutagenesis studies coupled with FRET assays. These showed that changing key catalytic amino acids impaired homomer formation in vivo. The wild-type human B4GalT1 structure also explains why the variant proteins used for crystallization in earlier studies failed to reveal the homodimers described in this study.
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Affiliation(s)
- Deborah Harrus
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Fawzi Khoder-Agha
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Miika Peltoniemi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Lloyd Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland
- * E-mail:
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15
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Tykesson E, Hassinen A, Zielinska K, Thelin MA, Frati G, Ellervik U, Westergren-Thorsson G, Malmström A, Kellokumpu S, Maccarana M. Dermatan sulfate epimerase 1 and dermatan 4- O-sulfotransferase 1 form complexes that generate long epimerized 4- O-sulfated blocks. J Biol Chem 2018; 293:13725-13735. [PMID: 29976758 DOI: 10.1074/jbc.ra118.003875] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/11/2018] [Indexed: 01/14/2023] Open
Abstract
During the biosynthesis of chondroitin/dermatan sulfate (CS/DS), a variable fraction of glucuronic acid is converted to iduronic acid through the activities of two epimerases, dermatan sulfate epimerases 1 (DS-epi1) and 2 (DS-epi2). Previous in vitro studies indicated that without association with other enzymes, DS-epi1 activity produces structures that have only a few adjacent iduronic acid units. In vivo, concomitant with epimerization, dermatan 4-O-sulfotransferase 1 (D4ST1) sulfates the GalNAc adjacent to iduronic acid. This sulfation facilitates DS-epi1 activity and enables the formation of long blocks of sulfated iduronic acid-containing domains, which can be major components of CS/DS. In this report, we used recombinant enzymes to confirm the concerted action of DS-epi1 and D4ST1. Confocal microscopy revealed that these two enzymes colocalize to the Golgi, and FRET experiments indicated that they physically interact. Furthermore, FRET, immunoprecipitation, and cross-linking experiments also revealed that DS-epi1, DS-epi2, and D4ST1 form homomers and are all part of a hetero-oligomeric complex where D4ST1 directly interacts with DS-epi1, but not with DS-epi2. The cooperation of DS-epi1 with D4ST1 may therefore explain the processive mode of the formation of iduronic acid blocks. In conclusion, the iduronic acid-forming enzymes operate in complexes, similar to other enzymes active in glycosaminoglycan biosynthesis. This knowledge shed light on regulatory mechanisms controlling the biosynthesis of the structurally diverse CS/DS molecule.
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Affiliation(s)
- Emil Tykesson
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland, and
| | - Katarzyna Zielinska
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden
| | - Martin A Thelin
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden
| | - Giacomo Frati
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden
| | - Ulf Ellervik
- Department of Chemistry, Lund University, SE-221 00, Lund, Sweden
| | | | - Anders Malmström
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland
| | - Marco Maccarana
- From the Department of Experimental Medical Science, Lund University, SE-221 00, Lund, Sweden,
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16
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Benedetti E, Pučić-Baković M, Keser T, Wahl A, Hassinen A, Yang JY, Liu L, Trbojević-Akmačić I, Razdorov G, Štambuk J, Klarić L, Ugrina I, Selman MHJ, Wuhrer M, Rudan I, Polasek O, Hayward C, Grallert H, Strauch K, Peters A, Meitinger T, Gieger C, Vilaj M, Boons GJ, Moremen KW, Ovchinnikova T, Bovin N, Kellokumpu S, Theis FJ, Lauc G, Krumsiek J. Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway. Nat Commun 2017; 8:1483. [PMID: 29133956 PMCID: PMC5684356 DOI: 10.1038/s41467-017-01525-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 09/25/2016] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Immunoglobulin G (IgG) is a major effector molecule of the human immune response, and aberrations in IgG glycosylation are linked to various diseases. However, the molecular mechanisms underlying protein glycosylation are still poorly understood. We present a data-driven approach to infer reactions in the IgG glycosylation pathway using large-scale mass-spectrometry measurements. Gaussian graphical models are used to construct association networks from four cohorts. We find that glycan pairs with high partial correlations represent enzymatic reactions in the known glycosylation pathway, and then predict new biochemical reactions using a rule-based approach. Validation is performed using data from a GWAS and results from three in vitro experiments. We show that one predicted reaction is enzymatically feasible and that one rejected reaction does not occur in vitro. Moreover, in contrast to previous knowledge, enzymes involved in our predictions colocalize in the Golgi of two cell lines, further confirming the in silico predictions.
