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Scala M, Tomati V, Ferla M, Lena M, Cohen JS, Fatemi A, Brokamp E, Bican A, Phillips JA, Koziura ME, Nicouleau M, Rio M, Siquier K, Boddaert N, Musante I, Tamburro S, Baldassari S, Iacomino M, Scudieri P, Rosenfeld JA, Bellus G, Reed S, Al Saif H, Russo RS, Walsh MB, Cantagrel V, Crunk A, Gustincich S, Ruggiero SM, Fitzgerald MP, Helbig I, Striano P, Severino M, Salpietro V, Pedemonte N, Zara F. De novo variants in DENND5B cause a neurodevelopmental disorder. Am J Hum Genet 2024; 111:529-543. [PMID: 38387458 PMCID: PMC10940048 DOI: 10.1016/j.ajhg.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
The Rab family of guanosine triphosphatases (GTPases) includes key regulators of intracellular transport and membrane trafficking targeting specific steps in exocytic, endocytic, and recycling pathways. DENND5B (Rab6-interacting Protein 1B-like protein, R6IP1B) is the longest isoform of DENND5, an evolutionarily conserved DENN domain-containing guanine nucleotide exchange factor (GEF) that is highly expressed in the brain. Through exome sequencing and international matchmaking platforms, we identified five de novo variants in DENND5B in a cohort of five unrelated individuals with neurodevelopmental phenotypes featuring cognitive impairment, dysmorphism, abnormal behavior, variable epilepsy, white matter abnormalities, and cortical gyration defects. We used biochemical assays and confocal microscopy to assess the impact of DENND5B variants on protein accumulation and distribution. Then, exploiting fluorescent lipid cargoes coupled to high-content imaging and analysis in living cells, we investigated whether DENND5B variants affected the dynamics of vesicle-mediated intracellular transport of specific cargoes. We further generated an in silico model to investigate the consequences of DENND5B variants on the DENND5B-RAB39A interaction. Biochemical analysis showed decreased protein levels of DENND5B mutants in various cell types. Functional investigation of DENND5B variants revealed defective intracellular vesicle trafficking, with significant impairment of lipid uptake and distribution. Although none of the variants affected the DENND5B-RAB39A interface, all were predicted to disrupt protein folding. Overall, our findings indicate that DENND5B variants perturb intracellular membrane trafficking pathways and cause a complex neurodevelopmental syndrome with variable epilepsy and white matter involvement.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Matteo Ferla
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Mariateresa Lena
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Nicouleau
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Marlene Rio
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France; Service de Génétique, Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Pairs, Paris, France
| | - Karine Siquier
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | - Nathalie Boddaert
- Département de Radiologie Pédiatrique, INSERM UMR 1163 and INSERM U1000, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Ilaria Musante
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | | | | | | | - Paolo Scudieri
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Gary Bellus
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Sara Reed
- Clinical Genetics, Geisinger Medical Center, Danville, PA 17822, USA
| | - Hind Al Saif
- Department of Human and Molecular Genetics, Division of Clinical Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | | | - Matthew B Walsh
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Vincent Cantagrel
- Université Paris Cité, Imagine Institute, Developmental Brain Disorders Laboratory, INSERM UMR 1163, 75015 Paris, France
| | | | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Sarah M Ruggiero
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark P Fitzgerald
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | | | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
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2
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Wang S, Zhang Y, Zhang L, Huang Y, Zhang J, Zhang K, Huang Y, Su G, Chen L, Yan B. Unraveling the complex dynamics of signaling molecules in cellular signal transduction. PNAS Nexus 2024; 3:pgae020. [PMID: 38274121 PMCID: PMC10810328 DOI: 10.1093/pnasnexus/pgae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Signaling molecules in cellular responses to foreign stimuli are described as static up- or down-concentration changes during signal transduction. This is because analytical methods for transducing molecules are much slower than the signaling events. In this study, we develop a dynamic cell model and reveal the temporal regulation of signal transduction events in response to reactive oxygen species (ROS). The model contained a set of 10 batches of redox-modified cells that mimic the temporal ROS accumulation events. Validating this dynamic cell model, we discover that cells survive early ROS attacks by activating the Nrf2/polysulfide/p62/CDK1 pathway. Nearly all signaling molecules exhibit time-dependent V-shape or inverse V-shape activation/feedback regulation dynamics in response to ROS accumulation. The results show that the dynamic cell model approach is invaluable for revealing complex signal intensity- and time-dependent cell signaling events.
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Affiliation(s)
- Shenqing Wang
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yi Zhang
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Liangwei Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yan Huang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jie Zhang
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Kena Zhang
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yujie Huang
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Bing Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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Wei J, Nie Y, Du H, Xu Y. Serine Improves Lactic Acid Stress Tolerance and Ethanol Production in Zygosaccharomyces bailii in Baijiu Fermentation. J Agric Food Chem 2023; 71:20295-20303. [PMID: 37929595 DOI: 10.1021/acs.jafc.3c06246] [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] [Indexed: 11/07/2023]
Abstract
Lactic acid is the primary inhibitor of the growth and ethanol production of yeasts in Baijiu fermentation. Certain amino acids have been found to be related to stress tolerance in yeasts. This study explored the effect of lactic acid stress on the ethanol-producing yeast Zygosaccharomyces bailii and evaluated the ability of serine to increase the lactic acid tolerance of Z. bailii in vitro. Serine significantly improved Z. bailii viability by 16.5% and ethanol production by 226.6% under lactic acid stress. Under lactic acid stress, serine supplementation led to an increase of 41.9% in cell wall integrity, 31.9% in cell membrane integrity, 296.6% in intracellular adenosine triphosphate (ATP), and 18.4% in the mitochondrial membrane potential. Finally, field emission scanning electron microscopy (FESEM) indicated that serine supplementation maintained the cell shape and reduced cell leakage. This study revealed a novel lactic acid tolerance mechanism of core functional yeasts during Jiang-flavor Baijiu fermentation.
