1
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Gonzalez-de-Miguel J, Montero-Blay A, Ciampi L, Rodriguez-Arce I, Serrano L. Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris. Microb Cell Fact 2024; 23:124. [PMID: 38689251 PMCID: PMC11059754 DOI: 10.1186/s12934-024-02392-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial genus offers a set of relevant properties that make it an interesting chassis for such purposes, the main one being the absence of a cell wall. However, due to their slow growth, they have rarely been considered as a potential platform in this respect. This notion may be challenged with the recent discovery of Mycoplasma feriruminatoris, a species with a dividing time close to that of common microbial workhorses. So far, no tools for heterologous protein expression nor secretion have been described for it. RESULTS The work presented here develops the fast-dividing M. feriruminatoris as a tool for secreting functional biomolecules of therapeutic interest that could be used for screening functional mutants as well as potentially for protein-protein interactions. Based on RNAseq, quantitative proteomics and promoter sequence comparison we have rationally designed optimal promoter sequences. Then, using in silico analysis, we have identified putative secretion signals that we validated using a luminescent reporter. The potential of the resulting secretion cassette has been shown with set of active clinically relevant proteins (interleukins and nanobodies). CONCLUSIONS We have engineered Mycoplasma feriruminatoris for producing and secreting functional proteins of medical interest.
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Affiliation(s)
- Javier Gonzalez-de-Miguel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Orikine Bio, Dr Aiguader 88, Barcelona, 08003, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
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2
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Broto A, Piñero-Lambea C, Segura-Morales C, Tio-Gillen AP, Unger WWJ, Burgos R, Mazzolini R, Miravet-Verde S, Jacobs BC, Casas J, Huizinga R, Lluch-Senar M, Serrano L. Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome. Microbes Infect 2024:105342. [PMID: 38679229 DOI: 10.1016/j.micinf.2024.105342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 03/08/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
A non-pathogenic Mycoplasma pneumoniae-based chassis is leading the development of live biotherapeutics (LBPs) for respiratory diseases. However, reports connecting Guillain-Barré syndrome (GBS) cases to prior M. pneumoniae infections represent a concern for exploiting such a chassis. Galactolipids, especially galactocerebroside (GalCer), are considered the most likely M. pneumoniae antigens triggering autoimmune responses associated with GBS development. In this work, we generated different strains lacking genes involved in galactolipids biosynthesis. Glycolipid profiling of the strains demonstrated that some mutants show a complete lack of galactolipids. Cross-reactivity assays with sera from GBS patients with prior M. pneumoniae infection showed that certain engineered strains exhibit reduced antibody recognition. However, correlation analyses of these results with the glycolipid profile of the engineered strains suggest that other factors different from GalCer contribute to sera recognition, including total ceramide levels, dihexosylceramide (DHCer), and diglycosyldiacylglycerol (DGDAG). Finally, we discuss the best candidate strains as potential GBS-free Mycoplasma chassis.
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Affiliation(s)
- Alicia Broto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Pulmobiotics ltd, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Carolina Segura-Morales
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anne P Tio-Gillen
- Department of Immunology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands; Department of Neurology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Wendy W J Unger
- Department of Pediatrics, Laboratory of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Centre, Rotterdam, The Netherlands
| | - Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rocco Mazzolini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Pulmobiotics ltd, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Bart C Jacobs
- Department of Immunology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands; Department of Neurology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | | | - Ruth Huizinga
- Department of Immunology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Pulmobiotics ltd, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, 08002, Spain; ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain.
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3
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Superti-Furga G, Agostinho M, Bury J, Cook S, Durinx C, Ender A, van Luenen H, Lund AH, Medema RH, Miączyńska M, Nickel D, Pelicci PG, Puisieux A, Ripatti S, Sander M, Schubeler D, Serrano L, Sommer T, Sonne-Hansen K, Tomančák P, Vives J, Vontas J, Bettencourt-Dias M. EU-LIFE charter of independent life science research institutes. FEBS Lett 2024; 598:719-724. [PMID: 38514456 DOI: 10.1002/1873-3468.14855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
The diverse range of organizations contributing to the global research ecosystem is believed to enhance the overall quality and resilience of its output. Mid-sized autonomous research institutes, distinct from universities, play a crucial role in this landscape. They often lead the way in new research fields and experimental methods, including those in social and organizational domains, which are vital for driving innovation. The EU-LIFE alliance was established with the goal of fostering excellence by developing and disseminating best practices among European biomedical research institutes. As directors of the 15 EU-LIFE institutes, we have spent a decade comparing and refining our processes. Now, we are eager to share the insights we've gained. To this end, we have crafted this Charter, outlining 10 principles we deem essential for research institutes to flourish and achieve ground-breaking discoveries. These principles, detailed in the Charter, encompass excellence, independence, training, internationality and inclusivity, mission focus, technological advancement, administrative innovation, cooperation, societal impact, and public engagement. Our aim is to inspire the establishment of new institutes that adhere to these principles and to raise awareness about their significance. We are convinced that they should be viewed a crucial component of any national and international innovation strategies.
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Affiliation(s)
- Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Marta Agostinho
- EU-LIFE, Alliance of Independent Research Institutes in the Life Sciences Across Europe, Barcelona, Spain
| | - Jo Bury
- VIB Flanders Institute for Biotechnology, Ghent, Belgium
| | | | | | - Anita Ender
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Anders H Lund
- The University of Copenhagen Biotech Research & Innovation Centre, Denmark
| | - René H Medema
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marta Miączyńska
- International Institute of Molecular and Cell biology, Warsaw, Poland
| | | | | | | | | | - Maike Sander
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Dirk Schubeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Thomas Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Pavel Tomančák
- Central European Institute of Technology, Brno, Czech Republic
| | - Joan Vives
- Center for Genomic Regulation, Barcelona, Spain
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Heraklion, Greece
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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5
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Orlando G, Serrano L, Schymkowitz J, Rousseau F. Integrating physics in deep learning algorithms: a force field as a PyTorch module. Bioinformatics 2024; 40:btae160. [PMID: 38514422 PMCID: PMC11007235 DOI: 10.1093/bioinformatics/btae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/08/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
MOTIVATION Deep learning algorithms applied to structural biology often struggle to converge to meaningful solutions when limited data is available, since they are required to learn complex physical rules from examples. State-of-the-art force-fields, however, cannot interface with deep learning algorithms due to their implementation. RESULTS We present MadraX, a forcefield implemented as a differentiable PyTorch module, able to interact with deep learning algorithms in an end-to-end fashion. AVAILABILITY AND IMPLEMENTATION MadraX documentation, together with tutorials and installation guide, is available at madrax.readthedocs.io.
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Affiliation(s)
- Gabriele Orlando
- Switch Laboratory, VIB Center for Brain and Disease Research, VIB, Leuven 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
- Switch Laboratory, VIB Center for AI & Computational Biology, VIB, Leuven 3000, Belgium
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- IC REA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, VIB, Leuven 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
- Switch Laboratory, VIB Center for AI & Computational Biology, VIB, Leuven 3000, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, VIB, Leuven 3000, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
- Switch Laboratory, VIB Center for AI & Computational Biology, VIB, Leuven 3000, Belgium
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6
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Miravet-Verde S, Mazzolini R, Segura-Morales C, Broto A, Lluch-Senar M, Serrano L. ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs. Nat Commun 2024; 15:2091. [PMID: 38453908 PMCID: PMC10920889 DOI: 10.1038/s41467-024-46112-2] [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: 11/18/2022] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.
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Affiliation(s)
- Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
| | | | - Carolina Segura-Morales
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Alicia Broto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Maria Lluch-Senar
- Pulmobiotics, Dr Aiguader 88, 08003, Barcelona, Spain.
- Institute of Biotechnology and Biomedicine "Vicent Villar Palasi" (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
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7
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Montero-Blay A, Blanco JD, Rodriguez-Arce I, Lastrucci C, Piñero-Lambea C, Lluch-Senar M, Serrano L. Author Correction: Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation. Mol Syst Biol 2024; 20:291-292. [PMID: 38351407 PMCID: PMC10912753 DOI: 10.1038/s44320-023-00008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Javier Delgado Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Claire Lastrucci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, 08002, Spain.
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain.
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8
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Ramirez Marquez E, Santiago A, Torres AG, Colon Y, Velez R, Serrano L, Campbell J, Rodriguez Rosa R. Bilateral Inferior Rectus Schwannoma and Strabismus: A Case Report. Cureus 2024; 16:e55582. [PMID: 38576694 PMCID: PMC10994566 DOI: 10.7759/cureus.55582] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
Schwannomas, also known as neurilemomas, are peripheral nerve sheath neoplasms. They can be sporadic or associated with genetic syndromes including neurofibromatosis type 2 (NF2). Schwannomas may lead to symptoms by exerting pressure on nearby structures, such as nerve and muscle fibers. In this study, we present the case of a 22-year-old female with a history of NF2 who, upon examination, presented with a visibly enlarged salmon-colored mass involving the left inferior rectus that she had since the age of 12 years. Ocular examinations revealed a small left hypertropia and exotropia in all gazes. Magnetic resonance imaging confirmed bilateral involvement of the inferior rectus muscles. She had a partial excisional biopsy of the mass involving the left inferior rectus muscle that confirmed the presence of schwannoma. This case highlights the importance of comprehensive evaluation of sensory and motor functions as well as considering orbital schwannomas in cases of strabismus, especially within the context of neurofibromatosis.
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Affiliation(s)
| | - Alejandra Santiago
- Ophthalmology, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Angel G Torres
- Ophthalmology, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Yannina Colon
- Pathology and Laboratory Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Roman Velez
- Pathology and Laboratory Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Luis Serrano
- Neuro-Ophthalmology, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Joseph Campbell
- Ophthalmology, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
| | - Ricardo Rodriguez Rosa
- Pediatric Ophthalmology, University of Puerto Rico, Medical Sciences Campus, San Juan, USA
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9
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Contreras E, Jurado-Ezqueta M, Pimentel R, Serrano L, Hidalgo C, Jiménez A, Polo MJ. Assessment of seasonal and annual patterns in phosphorus content in a monitored catchment through a partitioning approach based on hydrometeorological data. Environ Res 2024; 242:117501. [PMID: 37996003 DOI: 10.1016/j.envres.2023.117501] [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] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
High amounts of phosphorus (P) in rivers come mainly from two sources: fertilizers washed off from agricultural and urban areas by runoff water (non-point sources) and urban and industrial development which are translated in P discharges from wastewater treatment plants (WWTP). This work analyses the content of P in water for nearly 40 years inquiring into the origin of the sources, based on the hypothesis of runoff generation from the detection of river streamflow increases during the P contribution episode and the previous precipitation. For this purpose, the Guadaira River, which is located in the South of Spain and has a drainage surface of 1524 km2, was selected. In this watershed agricultural land use converges with numerous human activities resulting in high pressures on water quality. We found 40% of the P contribution episodes found seem to come from the runoff generated after the heaviest rainfall events, which normally occur between November and May. The remaining 60% of the P contribution episodes were found to be linked to point sources, which become more relevant from June to September, reaching the highest concentration values (6-17 mg/L). The results highlight that the target phosphate concentration value of 0.34 mg PO4/L imposed by the national legislation for a good state following the Water Framework Directive 2000/60/EC is exceeded by 96% of the measurements during the period from 1981 to 2022. On a monthly basis, PO4 loads showed a linear relationship with river streamflow (R2 = 0.94). However, on field measurements scale, a potential relationship between both variables was found, which changed according to the improvement in the wastewater treatment and facilities for 1982-1994, 1995-2017 and 2018-2022. In these three periods, different significant decreasing trends of the P content were found, mainly marked by the setup of each individual WWTP.
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Affiliation(s)
- E Contreras
- Fluvial Dynamics and Hydrology Research Group, Andalusian Institute for Earth System Research, University of Cordoba, Cordoba, Spain.
| | - M Jurado-Ezqueta
- Fluvial Dynamics and Hydrology Research Group, Andalusian Institute for Earth System Research, University of Cordoba, Cordoba, Spain.
| | - R Pimentel
- Fluvial Dynamics and Hydrology Research Group, Andalusian Institute for Earth System Research, University of Cordoba, Cordoba, Spain.
| | - L Serrano
- Plant Biology and Ecology Department, Faculty of Biology, University of Seville, Seville, Spain.
| | - C Hidalgo
- Physical, Chemical and Natural Systems Department, Pablo de Olavide University, Seville, Spain.
| | - A Jiménez
- Physical, Chemical and Natural Systems Department, Pablo de Olavide University, Seville, Spain.
| | - M J Polo
- Fluvial Dynamics and Hydrology Research Group, Andalusian Institute for Earth System Research, University of Cordoba, Cordoba, Spain.
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10
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Pascual‐Reguant L, Serra‐Camprubí Q, Datta D, Cianferoni D, Kourtis S, Gañez‐Zapater A, Cannatá C, Espinar L, Querol J, García‐López L, Musa‐Afaneh S, Guirola M, Gkanogiannis A, Miró Canturri A, Guzman M, Rodríguez O, Herencia‐Ropero A, Arribas J, Serra V, Serrano L, Tian TV, Peiró S, Sdelci S. Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. EMBO Mol Med 2023; 15:e18459. [PMID: 37937685 PMCID: PMC10701626 DOI: 10.15252/emmm.202318459] [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: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Triple-negative breast cancer (TNBC) often develops resistance to single-agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B-MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co-inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4-MED1 colocalization, and the transcription of cell cycle genes, thus suppressing TNBC cell proliferation. Targeting the interaction between BRD4S and LOXL2 could be a starting point for the development of new anticancer strategies for the treatment of TNBC.
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Affiliation(s)
- Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Debayan Datta
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez‐Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Cannatá
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Lorena Espinar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Laura García‐López
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sara Musa‐Afaneh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Guirola
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Anestis Gkanogiannis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andrea Miró Canturri
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Marta Guzman
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Olga Rodríguez
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Joaquin Arribas
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de CáncerMonforte de LemosMadridSpain
- Department of Biochemistry and Molecular BiologyUniversitat Autónoma de BarcelonaBellaterraSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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11
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Pirozzi A, Rincón E, Espinosa E, Donsì F, Serrano L. Nanostructured Cellulose-Based Aerogels: Influence of Chemical/Mechanical Cascade Processes on Quality Index for Benchmarking Dye Pollutant Adsorbents in Wastewater Treatment. Gels 2023; 9:958. [PMID: 38131944 PMCID: PMC10742814 DOI: 10.3390/gels9120958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
(1) Background: Nanostructured cellulose has emerged as an efficient bio-adsorbent aerogel material, offering biocompatibility and renewable sourcing advantages. This study focuses on isolating (ligno)cellulose nanofibers ((L)CNFs) from barley straw and producing aerogels to develop sustainable and highly efficient decontamination systems. (2) Methods: (Ligno)cellulose pulp has been isolated from barley straw through a pulping process, and was subsequently deconstructed into nanofibers employing various pre-treatment methods (TEMPO-mediated oxidation process or PFI beater mechanical treatment) followed by the high-pressure homogenization (HPH) process. (3) Results: The aerogels made by (L)CNFs, with a higher crystallinity degree, larger aspect ratio, lower shrinkage rate, and higher Young's modulus than cellulose aerogels, successfully adsorb and remove organic dye pollutants from wastewater. (L)CNF-based aerogels, with a quality index (determined using four characterization parameters) above 70%, exhibited outstanding contaminant removal capacity over 80%. The high specific surface area of nanocellulose isolated using the TEMPO oxidation process significantly enhanced the affinity and interactions between hydroxyl and carboxyl groups of nanofibers and cationic groups of contaminants. The efficacy in adsorbing cationic dyes in wastewater onto the aerogels was verified by the Langmuir adsorption isotherm model. (4) Conclusions: This study offers insights into designing and applying advanced (L)CNF-based aerogels as efficient wastewater decontamination and environmental remediation platforms.
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Affiliation(s)
- Annachiara Pirozzi
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Esther Rincón
- BioPrEn Group (RNM 940), Chemical Engineering Department, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Faculty of Science, Universidad de Córdoba, 14014 Córdoba, Spain; (E.R.); (E.E.)
| | - Eduardo Espinosa
- BioPrEn Group (RNM 940), Chemical Engineering Department, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Faculty of Science, Universidad de Córdoba, 14014 Córdoba, Spain; (E.R.); (E.E.)
| | - Francesco Donsì
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Luis Serrano
- BioPrEn Group (RNM 940), Chemical Engineering Department, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Faculty of Science, Universidad de Córdoba, 14014 Córdoba, Spain; (E.R.); (E.E.)
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12
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Weber M, Sogues A, Yus E, Burgos R, Gallo C, Martínez S, Lluch‐Senar M, Serrano L. Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium. Mol Syst Biol 2023; 19:e11301. [PMID: 37642167 PMCID: PMC10568206 DOI: 10.15252/msb.202211301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Adrià Sogues
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martínez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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13
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Najle SR, Grau-Bové X, Elek A, Navarrete C, Cianferoni D, Chiva C, Cañas-Armenteros D, Mallabiabarrena A, Kamm K, Sabidó E, Gruber-Vodicka H, Schierwater B, Serrano L, Sebé-Pedrós A. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 2023; 186:4676-4693.e29. [PMID: 37729907 PMCID: PMC10580291 DOI: 10.1016/j.cell.2023.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 02/16/2023] [Revised: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
The assembly of the neuronal and other major cell type programs occurred early in animal evolution. We can reconstruct this process by studying non-bilaterians like placozoans. These small disc-shaped animals not only have nine morphologically described cell types and no neurons but also show coordinated behaviors triggered by peptide-secreting cells. We investigated possible neuronal affinities of these peptidergic cells using phylogenetics, chromatin profiling, and comparative single-cell genomics in four placozoans. We found conserved cell type expression programs across placozoans, including populations of transdifferentiating and cycling cells, suggestive of active cell type homeostasis. We also uncovered fourteen peptidergic cell types expressing neuronal-associated components like the pre-synaptic scaffold that derive from progenitor cells with neurogenesis signatures. In contrast, earlier-branching animals like sponges and ctenophores lacked this conserved expression. Our findings indicate that key neuronal developmental and effector gene modules evolved before the advent of cnidarian/bilaterian neurons in the context of paracrine cell signaling.
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Affiliation(s)
- Sebastián R Najle
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Damiano Cianferoni
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Chiva
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Didac Cañas-Armenteros
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Arrate Mallabiabarrena
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany; American Museum of Natural History, Richard Gilder Graduate School, NY, USA
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain.
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14
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Peña-Ortiz M, Serrano L, Romero AA, García A. Bay Leaves Extracts as Active Additive for Food Protective Coatings. Foods 2023; 12:3741. [PMID: 37893634 PMCID: PMC10606290 DOI: 10.3390/foods12203741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Ethanolic extracts of bay leaves were obtained using the Soxhlet method (extraction yield of 22.3 ± 1.2%) and further analyzed through different methods, thus determining the chemical composition with gas chromatography, phenolic content with the Folin-Ciocalteu technique (11.8 ± 0.4% wt.) and antioxidant power with the radical 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) method (75.06%). Furthermore, its effect on the growth of two bacteria, Escherichia coli and Bacillus cereus, and on two yeasts, Candida glabrata and Saccharomyces cerevisiae, was determined, showing a minimum inhibitory concentration of 0.65 mg/mL on the growth of B. cereus. Finally, edible films were prepared using different polymers (carboxymethyl cellulose, gum Arabic, polyvinyl pyrrolidone, and polyvinyl alcohol) containing 0, 5, 10, or 15% wt. of bay leaf extract as troubleshooting for perishable fruits, specifically for cultivated strawberry. The prepared composites presented reduced water vapor permeabilities (up to 4.3 × 10-7 g·Pa-1·m-1·h-1), high specific transparencies (≈30%/mm), as well as the effective blocking of ultraviolet radiation (>99.9%). In vivo tests showed that the most suitable treatment for strawberry protection was the impregnation with a composite comprising polyvinyl alcohol and a 15% wt. bay leaf extract, resulting in a noteworthy reduction in mass loss (22% after 6 days). It can be asserted that food packaging with the designed composites would be an effective alternative for the reduction in postharvest losses.
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Affiliation(s)
- Manuel Peña-Ortiz
- FQM-383 NANOVAL Group, Organic Chemistry Department, University of Córdoba, Campus de Rabanales, Marie Curie Building, Ctra. Nnal. IV-A, Km 396, 14014 Córdoba, Spain; (M.P.-O.); (A.A.R.)
- BioPrEn Group (RNM 940), Chemical Engineering Department, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Faculty of Science, University of Córdoba, 14014 Córdoba, Spain
| | - Luis Serrano
- BioPrEn Group (RNM 940), Chemical Engineering Department, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Faculty of Science, University of Córdoba, 14014 Córdoba, Spain
| | - Antonio A. Romero
- FQM-383 NANOVAL Group, Organic Chemistry Department, University of Córdoba, Campus de Rabanales, Marie Curie Building, Ctra. Nnal. IV-A, Km 396, 14014 Córdoba, Spain; (M.P.-O.); (A.A.R.)
| | - Araceli García
- FQM-383 NANOVAL Group, Organic Chemistry Department, University of Córdoba, Campus de Rabanales, Marie Curie Building, Ctra. Nnal. IV-A, Km 396, 14014 Córdoba, Spain; (M.P.-O.); (A.A.R.)
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15
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Bronte O, García-García F, Lee DJ, Urrutia I, Uranga A, Nieves M, Martínez-Minaya J, Quintana JM, Arostegui I, Zalacain R, Ruiz-Iturriaga LA, Serrano L, Menéndez R, Méndez R, Torres A, Cilloniz C, España PP. Impact of outdoor air pollution on severity and mortality in COVID-19 pneumonia. Sci Total Environ 2023; 894:164877. [PMID: 37331396 PMCID: PMC10275649 DOI: 10.1016/j.scitotenv.2023.164877] [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] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/23/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
The relationship between exposure to air pollution and the severity of coronavirus disease 2019 (COVID-19) pneumonia and other outcomes is poorly understood. Beyond age and comorbidity, risk factors for adverse outcomes including death have been poorly studied. The main objective of our study was to examine the relationship between exposure to outdoor air pollution and the risk of death in patients with COVID-19 pneumonia using individual-level data. The secondary objective was to investigate the impact of air pollutants on gas exchange and systemic inflammation in this disease. This cohort study included 1548 patients hospitalised for COVID-19 pneumonia between February and May 2020 in one of four hospitals. Local agencies supplied daily data on environmental air pollutants (PM10, PM2.5, O3, NO2, NO and NOX) and meteorological conditions (temperature and humidity) in the year before hospital admission (from January 2019 to December 2019). Daily exposure to pollution and meteorological conditions by individual postcode of residence was estimated using geospatial Bayesian generalised additive models. The influence of air pollution on pneumonia severity was studied using generalised additive models which included: age, sex, Charlson comorbidity index, hospital, average income, air temperature and humidity, and exposure to each pollutant. Additionally, generalised additive models were generated for exploring the effect of air pollution on C-reactive protein (CRP) level and SpO2/FiO2 at admission. According to our results, both risk of COVID-19 death and CRP level increased significantly with median exposure to PM10, NO2, NO and NOX, while higher exposure to NO2, NO and NOX was associated with lower SpO2/FiO2 ratios. In conclusion, after controlling for socioeconomic, demographic and health-related variables, we found evidence of a significant positive relationship between air pollution and mortality in patients hospitalised for COVID-19 pneumonia. Additionally, inflammation (CRP) and gas exchange (SpO2/FiO2) in these patients were significantly related to exposure to air pollution.
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Affiliation(s)
- O Bronte
- Galdakao-Usansolo University Hospital, Pulmonology Department, Galdakao, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain.
| | | | - D-J Lee
- Basque Center for Applied Mathematics (BCAM), Bilbao, Spain
| | - I Urrutia
- Galdakao-Usansolo University Hospital, Pulmonology Department, Galdakao, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | - A Uranga
- Galdakao-Usansolo University Hospital, Pulmonology Department, Galdakao, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | - M Nieves
- Galdakao-Usansolo University Hospital, Pulmonology Department, Galdakao, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | | | - J M Quintana
- Galdakao-Usansolo University Hospital, Research Unit, Galdakao, Spain
| | - I Arostegui
- University of the Basque Country (UPV/EHU), Department of Applied Mathematics, Statistics and Operative Research, Leioa, Spain; Basque Center for Applied Mathematics (BCAM), Bilbao, Spain
| | - R Zalacain
- Cruces University Hospital, Pulmonology Department, Baracaldo, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | - L A Ruiz-Iturriaga
- Cruces University Hospital, Pulmonology Department, Baracaldo, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | - L Serrano
- Cruces University Hospital, Pulmonology Department, Baracaldo, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
| | - R Menéndez
- Hospital Universitari i Politècnic La Fe de Valencia, Pulmonology Department, Valencia, Spain
| | - R Méndez
- Hospital Universitari i Politècnic La Fe de Valencia, Pulmonology Department, Valencia, Spain
| | - A Torres
- Hospital Clínic i Provincial de Barcelona, Pulmonology Department, University of Barcelona, Barcelona, Spain
| | - C Cilloniz
- Hospital Clínic i Provincial de Barcelona, Pulmonology Department, University of Barcelona, Barcelona, Spain; Faculty of Health Sciences, Continental University, Huancayo, Peru
| | - P P España
- Galdakao-Usansolo University Hospital, Pulmonology Department, Galdakao, Spain; BioCruces Bizkaia Health Research Institute, Baracaldo, Spain
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16
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Palmier E, De Miguel R, Montejano R, Busca C, Micán R, Ramos L, Cadiñanos J, Serrano L, Bernardino JI, Pérez-Valero I, Valencia E, Arribas JR, Montes ML, González-García J, Martín-Carbonero L. Three-year efficacy of switching to dolutegravir plus lamivudine: A real-world study. HIV Med 2023; 24:1013-1019. [PMID: 37194419 DOI: 10.1111/hiv.13500] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Dolutegravir (DTG) plus lamivudine (3TC) has proven highly efficacious as a switching strategy in virologically suppressed people with HIV (PWH). As this strategy was introduced relatively recently, real-world, long-term durability studies are lacking. METHODS We performed a retrospective review of treatment-experienced patients who started DTG + 3TC in a cohort of PWH. HIV-RNA <50 copies/mL was analysed at 144 weeks in an intention-to-treat (ITT) analysis (missing = failure) and a per-protocol (PP) analysis (patients with missing data or changes for reasons other than virological failure were excluded). RESULTS The study population comprised 358 PWH (19% women). Median age and time with HIV infection were 51.7 and 13.4 years, respectively. The median number of previous antiretroviral combinations was three. Previous virological failure was reported in 27.1% of patients, and the M184V resistance mutation was detected in 17 patients. At 144 weeks, the percentage of individuals with HIV-RNA <50 copies/mL was 77.4% (277/358) in the ITT analysis and 95.5% (277/290) in the PP analysis. A total of 68 participants were excluded from the PP analysis (data missing, 25, discontinuation due to toxicity, 19; other, 16; death, 8). Two people with virological failure selected resistance-associated mutations (M184V and M184V + R263K). HIV-RNA remained undetectable in 17 patients with a previous history of the M184V mutation. CONCLUSION Our results confirm the real-world, long-term efficacy, tolerability and high genetic barrier of DTG + 3TC in treatment-experienced PWH. Although scarce, mutations causing resistance to nucleosides and integrase can emerge.
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Affiliation(s)
- E Palmier
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - R De Miguel
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - R Montejano
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - C Busca
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - R Micán
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - L Ramos
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - J Cadiñanos
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - L Serrano
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - J I Bernardino
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | | | - E Valencia
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - J R Arribas
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - M L Montes
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - J González-García
- Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBER Infectious Diseases (CIBERINFEC), Madrid, Spain
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17
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Mazzolini R, Rodríguez-Arce I, Fernández-Barat L, Piñero-Lambea C, Garrido V, Rebollada-Merino A, Motos A, Torres A, Grilló MJ, Serrano L, Lluch-Senar M. Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms. Nat Biotechnol 2023; 41:1089-1098. [PMID: 36658340 PMCID: PMC10421741 DOI: 10.1038/s41587-022-01584-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 03/22/2021] [Accepted: 10/21/2022] [Indexed: 01/21/2023]
Abstract
Engineered live bacteria could provide a new modality for treating lung infections, a major cause of mortality worldwide. In the present study, we engineered a genome-reduced human lung bacterium, Mycoplasma pneumoniae, to treat ventilator-associated pneumonia, a disease with high hospital mortality when associated with Pseudomonas aeruginosa biofilms. After validating the biosafety of an attenuated M. pneumoniae chassis in mice, we introduced four transgenes into the chromosome by transposition to implement bactericidal and biofilm degradation activities. We show that this engineered strain has high efficacy against an acute P. aeruginosa lung infection in a mouse model. In addition, we demonstrated that the engineered strain could dissolve biofilms formed in endotracheal tubes of patients with ventilator-associated pneumonia and be combined with antibiotics targeting the peptidoglycan layer to increase efficacy against Gram-positive and Gram-negative bacteria. We expect our M. pneumoniae-engineered strain to be able to treat biofilm-associated infections in the respiratory tract.