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Affiliation(s)
- Elisa Benedetti
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Annika Wahl
- Institute of Epidemiology 2, Research Unit Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology 2, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | | | | | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Lucija Klarić
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Ivo Ugrina
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
- Faculty of Science, University of Split, 21000 Split, Croatia
- Intellomics Ltd., 10000 Zagreb, Croatia
| | | | - Manfred Wuhrer
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, EH8 9AG Edinburgh, UK
| | - Ozren Polasek
- University of Split School of Medicine, 21000 Split, Croatia
- Gen-info Ltd., 10000 Zagreb, Croatia
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Harald Grallert
- Institute of Epidemiology 2, Research Unit Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology 2, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 40225 Düsseldorf, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians Universität, 81577 Munich, Germany
| | - Annette Peters
- Institute of Epidemiology 2, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Christian Gieger
- Institute of Epidemiology 2, Research Unit Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology 2, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Marija Vilaj
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Tatiana Ovchinnikova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nicolai Bovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Mathematics, Technical University Munich, 85748 Garching bei München, Germany
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 40225 Düsseldorf, Germany
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17
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Halonen N, Kilpijärvi J, Sobocinski M, Datta-Chaudhuri T, Hassinen A, Prakash SB, Möller P, Abshire P, Kellokumpu S, Lloyd Spetz A. Low temperature co-fired ceramic packaging of CMOS capacitive sensor chip towards cell viability monitoring. Beilstein J Nanotechnol 2016; 7:1871-1877. [PMID: 28144536 PMCID: PMC5238666 DOI: 10.3762/bjnano.7.179] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/10/2016] [Indexed: 05/26/2023]
Abstract
Cell viability monitoring is an important part of biosafety evaluation for the detection of toxic effects on cells caused by nanomaterials, preferably by label-free, noninvasive, fast, and cost effective methods. These requirements can be met by monitoring cell viability with a capacitance-sensing integrated circuit (IC) microchip. The capacitance provides a measurement of the surface attachment of adherent cells as an indication of their health status. However, the moist, warm, and corrosive biological environment requires reliable packaging of the sensor chip. In this work, a second generation of low temperature co-fired ceramic (LTCC) technology was combined with flip-chip bonding to provide a durable package compatible with cell culture. The LTCC-packaged sensor chip was integrated with a printed circuit board, data acquisition device, and measurement-controlling software. The packaged sensor chip functioned well in the presence of cell medium and cells, with output voltages depending on the medium above the capacitors. Moreover, the manufacturing of microfluidic channels in the LTCC package was demonstrated.
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Affiliation(s)
- Niina Halonen
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, P.O.Box 4500, FI-90014 University of Oulu, Finland
| | - Joni Kilpijärvi
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, P.O.Box 4500, FI-90014 University of Oulu, Finland
| | - Maciej Sobocinski
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, P.O.Box 4500, FI-90014 University of Oulu, Finland
| | - Timir Datta-Chaudhuri
- Department of Electrical & Computer Engineering and the Institute for Systems Research, University of Maryland, College Park, MD 20742, USA
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014 University of Oulu, Finland
| | - Someshekar B Prakash
- Department of Electrical & Computer Engineering and the Institute for Systems Research, University of Maryland, College Park, MD 20742, USA
- Advanced Design Organization, Intel Corporation, Hillsboro, USA
| | - Peter Möller
- Division of Applied Sensor Science, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
| | - Pamela Abshire
- Department of Electrical & Computer Engineering and the Institute for Systems Research, University of Maryland, College Park, MD 20742, USA
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014 University of Oulu, Finland
| | - Anita Lloyd Spetz
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, P.O.Box 4500, FI-90014 University of Oulu, Finland
- Division of Applied Sensor Science, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