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Affiliation(s)
- Junlin Wei
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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4
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Povo-Retana A, Landauro-Vera R, Fariñas M, Sánchez-García S, Alvarez-Lucena C, Marin S, Cascante M, Boscá L. Defining the metabolic signatures associated with human macrophage polarisation. Biochem Soc Trans 2023; 51:1429-1436. [PMID: 37449892 PMCID: PMC10586766 DOI: 10.1042/bst20220504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Macrophages are essential components of the innate immune system that play both homeostatic roles in healthy organs, and host defence functions against pathogens after tissue injury. To accomplish their physiological role, macrophages display different profiles of gene expression, immune function, and metabolic phenotypes that allow these cells to participate in different steps of the inflammatory reaction, from the initiation to the resolution phase. In addition, significant differences exist in the phenotype of macrophages depending on the tissue in which they are present and on the mammalian species. From a metabolic point of view, macrophages are essentially glycolytic cells; however, their metabolic fluxes are dependent on the functional polarisation of these cells. This metabolic and cellular plasticity offers the possibility to interfere with the activity of macrophages to avoid harmful effects due to persistent activation or the release of molecules that delay tissue recovery after injury.
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Affiliation(s)
- Adrián Povo-Retana
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - Rodrigo Landauro-Vera
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - Marco Fariñas
- Department of Biochemistry and Molecular Biomedicine-Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Sergio Sánchez-García
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - Carlota Alvarez-Lucena
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine-Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine-Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Lisardo Boscá
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
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5
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Fort L. Messenger functions of cell death during development and homeostasis. Biochem Soc Trans 2023; 51:759-769. [PMID: 37021685 DOI: 10.1042/bst20220925] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 04/27/2023]
Abstract
In our human society, would you not want to know if your neighbor suddenly passed away? Tissues and cells are not that different. Cell death is an inevitable part of tissue homeostasis and comes in different flavors that can either be a consequence of an injury or a regulated phenomenon (such as programed cell death). Historically, cell death was viewed as a way to discard cells, without functional consequences. Today, this view has evolved and recognizes an extra layer of complexity: dying cells can provide physical or chemical signals to notify their neighbors. Like any type of communication, signals can only be read if surrounding tissues have evolved to recognize them and functionally adapt. This short review aims to provide a summary of recent work interrogating the messenger functions and consequences of cell death in various model organisms.
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Affiliation(s)
- Loic Fort
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, U.S.A
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6
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Romero-Olivares AL, Frey SD, Treseder KK. Tracking fungal species-level responses in soil environments exposed to long-term warming and associated drying. FEMS Microbiol Lett 2023; 370:fnad128. [PMID: 38059856 DOI: 10.1093/femsle/fnad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Climate change is affecting fungal communities and their function in terrestrial ecosystems. Despite making progress in the understanding of how the fungal community responds to global change drivers in natural ecosystems, little is known on how fungi respond at the species level. Understanding how fungal species respond to global change drivers, such as warming, is critical, as it could reveal adaptation pathways to help us to better understand ecosystem functioning in response to global change. Here, we present a model study to track species-level responses of fungi to warming-and associated drying-in a decade-long global change field experiment; we focused on two free-living saprotrophic fungi which were found in high abundance in our site, Mortierella and Penicillium. Using microbiological isolation techniques, combined with whole genome sequencing of fungal isolates, and community level metatranscriptomics, we investigated transcription-level differences of functional categories and specific genes involved in catabolic processes, cell homeostasis, cell morphogenesis, DNA regulation and organization, and protein biosynthesis. We found that transcription-level responses were mostly species-specific but that under warming, both fungi consistently invested in the transcription of critical genes involved in catabolic processes, cell morphogenesis, and protein biosynthesis, likely allowing them to withstand a decade of chronic stress. Overall, our work supports the idea that fungi that invest in maintaining their catabolic rates and processes while growing and protecting their cells may survive under global climate change.
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Affiliation(s)
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, Unites States
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, United States
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Roberty S, Plumier JC. Bleaching physiology: who's the 'weakest link' - host vs. symbiont? Emerg Top Life Sci 2022:ETLS20210228. [PMID: 35179208 DOI: 10.1042/ETLS20210228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
Abstract
Environmental stress, such as an increase in the sea surface temperature, triggers coral bleaching, a profound dysfunction of the mutualist symbiosis between the host cnidarians and their photosynthetic dinoflagellates of the Family Symbiodiniaceae. Because of climate change, mass coral bleaching events will increase in frequency and severity in the future, threatening the persistence of this iconic marine ecosystem at global scale. Strategies adapted to coral reefs preservation and restoration may stem from the identification of the succession of events and of the different molecular and cellular contributors to the bleaching phenomenon. To date, studies aiming to decipher the cellular cascade leading to temperature-related bleaching, emphasized the involvement of reactive species originating from compromised bioenergetic pathways (e.g. cellular respiration and photosynthesis). These molecules are responsible for damage to various cellular components causing the dysregulation of cellular homeostasis and the breakdown of symbiosis. In this review, we synthesize the current knowledge available in the literature on the cellular mechanisms caused by thermal stress, which can initiate or participate in the cell cascade leading to the loss of symbionts, with a particular emphasis on the role of each partner in the initiating processes.
