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Hakami N, Burgstaller A, Gao N, Rutz A, Mann S, Staufer O. Functional Integration of Synthetic Cells into 3D Microfluidic Devices for Artificial Organ-On-Chip Technologies. Adv Healthc Mater 2024; 13:e2303334. [PMID: 38794823 DOI: 10.1002/adhm.202303334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Microfluidics plays a pivotal role in organ-on-chip technologies and in the study of synthetic cells, especially in the development and analysis of artificial cell models. However, approaches that use synthetic cells as integral functional components for microfluidic systems to shape the microenvironment of natural living cells cultured on-chip are not explored. Here, colloidosome-based synthetic cells are integrated into 3D microfluidic devices, pioneering the concept of synthetic cell-based microenvironments for organs-on-chip. Methods are devised to create dense and stable networks of silica colloidosomes, enveloped by supported lipid bilayers, within microfluidic channels. These networks promote receptor-ligand interactions with on-chip cultured cells. Furthermore, a technique is introduced for the controlled release of growth factors from the synthetic cells into the channels, using a calcium alginate-based hydrogel formation within the colloidosomes. To demonstrate the potential of the technology, a modular plug-and-play lymph-node-on-a-chip prototype that guides the expansion of primary human T cells by stimulating receptor ligands on the T cells and modulating their cytokine environment is presented. This integration of synthetic cells into microfluidic systems offers a new direction for organ-on-chip technologies and suggests further avenues for exploration in potential therapeutic applications.
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Affiliation(s)
- Niki Hakami
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Anna Burgstaller
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Ning Gao
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Angela Rutz
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, Bristol, BS8 1TS, UK
| | - Oskar Staufer
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, Bristol, BS8 1TS, UK
- Center for Biophysics, Saarland University, Campus Saarland, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Campus E8 1, 66123, Saarbrücken, Germany
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Tatulian SA. Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy. Phys Chem Chem Phys 2024; 26:21930-21953. [PMID: 39108200 DOI: 10.1039/d4cp01136h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA.
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Lu HJ, Koju N, Sheng R. Mammalian integrated stress responses in stressed organelles and their functions. Acta Pharmacol Sin 2024; 45:1095-1114. [PMID: 38267546 PMCID: PMC11130345 DOI: 10.1038/s41401-023-01225-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
The integrated stress response (ISR) triggered in response to various cellular stress enables mammalian cells to effectively cope with diverse stressful conditions while maintaining their normal functions. Four kinases (PERK, PKR, GCN2, and HRI) of ISR regulate ISR signaling and intracellular protein translation via mediating the phosphorylation of eukaryotic translation initiation factor 2 α (eIF2α) at Ser51. Early ISR creates an opportunity for cells to repair themselves and restore homeostasis. This effect, however, is reversed in the late stages of ISR. Currently, some studies have shown the non-negligible impact of ISR on diseases such as ischemic diseases, cognitive impairment, metabolic syndrome, cancer, vanishing white matter, etc. Hence, artificial regulation of ISR and its signaling with ISR modulators becomes a promising therapeutic strategy for relieving disease symptoms and improving clinical outcomes. Here, we provide an overview of the essential mechanisms of ISR and describe the ISR-related pathways in organelles including mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes. Meanwhile, the regulatory effects of ISR modulators and their potential application in various diseases are also enumerated.
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Affiliation(s)
- Hao-Jun Lu
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123, China
| | - Nirmala Koju
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123, China
| | - Rui Sheng
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences of Soochow University, Suzhou, 215123, China.