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Affiliation(s)
- Rocco Mazzolini
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Irene Rodríguez-Arce
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Laia Fernández-Barat
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd, Barcelona, Spain
| | - Victoria Garrido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Agrobiotechnology, CSIC-Navarra Government, Navarra, Spain
| | - Agustín Rebollada-Merino
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Anna Motos
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, SpainICREA, Barcelona, Spain
| | | | - Luis Serrano
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Maria Lluch-Senar
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Pulmobiotics Ltd, Barcelona, Spain.
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain.
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18
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Burgos R, Garcia-Ramallo E, Shaw D, Lluch-Senar M, Serrano L. Development of a Serum-Free Medium To Aid Large-Scale Production of Mycoplasma-Based Therapies. Microbiol Spectr 2023; 11:e0485922. [PMID: 37097155 PMCID: PMC10269708 DOI: 10.1128/spectrum.04859-22] [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: 11/25/2022] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
To assist in the advancement of the large-scale production of safe Mycoplasma vaccines and other Mycoplasma-based therapies, we developed a culture medium free of animal serum and other animal components for Mycoplasma pneumoniae growth. By establishing a workflow method to systematically test different compounds and concentrations, we provide optimized formulations capable of supporting serial passaging and robust growth reaching 60 to 70% of the biomass obtained in rich medium. Global transcriptomic and proteomic analysis showed minor physiological changes upon cell culture in the animal component-free medium, supporting its suitability for the production of M. pneumoniae-based therapies. The major contributors to growth performance were found to be glucose as a carbon source, glycerol, cholesterol, and phospholipids as a source of fatty acids. Bovine serum albumin or cyclodextrin (in the animal component-free medium) were required as lipid carriers to prevent lipid toxicity. Connaught Medical Research Laboratories medium (CMRL) used to simplify medium preparation as a source of amino acids, nucleotide precursors, vitamins, and other cofactors could be substituted by cysteine. In fact, the presence of protein hydrolysates such as yeastolate or peptones was found to be essential and preferred over free amino acids, except for the cysteine. Supplementation of nucleotide precursors and vitamins is not strictly necessary in the presence of yeastolate, suggesting that this animal origin-free hydrolysate serves as an efficient source for these compounds. Finally, we adapted the serum-free medium formulation to support growth of Mycoplasma hyopneumoniae, a swine pathogen for which inactivated whole-cell vaccines are available. IMPORTANCE Mycoplasma infections have a significant negative impact on both livestock production and human health. Vaccination is often the first option to control disease and alleviate the economic impact that some Mycoplasma infections cause on milk production, weight gain, and animal health. The fastidious nutrient requirements of these bacteria, however, challenges the industrial production of attenuated or inactivated whole-cell vaccines, which depends on the use of animal serum and other animal raw materials. Apart from their clinical relevance, some Mycoplasma species have become cellular models for systems and synthetic biology, owing to the small size of their genomes and the absence of a cell wall, which offers unique opportunities for the secretion and delivery of biotherapeutics. This study proposes medium formulations free of serum and animal components with the potential of supporting large-scale production upon industrial optimization, thus contributing to the development of safe vaccines and other Mycoplasma-based therapies.
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Daniel Shaw
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pulmobiotics Ltd., Barcelona, Spain
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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Gurriaran-Rodriguez U, Datzkiw D, Radusky LG, Esper M, Xiao F, Ming H, Fisher S, Rojas MA, De Repentigny Y, Kothary R, Rojas AL, Serrano L, Hierro A, Rudnicki MA. Wnt binding to Coatomer proteins directs secretion on exosomes independently of palmitoylation. bioRxiv 2023:2023.05.30.542914. [PMID: 37398399 PMCID: PMC10312507 DOI: 10.1101/2023.05.30.542914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wnt proteins are secreted hydrophobic glycoproteins that act over long distances through poorly understood mechanisms. We discovered that Wnt7a is secreted on extracellular vesicles (EVs) following muscle injury. Structural analysis identified the motif responsible for Wnt7a secretion on EVs that we term the Exosome Binding Peptide (EBP). Addition of the EBP to an unrelated protein directed secretion on EVs. Disruption of palmitoylation, knockdown of WLS, or deletion of the N-terminal signal peptide did not affect Wnt7a secretion on purified EVs. Bio-ID analysis identified Coatomer proteins as candidates responsible for loading Wnt7a onto EVs. The crystal structure of EBP bound to the COPB2 coatomer subunit, the binding thermodynamics, and mutagenesis experiments, together demonstrate that a dilysine motif in the EBP mediates binding to COPB2. Other Wnts contain functionally analogous structural motifs. Mutation of the EBP results in a significant impairment in the ability of Wnt7a to stimulate regeneration, indicating that secretion of Wnt7a on exosomes is critical for normal regeneration in vivo . Our studies have defined the structural mechanism that mediates binding of Wnt7a to exosomes and elucidated the singularity of long-range Wnt signalling.
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Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, Radusky L, Senger G, Calvet F, Weghorn D, Irimia M, Schaefer MH, Serrano L. Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Syst 2023; 14:312-323.e3. [PMID: 36889307 DOI: 10.1016/j.cels.2023.02.002] [Citation(s) in RCA: 3] [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: 01/25/2022] [Revised: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
Codon usage influences gene expression distinctly depending on the cell context. Yet, the importance of codon bias in the simultaneous turnover of specific groups of protein-coding genes remains to be investigated. Here, we find that genes enriched in A/T-ending codons are expressed more coordinately in general and across tissues and development than those enriched in G/C-ending codons. tRNA abundance measurements indicate that this coordination is linked to the expression changes of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition are more likely to be part of the same protein complex, especially for genes with A/T-ending codons. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.
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Affiliation(s)
- Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Gökçe Senger
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Donate Weghorn
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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21
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Hernandez-Alias X, Benisty H, Radusky LG, Serrano L, Schaefer MH. Using protein-per-mRNA differences among human tissues in codon optimization. Genome Biol 2023; 24:34. [PMID: 36829202 PMCID: PMC9951436 DOI: 10.1186/s13059-023-02868-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in their transcriptomes, the effect of tissue-specific codon optimality on protein synthesis remains elusive. RESULTS We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. We detect two clusters of tissues with an opposite pattern of codon preferences. We then use these identified patterns for the development of CUSTOM, a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In human cell-line models, we provide evidence that codon optimization should take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles. CONCLUSIONS We provide proof-of-concept evidence that codon preferences exist in tissue-specific protein synthesis and demonstrate its application to synthetic gene design. We show that CUSTOM can be of benefit in biological and biotechnological applications, such as in the design of tissue-targeted therapies and vaccines.
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Affiliation(s)
- Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Leandro G Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain. .,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Martin H Schaefer
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139, Milan, Italy.
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Hernandez-Alias X, Katanski CD, Zhang W, Assari M, Watkins CP, Schaefer MH, Serrano L, Pan T. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res 2023; 51:e17. [PMID: 36537222 PMCID: PMC9943672 DOI: 10.1093/nar/gkac1185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylation and modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.
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Affiliation(s)
- Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Christopher D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mahdi Assari
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Christopher P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Martin H Schaefer
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan 20139, Italy
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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23
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Rincón E, Espinosa E, Pinillos M, Serrano L. Bioactive Absorbent Chitosan Aerogels Reinforced with Bay Tree Pruning Waste Nanocellulose with Antioxidant Properties for Burger Meat Preservation. Polymers (Basel) 2023; 15:polym15040866. [PMID: 36850149 PMCID: PMC9964863 DOI: 10.3390/polym15040866] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
As a transition strategy towards sustainability, food packaging plays a crucial role in the current era. This, carried out in a biorefinery context of agricultural residues, involves not only obtaining desirable products but a comprehensive utilization of biomass that contributes to the circular bioeconomy. The present work proposes the preparation of bioactive absorbent food pads through a multi-product biorefinery approach from bay tree pruning waste (BTPW). In a first step, chitosan aerogels reinforced with lignocellulose and cellulose micro/nanofibers from BTPW were prepared, studying the effect of residual lignin on the material's properties. The presence of micro/nanofibers improved the mechanical performance (up to 60%) in addition to increasing the water uptake (42%) when lignin was present. The second step was to make them bioactive by incorporating bay leaf extract. The residual lignin in the micro/nanofibers was decisive, since when present, the release profiles of the extract were faster, reaching an antioxidant power of more than 85% after only 30 min. Finally, these bioactive aerogels were used as absorbent pads for fresh meat. With the use of the bioactive aerogels (with ≥2% extract), the meat remained fresh for 10 days as a result of delayed oxidation of the food during storage (20% metmyoglobin proportion).
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Montero‐Blay A, Blanco JD, Rodriguez‐Arce I, Lastrucci C, Piñero‐Lambea C, Lluch‐Senar M, Serrano L. Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation. Mol Syst Biol 2023; 19:e11037. [PMID: 36598022 PMCID: PMC9834763 DOI: 10.15252/msb.202211037] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 01/05/2023] Open
Abstract
Interleukin-10 (IL-10) is an anti-inflammatory cytokine that is active as a swapped domain dimer and is used in bacterial therapy of gut inflammation. IL-10 can be used as treatment of a wide range of pulmonary diseases. Here we have developed a non-pathogenic chassis (CV8) of the human lung bacterium Mycoplasma pneumoniae (MPN) to treat lung diseases. We find that IL-10 expression by MPN has a limited impact on the lung inflammatory response in mice. To solve these issues, we rationally designed a single-chain IL-10 (SC-IL10) with or without surface mutations, using our protein design software (ModelX and FoldX). As compared to the IL-10 WT, the designed SC-IL10 molecules increase the effective expression in MPN four-fold, and the activity in mouse and human cell lines between 10 and 60 times, depending on the cell line. The SC-IL10 molecules expressed in the mouse lung by CV8 in vivo have a powerful anti-inflammatory effect on Pseudomonas aeruginosa lung infection. This rational design strategy could be used to other molecules with immunomodulatory properties used in bacterial therapy.
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Affiliation(s)
- Ariadna Montero‐Blay
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Javier Delgado Blanco
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Irene Rodriguez‐Arce
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Claire Lastrucci
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carlos Piñero‐Lambea
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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Quiat D, Timberlake AT, Curran JJ, Cunningham ML, McDonough B, Artunduaga MA, DePalma SR, Duenas-Roque MM, Gorham JM, Gustafson JA, Hamdan U, Hing AV, Hurtado-Villa P, Nicolau Y, Osorno G, Pachajoa H, Porras-Hurtado GL, Quintanilla-Dieck L, Serrano L, Tumblin M, Zarante I, Luquetti DV, Eavey RD, Heike CL, Seidman JG, Seidman CE. Damaging variants in FOXI3 cause microtia and craniofacial microsomia. Genet Med 2023; 25:143-150. [PMID: 36260083 PMCID: PMC9885525 DOI: 10.1016/j.gim.2022.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Craniofacial microsomia (CFM) represents a spectrum of craniofacial malformations, ranging from isolated microtia with or without aural atresia to underdevelopment of the mandible, maxilla, orbit, facial soft tissue, and/or facial nerve. The genetic causes of CFM remain largely unknown. METHODS We performed genome sequencing and linkage analysis in patients and families with microtia and CFM of unknown genetic etiology. The functional consequences of damaging missense variants were evaluated through expression of wild-type and mutant proteins in vitro. RESULTS We studied a 5-generation kindred with microtia, identifying a missense variant in FOXI3 (p.Arg236Trp) as the cause of disease (logarithm of the odds = 3.33). We subsequently identified 6 individuals from 3 additional kindreds with microtia-CFM spectrum phenotypes harboring damaging variants in FOXI3, a regulator of ectodermal and neural crest development. Missense variants in the nuclear localization sequence were identified in cases with isolated microtia with aural atresia and found to affect subcellular localization of FOXI3. Loss of function variants were found in patients with microtia and mandibular hypoplasia (CFM), suggesting dosage sensitivity of FOXI3. CONCLUSION Damaging variants in FOXI3 are the second most frequent genetic cause of CFM, causing 1% of all cases, including 13% of familial cases in our cohort.
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Affiliation(s)
- Daniel Quiat
- Department of Cardiology, Boston Children’s Hospital, Boston, MA,Department of Pediatrics, Harvard Medical School, Boston, MA,Department of Genetics, Harvard Medical School, Boston, MA
| | - Andrew T. Timberlake
- Hansjörg Wyss Department of Plastic and Reconstructive Surgery, NYU Langone Medical Center, New York, NY
| | | | - Michael L. Cunningham
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | | | | | | | | | | | - Jonas A. Gustafson
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | | | - Anne V. Hing
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Gabriel Osorno
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Harry Pachajoa
- Servicio de Genética Médica, Fundación Valle del Lili, Cali, Colombia,Centro de Investigación en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia
| | | | - Lourdes Quintanilla-Dieck
- Department of Otolaryngology Head and Neck Surgery, Oregon Health & Science University, Portland, OR
| | | | | | - Ignacio Zarante
- Human Genomics Institute, Pontificia Universidad Javeriana, Bogotá, Colombia,Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Daniela V. Luquetti
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Roland D. Eavey
- Department of Otolaryngology–Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Carrie L. Heike
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Jonathan G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA,Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA,Howard Hughes Medical Institute, Chevy Chase, MD,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
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Anglada-Girotto M, Miravet-Verde S, Serrano L, Head SA. robustica: customizable robust independent component analysis. BMC Bioinformatics 2022; 23:519. [PMID: 36471244 PMCID: PMC9721028 DOI: 10.1186/s12859-022-05043-9] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Independent Component Analysis (ICA) allows the dissection of omic datasets into modules that help to interpret global molecular signatures. The inherent randomness of this algorithm can be overcome by clustering many iterations of ICA together to obtain robust components. Existing algorithms for robust ICA are dependent on the choice of clustering method and on computing a potentially biased and large Pearson distance matrix. RESULTS We present robustica, a Python-based package to compute robust independent components with a fully customizable clustering algorithm and distance metric. Here, we exploited its customizability to revisit and optimize robust ICA systematically. Of the 6 popular clustering algorithms considered, DBSCAN performed the best at clustering independent components across ICA iterations. To enable using Euclidean distances, we created a subroutine that infers and corrects the components' signs across ICA iterations. Our subroutine increased the resolution, robustness, and computational efficiency of the algorithm. Finally, we show the applicability of robustica by dissecting over 500 tumor samples from low-grade glioma (LGG) patients, where we define two new gene expression modules with key modulators of tumor progression upon IDH1 and TP53 mutagenesis. CONCLUSION robustica brings precise, efficient, and customizable robust ICA into the Python toolbox. Through its customizability, we explored how different clustering algorithms and distance metrics can further optimize robust ICA. Then, we showcased how robustica can be used to discover gene modules associated with combinations of features of biological interest. Taken together, given the broad applicability of ICA for omic data analysis, we envision robustica will facilitate the seamless computation and integration of robust independent components in large pipelines.
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Affiliation(s)
- Miquel Anglada-Girotto
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Samuel Miravet-Verde
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Pg. LLuís Companys 23, 08010 Barcelona, Spain
| | - Sarah A. Head
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
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Piñero-Lambea C, Garcia-Ramallo E, Miravet-Verde S, Burgos R, Scarpa M, Serrano L, Lluch-Senar M. SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome. Nucleic Acids Res 2022; 50:e127. [PMID: 36215032 PMCID: PMC9825166 DOI: 10.1093/nar/gkac836] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/03/2022] [Accepted: 09/28/2022] [Indexed: 01/29/2023] Open
Abstract
The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a multi-recombinase engineering rationale combining oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We test this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombination machinery. Using SURE editing, we can seamlessly generate, in a single step, a wide variety of genome modifications at high efficiencies, including the largest possible deletion of this genome (30 Kb) and the targeted complementation of essential genes in the deletion of a region of interest. Additional steps can be taken to remove the selector plasmid from the edited area, to obtain markerless or even scarless edits. Of note, SURE editing is compatible with different site-specific recombinases for mediating transient plasmid integration. This battery of selector plasmids can be used to select different edits, regardless of the target sequence, which significantly reduces the cloning load associated to genome engineering projects. Given the proven functionality in several microorganisms of the machinery behind the SURE editing logic, this method is likely to represent a valuable advance for the synthetic biology field.
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Affiliation(s)
| | | | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain,ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Correspondence may also be addressed to Maria Lluch-Senar. Tel: +34 661963680;
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Pascual Reguant L, Tian T, Datta D, Cianferoni D, Kourtis S, Gañez-Zapater A, Cannatá C, Serra-Camprubi Q, Espinar L, Guirola M, Querol J, Miró-Canturri A, Arribas J, Serrano L, Peiró S, Sdelci S. Interactions between BRD4 short, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rincón E, Bautista JM, Espinosa E, Serrano L. Biopolymer‐based sachets enriched with acorn shell extracts produced by ultrasound‐assisted extraction for active packaging. J Appl Polym Sci 2022. [DOI: 10.1002/app.53102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Esther Rincón
- Biopren Group, Inorganic Chemistry and Chemical Engineering Department Nanochemistry University Institute (IUNAN), Universidad de Córdoba Córdoba Spain
| | - Juana M. Bautista
- Biopren Group, Inorganic Chemistry and Chemical Engineering Department Nanochemistry University Institute (IUNAN), Universidad de Córdoba Córdoba Spain
| | - Eduardo Espinosa
- Biopren Group, Inorganic Chemistry and Chemical Engineering Department Nanochemistry University Institute (IUNAN), Universidad de Córdoba Córdoba Spain
| | - Luis Serrano
- Biopren Group, Inorganic Chemistry and Chemical Engineering Department Nanochemistry University Institute (IUNAN), Universidad de Córdoba Córdoba Spain
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Elfmann C, Zhu B, Pedreira T, Hoßbach B, Lluch-Senar M, Serrano L, Stülke J. MycoWiki: Functional annotation of the minimal model organism Mycoplasma pneumoniae. Front Microbiol 2022; 13:935066. [PMID: 35958127 PMCID: PMC9358437 DOI: 10.3389/fmicb.2022.935066] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
The human pathogen Mycoplasma pneumoniae is viable independently from host cells or organisms, despite its strongly reduced genome with only about 700 protein-coding genes. The investigation of M. pneumoniae can therefore help to obtain general insights concerning the basic requirements for cellular life. Accordingly, M. pneumoniae has become a model organism for systems biology in the past decade. To support the investigation of the components of this minimal bacterium, we have generated the database MycoWiki. (http://mycowiki.uni-goettingen.de) MycoWiki organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae. Interestingly, M. pneumoniae has undergone an evolution that resulted in the limited similarity of many proteins to proteins of model organisms. To facilitate the analysis of the functions of M. pneumoniae proteins, we have integrated structure predictions from the AlphaFold Protein Structure Database for most proteins, structural information resulting from in vivo cross-linking, and protein-protein interactions based on a global in vivo study. MycoWiki is an important tool for the systems and synthetic biology community that will support the comprehensive understanding of a minimal organism and the functional annotation of so far uncharacterized proteins.