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18
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Deen AJ, Arasu UT, Pasonen-Seppänen S, Hassinen A, Takabe P, Wojciechowski S, Kärnä R, Rilla K, Kellokumpu S, Tammi R, Tammi M, Oikari S. UDP-sugar substrates of HAS3 regulate its O-GlcNAcylation, intracellular traffic, extracellular shedding and correlate with melanoma progression. Cell Mol Life Sci 2016; 73:3183-204. [PMID: 26883802 DOI: 10.1007/s00018-016-2158-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/25/2016] [Accepted: 02/04/2016] [Indexed: 01/06/2023]
Abstract
Hyaluronan content is a powerful prognostic factor in many cancer types, but the molecular basis of its synthesis in cancer still remains unclear. Hyaluronan synthesis requires the transport of hyaluronan synthases (HAS1-3) from Golgi to plasma membrane (PM), where the enzymes are activated. For the very first time, the present study demonstrated a rapid recycling of HAS3 between PM and endosomes, controlled by the cytosolic levels of the HAS substrates UDP-GlcUA and UDP-GlcNAc. Depletion of UDP-GlcNAc or UDP-GlcUA shifted the balance towards HAS3 endocytosis, and inhibition of hyaluronan synthesis. In contrast, UDP-GlcNAc surplus suppressed endocytosis and lysosomal decay of HAS3, favoring its retention in PM, stimulating hyaluronan synthesis, and HAS3 shedding in extracellular vesicles. The concentration of UDP-GlcNAc also controlled the level of O-GlcNAc modification of HAS3. Increasing O-GlcNAcylation reproduced the effects of UDP-GlcNAc surplus on HAS3 trafficking, while its suppression showed the opposite effects, indicating that O-GlcNAc signaling is associated to UDP-GlcNAc supply. Importantly, a similar correlation existed between the expression of GFAT1 (the rate limiting enzyme in UDP-GlcNAc synthesis) and hyaluronan content in early and deep human melanomas, suggesting the association of UDP-sugar metabolism in initiation of melanomagenesis. In general, changes in glucose metabolism, realized through UDP-sugar contents and O-GlcNAc signaling, are important in HAS3 trafficking, hyaluronan synthesis, and correlates with melanoma progression.
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Affiliation(s)
- Ashik Jawahar Deen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland.
| | - Uma Thanigai Arasu
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Sanna Pasonen-Seppänen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014, Oulu, Finland
| | - Piia Takabe
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Sara Wojciechowski
- A. I. Virtanen Institute for Molecular Sciences, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Riikka Kärnä
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Kirsi Rilla
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014, Oulu, Finland
| | - Raija Tammi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Markku Tammi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Sanna Oikari
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland.
- Institute of Dentistry, School of Medicine, University of Eastern Finland, 70210, Kuopio, Finland.
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19
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Kellokumpu S, Hassinen A, Glumoff T. Glycosyltransferase complexes in eukaryotes: long-known, prevalent but still unrecognized. Cell Mol Life Sci 2015; 73:305-25. [PMID: 26474840 PMCID: PMC7079781 DOI: 10.1007/s00018-015-2066-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 06/09/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 01/08/2023]
Abstract
Glycosylation is the most common and complex cellular modification of proteins and lipids. It is critical for multicellular life and its abrogation often leads to a devastating disease. Yet, the underlying mechanistic details of glycosylation in both health and disease remain unclear. Partly, this is due to the complexity and dynamicity of glycan modifications, and the fact that not all the players are taken into account. Since late 1960s, a vast number of studies have demonstrated that glycosyltransferases typically form homomeric and heteromeric complexes with each other in yeast, plant and animal cells. To propagate their acceptance, we will summarize here accumulated data for their prevalence and potential functional importance for glycosylation focusing mainly on their mutual interactions, the protein domains mediating these interactions, and enzymatic activity changes that occur upon complex formation. Finally, we will highlight the few existing 3D structures of these enzyme complexes to pinpoint their individual nature and to emphasize that their lack is the main obstacle for more detailed understanding of how these enzyme complexes interact and function in a eukaryotic cell.
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Affiliation(s)
- Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220, Oulu, Finland.