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Sidibé A, Charles MT, Lucier JF, Xu Y, Beaulieu C. Preharvest UV-C Hormesis Induces Key Genes Associated With Homeostasis, Growth and Defense in Lettuce Inoculated With Xanthomonas campestris pv. vitians. Front Plant Sci 2022; 12:793989. [PMID: 35111177 PMCID: PMC8801786 DOI: 10.3389/fpls.2021.793989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Preharvest application of hormetic doses of ultraviolet-C (UV-C) generates beneficial effects in plants. In this study, within 1 week, four UV-C treatments of 0.4 kJ/m2 were applied to 3-week-old lettuce seedlings. The leaves were inoculated with a virulent strain of Xanthomonas campestris pv. vitians (Xcv) 48 h after the last UV-C application. The extent of the disease was tracked over time and a transcriptomic analysis was performed on lettuce leaf samples. Samples of lettuce leaves, from both control and treated groups, were taken at two different times corresponding to T2, 48 h after the last UV-C treatment and T3, 24 h after inoculation (i.e., 72 h after the last UV-C treatment). A significant decrease in disease severity between the UV-C treated lettuce and the control was observed on days 4, 8, and 14 after pathogen inoculation. Data from the transcriptomic study revealed, that in response to the effect of UV-C alone and/or UV-C + Xcv, a total of 3828 genes were differentially regulated with fold change (|log2-FC|) > 1.5 and false discovery rate (FDR) < 0.05. Among these, of the 2270 genes of known function 1556 were upregulated and 714 were downregulated. A total of 10 candidate genes were verified by qPCR and were generally consistent with the transcriptomic results. The differentially expressed genes observed in lettuce under the conditions of the present study were associated with 14 different biological processes in the plant. These genes are involved in a series of metabolic pathways associated with the ability of lettuce treated with hormetic doses of UV-C to resume normal growth and to defend themselves against potential stressors. The results indicate that the hormetic dose of UV-C applied preharvest on lettuce in this study, can be considered as an eustress that does not interfere with the ability of the treated plants to carry on a set of key physiological processes namely: homeostasis, growth and defense.
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Affiliation(s)
- Amadou Sidibé
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Thérèse Charles
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | | | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agri-Food Processing, Zhejiang University, Hangzhou, China
| | - Carole Beaulieu
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
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Harding BW, Ewbank JJ. An integrated view of innate immune mechanisms in C. elegans. Biochem Soc Trans 2021; 49:2307-17. [PMID: 34623403 DOI: 10.1042/BST20210399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022]
Abstract
The simple notion 'infection causes an immune response' is being progressively refined as it becomes clear that immune mechanisms cannot be understood in isolation, but need to be considered in a more global context with other cellular and physiological processes. In part, this reflects the deployment by pathogens of virulence factors that target diverse cellular processes, such as translation or mitochondrial respiration, often with great molecular specificity. It also reflects molecular cross-talk between a broad range of host signalling pathways. Studies with the model animal C. elegans have uncovered a range of examples wherein innate immune responses are intimately connected with different homeostatic mechanisms, and can influence reproduction, ageing and neurodegeneration, as well as various other aspects of its biology. Here we provide a short overview of a number of such connections, highlighting recent discoveries that further the construction of a fully integrated view of innate immunity.
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Yu H, Yang Z, Sui M, Cui C, Hu Y, Hou X, Xing Q, Huang X, Bao Z. Identification and Characterization of HSP90 Gene Family Reveals Involvement of HSP90, GRP94 and Not TRAP1 in Heat Stress Response in Chlamys farreri. Genes (Basel) 2021; 12:1592. [PMID: 34680986 PMCID: PMC8535295 DOI: 10.3390/genes12101592] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/15/2023] Open
Abstract
Heat shock proteins 90 (HSP90s) are a class of ubiquitous, highly conserved, and multi-functional molecular chaperones present in all living organisms. They assist protein folding processes to form functional proteins. In the present study, three HSP90 genes, CfHSP90, CfGRP94 and CfTRAP1, were successfully identified in the genome of Chlamys farreri. The length of CfHSP90, CfGRP94 and CfTRAP1 were 7211 bp, 26,457 bp, and 28,699 bp, each containing an open reading frame (ORF) of 2181 bp, 2397 bp, and 2181 bp, and encoding proteins of 726, 798, and 726 amino acids, respectively. A transcriptomic database demonstrated that CfHSP90 and CfGRP94 were the primary functional executors with high expression during larval development and in adult tissues, while CfTRAP1 expression was low. Furthermore, all of the three CfHSP90s showed higher expression in gonads and ganglia as compared with other tissues, which indicated their probable involvement in gametogenesis and nerve signal transmission in C. farreri. In addition, under heat stress, the expressions of CfHSP90 and CfGRP94 were significantly up-regulated in the mantle, gill, and blood, but not in the heart. Nevertheless, the expression of CfTRAP1 did not change significantly in the four tested tissues. Taken together, in coping with heat stress, CfHSP90 and CfGRP94 could help correct protein folding or salvage damaged proteins for cell homeostasis in C. farreri. Collectively, a comprehensive analysis of CfHSP90s in C. farreri was conducted. The study indicates the functional diversity of CfHSP90s in growth, development, and environmental response, and our findings may have implications for the subsequent in-depth exploration of HSP90s in invertebrates.