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Affiliation(s)
- Christoph Elfmann
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Tiago Pedreira
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Ben Hoßbach
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jörg Stülke
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
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31
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Iribarne-Durán LM, Serrano L, Peinado FM, Peña-Caballero M, Hurtado JA, Vela-Soria F, Fernández MF, Freire C, Artacho-Cordón F, Olea N. Biomonitoring bisphenols, parabens, and benzophenones in breast milk from a human milk bank in Southern Spain. Sci Total Environ 2022; 830:154737. [PMID: 35337871 DOI: 10.1016/j.scitotenv.2022.154737] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 11/19/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Human breast milk is considered the optimal source of nutrition for infants. Milk from breast milk banks offers an alternative to infant formulas for vulnerable hospitalized neonates most likely to benefit from exclusive human milk feeding. However, breast milk can also be a source of exposure to environmental contaminants, including endocrine-disrupting chemicals (EDCs). AIM To evaluate concentrations of phenolic EDCs, including bisphenols, parabens (PBs), and benzophenones (BPs), in samples from a human milk bank in Granada, Southern Spain and to explore sociodemographic, reproductive, and lifestyle factors related to their concentrations in the milk. METHODS Concentrations of three bisphenols [bisphenol A (BPA), bisphenol F (BPF), and bisphenol S (BPS)], four PBs [methyl- (MeP), ethyl- (EtP), propyl- (n-PrP), and butyl-paraben (n-BuP)], and six BPs [BP-1, BP-2, BP-3, BP-6, BP-8, and 4-hydroxy-BP] were determined in milk samples from 83 donors. Information on potential explanatory variables was gathered using the milk bank donor form and an ad hoc questionnaire. Multiple linear and logistic regression models were fitted. RESULTS Detectable concentrations were found of at least one of the analyzed compounds in all donor breast milk samples and at least five compounds in one-fifth of them. The most frequently detected compounds were MeP (90.5%), BP-3 (75.0%), EtP (51.2%), n-PrP (46.4%), and BPA (41.7%). Median concentrations ranged between <0.10 ng/mL (n-PrP, n-BuP, BP-1) and 0.59 ng/mL (BP-3). No sample contained detectable concentrations of BPF, BPS, or most BPs (BP-2, BP-6, BP-8, and 4- hydroxy-BP). Breast milk phenol concentrations were associated with parity, the utilization of deodorants, mouthwash, skin care products, and cosmetics, and the intake of nutritional supplements. CONCLUSIONS Results reveal the widespread presence of BPA, PBs, and BP-3 in donor breast milk samples, highlighting the need for preventive measures to enhance the benefits of breast milk from milk banks and from breastfeeding women in general.
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Affiliation(s)
- L M Iribarne-Durán
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain
| | - L Serrano
- Neonatal Intensive Care Unit, Virgen de las Nieves University Hospital, E-18012 Granada, Spain
| | - F M Peinado
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain
| | - M Peña-Caballero
- Neonatal Intensive Care Unit, Virgen de las Nieves University Hospital, E-18012 Granada, Spain
| | - J A Hurtado
- Neonatal Intensive Care Unit, Virgen de las Nieves University Hospital, E-18012 Granada, Spain
| | - F Vela-Soria
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain
| | - M F Fernández
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), E-28029 Madrid, Spain; Department of Radiology and Physical Medicine, University of Granada, E-18016 Granada, Spain
| | - C Freire
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), E-28029 Madrid, Spain.
| | - F Artacho-Cordón
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), E-28029 Madrid, Spain; Department of Radiology and Physical Medicine, University of Granada, E-18016 Granada, Spain.
| | - N Olea
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18012 Granada, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), E-28029 Madrid, Spain; Department of Radiology and Physical Medicine, University of Granada, E-18016 Granada, Spain; Nuclear Medicine Unit, San Cecilio University Hospital, E-18016 Granada, Spain
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32
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Serrano L, Algarate S, Herrero-Cortina B, Bueno J, González-Barriga MT, Ducons M, Montero-Marco J, Acha B, Taboada A, Sanz-Burillo P, Yuste C, Benito R, Serrano L, González T, Acha B, Yuste C, Sanz P, Taboada A, Ferrández CI, Sahuquillo P, Zueco E, Montero-Marco J, Charlo M, Redondo M, Fernández L, Inglés C, Bueno J, Benito R, Algarate S, Herrero-Cortina B. Assessment of humoral immune response to two mRNA SARS-CoV-2 VACCINES (Moderna and Pfizer) in healthcare workers fully vaccinated with and without a history of previous infection. J Appl Microbiol 2022; 133:1969-1974. [PMID: 35801660 PMCID: PMC9350023 DOI: 10.1111/jam.15699] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Aims Presence of anti‐S1 region of SARS‐CoV‐2 spike protein was analysed, at two and eight months, in 477 immunocompetent healthcare workers in Zaragoza, Spain, vaccinated with mRNA‐1273 (Moderna) or BNT162b2 (Pfizer). Methods and results Antibody analysis was performed with Alinity i System (Abbott). At 2 months, 100% of vaccinated had anti‐S1 IgG (mean = 13,285 AU ml−1). This value was significantly higher with Moderna (18,192 AU ml−1) than with Pfizer (10,441 AU ml−1). The mean value of anti‐S1 IgG after vaccination was significantly higher in patients with than without previous infection (18,539 vs. 7919 AU ml−1); in both groups was significantly higher with Moderna than with Pfizer (21,881 vs. 15,733 AU ml−1 and 11,949 vs. 6387 AU ml−1), respectively. At 8 months, 100% of patients were IgG positive, with higher levels with Moderna than with Pfizer. Nevertheless, in ensemble of cases, a mean decrease of antibody levels of 11,025 AU ml−1 was observed. Conclusion At 2 and 8 months after vaccination, IgG response persists with both vaccines but with important decrease which suggests the need for revaccination. Significance and impact of study The study contributes to know the immune status after vaccination with two of more used anti‐SARS‐CoV‐2 vaccines. This knowledge is important for establishing the best vaccination strategy
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Affiliation(s)
- Laura Serrano
- Occupational Health Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Sonia Algarate
- Microbiology Department, Lozano Blesa University Hospital, Zaragoza, Spain.,Microbiology Department, Zaragoza University, Spain
| | - Beatriz Herrero-Cortina
- Investigation Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain.,Universidad San Jorge, Villanueva de Gállego, Zaragoza, Spain
| | - Jessica Bueno
- Microbiology Department, Lozano Blesa University Hospital, Zaragoza, Spain
| | | | - María Ducons
- Microbiology Department, Lozano Blesa University Hospital, Zaragoza, Spain
| | - Jesica Montero-Marco
- Investigation Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Beatriz Acha
- Occupational Health Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Ana Taboada
- Occupational Health Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Pilar Sanz-Burillo
- Occupational Health Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Cristina Yuste
- Occupational Health Unit, Lozano Blesa University Hospital, Zaragoza, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
| | - Rafael Benito
- Microbiology Department, Lozano Blesa University Hospital, Zaragoza, Spain.,Microbiology Department, Zaragoza University, Spain.,Institute for Health Research Aragón, Zaragoza, Spain
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Quiat D, Kim SW, Zhang Q, Morton SU, Pereira AC, DePalma SR, Willcox JAL, McDonough B, DeLaughter DM, Gorham JM, Curran JJ, Tumblin M, Nicolau Y, Artunduaga MA, Quintanilla-Dieck L, Osorno G, Serrano L, Hamdan U, Eavey RD, Seidman CE, Seidman JG. An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations. Proc Natl Acad Sci U S A 2022; 119:e2203928119. [PMID: 35584116 PMCID: PMC9173816 DOI: 10.1073/pnas.2203928119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 01/14/2023] Open
Abstract
Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although the contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map an ∼10-kb microtia locus (odds ratio = 4.7; P = 6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526 to 78555137). While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%). We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals. The locus is located near a chromatin loop region that regulates ROBO1 and ROBO2 expression in induced pluripotent stem cell–derived neural crest cells. Furthermore, we use single nuclear RNA sequencing to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and is shared by some East Asian subjects with craniofacial malformations, we propose that both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.
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Affiliation(s)
- Daniel Quiat
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sarah U. Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, 05508-060, Brazil
| | | | | | | | | | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Justin J. Curran
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | | | | | - Lourdes Quintanilla-Dieck
- Department of Otolaryngology Head and Neck Surgery, Oregon Health & Science University, Portland, OR 97239
| | - Gabriel Osorno
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | | | | | - Roland D. Eavey
- Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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Radusky LG, Serrano L. pyFoldX: enabling biomolecular analysis and engineering along structural ensembles. Bioinformatics 2022; 38:2353-2355. [PMID: 35176149 PMCID: PMC9004634 DOI: 10.1093/bioinformatics/btac072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/19/2021] [Accepted: 02/09/2022] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software has proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modelling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module and an easy integration with the data analysis ecosystem of the python programming language. AVAILABILITY AND IMPLEMENTATION pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http://foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality and the scripts used to generate the data and figures presented in this paper are available at https://github.com/leandroradusky/pyFoldX. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Leandro G Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
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35
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Cova CM, Rincón E, Espinosa E, Serrano L, Zuliani A. Paving the Way for a Green Transition in the Design of Sensors and Biosensors for the Detection of Volatile Organic Compounds (VOCs). Biosensors (Basel) 2022; 12:51. [PMID: 35200311 PMCID: PMC8869180 DOI: 10.3390/bios12020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 05/06/2023]
Abstract
The efficient and selective detection of volatile organic compounds (VOCs) provides key information for various purposes ranging from the toxicological analysis of indoor/outdoor environments to the diagnosis of diseases or to the investigation of biological processes. In the last decade, different sensors and biosensors providing reliable, rapid, and economic responses in the detection of VOCs have been successfully conceived and applied in numerous practical cases; however, the global necessity of a sustainable development, has driven the design of devices for the detection of VOCs to greener methods. In this review, the most recent and innovative VOC sensors and biosensors with sustainable features are presented. The sensors are grouped into three of the main industrial sectors of daily life, including environmental analysis, highly important for toxicity issues, food packaging tools, especially aimed at avoiding the spoilage of meat and fish, and the diagnosis of diseases, crucial for the early detection of relevant pathological conditions such as cancer and diabetes. The research outcomes presented in the review underly the necessity of preparing sensors with higher efficiency, lower detection limits, improved selectivity, and enhanced sustainable characteristics to fully address the sustainable manufacturing of VOC sensors and biosensors.