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220, Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220, Oulu, Finland
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20
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Huang HH, Hassinen A, Sundaram S, Spiess AN, Kellokumpu S, Stanley P. GnT1IP-L specifically inhibits MGAT1 in the Golgi via its luminal domain. eLife 2015; 4. [PMID: 26371870 PMCID: PMC4572887 DOI: 10.7554/elife.08916] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 05/21/2015] [Accepted: 08/12/2015] [Indexed: 12/15/2022] Open
Abstract
Mouse GnT1IP-L, and membrane-bound GnT1IP-S (MGAT4D) expressed in cultured cells
inhibit MGAT1, the N-acetylglucosaminyltransferase that initiates the synthesis of
hybrid and complex N-glycans. However, it is not known where in the secretory pathway
GnT1IP-L inhibits MGAT1, nor whether GnT1IP-L inhibits other N-glycan branching
N-acetylglucosaminyltransferases of the medial Golgi. We show here that the luminal
domain of GnT1IP-L contains its inhibitory activity. Retention of GnT1IP-L in the
endoplasmic reticulum (ER) via the N-terminal region of human invariant chain p33,
with or without C-terminal KDEL, markedly reduced inhibitory activity. Dynamic
fluorescent resonance energy transfer (FRET) and bimolecular fluorescence
complementation (BiFC) assays revealed homomeric interactions for GnT1IP-L in the ER,
and heteromeric interactions with MGAT1 in the Golgi. GnT1IP-L did not generate a
FRET signal with MGAT2, MGAT3, MGAT4B or MGAT5 medial Golgi GlcNAc-tranferases.
GnT1IP/Mgat4d transcripts are expressed predominantly in
spermatocytes and spermatids in mouse, and are reduced in men with impaired
spermatogenesis. DOI:http://dx.doi.org/10.7554/eLife.08916.001 Proteins are made up of chains of amino acids that fold into three-dimensional shapes
and many are assembled in a cell compartment known as the endoplasmic reticulum. From
here, these new proteins move to another compartment called the Golgi, where they may
be further modified before they are transported to their final destination in the
cell. One way that proteins may be modified is known as glycosylation, in which sugar
molecules are attached to specific amino acids. Some sugar molecules can act as
labels that ensure the new proteins are transported to the correct destination in the
cell. For proteins that are delivered to the surface of the cell, the sugar molecules
can also play important roles in communication with other cells. A simple sugar molecule, or a complex arrangement of many sugar molecules, may be
attached to an amino acid by glycosylation. An enzyme called MGAT1 controls the
synthesis of sugars called complex N-glycans in the Golgi. In 2010, researchers
reported that a glycoprotein called GnT1IP-L binds to MGAT1 and inhibits its
activity, thereby blocking the production of complex N-glycans. GnT1IP-L was found in
the endoplasmic reticulum and Golgi, but it was not clear how it inhibits MGAT1. Huang et al.—including some of the researchers from the 2010 study—have
now investigated the activity of GnT1IP-L in cells grown in the laboratory using
several biochemical techniques. The experiments show that GnT1IP-L only binds to
MGAT1 when both proteins are in the Golgi. There are three sections (or
‘domains’) in GnT1IP-L, but Huang et al. found that only the domain
that is on the inside of the Golgi is involved in this interaction. Previous work indicated that GnT1IP-L may be involved in the formation of sperm in
mice. Huang et al. have now analyzed previously published data on samples of testis
tissue from human patients and found that the gene that encodes GnT1IP-L is present
in very low amounts in patients whose sperm do not develop properly. Huang et al.'s findings suggest that GnT1IP-L may inhibit MGAT1 to control the
glycosylation of proteins in the Golgi of developing sperm. The next step is to test
this hypothesis by generating mutant mice that lack GnT1IP-L, or to make GnT1P-L in
other cells in which it is not normally made, to find out if this affects the
production of sperm. DOI:http://dx.doi.org/10.7554/eLife.08916.002
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Affiliation(s)
- Hung-Hsiang Huang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, United States
| | - Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Subha Sundaram
- Department of Cell Biology, Albert Einstein College of Medicine, New York, United States
| | | | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, United States
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21
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Bart G, Vico NO, Hassinen A, Pujol FM, Deen AJ, Ruusala A, Tammi RH, Squire A, Heldin P, Kellokumpu S, Tammi MI. Fluorescence resonance energy transfer (FRET) and proximity ligation assays reveal functionally relevant homo- and heteromeric complexes among hyaluronan synthases HAS1, HAS2, and HAS3. J Biol Chem 2015; 290:11479-90. [PMID: 25795779 DOI: 10.1074/jbc.m115.640581] [Citation(s) in RCA: 27] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Indexed: 01/04/2023] Open
Abstract