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Bothe A, Ban N. A highly optimized human in vitro translation system. CELL REPORTS METHODS 2024; 4:100755. [PMID: 38608690 PMCID: PMC11046033 DOI: 10.1016/j.crmeth.2024.100755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
In vitro translation is an important method for studying fundamental aspects of co- and post-translational gene regulation, as well as for protein expression in the laboratory and on an industrial scale. Here, by re-examining and improving a human in vitro translation system (HITS), we were able to develop a minimal system where only four components are needed to supplement human cell lysates. Functional characterization of our improved HITS revealed the synergistic effect of mRNA capping and polyadenylation. Furthermore, we found that mRNAs are translated with an efficiency equal to or higher than existing state-of-the-art mammalian in vitro translation systems. Lastly, we present an easy preparation procedure for cytoplasmic extracts from cultured HeLa cells, which can be performed in any cell culture laboratory. These methodological advances will allow HITSs to become a widespread tool in basic molecular biology research.
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Affiliation(s)
- Adrian Bothe
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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Karousis ED. The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections. Biochem Soc Trans 2024; 52:481-490. [PMID: 38385526 PMCID: PMC10903449 DOI: 10.1042/bst20231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Non-structural protein 1 (Nsp1) is one of the first proteins produced during coronaviral infections. It plays a pivotal role in hijacking and rendering the host gene expression under the service of the virus. With a focus on SARS-CoV-2, this review presents how Nsp1 selectively inhibits host protein synthesis and induces mRNA degradation of host but not viral mRNAs and blocks nuclear mRNA export. The clinical implications of this protein are highlighted by showcasing the pathogenic role of Nsp1 through the repression of interferon expression pathways and the features of viral variants with mutations in the Nsp1 coding sequence. The ability of SARS-CoV-2 Nsp1 to hinder host immune responses at an early step, the absence of homology to any human proteins, and the availability of structural information render this viral protein an ideal drug target with therapeutic potential.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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Koehler JK, Schmager S, Bender V, Steiner D, Massing U. Preparation of Nanosized Pharmaceutical Formulations by Dual Centrifugation. Pharmaceuticals (Basel) 2023; 16:1519. [PMID: 38004385 PMCID: PMC10675754 DOI: 10.3390/ph16111519] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Dual centrifugation (DC) is an innovative in-vial homogenization and in-vial nanomilling technique that has been in use for the preparation of liposomes for more than one decade. Since then, DC has continuously been developed for preparing various liposomes and other lipid nanoparticles including emulsions and solid lipid nanoparticles (SLNs) as well as polymersomes and nanocrystals. Improvements in equipment technology have been achieved over the past decade, so that DC is now on its way to becoming the quasi-standard for the simple, fast, and aseptic production of lipid nanoparticles and nanocrystals in small and medium batch sizes, including the possibility of simple and fast formulation screening or bedside preparations of therapeutic nanoparticles. More than 68 publications in which DC was used to produce nanoparticles have appeared since then, justifying an initial review of the use of DC for pharmaceutical nanotechnology.
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Affiliation(s)
- Jonas K. Koehler
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.K.K.); (S.S.); (V.B.)
| | - Stefanie Schmager
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.K.K.); (S.S.); (V.B.)
| | - Valentin Bender
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.K.K.); (S.S.); (V.B.)
| | - Denise Steiner
- Department of Pharmaceutical Technology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Institute of Pharmaceutical Technology and Biopharmacy, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Ulrich Massing
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany; (J.K.K.); (S.S.); (V.B.)
- Andreas Hettich GmbH & Co. KG, 78532 Tuttlingen, Germany
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Schubert K, Karousis ED, Ban I, Lapointe CP, Leibundgut M, Bäumlin E, Kummerant E, Scaiola A, Schönhut T, Ziegelmüller J, Puglisi JD, Mühlemann O, Ban N. Universal features of Nsp1-mediated translational shutdown by coronaviruses. Mol Cell 2023; 83:3546-3557.e8. [PMID: 37802027 PMCID: PMC10575594 DOI: 10.1016/j.molcel.2023.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.
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Affiliation(s)
- Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern 3012, Switzerland.
| | - Ivo Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Emilie Bäumlin
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern 3012, Switzerland
| | - Eric Kummerant
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Jana Ziegelmüller
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland.
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