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Affiliation(s)
- Camilla Maria Cova
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
| | - Esther Rincón
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Eduardo Espinosa
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Luis Serrano
- BioPren Group, Inorganic Chemistry and Chemical Engineering Department, Faculty of Sciences, University of Cordoba, 14014 Cordoba, Spain; (E.R.); (E.E.); (L.S.)
| | - Alessio Zuliani
- Department of Chemistry, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy;
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36
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Varadi M, Anyango S, Armstrong D, Berrisford J, Choudhary P, Deshpande M, Nadzirin N, Nair SS, Pravda L, Tanweer A, Al-Lazikani B, Andreini C, Barton GJ, Bednar D, Berka K, Blundell T, Brock KP, Carazo JM, Damborsky J, David A, Dey S, Dunbrack R, Recio JF, Fraternali F, Gibson T, Helmer-Citterich M, Hoksza D, Hopf T, Jakubec D, Kannan N, Krivak R, Kumar M, Levy ED, London N, Macias JR, Srivatsan MM, Marks DS, Martens L, McGowan SA, McGreig JE, Modi V, Parra RG, Pepe G, Piovesan D, Prilusky J, Putignano V, Radusky LG, Ramasamy P, Rausch AO, Reuter N, Rodriguez LA, Rollins NJ, Rosato A, Rubach P, Serrano L, Singh G, Skoda P, Sorzano COS, Stourac J, Sulkowska JI, Svobodova R, Tichshenko N, Tosatto SCE, Vranken W, Wass MN, Xue D, Zaidman D, Thornton J, Sternberg M, Orengo C, Velankar S. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res 2022; 50:D534-D542. [PMID: 34755867 PMCID: PMC8728252 DOI: 10.1093/nar/gkab988] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.
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37
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Shaw D, Miravet‐Verde S, Piñero‐Lambea C, Serrano L, Lluch‐Senar M. LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions. Microb Biotechnol 2021; 14:2403-2419. [PMID: 33325626 PMCID: PMC8601177 DOI: 10.1111/1751-7915.13714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
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Affiliation(s)
- Daniel Shaw
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Samuel Miravet‐Verde
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Carlos Piñero‐Lambea
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Present address:
Pulmobiotics ltdDr. Aiguader 88Barcelona08003Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Universitat Pompeu Fabra (UPF)Barcelona08002Spain
- ICREAPg. Lluís Companys 23Barcelona08010Spain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Basic Sciences DepartmentFaculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaSant Cugat del Vallès08195Spain
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Garrido V, Piñero-Lambea C, Rodriguez-Arce I, Paetzold B, Ferrar T, Weber M, Garcia-Ramallo E, Gallo C, Collantes M, Peñuelas I, Serrano L, Grilló MJ, Lluch-Senar M. Engineering a genome-reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo. Mol Syst Biol 2021; 17:e10145. [PMID: 34612607 PMCID: PMC8493563 DOI: 10.15252/msb.202010145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/25/2023] Open
Abstract
Bacteria present a promising delivery system for treating human diseases. Here, we engineered the genome‐reduced human lung pathogen Mycoplasma pneumoniae as a live biotherapeutic to treat biofilm‐associated bacterial infections. This strain has a unique genetic code, which hinders gene transfer to most other bacterial genera, and it lacks a cell wall, which allows it to express proteins that target peptidoglycans of pathogenic bacteria. We first determined that removal of the pathogenic factors fully attenuated the chassis strain in vivo. We then designed synthetic promoters and identified an endogenous peptide signal sequence that, when fused to heterologous proteins, promotes efficient secretion. Based on this, we equipped the chassis strain with a genetic platform designed to secrete antibiofilm and bactericidal enzymes, resulting in a strain capable of dissolving Staphylococcus aureus biofilms preformed on catheters in vitro, ex vivo, and in vivo. To our knowledge, this is the first engineered genome‐reduced bacterium that can fight against clinically relevant biofilm‐associated bacterial infections.
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Affiliation(s)
- Victoria Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain
| | - Irene Rodriguez-Arce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - Bernhard Paetzold
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,S-Biomedic N.V., Beerse, Belgium
| | - Tony Ferrar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - María Collantes
- RADIOMIN Research Group, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Iván Peñuelas
- RADIOMIN Research Group, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - María-Jesús Grilló
- Institute of Agrobiotechnology (IdAB; CSIC-Navarra Government), Mutilva, Spain
| | - María Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Pulmobiotics Ltd, Barcelona, Spain.,Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
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Burgos R, Weber M, Gallo C, Lluch-Senar M, Serrano L. Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control. iScience 2021; 24:102985. [PMID: 34485867 PMCID: PMC8403727 DOI: 10.1016/j.isci.2021.102985] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand. Lon degrades efficiently tmRNA-tagged proteins in a genome-reduced bacterium tmRNA-tag mutants are viable and reveal extensive tagging activity in M. pneumoniae Co-evolution of Lon and their substrates offer simple mechanisms of regulation Chaperone and Lon relative levels correlate with bacterial growth rates
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author
| | - Marc Weber
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author
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Martínez-Torró C, Torres-Puig S, Marcos-Silva M, Huguet-Ramón M, Muñoz-Navarro C, Lluch-Senar M, Serrano L, Querol E, Piñol J, Pich OQ. Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium. Front Microbiol 2021; 12:695572. [PMID: 34589065 PMCID: PMC8475190 DOI: 10.3389/fmicb.2021.695572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/10/2021] [Indexed: 12/03/2022] Open
Abstract
It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.
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Affiliation(s)
- Carlos Martínez-Torró
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Torres-Puig
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Marcos-Silva
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Huguet-Ramón
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Navarro
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Q. Pich
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d’Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Sabadell, Spain
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Suay-Corredera C, Pricolo MR, Herrero-Galán E, Velázquez-Carreras D, Sánchez-Ortiz D, García-Giustiniani D, Delgado J, Galano-Frutos JJ, García-Cebollada H, Vilches S, Domínguez F, Molina MS, Barriales-Villa R, Frisso G, Sancho J, Serrano L, García-Pavía P, Monserrat L, Alegre-Cebollada J. Protein haploinsufficiency drivers identify MYBPC3 variants that cause hypertrophic cardiomyopathy. J Biol Chem 2021; 297:100854. [PMID: 34097875 PMCID: PMC8260873 DOI: 10.1016/j.jbc.2021.100854] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease. Variants in MYBPC3, the gene encoding cardiac myosin-binding protein C (cMyBP-C), are the leading cause of HCM. However, the pathogenicity status of hundreds of MYBPC3 variants found in patients remains unknown, as a consequence of our incomplete understanding of the pathomechanisms triggered by HCM-causing variants. Here, we examined 44 nontruncating MYBPC3 variants that we classified as HCM-linked or nonpathogenic according to cosegregation and population genetics criteria. We found that around half of the HCM-linked variants showed alterations in RNA splicing or protein stability, both of which can lead to cMyBP-C haploinsufficiency. These protein haploinsufficiency drivers associated with HCM pathogenicity with 100% and 94% specificity, respectively. Furthermore, we uncovered that 11% of nontruncating MYBPC3 variants currently classified as of uncertain significance in ClinVar induced one of these molecular phenotypes. Our strategy, which can be applied to other conditions induced by protein loss of function, supports the idea that cMyBP-C haploinsufficiency is a fundamental pathomechanism in HCM.
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Affiliation(s)
| | - Maria Rosaria Pricolo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
| | | | | | | | | | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan José Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Helena García-Cebollada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Vilches
- Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain
| | - Fernando Domínguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - María Sabater Molina
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Hospital C. Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain
| | - Roberto Barriales-Villa
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Unidad de Cardiopatías Familiares, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña, Servizo Galego de Saúde (SERGAS), Universidade da Coruña, A Coruña, Spain
| | - Giulia Frisso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; CEINGE Biotecnologie Avanzate, scarl, Naples, Italy
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Pablo García-Pavía
- Heart Failure and Inherited Cardiac Diseases Unit. Department of Cardiology. Hospital Universitario Puerta de Hierro, Madrid, Spain; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, Spain
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Serrano L, López AC, González SP, Palacios S, Dexeus D, Centeno-Mediavilla C, Coronado P, de la Fuente J, López JA, Vanrell C, Cortés J. Efficacy of a Coriolus versicolor-Based Vaginal Gel in Women With Human Papillomavirus-Dependent Cervical Lesions: The PALOMA Study. J Low Genit Tract Dis 2021; 25:130-136. [PMID: 33746195 PMCID: PMC7984756 DOI: 10.1097/lgt.0000000000000596] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The aim of the study was to evaluate the efficacy of Papilocare, a Coriolus versicolor-based vaginal gel, in repairing human papillomavirus (HPV)-related low-grade cervical lesions. METHODS The study is a multicenter, open-label, randomized, parallel-group, watchful waiting approach-controlled trial involving 91 HPV-positive women with low-grade Pap smear alterations and consistent colposcopy. RESULTS The percentage of patients with normal Pap smear and concordant colposcopy 3 and 6 months after receiving treatment (78.0% and 84.9%) was significantly higher than without treatment (54.8% and 64.5%), especially in high-risk HPV patients (79.5% and 87.8% vs 52.0% and 56.0%). At 6-month visit, overall HPV clearance was achieved by a greater number of patients receiving treatment (59.6%) compared with those without treatment (41.9%), especially high-risk HPV ones (62.5% vs 40.0%). The cervical re-epithelization score was significantly higher with treatment (mean = 4.5) than without (mean = 4.1). Compared with baseline, perceived stress decreased in the treatment group (from 21.1 to 19.0) and increased in the control group (from 17.7 to 20.7). A total of 7 possible or probable treatment-related adverse events were reported, most of them (n = 6) being mild or moderate in severity. CONCLUSIONS Treatment with Papilocare has demonstrated a better clinical benefit than the conventional watchful waiting approach in clinical practice for total and high-risk HPV patients in terms of its efficacy to treat HPV-related cervical lesions and to clear all HPV strains after a single 6-month period. It has demonstrated an adequate safety and tolerability and confers additional benefits such as higher re-epithelization, stress reduction, and high treatment adherence.