In vertebrates, hyaluronan is produced in the plasma membrane from cytosolic UDP-sugar substrates by hyaluronan synthase 1-3 (HAS1-3) isoenzymes that transfer N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcUA) in alternative positions in the growing polysaccharide chain during its simultaneous extrusion into the extracellular space. It has been shown that HAS2 immunoprecipitates contain functional HAS2 homomers and also heteromers with HAS3 (Karousou, E., Kamiryo, M., Skandalis, S. S., Ruusala, A., Asteriou, T., Passi, A., Yamashita, H., Hellman, U., Heldin, C. H., and Heldin, P. (2010) The activity of hyaluronan synthase 2 is regulated by dimerization and ubiquitination. J. Biol. Chem. 285, 23647-23654). Here we have systematically screened in live cells, potential interactions among the HAS isoenzymes using fluorescence resonance energy transfer (FRET) and flow cytometric quantification. We show that all HAS isoenzymes form homomeric and also heteromeric complexes with each other. The same complexes were detected both in Golgi apparatus and plasma membrane by using FRET microscopy and the acceptor photobleaching method. Proximity ligation assays with HAS antibodies confirmed the presence of HAS1-HAS2, HAS2-HAS2, and HAS2-HAS3 complexes between endogenously expressed HASs. C-terminal deletions revealed that the enzymes interact mainly via uncharacterized N-terminal 86-amino acid domain(s), but additional binding site(s) probably exist in their C-terminal parts. Of all the homomeric complexes HAS1 had the lowest and HAS3 the highest synthetic activity. Interestingly, HAS1 transfection reduced the synthesis of hyaluronan obtained by HAS2 and HAS3, suggesting functional cooperation between the isoenzymes. These data indicate a general tendency of HAS isoenzymes to form both homomeric and heteromeric complexes with potentially important functional consequences on hyaluronan synthesis.
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Affiliation(s)
- Geneviève Bart
- From the Institute of Biomedicine/Anatomy, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Nuria Ortega Vico
- the Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Antti Hassinen
- the Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Francois M Pujol
- the Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Ashik Jawahar Deen
- From the Institute of Biomedicine/Anatomy, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Aino Ruusala
- the Ludwig Institute for Cancer Research, Uppsala University, SE-75124, Uppsala, Sweden, and
| | - Raija H Tammi
- From the Institute of Biomedicine/Anatomy, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Anthony Squire
- the Institute for Experimental Immunology and Imaging, University Clinic Essen, 45147 Essen, Germany
| | - Paraskevi Heldin
- the Ludwig Institute for Cancer Research, Uppsala University, SE-75124, Uppsala, Sweden, and
| | - Sakari Kellokumpu
- the Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Markku I Tammi
- From the Institute of Biomedicine/Anatomy, University of Eastern Finland, FI-70211 Kuopio, Finland,
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22
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Hartmann-Fatu C, Trusch F, Moll CN, Michin I, Hassinen A, Kellokumpu S, Bayer P. Heterodimers of Tyrosylprotein Sulfotransferases Suggest Existence of a Higher Organization Level of Transferases in the Membrane of the trans-Golgi Apparatus. J Mol Biol 2015; 427:1404-1412. [DOI: 10.1016/j.jmb.2015.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/22/2015] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
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23
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Hassinen A, Kellokumpu S. Organizational interplay of Golgi N-glycosyltransferases involves organelle microenvironment-dependent transitions between enzyme homo- and heteromers. J Biol Chem 2014; 289:26937-26948. [PMID: 25135644 DOI: 10.1074/jbc.m114.595058] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glycosylation of proteins and lipids takes place in the Golgi apparatus by the consecutive actions of functionally distinct glycosidases and glycosyltransferases. Current evidence indicates that they function as enzyme homomers and/or heteromers in the living cell. Here we investigate their organizational interplay and show that glycosyltransferase homomers are assembled in the endoplasmic reticulum. Upon transport to the Golgi, the majority of homomers are disassembled to allow the formation of enzyme heteromers between sequentially acting medial-Golgi enzymes GnT-I and GnT-II or trans-Golgi enzymes GalT-I and ST6Gal-I. This transition is driven by the acidic Golgi environment, as it was markedly inhibited by raising Golgi luminal pH with chloroquine. Our FRAP (fluorescence recovery after photobleaching) measurements showed that the complexes remain mobile Golgi membrane constituents that can relocate to the endoplasmic reticulum or to the scattered Golgi mini-stacks upon brefeldin A or nocodazole treatment, respectively. During this relocation, heteromers undergo a reverse transition back to enzyme homomers. These data unveil an unprecedented organizational interplay between Golgi N-glycosyltransferases that involves dynamic and organelle microenvironment-driven transitions between enzyme homomers and heteromers during their trafficking within the early secretory compartments.
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Affiliation(s)
- Antti Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland.
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24
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Hassinen A, Moreels I, De Nolf K, Smet PF, Martins JC, Hens Z. Short-Chain Alcohols Strip X-Type Ligands and Quench the Luminescence of PbSe and CdSe Quantum Dots, Acetonitrile Does Not. J Am Chem Soc 2012. [DOI: 10.1021/ja308861d] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Antti Hassinen
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
| | - Iwan Moreels
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
| | - Kim De Nolf
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
| | - Philippe F. Smet
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
| | - José C. Martins
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
| | - Zeger Hens
- Physics
and Chemistry of Nanostructures, ‡Center for Nano and Biophotonics, §Lumilab, and ∥NMR and Structure
Analysis, Ghent University, Belgium
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25
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Rainò G, Moreels I, Hassinen A, Stöferle T, Hens Z, Mahrt RF. Exciton dynamics within the band-edge manifold states: the onset of an acoustic phonon bottleneck. Nano Lett 2012; 12:5224-5229. [PMID: 23016932 DOI: 10.1021/nl302390b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Exciton dynamics within the band-edge state manifold of CdSe/ZnS and CdSe/CdS quantum dots (QDs) have been investigated. Low-temperature time-resolved photoluminescence (PL) experiments demonstrate that exciton relaxation is mediated by LO phonons, whereas an acoustic phonon bottleneck is observed for splitting energies lower than the optical phonon energy. This has important implications since the main source affecting exciton dephasing is considered to be a spin-flip process. Our results concur with recent observations of long exciton dephasing times in CdSe/CdS QDs and show a way to engineer nanoparticles with enhanced coherence time, a prerequisite for their use in quantum optical applications.
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Affiliation(s)
- Gabriele Rainò
- IBM Research -Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland.
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26
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Abstract
Most organelles within the exocytic and endocytic pathways typically acidify their interiors, a phenomenon that is known to be crucial for their optimal functioning in eukaryotic cells. This review highlights recent advances in our understanding of how Golgi acidity is maintained and regulated, and how its misregulation contributes to organelle dysfunction and disease. Both its biosynthetic products (glycans) and protein-sorting events are highly sensitive to changes in Golgi luminal pH and are affected in certain human disease states such as cancers and cutis laxa. Other potential disease states that are caused by, or are associated with, Golgi pH misregulation will also be discussed.
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Affiliation(s)
- Antti Rivinoja
- Department of Biochemistry, University of Oulu, Oulu, Finland
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27
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Hassinen A, Pujol FM, Kokkonen N, Pieters C, Kihlström M, Korhonen K, Kellokumpu S. Functional organization of Golgi N- and O-glycosylation pathways involves pH-dependent complex formation that is impaired in cancer cells. J Biol Chem 2011; 286:38329-38340. [PMID: 21911486 DOI: 10.1074/jbc.m111.277681] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glycosylation is one of the most common modifications of proteins and lipids and also a major source of biological diversity in eukaryotes. It is critical for many basic cellular functions and recognition events that range from protein folding to cell signaling, immunological defense, and the development of multicellular organisms. Glycosylation takes place mainly in the endoplasmic reticulum and Golgi apparatus and involves dozens of functionally distinct glycosidases and glycosyltransferases. How the functions of these enzymes, which act sequentially and often competitively, are coordinated to faithfully synthesize a vast array of different glycan structures is currently unclear. Here, we investigate the supramolecular organization of the Golgi N- and O-glycosylation pathways in live cells using a FRET flow cytometric quantification approach. We show that the enzymes form enzymatically active homo- and/or heteromeric complexes within each pathway. However, no complexes composed of enzymes that operate in different pathways, were detected, which suggests that the pathways are physically distinct. In addition, we show that complex formation is mediated almost exclusively by the catalytic domains of the interacting enzymes. Our data also suggest that the heteromeric complexes are functionally more important than enzyme homomers. Heteromeric complex formation was found to be dependent on Golgi acidity, markedly impaired in acidification-defective cancer cells, and required for the efficient synthesis of cell surface glycans. Collectively, the results emphasize that the Golgi glycosylation pathways are functionally organized into complexes that are important for glycan synthesis.