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Affiliation(s)
- Haitao Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Mingyi Sui
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Chang Cui
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Yuqing Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (H.Y.); (Z.Y.); (M.S.); (C.C.); (Y.H.); (X.H.); (Q.X.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, SANYA Oceanographic Institution of the Ocean University of CHINA (SOI-OUC), Sanya 572000, China
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11
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Yang Z, Li Z, Teasdale RD. Retromer dependent changes in cellular homeostasis and Parkinson's disease. Essays Biochem 2021:EBC20210023. [PMID: 34528672 DOI: 10.1042/EBC20210023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022]
Abstract
To date, mechanistic treatments targeting the initial cause of Parkinson's disease (PD) are limited due to the underlying biological cause(s) been unclear. Endosomes and their associated cellular homeostasis processes have emerged to have a significant role in the pathophysiology associated with PD. Several variants within retromer complex have been identified and characterised within familial PD patients. The retromer complex represents a key sorting platform within the endosomal system that regulates cargo sorting that maintains cellular homeostasis. In this review, we summarise the current understandings of how PD-associated retromer variants disrupt cellular trafficking and how the retromer complex can interact with other PD-associated genes to contribute to the disease progression.
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12
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Arif Y, Singh P, Bajguz A, Hayat S. Phytocannabinoids Biosynthesis in Angiosperms, Fungi, and Liverworts and Their Versatile Role. Plants (Basel) 2021; 10:1307. [PMID: 34203173 PMCID: PMC8309193 DOI: 10.3390/plants10071307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022]
Abstract
Phytocannabinoids are a structurally diverse class of bioactive naturally occurring compounds found in angiosperms, fungi, and liverworts and produced in several plant organs such as the flower and glandular trichrome of Cannabis sativa, the scales in Rhododendron, and oil bodies of liverworts such as Radula species; they show a diverse role in humans and plants. Moreover, phytocannabinoids are prenylated polyketides, i.e., terpenophenolics, which are derived from isoprenoid and fatty acid precursors. Additionally, targeted productions of active phytocannabinoids have beneficial properties via the genes involved and their expression in a heterologous host. Bioactive compounds show a remarkable non-hallucinogenic biological property that is determined by the variable nature of the side chain and prenyl group defined by the enzymes involved in their biosynthesis. Phytocannabinoids possess therapeutic, antibacterial, and antimicrobial properties; thus, they are used in treating several human diseases. This review gives the latest knowledge on their role in the amelioration of abiotic (heat, cold, and radiation) stress in plants. It also aims to provide synthetic and biotechnological approaches based on combinatorial biochemical and protein engineering to synthesize phytocannabinoids with enhanced properties.
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Affiliation(s)
- Yamshi Arif
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (Y.A.); (P.S.); (S.H.)
| | - Priyanka Singh
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (Y.A.); (P.S.); (S.H.)
| | - Andrzej Bajguz
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
| | - Shamsul Hayat
- Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India; (Y.A.); (P.S.); (S.H.)
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13
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Armaos A, Zacco E, Sanchez de Groot N, Tartaglia GG. RNA-protein interactions: Central players in coordination of regulatory networks. Bioessays 2020; 43:e2000118. [PMID: 33284474 DOI: 10.1002/bies.202000118] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Changes in the abundance of protein and RNA molecules can impair the formation of complexes in the cell leading to toxicity and death. Here we exploit the information contained in protein, RNA and DNA interaction networks to provide a comprehensive view of the regulation layers controlling the concentration-dependent formation of assemblies in the cell. We present the emerging concept that RNAs can act as scaffolds to promote the formation ribonucleoprotein complexes and coordinate the post-transcriptional layer of gene regulation. We describe the structural and interaction network properties that characterize the ability of protein and RNA molecules to interact and phase separate in liquid-like compartments. Finally, we show that presence of structurally disordered regions in proteins correlate with the propensity to undergo liquid-to-solid phase transitions and cause human diseases. Also see the video abstract here https://youtu.be/kfpqibsNfS0.
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Affiliation(s)
- Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Elsa Zacco
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Natalia Sanchez de Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Biology 'Charles Darwin', Sapienza University of Rome, Rome, Italy.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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14
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Morin G, Pinel K, Dias K, Seiliez I, Beaumatin F. RTH-149 Cell Line, a Useful Tool to Decipher Molecular Mechanisms Related to Fish Nutrition. Cells 2020; 9:cells9081754. [PMID: 32707879 PMCID: PMC7463835 DOI: 10.3390/cells9081754] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 06/22/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Nowadays, aquaculture provides more than 50% of fish consumed worldwide but faces new issues that challenge its sustainability. One of them relies on the replacement of fish meal (FM) in aquaculture feeds by other protein sources without deeply affecting the whole organism's homeostasis. Multiple strategies have already been tested using in vivo approaches, but they hardly managed to cope with the multifactorial problems related to the complexities of fish biology together with new feed formulations. In this context, rainbow trout (RT) is particularly concerned by these problems, since, as a carnivorous fish, dietary proteins provide the amino acids required to supply most of its energetic metabolism. Surprisingly, we noticed that in vitro approaches considering RT cell lines as models to study RT amino acid metabolism were never previously used. Therefore, we decided to investigate if, and how, three major pathways described, in other species, to be regulated by amino acid and to control cellular homeostasis were functional in a RT cell line called RTH-149-namely, the mechanistic Target Of Rapamycin (mTOR), autophagy and the general control nonderepressible 2 (GCN2) pathways. Our results not only demonstrated that these three pathways were functional in RTH-149 cells, but they also highlighted some RT specificities with respect to the time response, amino acid dependencies and the activation levels of their downstream targets. Altogether, this article demonstrated, for the first time, that RT cell lines could represent an interesting alternative of in vivo experimentations for the study of fish nutrition-related questions.
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15
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Medina MV, Sapochnik D, Garcia Solá M, Coso O. Regulation of the Expression of Heme Oxygenase-1: Signal Transduction, Gene Promoter Activation, and Beyond. Antioxid Redox Signal 2020; 32:1033-1044. [PMID: 31861960 PMCID: PMC7153632 DOI: 10.1089/ars.2019.7991] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 02/06/2023]
Abstract
Significance: Heme oxygenase-1 (HO-1) is a ubiquitous 32-kDa protein expressed in many tissues and highly inducible. They catalyze the degradation of the heme group and the release of free iron, carbon monoxide, and biliverdin; the latter converted to bilirubin by biliverdin reductase. Its role in the regulation of cellular homeostasis is widely documented. Studying regulation of HO-1 expression is important not only to understand the life of healthy cells but also the unbalances in cell metabolism that lead to disease. Recent Advances: The regulation of its enzymatic activity depends heavily upon changes in expression studied mainly at the transcriptional level. Current knowledge regarding HO-1 gene expression focuses primarily on transcription factors such as Nrf2 (nuclear factor erythroid 2-related factor 2), AP-1 (activator protein-1), and hypoxia-inducible factor, which collect signal transduction pathway information at the HO-1 gene promoter. Understanding of gene expression regulation is not limited to transcription factor activity but also involves an extended range of post- or cotranscriptional regulated events. Critical Issues: In addition to the regulation of gene promoter activity, alternative splicing, alternative polyadenylation, and regulation of messenger RNA stability play critical roles in changes in HO-1 gene expression levels, involving specific factors, proteins, and microRNAs. All potential targets for diagnosis or treatment of diseases are related to HO-1 dysregulation. Future Directions: Unbalances in the tightly regulated gene expression mechanisms lead to cell transformation and cancer development. Knowledge of these events and signal transduction cascades triggered by oncogenes in which HO-1 plays a critical role is of upmost importance for research in this field.
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Affiliation(s)
- María Victoria Medina
- Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daiana Sapochnik
- Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martín Garcia Solá
- Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Omar Coso
- Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Parlato R, Tucker KL. Editorial: Emerging Cellular Stress Sensors in Neurological Disorders: Closing in on the Nucleolus and the Primary Cilium. Front Cell Neurosci 2020; 14:64. [PMID: 32265665 PMCID: PMC7100531 DOI: 10.3389/fncel.2020.00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/04/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Ulm, Germany.,Institute of Anatomy and Cell Biology, Department of Medical Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Kerry L Tucker
- Department of Biomedical Sciences, Center for Excellence in the Neurosciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, United States
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17
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Cordaro M, Cuzzocrea S, Crupi R. An Update of Palmitoylethanolamide and Luteolin Effects in Preclinical and Clinical Studies of Neuroinflammatory Events. Antioxidants (Basel) 2020; 9:antiox9030216. [PMID: 32150935 PMCID: PMC7139331 DOI: 10.3390/antiox9030216] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 01/29/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
The inflammation process represents of a dynamic series of phenomena that manifest themselves with an intense vascular reaction. Neuroinflammation is a reply from the central nervous system (CNS) and the peripheral nervous system (PNS) to a changed homeostasis. There are two cell systems that mediate this process: the glia of the CNS and the lymphocites, monocytes, and macrophages of the hematopoietic system. In both the peripheral and central nervous systems, neuroinflammation plays an important role in the pathogenesis of neurodegenerative diseases, such as Parkinson’s and Alzheimer’s diseases, and in neuropsychiatric illnesses, such as depression and autism spectrum disorders. The resolution of neuroinflammation is a process that allows for inflamed tissues to return to homeostasis. In this process the important players are represented by lipid mediators. Among the naturally occurring lipid signaling molecules, a prominent role is played by the N-acylethanolamines, namely N-arachidonoylethanolamine and its congener N-palmitoylethanolamine, which is also named palmitoylethanolamide or PEA. PEA possesses a powerful neuroprotective and anti-inflammatory power but has no antioxidant effects per se. For this reason, its co-ultramicronization with the flavonoid luteolin is more efficacious than either molecule alone. Inhibiting or modulating the enzymatic breakdown of PEA represents a complementary therapeutic approach to treating neuroinflammation. The aim of this review is to discuss the role of ultramicronized PEA and co-ultramicronized PEA with luteolin in several neurological diseases using preclinical and clinical approaches.