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Serrano L, Saad AR, DuCoin C, Velanovich V. After the hiatal hernia repair: fundoplication, yes or no? Partial or complete? Ann Laparosc Endosc Surg 2021. [DOI: 10.21037/ales.2020.03.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hernandez-Alias X, Benisty H, Schaefer MH, Serrano L. Translational adaptation of human viruses to the tissues they infect. Cell Rep 2021; 34:108872. [PMID: 33730572 PMCID: PMC7962955 DOI: 10.1016/j.celrep.2021.108872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
Viruses need to hijack the translational machinery of the host cell for a productive infection to happen. However, given the dynamic landscape of tRNA pools among tissues, it is unclear whether different viruses infecting different tissues have adapted their codon usage toward their tropism. Here, we collect the coding sequences of 502 human-infecting viruses and determine that tropism explains changes in codon usage. Using the tRNA abundances across 23 human tissues from The Cancer Genome Atlas (TCGA), we build an in silico model of translational efficiency that validates the correspondence of the viral codon usage with the translational machinery of their tropism. For instance, we detect that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is specifically adapted to the upper respiratory tract and alveoli. Furthermore, this correspondence is specifically defined in early viral proteins. The observed tissue-specific translational efficiency could be useful for the development of antiviral therapies and vaccines.
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Affiliation(s)
- Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Martin H Schaefer
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, Milan 20139, Italy.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain.
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Hernandez‐Alias X, Benisty H, Schaefer MH, Serrano L. Translational efficiency across healthy and tumor tissues is proliferation-related. Mol Syst Biol 2021; 17:e10097. [PMID: 33759329 PMCID: PMC7988298 DOI: 10.15252/msb.202010097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/27/2021] [Indexed: 11/09/2022] Open
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Head SA, Hernandez-Alias X, Yang JS, Ciampi L, Beltran-Sastre V, Torres-Méndez A, Irimia M, Schaefer MH, Serrano L. Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers. PLoS Biol 2021; 19:e3001138. [PMID: 33621242 PMCID: PMC7935315 DOI: 10.1371/journal.pbio.3001138] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 03/05/2021] [Accepted: 02/04/2021] [Indexed: 01/14/2023] Open
Abstract
RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3–27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the SF Serine/Arginine Repetitive Matrix 4 (SRRM4), whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here, we demonstrate that despite having low expression in normal nonneural tissues, SRRM4 is further silenced in tumors, resulting in the suppression of normal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced SF across all tumor types analyzed, implying a general advantage of microexon down-regulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and up-regulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and toward differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake. Using data from The Cancer Genome Atlas, this study shows that the splicing factor SRRM4 and its program of differentiation-promoting microexons are downregulated across tumor types with remarkable consistency, providing tumors with a proliferative advantage.
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Affiliation(s)
- Sarah A. Head
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jae-Seong Yang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Violeta Beltran-Sastre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Méndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Martin H. Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- * E-mail: (SAH); (MHS); (LS)
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
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Affiliation(s)
- Esther Rincón
- Departamento de Química Orgánica Universidad de Córdoba Córdoba Spain
- Departamento de Química Inorgánica e Ingeniería Química Universidad de Córdoba Córdoba Spain
| | - Alina M. Balu
- Departamento de Química Orgánica Universidad de Córdoba Córdoba Spain
| | - Rafael Luque
- Departamento de Química Orgánica Universidad de Córdoba Córdoba Spain
| | - Luis Serrano
- Departamento de Química Inorgánica e Ingeniería Química Universidad de Córdoba Córdoba Spain
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48
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Pickering KA, Gilroy K, Cassidy JW, Fey SK, Najumudeen AK, Zeiger LB, Vincent DF, Gay DM, Johansson J, Fordham RP, Miller B, Clark W, Hedley A, Unal EB, Kiel C, McGhee E, Machesky LM, Nixon C, Johnsson AE, Bain M, Strathdee D, van Hoof SR, Medema JP, Anderson KI, Brachmann SM, Stucke VM, Malliri A, Drysdale M, Turner M, Serrano L, Myant K, Campbell AD, Sansom OJ. A RAC-GEF network critical for early intestinal tumourigenesis. Nat Commun 2021; 12:56. [PMID: 33397922 PMCID: PMC7782582 DOI: 10.1038/s41467-020-20255-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/17/2020] [Indexed: 01/29/2023] Open
Abstract
RAC1 activity is critical for intestinal homeostasis, and is required for hyperproliferation driven by loss of the tumour suppressor gene Apc in the murine intestine. To avoid the impact of direct targeting upon homeostasis, we reasoned that indirect targeting of RAC1 via RAC-GEFs might be effective. Transcriptional profiling of Apc deficient intestinal tissue identified Vav3 and Tiam1 as key targets. Deletion of these indicated that while TIAM1 deficiency could suppress Apc-driven hyperproliferation, it had no impact upon tumourigenesis, while VAV3 deficiency had no effect. Intriguingly, deletion of either gene resulted in upregulation of Vav2, with subsequent targeting of all three (Vav2-/- Vav3-/- Tiam1-/-), profoundly suppressing hyperproliferation, tumourigenesis and RAC1 activity, without impacting normal homeostasis. Critically, the observed RAC-GEF dependency was negated by oncogenic KRAS mutation. Together, these data demonstrate that while targeting RAC-GEF molecules may have therapeutic impact at early stages, this benefit may be lost in late stage disease.
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Affiliation(s)
- K A Pickering
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - K Gilroy
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - J W Cassidy
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK
| | - S K Fey
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - A K Najumudeen
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - L B Zeiger
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - D F Vincent
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - D M Gay
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - J Johansson
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - R P Fordham
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - B Miller
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - W Clark
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - A Hedley
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - E B Unal
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRC), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - C Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRC), Barcelona, Spain
| | - E McGhee
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - L M Machesky
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - C Nixon
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - A E Johnsson
- The Babraham Institute, Babraham Hall, Babraham, Cambridge, CB22 3AT, UK
| | - M Bain
- IBAHCM and School of Veterinary Medicine, 464 Bearsden Road, Bearsden, Glasgow, G61 1QH, UK
| | - D Strathdee
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - S R van Hoof
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM) and Cancer Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
- Oncode Institute, Academic Medical Center, Amsterdam, The Netherlands
| | - J P Medema
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM) and Cancer Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
- Oncode Institute, Academic Medical Center, Amsterdam, The Netherlands
| | - K I Anderson
- The Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, UK
| | - S M Brachmann
- Novartis Institutes for BioMedical Research, Klybeckstrasse, 141, 4002, Basel, Switzerland
| | - V M Stucke
- Novartis Institutes for BioMedical Research, Klybeckstrasse, 141, 4002, Basel, Switzerland
| | - A Malliri
- CRUK Manchester Institute, 553 Wilmslow Road, Manchester, M20 4BX, UK
| | - M Drysdale
- Broad Institute, 415 Main St, Cambridge, MA, 02142, United States
| | - M Turner
- The Babraham Institute, Babraham Hall, Babraham, Cambridge, CB22 3AT, UK
| | - L Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRC), Barcelona, Spain
| | - K Myant
- Edinburgh Research Centre, The Institute of Genetics and Molecular Medicine, Crewe Road South, Edinburgh, EH4 2XR, UK.
| | - A D Campbell
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - O J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK.
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49
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Shaw D, Serrano L, Lluch-Senar M. Lox'd in translation: contradictions in the nomenclature surrounding common lox-site mutants and their implications in experiments. Microbiology (Reading) 2021; 167:000997. [PMID: 33284099 PMCID: PMC8116776 DOI: 10.1099/mic.0.000997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/13/2020] [Indexed: 11/20/2022]
Abstract
The Cre-Lox system is a highly versatile and powerful DNA recombinase mechanism, mainly used in genetic engineering to insert or remove desired DNA sequences. It is widely utilized across multiple fields of biology, with applications ranging from plants, to mammals, to microbes. A key feature of this system is its ability to allow recombination between mutant lox sites. Two of the most commonly used mutant sites are named lox66 and lox71, which recombine to create a functionally inactive double mutant lox72 site. However, a large portion of the published literature has incorrectly annotated these mutant lox sites, which in turn can lead to difficulties in replication of methods, design of proper vectors and confusion over the proper nomenclature. Here, we demonstrate common errors in annotations, the impacts they can have on experimental viability, and a standardized naming convention. We also show an example of how this incorrect annotation can induce toxic effects in bacteria that lack optimal DNA repair systems, exemplified by Mycoplasma pneumoniae.
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Affiliation(s)
- Daniel Shaw
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Pulmobiotics SL, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
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50
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Burgos R, Weber M, Martinez S, Lluch‐Senar M, Serrano L. Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. Mol Syst Biol 2020; 16:e9530. [PMID: 33320415 PMCID: PMC7737663 DOI: 10.15252/msb.20209530] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Protein degradation is a crucial cellular process in all-living systems. Here, using Mycoplasma pneumoniae as a model organism, we defined the minimal protein degradation machinery required to maintain proteome homeostasis. Then, we conditionally depleted the two essential ATP-dependent proteases. Whereas depletion of Lon results in increased protein aggregation and decreased heat tolerance, FtsH depletion induces cell membrane damage, suggesting a role in quality control of membrane proteins. An integrative comparative study combining shotgun proteomics and RNA-seq revealed 62 and 34 candidate substrates, respectively. Cellular localization of substrates and epistasis studies supports separate functions for Lon and FtsH. Protein half-life measurements also suggest a role for Lon-modulated protein decay. Lon plays a key role in protein quality control, degrading misfolded proteins and those not assembled into functional complexes. We propose that regulating complex assembly and degradation of isolated proteins is a mechanism that coordinates important cellular processes like cell division. Finally, by considering the entire set of proteases and chaperones, we provide a fully integrated view of how a minimal cell regulates protein folding and degradation.
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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