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Affiliation(s)
- Antti Hassinen
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Francois M Pujol
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Nina Kokkonen
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Caroline Pieters
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Minna Kihlström
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Kati Korhonen
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland
| | - Sakari Kellokumpu
- Department of Biochemistry and the Finnish Glycoscience Graduate School, University of Oulu, FIN-90014 Oulu, Finland.
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28
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Hassinen A, Rivinoja A, Kauppila A, Kellokumpu S. Golgi N-glycosyltransferases form both homo- and heterodimeric enzyme complexes in live cells. J Biol Chem 2010; 285:17771-7. [PMID: 20378551 DOI: 10.1074/jbc.m110.103184] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycans (i.e. oligosaccharide chains attached to cellular proteins and lipids) are crucial for nearly all aspects of life, including the development of multicellular organisms. They come in multiple forms, and much of this diversity between molecules, cells, and tissues is generated by Golgi-resident glycosidases and glycosyltransferases. However, their exact mode of functioning in glycan processing is currently unclear. Here we investigate the supramolecular organization of the N-glycosylation pathway in live cells by utilizing the bimolecular fluorescence complementation approach. We show that all four N-glycosylation enzymes tested (beta-1,2-N-acetylglucosaminyltransferase I, beta-1,2-N-acetylglucosaminyltransferase II, 1,4-galactosyltransferase I, and alpha-2,6-sialyltransferase I) form Golgi-localized homodimers. Intriguingly, the same enzymes also formed two distinct and functionally relevant heterodimers between the medial Golgi enzymes beta-1,2-N-acetylglucosaminyltransferase I and beta-1,2-N-acetylglucosaminyltransferase II and the trans-Golgi enzymes 1,4-galactosyltransferase I and alpha-2,6-sialyltransferase I. Given their strict Golgi localization and sequential order of function, the two heterodimeric complexes are probably responsible for the processing and maturation of N-glycans in live cells.
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Affiliation(s)
- Antti Hassinen
- Department of Biochemistry, University of Oulu and the Glycoscience Graduate School Finland, PO Box 3000, Linnanmaa, FIN-90014 Oulu, Finland
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29
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Rivinoja A, Hassinen A, Kokkonen N, Kauppila A, Kellokumpu S. Elevated Golgi pH impairs terminal N-glycosylation by inducing mislocalization of Golgi glycosyltransferases. J Cell Physiol 2009; 220:144-54. [PMID: 19277980 DOI: 10.1002/jcp.21744] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Acidic pH of the Golgi lumen is known to be crucial for correct glycosylation, transport and sorting of proteins and lipids during their transit through the organelle. To better understand why Golgi acidity is important for these processes, we have examined here the most pH sensitive events in N-glycosylation by sequentially raising Golgi luminal pH with chloroquine (CQ), a weak base. We show that only a 0.2 pH unit increase (20 microM CQ) is sufficient to markedly impair terminal alpha(2,3)-sialylation of an N-glycosylated reporter protein (CEA), and to induce selective mislocalization of the corresponding alpha(2,3)-sialyltransferase (ST3) into the endosomal compartments. Much higher pH increase was required to impair alpha(2,6)-sialylation, or the proximal glycosylation steps such as beta(1,4)-galactosylation or acquisition of Endo H resistance, and the steady-state localization of the key enzymes responsible for these modifications (ST6, GalT I, MANII). The overall Golgi morphology also remained unaltered, except when Golgi pH was raised close to neutral. By using transmembrane domain chimeras between the ST6 and ST3, we also show that the luminal domain of the ST6 is mainly responsible for its less pH sensitive localization in the Golgi. Collectively, these results emphasize that moderate Golgi pH alterations such as those detected in cancer cells can impair N-glycosylation by inducing selective mislocalization of only certain Golgi glycosyltransferases.
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Affiliation(s)
- Antti Rivinoja
- Department of Biochemistry and The Finnish Glycoscience Graduate School, University of Oulu, Oulu, Finland
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30
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Bhaumik P, Schmitz W, Hassinen A, Hiltunen JK, Conzelmann E, Wierenga RK. The catalysis of the 1,1-proton transfer by alpha-methyl-acyl-CoA racemase is coupled to a movement of the fatty acyl moiety over a hydrophobic, methionine-rich surface. J Mol Biol 2007; 367:1145-61. [PMID: 17320106 DOI: 10.1016/j.jmb.2007.01.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [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: 10/16/2006] [Revised: 01/23/2007] [Accepted: 01/24/2007] [Indexed: 10/23/2022]
Abstract
Alpha-methylacyl-CoA racemases are essential enzymes for branched-chain fatty acid metabolism. Their reaction mechanism and the structural basis of their wide substrate specificity are poorly understood. High-resolution crystal structures of Mycobacterium tuberculosis alpha-methylacyl-CoA racemase (MCR) complexed with substrate molecules show the active site geometry required for catalysis of the interconversion of (2S) and (2R)-methylacyl-CoA. The thioester oxygen atom and the 2-methyl group are in a cis-conformation with respect to each other. The thioester oxygen atom fits into an oxyanion hole and the 2-methyl group points into a hydrophobic pocket. The active site geometry agrees with a 1,1-proton transfer mechanism in which the acid/base-pair residues are His126 and Asp156. The structures of the complexes indicate that the acyl chains of the S-substrate and the R-substrate bind in an S-pocket and an R-pocket, respectively. A unique feature of MCR is a large number of methionine residues in the acyl binding region, located between the S-pocket and the R-pocket. It appears that the (S) to (R) interconversion of the 2-methylacyl chiral center is coupled to a movement of the acyl group over this hydrophobic, methionine-rich surface, when moving from its S-pocket to its R-pocket, whereas the 2-methyl moiety and the CoA group remain fixed in their respective pockets.
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Affiliation(s)
- Prasenjit Bhaumik
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Linnanmaa, P.O. Box 3000, FIN-90014 University of Oulu, Finland
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31
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Miglietta F, Hoosbeek MR, Foot J, Gigon F, Hassinen A, Heijmans M, Peressotti A, Saarinen T, Van Breemen N, Wallén B. Spatial and temporal performance of the miniface (free air CO2 enrichment) system on Bog Ecosystems in northern and Central Europe. Environ Monit Assess 2001; 66:107-127. [PMID: 11214346 DOI: 10.1023/a:1026495830251] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Bog Ecosystem Research Initiative (BERI) project was initiated to investigate, at five climatically different sites across Europe, the effects of elevated CO2 and N deposition on the net exchange of CO2 and CH4 between bogs and the atmosphere, and to study the effects of elevated CO2 and N deposition on the plant biodiversity of bog communities. A major challenge to investigate the effects of elevated CO2 on vegetation and ecosystems is to apply elevated CO2 concentrations to growing vegetation without changing the physical conditions like climate and radiation. Most available CO2 enrichment methods disturb the natural conditions to some degree, for instance closed chambers or open top chambers. Free Air CO2 Enrichment (FACE) systems have proven to be suitable to expose plants to elevated CO2 concentrations with minimal disturbance of their natural environment. The size and spatial scale of the vegetation studied within the BERI project allowed the use of a modified version of a small FACE system called MiniFACE. This paper describes the BERI MiniFACE design as well as its temporal and spatial performance at the five BERI field locations. The temporal performance of the MiniFACE system largely met the quality criteria defined by the FACE Protocol. One minute average CO2 concentrations measured at the centre of the ring stayed within 20% of the pre-set target for more than 95% of the time. Increased wind speeds were found to improve the MiniFACE system's temporal performance. Spatial analyses showed no apparent CO2 gradients across a ring during a 4 day period and the mean differences between each sampling point and the centre of the ring did not exceed 10%. Observations made during a windy day, causing a CO2 concentration gradient, and observations made during a calm day indicated that short term gradients tend to average out over longer periods of time. On a day with unidirectional strong winds, CO2 concentrations at the upwind side of the ring centre were higher than those made at the centre and at the downwind side of the ring centre, but the bell-shaped distribution was found basically the same for the centre and the four surrounding measurement points, implying that the short term (1 sec) variability of CO2 concentrations across the MiniFACE ring is almost the same at any point in the ring. Based on gas dispersion simulations and measured CO2 concentration profiles, the possible interference between CO2-enriched and control rings was found to be negligible beyond a centre-to-centre ring distance of 6 m.
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Affiliation(s)
- F Miglietta
- IATA-CNR, Institute of Agrometeorology and Environmental Analysis, National Research Council, P. le delle Cascine 18, 50144 Firenze, Italy
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