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Affiliation(s)
- Marika Cordaro
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98100 Messina, Italy;
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Via F. Stagno D’Alcontres 31, 98166 Messina, Italy;
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, MO 63103, USA
- Correspondence: ; Tel.: +390-906-765-208
| | - Rosalia Crupi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Via F. Stagno D’Alcontres 31, 98166 Messina, Italy;
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18
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Morris AR, Stanton DL, Roman D, Liu AC. Systems Level Understanding of Circadian Integration with Cell Physiology. J Mol Biol 2020; 432:3547-3564. [PMID: 32061938 DOI: 10.1016/j.jmb.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 11/05/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
The mammalian circadian clock regulates a wide variety of physiological and behavioral processes. In turn, its disruption is associated with sleep deficiency, metabolic syndrome, neurological and psychiatric disorders, and cancer. At the turn of the century, the circadian clock was determined to be regulated by a transcriptional negative feedback mechanism composed of a dozen core clock genes. More recently, large-scale genomic studies have expanded the clock into a complex network composed of thousands of gene outputs and inputs. A major task of circadian research is to utilize systems biological approaches to uncover the governing principles underlying cellular oscillatory behavior and advance understanding of biological functions at the genomic level with spatiotemporal resolution. This review focuses on the genes and pathways that provide inputs to the circadian clock. Several emerging examples include AMP-activated protein kinase AMPK, nutrient/energy sensor mTOR, NAD+-dependent deacetylase SIRT1, hypoxia-inducible factor HIF1α, oxidative stress-inducible factor NRF2, and the proinflammatory factor NF-κB. Among others that continue to be revealed, these input pathways reflect the extensive interplay between the clock and cell physiology through the regulation of core clock genes and proteins. While the scope of this crosstalk is well-recognized, precise molecular links are scarce, and the underlying regulatory mechanisms are not well understood. Future research must leverage genetic and genomic tools and technologies, network analysis, and computational modeling to characterize additional modifiers and input pathways. This systems-based framework promises to advance understanding of the circadian timekeeping system and may enable the enhancement of circadian functions through related input pathways.
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Affiliation(s)
- Andrew R Morris
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Daniel L Stanton
- Department of Animal Sciences, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, United States of America
| | - Destino Roman
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Andrew C Liu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States of America.
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19
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Jakubovics NS. An ion for an iron: streptococcal metal homeostasis under oxidative stress. Biochem J 2019; 476:699-703. [PMID: 30819932 DOI: 10.1042/BCJ20190017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 11/17/2022]
Abstract
The ability of opportunistic pathogens such as Group A Streptococcus (GAS) to transition between mucosal colonisation and invasive disease requires complex systems for adapting to markedly different host environments. The battle to acquire essential trace metals such as manganese and iron from the host is central to pathogenesis. Using a molecular genetic approach, Turner et al. [Biochem. J. (2019) 476, 595-611] show that it is not just individual metal concentrations that are important, but the ratio of iron to manganese within cells. Increasing this ratio by knocking out pmtA, encoding the Fe(II) exporter PmtA, or by disrupting mtsA, encoding an MtsABC Mn(II)-import system component, led to reductions in superoxide dismutase (SodA) activity and increased sensitivity to oxidative stress. The authors show that SodA is at least 4-fold more active with Mn bound than with Fe and speculate that high intracellular Fe:Mn ratios reduce superoxide dismutase activity through the mismetalation of SodA. Challenging wild-type GAS with 1 mM H2O2 led to a decrease in Fe:Mn ratio and a 3-fold increase in SodA activity, indicating that modulation of the balance between intracellular Fe and Mn may play an important role in adaptation to oxidative stress. This work unravels some of the key mechanisms for maintaining appropriate Mn and Fe concentrations within bacterial cells and underscores the need for future studies that take an holistic view to metal ion homeostasis in bacteria. Strategies aimed at interfering with the balance of intracellular metal ions represent a promising approach for the control of invasive microbial infections.
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20
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Affandi T, McEvoy MM. Mechanism of metal ion-induced activation of a two-component sensor kinase. Biochem J 2019; 476:115-35. [PMID: 30530842 DOI: 10.1042/BCJ20180577] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Two-component systems (TCSs) are essential for bacteria to sense, respond, and adapt to changing environments, such as elevation of Cu(I)/Ag(I) ions in the periplasm. In Escherichia coli, the CusS-CusR TCS up-regulates the cusCFBA genes under increased periplasmic Cu(I)/Ag(I) concentrations to help maintain metal ion homeostasis. The CusS histidine kinase is a homodimeric integral membrane protein that binds to periplasmic Cu(I)/Ag(I) and transduces a signal to its cytoplasmic kinase domain. However, the mechanism of how metal binding in the periplasm activates autophosphorylation in the cytoplasm is unknown. Here, we report that only one of the two metal ion-binding sites in CusS enhances dimerization of the sensor domain. Utilizing nanodisc technology to study full-length CusS, we show that metal-induced dimerization in the sensor domain triggers kinase activity in the cytoplasmic domain. We also investigated autophosphorylation in the cytoplasmic domain of CusS and phosphotransfer between CusS and CusR. In vitro analyses show that CusS autophosphorylates its conserved H271 residue at the N1 position of the histidine imidazole. The phosphoryl group is removed by the response regulator CusR in a reaction that requires a conserved aspartate at position 51. Functional analyses in vivo of CusS and CusR variants with mutations in the autophosphorylation or phosphoacceptor residues suggest that the phosphotransfer event is essential for metal resistance in E. coli Biochemical analysis shows that the CusS dimer autophosphorylates using a cis mechanism. Our results support a signal transduction model in which rotation and bending movements in the cytoplasmic domain maintain the mode of autophosphorylation.
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21
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Abstract
Macroautophagy/autophagy is vital for intracellular quality control and homeostasis. Therefore, careful regulation of autophagy is very important. In the past 10 years, a number of studies have reported that estrogenic effectors affect autophagy. However, some results, especially those regarding the modulatory effect of 17β-estradiol (E2) on autophagy seem inconsistent. Moreover, several clinical trials are already in place combining both autophagy inducers and autophagy inhibitors with endocrine therapies for breast cancer. Not all patients experience benefit, which further confuses and complicates our understanding of the main effects of autophagy in estrogen-related cancer. In view of the importance of the crosstalk between estrogen signaling and autophagy, this review summarizes the estrogenic effectors reported to affect autophagy, subcellular distribution and translocation of estrogen receptors, autophagy-targeted transcription factors (TFs), miRNAs, and histone modifications regulated by E2. Upon stimulation with estrogen, there will always be opposing functional actions, which might occur between different receptors, receptors on TFs, TFs on autophagy genes, or even histone modifications on transcription. The huge signaling network downstream of estrogen can promote autophagy and reduce overstimulated autophagy at the same time, which allows autophagy to be regulated by estrogen in a restricted range. To help understand how the estrogenic regulation of autophagy affects cell fate, a hypothetical model is presented here. Finally, we discuss some exciting new directions in the field. We hope this might help to better understand the multiple associations between estrogen and autophagy, the pathogenic mechanisms of many estrogen-related diseases, and to design novel and efficacious therapeutics. Abbreviations: AP-1, activator protein-1; HATs, histone acetyltransferases; HDAC, histone deacetylases; HOTAIR, HOX transcript antisense RNA.
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Affiliation(s)
- Jin Xiang
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Xiang Liu
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Jing Ren
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Kun Chen
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Hong-Lu Wang
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Yu-Yang Miao
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Miao-Miao Qi
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
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22
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Abstract
Macroautophagy/autophagy is a catabolic process that is essential for cellular homeostasis. How autophagosomal vesicle forms in a spatio-temporally regulated manner remains elusive. Our recent study revealed that small GTPase, RAB37 (RAB37, member RAS oncogene family), functions as a key organizer of autophagosomal membrane biogenesis. RAB37 interacts with ATG5 (autophagy related 5) and promotes autophagosome formation by modulating ATG12-ATG5-ATG16L1 complex assembly. These findings provide new insights into autophagy regulation.
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Affiliation(s)
- Ying Song
- a Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences , Wuhan University , Wuhan , China
| | - Dantong Shang
- a Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences , Wuhan University , Wuhan , China
| | - Hanhua Cheng
- a Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences , Wuhan University , Wuhan , China
| | - Rongjia Zhou
- a Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences , Wuhan University , Wuhan , China
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23
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Abstract
Essays in Biochemistry volume 61 (issue 6), entitled Signalling Mechanisms in Autophagy, covers a range of topics in autophagy signalling, touching on emerging new details on the mechanisms of autophagy regulation, novel aspects of selective autophagy and how autophagy functions in organelle homeostasis. It also looks at how autophagy research is leading to better understanding of human disease and plant biology that can be exploited for the benefit of society.
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24
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Martinez Guimera A, Welsh C, Dalle Pezze P, Fullard N, Nelson G, Roger MF, Przyborski SA, Shanley DP. Systems modelling ageing: from single senescent cells to simple multi-cellular models. Essays Biochem 2017; 61:369-77. [PMID: 28698310 DOI: 10.1042/EBC20160087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 01/10/2023]
Abstract
Systems modelling has been successfully used to investigate several key molecular mechanisms of ageing. Modelling frameworks to allow integration of models and methods to enhance confidence in models are now well established. In this article, we discuss these issues and work through the process of building an integrated model for cellular senescence as a single cell and in a simple tissue context.
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Tundo GR, Sbardella D, Ciaccio C, Grasso G, Gioia M, Coletta A, Polticelli F, Di Pierro D, Milardi D, Van Endert P, Marini S, Coletta M. Multiple functions of insulin-degrading enzyme: a metabolic crosslight? Crit Rev Biochem Mol Biol 2017. [PMID: 28635330 DOI: 10.1080/10409238.2017.1337707] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degrade several other polypeptides, such as β-amyloid, amylin, and glucagon, envisaging the possible implication of IDE dys-regulation in the "aggregopathies" and, in particular, in neurodegenerative diseases. Over the last decade, a novel scenario on IDE biology has emerged, pointing out a multi-functional role of this enzyme in several basic cellular processes. In particular, latest advances indicate that IDE behaves as a heat shock protein and modulates the ubiquitin-proteasome system, suggesting a major implication in proteins turnover and cell homeostasis. In addition, recent observations have highlighted that the regulation of glucose metabolism by IDE is not merely based on its largely proposed role in the degradation of insulin in vivo. There is increasing evidence that improper IDE function, regulation, or trafficking might contribute to the etiology of metabolic diseases. In addition, the enzymatic activity of IDE is affected by metals levels, thus suggesting a role also in the metal homeostasis (metallostasis), which is thought to be tightly linked to the malfunction of the "quality control" machinery of the cell. Focusing on the physiological role of IDE, we will address a comprehensive vision of the very complex scenario in which IDE takes part, outlining its crucial role in interconnecting several relevant cellular processes.
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Affiliation(s)
- Grazia R Tundo
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Diego Sbardella
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Chiara Ciaccio
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Giuseppe Grasso
- d Department of Chemistry , University of Catania , Catania , Italy.,e CNR IBB , Catania , Italy
| | - Magda Gioia
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Andrea Coletta
- f Department of Chemistry , University of Aarhus , Aarhus , Denmark
| | | | - Donato Di Pierro
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | | | - Peter Van Endert
- h Université Paris Descartes, INSERM, U1151, CNRS , Paris , France
| | - Stefano Marini
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Massimo Coletta
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
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Abstract
The upregulation of autophagosome formation in response to nutrient deprivation requires significant intracellular membrane rearrangements that are poorly understood. Recent findings have implicated COPII-coated vesicles, well known as ER-Golgi cargo transport carriers, as key players in macroautophagy. The role of COPII vesicles in macroautophagy and how they interact with autophagy-related (Atg) proteins was unknown. In our recent report, we show that during nutrient deprivation, phosphorylation of the membrane-distal surface of the COPII coat subunit Sec24 facilitates the interaction of Sec24 with the Atg machinery (specifically, Atg9) to regulate the abundance of autophagosomes during starvation. Phosphorylation of Sec24 is specifically required for macroautophagy, but not ER-Golgi transport. These findings begin to unravel the unique function of COPII vesicles during starvation-induced macroautophagy.
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Affiliation(s)
- Juan Wang
- a College of Life Science and Bioengineering , Beijing University of Technology , Beijing , China
| | - Saralin Davis
- b Department of Cellular and Molecular Medicine , University of California at San Diego , La Jolla , CA , USA
| | - Ming Zhu
- b Department of Cellular and Molecular Medicine , University of California at San Diego , La Jolla , CA , USA
| | | | - Susan Ferro-Novick
- b Department of Cellular and Molecular Medicine , University of California at San Diego , La Jolla , CA , USA
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [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] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Lemoine R, Pachlopnik-Schmid J, Farin HF, Bigorgne A, Debré M, Sepulveda F, Héritier S, Lemale J, Talbotec C, Rieux-Laucat F, Ruemmele F, Morali A, Cathebras P, Nitschke P, Bole-Feysot C, Blanche S, Brousse N, Picard C, Clevers H, Fischer A, de Saint Basile G. Immune deficiency-related enteropathy-lymphocytopenia-alopecia syndrome results from tetratricopeptide repeat domain 7A deficiency. J Allergy Clin Immunol 2014; 134:1354-1364.e6. [PMID: 25174867 DOI: 10.1016/j.jaci.2014.07.019] [Citation(s) in RCA: 50] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/04/2014] [Accepted: 07/12/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is one of the most common chronic gastrointestinal diseases, but the underlying molecular mechanisms remain largely unknown. Studies of monogenic diseases can provide insight into the pathogenesis of IBD. OBJECTIVE We thought to determine the underlying molecular causes of IBD occurring in 2 unrelated families in association with an immune deficiency. METHODS We performed genetic linkage analysis and candidate gene sequencing on 13 patients from a large consanguineous family affected by early-onset IBD, progressive immune deficiency, and, in some cases, autoimmunity and alopecia, a condition we named enteropathy-lymphocytopenia-alopecia. The candidate gene was also sequenced in an unrelated patient with a similar phenotype. We performed histologic analysis of patients' intestinal biopsy specimens and carried out functional assays on PBMCs. Gut organoids derived from a patient's biopsy specimen were analyzed. RESULTS We identified biallelic missense mutations in tetratricopeptide repeat domain 7A (TTC7A) in all patients from both families. The resulting TTC7A depletion modified the proliferation, adhesion, and migratory capacities of lymphocytes through inappropriate activation of the RhoA signaling pathway. Normal function was restored by wild-type TTC7A expression or addition of a RhoA kinase inhibitor. The growth and polarity of gut epithelial organoids were also found to be dependent on the RhoA signaling pathway. CONCLUSIONS We show that TTC7A regulates the actin cytoskeleton dynamics in lymphocytes through the RhoA signaling pathway and is required in both lymphocytes and epithelial cells for maintaining equilibrium between cell proliferation, migration, polarization, and cell death. Our study highlights variability in the phenotypic expression resulting from TTC7A deficiency and outlines that impairment of both epithelial cells and lymphocytes cooperatively causes IBD.
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Affiliation(s)
- Roxane Lemoine
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Jana Pachlopnik-Schmid
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Henner F Farin
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Amélie Bigorgne
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Marianne Debré
- Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Fernando Sepulveda
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Sébastien Héritier
- Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Julie Lemale
- Unité de Nutrition et Gastroentérologie Pédiatriques, Hôpital Trousseau, Paris, France
| | - Cécile Talbotec
- Service de gastroentérologie, hépatologie et nutrition pédiatriques, Hôpital Necker-Enfants Malades, Paris, France
| | - Frédéric Rieux-Laucat
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Frank Ruemmele
- Service de gastroentérologie, hépatologie et nutrition pédiatriques, Hôpital Necker-Enfants Malades, Paris, France
| | - Alain Morali
- Unité d'Hépato-Gastro-Entérologie et Nutrition Pédiatriques, Hôpital d'Enfants, CHU Nancy Brabois-F 54500 Vandoeuvre les Nancy et Unité INSERM U954, Paris, France
| | - Pascal Cathebras
- Service de Médecine Interne, CHU de Saint Etienne, Saint Etienne, France
| | - Patrick Nitschke
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
| | | | - Stéphane Blanche
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Nicole Brousse
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Laboratoire d'Anatomie Pathologique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Capucine Picard
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France; Centre d'Etudes des Déficits Immunitaires, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Alain Fischer
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France; College de France, Paris, France
| | - Geneviève de Saint Basile
- INSERM, Unité U1163, Laboratoire Homéostasie normale et pathologique du système immunitaire, Hôpital Necker Enfants-Malades, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Paris, France; Unité d'Immunologie et Hématologie Pédiatrique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France; Centre d'Etudes des Déficits Immunitaires, Assistance Publique-Hôpitaux de Paris, Paris, France.
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