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Yu, Jingyou, and Shan-Lu Liu. "The Inhibition of HIV-1 Entry Imposed by Interferon Inducible Transmembrane Proteins Is Independent of Co-Receptor Usage." Viruses 10, no. 8 (August 7, 2018): 413. http://dx.doi.org/10.3390/v10080413.
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Interferon inducible transmembrane proteins (IFITMs) are one of several IFN-stimulated genes (ISGs) that restrict entry of enveloped viruses, including flaviviruses, filoviruses and retroviruses. It has been recently reported that in U87 glioblastoma cells IFITM proteins inhibit HIV-1 entry in a co-receptor-dependent manner, that is, IFITM1 is more inhibitory on CCR5 tropic HIV-1 whereas IFITM2/3 confers a greater suppression of CXCR4 counterparts. However, how entry of HIV-1 with distinct co-receptor usage is modulated by different IFITM orthologs in physiologically relevant CD4+ T cells and monocytes/macrophages has not been investigated in detail. Here, we report that overexpression of IFITM1, 2 and 3 in human CD4+ HuT78 cells, SupT1 cells, monocytic THP-1 cells and U87 cells expressing CD4 and co-receptor CCR5 or CXCR4, suppressed entry of CXCR4 tropic viruses NL4.3 and HXB2, CCR5 tropic viruses AD8 and JRFL, dual tropic 89.6 virus, as well as a panel of 32 transmitted founder (T/F) viruses, with a consistent order of potency, that is, IFITM3 > IFITM2 > IFITM1. Consistent with previous reports, we found that some CCR5-using HIV-1 isolates, such as AD8 and JRFL, were relatively resistant to inhibition by IFITM2 and IFITM3, although the effect can be cell-type dependent. However, in no case have we observed that IFITM1 had a stronger inhibition on entry of any HIV-1 strains tested, including those of CCR5-using T/Fs. We knocked down the endogenous IFITMs in peripheral blood mononuclear cells (PBMCs) and purified CD4+ T cells and observed that, while this treatment did greatly enhance the multiple-round of HIV-1 replication but had modest effect to rescue the single-round HIV-1 infection, reinforcing our previous conclusion that the predominant effect of IFITMs on HIV-1 infection is in viral producer cells, rather than in target cells to block viral entry. Overall, our results argue against the idea that IFITM proteins distinguish co-receptors CCR5 and CXCR4 to inhibit entry but emphasize that the predominant role of IFITMs on HIV-1 is in producer cells that intrinsically impair the viral infectivity.
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Franz, Sergej, Fabian Pott, Thomas Zillinger, Christiane Schüler, Sandra Dapa, Carlo Fischer, Vânia Passos, et al. "Human IFITM3 restricts chikungunya virus and Mayaro virus infection and is susceptible to virus-mediated counteraction." Life Science Alliance 4, no. 7 (June 2, 2021): e202000909. http://dx.doi.org/10.26508/lsa.202000909.
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Interferon-induced transmembrane (IFITM) proteins restrict membrane fusion and virion internalization of several enveloped viruses. The role of IFITM proteins during alphaviral infection of human cells and viral counteraction strategies are insufficiently understood. Here, we characterized the impact of human IFITMs on the entry and spread of chikungunya virus and Mayaro virus and provide first evidence for a CHIKV-mediated antagonism of IFITMs. IFITM1, 2, and 3 restricted infection at the level of alphavirus glycoprotein-mediated entry, both in the context of direct infection and cell-to-cell transmission. