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Article ; Online: SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns.

Redondo, Natalia / Zaldívar-López, Sara / Garrido, Juan J / Montoya, Maria

2021 Volume 12, Page(s) 708264

Abstract: There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the ... ...

Abstract	There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the current knowledge of SARS-CoV-2 accessory proteins is summarized updating new research that could be critical in understanding SARS-CoV-2 interaction with the host. Some accessory proteins such as ORF3b, ORF6, ORF7a and ORF8 have been shown to be important IFN-I antagonists inducing an impairment in the host immune response. In addition, ORF3a is involved in apoptosis whereas others like ORF9b and ORF9c interact with cellular organelles leading to suppression of the antiviral response in infected cells. However, possible roles of ORF7b and ORF10 are still awaiting to be described. Also, ORF3d has been reassigned. Relevant information on the knowns and the unknowns in these proteins is analyzed, which could be crucial for further understanding of SARS-CoV-2 pathogenesis and to design strategies counteracting their actions evading immune responses in COVID-19.
MeSH term(s)	COVID-19/immunology ; COVID-19/pathology ; Coronavirus/metabolism ; Coronavirus/pathogenicity ; Humans ; Immune Evasion ; Immunity ; Interferons/antagonists & inhibitors ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; Viral Regulatory and Accessory Proteins/immunology ; Viral Regulatory and Accessory Proteins/metabolism
Chemical Substances	Viral Regulatory and Accessory Proteins ; Interferons (9008-11-1)
Language	English
Publishing date	2021-07-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2021.708264
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Salmonella Typhimurium induces genome-wide expression and phosphorylation changes that modulate immune response, intracellular survival and vesicle transport in infected neutrophils

Zaldívar-López, Sara / Herrera-Uribe, Juber / Bautista, Rocío / Jiménez Soria, Angeles / Moreno, Ángela / Claros, M. Gonzalo / Garrido, Juan J.

Developmental and Comparative Immunology. 2023 Mar., v. 140 p.104597-

2023

Abstract: Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro ... ...

Abstract	Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro model of neutrophil infection to perform dual RNA-sequencing (both host and pathogen). In addition, and given that many pathogens interfere with kinase‐mediated phosphorylation in host signaling, we performed a phosphoproteomic analysis. The immune response was overall diminished in infected neutrophils, mainly JAK/STAT and toll-like receptor signaling pathways. We found decreased expression of proinflammatory cytokine receptor genes and predicted downregulation of the mitogen-activated protein (MAPK) signaling pathway. Also, Salmonella infection inhibited interferons I and II signaling pathways by upregulation of SOCS3 and subsequent downregulation of STAT1 and STAT2. Additionally, phosphorylation of PSMC2 and PSMC4, proteasome regulatory proteins, was decreased in infected neutrophils. Cell viability and survival was increased by p53 signaling, cell cycle arrest and NFkB-proteasome pathways activation. Combined analysis of RNA-seq and phosphoproteomics also revealed inhibited vesicle transport mechanisms mediated by dynein/dynactin and exocyst complexes, involved in ER-to-Golgi transport and centripetal movement of lysosomes and endosomes. Among the overexpressed virulence genes from Salmonella we found potential effectors responsible of these dysregulations, such as spiC, sopD2, sifA or pipB2, all of them involved in intracellular replication. Our results suggest that Salmonella induces (through overexpression of virulence factors) transcriptional and phosphorylation changes that increases neutrophil survival and shuts down immune response to minimize host response, and impairing intracellular vesicle transport likely to keep nutrients for replication and Salmonella-containing vacuole formation and maintenance.
Keywords	Salmonella Typhimurium ; Toll-like receptors ; cell cycle checkpoints ; cell viability ; cytokine receptors ; dynein ATPase ; endosomes ; food pathogens ; immune response ; lysosomes ; models ; neutrophils ; pathogenesis ; phosphorylation ; physiological transport ; proteasome endopeptidase complex ; proteomics ; salmonellosis ; sequence analysis ; transcription (genetics) ; vacuoles ; virulence ; Infection ; Transcriptomics ; Dual RNA-Seq ; Phosphoproteomics
Language	English
Dates of publication	2023-03
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2022.104597
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Article ; Online: Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use.

Ortiz Sanjuán, Juan M / Manzanilla, Edgar G / Cabrera-Rubio, Raúl / Crispie, Fiona / Cotter, Paul D / Garrido, Juan J / Ekhlas, Daniel / O'Neill, Lorcan / Argüello, Héctor

Frontiers in cellular and infection microbiology

2024 Volume 14, Page(s) 1354449

Abstract: Introduction: Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), ...

Abstract	Introduction: Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use. Methods: This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available. Results: The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Discussion: The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic
MeSH term(s)	Swine ; Animals ; Escherichia coli ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Zinc Oxide/pharmacology ; Zinc Oxide/therapeutic use ; Diarrhea/microbiology ; Microbiota
Chemical Substances	Anti-Bacterial Agents ; Zinc Oxide (SOI2LOH54Z)
Language	English
Publishing date	2024-02-07
Publishing country	Switzerland
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2024.1354449
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Article ; Online: Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs.

Ortiz Sanjuán, Juan M / Argüello, Héctor / Cabrera-Rubio, Raúl / Crispie, Fiona / Cotter, Paul D / Garrido, Juan J / Ekhlas, Daniel / Burgess, Catherine M / Manzanilla, Edgar G

Animal microbiome

2024 Volume 6, Issue 1, Page(s) 18

Abstract: Background: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to ... ...

Abstract	Background: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. Results: Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. Conclusion: Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article
ISSN	2524-4671
ISSN (online)	2524-4671
DOI	10.1186/s42523-024-00306-7
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Article ; Online: Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning.

Ortiz Sanjuán, Juan M / Manzanilla, Edgar G / Cabrera-Rubio, Raúl / Crispie, Fiona / Cotter, Paul D / Garrido, Juan J / Argüello, Héctor

Microbiology spectrum

2022 Volume 10, Issue 4, Page(s) e0159722

Abstract: Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies ... ...

Abstract	Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between
MeSH term(s)	Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Diarrhea/microbiology ; Escherichia coli ; Gastrointestinal Microbiome ; Nebramycin/analogs & derivatives ; Swine ; Zinc Oxide/pharmacology ; Zinc Oxide/therapeutic use
Chemical Substances	Anti-Bacterial Agents ; apramycin (388K3TR36Z) ; Nebramycin (11048-13-8) ; Zinc Oxide (SOI2LOH54Z)
Language	English
Publishing date	2022-08-11
Publishing country	United States
Document type	Journal Article ; Randomized Controlled Trial, Veterinary ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01597-22
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Article ; Online: Study of microRNA expression in Salmonella Typhimurium-infected porcine ileum reveals miR-194a-5p as an important regulator of the TLR4-mediated inflammatory response.

Herrera-Uribe, Juber / Zaldívar-López, Sara / Aguilar, Carmen / Entrenas-García, Carmen / Bautista, Rocío / Claros, M Gonzalo / Garrido, Juan J

Veterinary research

2022 Volume 53, Issue 1, Page(s) 35

Abstract: Infection with Salmonella Typhimurium (S. Typhimurium) is a common cause of food-borne zoonosis leading to acute gastroenteritis in humans and pigs, causing economic losses to producers and farmers, and generating a food security risk. In a previous ... ...

Abstract	Infection with Salmonella Typhimurium (S. Typhimurium) is a common cause of food-borne zoonosis leading to acute gastroenteritis in humans and pigs, causing economic losses to producers and farmers, and generating a food security risk. In a previous study, we demonstrated that S. Typhimurium infection produces a severe transcriptional activation of inflammatory processes in ileum. However, little is known regarding how microRNAs regulate this response during infection. Here, small RNA sequencing was used to identify 28 miRNAs differentially expressed (DE) in ileum of S. Typhimurium-infected pigs, which potentially regulate 14 target genes involved in immune system processes such as regulation of cytokine production, monocyte chemotaxis, or cellular response to interferon gamma. Using in vitro functional and gain/loss of function (mimics/CRISPR-Cas system) approaches, we show that porcine miR-194a-5p (homologous to human miR-194-5p) regulates TLR4 gene expression, an important molecule involved in pathogen virulence, recognition and activation of innate immunity in Salmonella infection.
MeSH term(s)	Animals ; Ileum ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Salmonella Infections, Animal ; Salmonella typhimurium/genetics ; Swine ; Toll-Like Receptor 4/metabolism
Chemical Substances	MicroRNAs ; Toll-Like Receptor 4
Language	English
Publishing date	2022-05-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1146298-x
ISSN	1297-9716 ; 0928-4249
ISSN (online)	1297-9716
ISSN	0928-4249
DOI	10.1186/s13567-022-01056-7
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Article ; Online: Salmonella Typhimurium induces genome-wide expression and phosphorylation changes that modulate immune response, intracellular survival and vesicle transport in infected neutrophils.

Zaldívar-López, Sara / Herrera-Uribe, Juber / Bautista, Rocío / Jiménez, Ángeles / Moreno, Ángela / Claros, M Gonzalo / Garrido, Juan J

Developmental and comparative immunology

2022 Volume 140, Page(s) 104597

Abstract	Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro model of neutrophil infection to perform dual RNA-sequencing (both host and pathogen). In addition, and given that many pathogens interfere with kinase-mediated phosphorylation in host signaling, we performed a phosphoproteomic analysis. The immune response was overall diminished in infected neutrophils, mainly JAK/STAT and toll-like receptor signaling pathways. We found decreased expression of proinflammatory cytokine receptor genes and predicted downregulation of the mitogen-activated protein (MAPK) signaling pathway. Also, Salmonella infection inhibited interferons I and II signaling pathways by upregulation of SOCS3 and subsequent downregulation of STAT1 and STAT2. Additionally, phosphorylation of PSMC2 and PSMC4, proteasome regulatory proteins, was decreased in infected neutrophils. Cell viability and survival was increased by p53 signaling, cell cycle arrest and NFkB-proteasome pathways activation. Combined analysis of RNA-seq and phosphoproteomics also revealed inhibited vesicle transport mechanisms mediated by dynein/dynactin and exocyst complexes, involved in ER-to-Golgi transport and centripetal movement of lysosomes and endosomes. Among the overexpressed virulence genes from Salmonella we found potential effectors responsible of these dysregulations, such as spiC, sopD2, sifA or pipB2, all of them involved in intracellular replication. Our results suggest that Salmonella induces (through overexpression of virulence factors) transcriptional and phosphorylation changes that increases neutrophil survival and shuts down immune response to minimize host response, and impairing intracellular vesicle transport likely to keep nutrients for replication and Salmonella-containing vacuole formation and maintenance.
MeSH term(s)	Animals ; Salmonella typhimurium ; Neutrophils/metabolism ; Phosphorylation ; Proteasome Endopeptidase Complex/metabolism ; Salmonella Infections ; Immunity ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Bacterial Proteins
Language	English
Publishing date	2022-11-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2022.104597
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Article: Study of microRNA expression in Salmonella Typhimurium-infected porcine ileum reveals miR-194a-5p as an important regulator of the TLR4-mediated inflammatory response

Herrera-Uribe, Juber / Zaldívar-López, Sara / Aguilar, Carmen / Entrenas-García, Carmen / Bautista, Rocío / Claros, M. Gonzalo / Garrido, Juan J.

Veterinary research. 2022 Dec., v. 53, no. 1

2022

Abstract	Infection with Salmonella Typhimurium (S. Typhimurium) is a common cause of food-borne zoonosis leading to acute gastroenteritis in humans and pigs, causing economic losses to producers and farmers, and generating a food security risk. In a previous study, we demonstrated that S. Typhimurium infection produces a severe transcriptional activation of inflammatory processes in ileum. However, little is known regarding how microRNAs regulate this response during infection. Here, small RNA sequencing was used to identify 28 miRNAs differentially expressed (DE) in ileum of S. Typhimurium-infected pigs, which potentially regulate 14 target genes involved in immune system processes such as regulation of cytokine production, monocyte chemotaxis, or cellular response to interferon gamma. Using in vitro functional and gain/loss of function (mimics/CRISPR-Cas system) approaches, we show that porcine miR-194a-5p (homologous to human miR-194-5p) regulates TLR4 gene expression, an important molecule involved in pathogen virulence, recognition and activation of innate immunity in Salmonella infection.
Keywords	Salmonella Typhimurium ; chemotaxis ; cytokines ; food security ; gastroenteritis ; gene expression ; humans ; ileum ; inflammation ; innate immunity ; interferon-gamma ; microRNA ; monocytes ; pathogens ; risk ; salmonellosis ; swine ; transcriptional activation ; veterinary medicine ; virulence ; zoonoses
Language	English
Dates of publication	2022-12
Size	p. 35.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	1146298-x
ISSN	1297-9716 ; 0928-4249
ISSN (online)	1297-9716
ISSN	0928-4249
DOI	10.1186/s13567-022-01056-7
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Article: CD9 expression in porcine blood CD4+ T cells delineates two subsets with phenotypic characteristics of central and effector memory cells

Álvarez, Belén / Revilla, Concepción / Moreno, Sara / Jiménez-Marín, Ángeles / Ramos, Elena / Martínez de la Riva, Paloma / Poderoso, Teresa / Garrido, Juan J. / Ezquerra, Ángel / Domínguez, Javier

Developmental and comparative immunology. 2022 Aug., v. 133

2022

Abstract: In this report, we describe the characterization of a new monoclonal antibody, named 4H5CR4, against porcine CD9. Its use in combination with antibodies to CD4, CD8α, and 2E3 allows to distinguish at least five main CD4⁺ T cell subsets. Analysis on these ...

Abstract	In this report, we describe the characterization of a new monoclonal antibody, named 4H5CR4, against porcine CD9. Its use in combination with antibodies to CD4, CD8α, and 2E3 allows to distinguish at least five main CD4⁺ T cell subsets. Analysis on these subsets of CD45RA, CD27, CD29, CD95, CCR7, and SLA-DR markers depicts a progressive model of CD4⁺ T cell development. CD4⁺ 2E3⁺ CD8α⁻ CD9⁻ cells are the least differentiated population of naïve cells, whereas the CD4⁺ 2E3⁻ CD8α⁺CD9⁺ and CD4⁺ 2E3⁻ CD8α⁺ CD9⁻ cells display phenotypic features of central and effector memory T helper cells, respectively. The latter subsets were able to produce IFN-γ after polyclonal activation with PMA/Ionomycin; however, in vitro virus-specific IFN-γ production of PBMCs collected at 38–44 days after pseudorabies virus vaccination was dominated by cells with a CD9⁺ phenotype. Therefore, CD9 appears to be a useful marker to investigate CD4⁺ T cell heterogeneity in swine.
Keywords	CD4-positive T-lymphocytes ; Suid alphaherpesvirus 1 ; models ; monoclonal antibodies ; phenotype ; swine ; vaccination
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2022.104431
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Article ; Online: Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains

Herrera-Uribe, Júber / Jiménez-Marín, Ángeles / Lacasta, Anna / Monteagudo, Paula L. / Pina-Pedrero, Sonia / Rodríguez, Fernando / Moreno, Ángela / Garrido, Juan J.

Veterinary Research

2023

Keywords	swine ; analysis ; virus ; african swine fever ; african swine fever virus ; strains ; fever ; nodes ; swine fever ; lymph ; swine fever virus
Publishing date	2023-03-10T14:40:10Z
Publisher	Springer
Publishing country	fr
Document type	Article ; Online
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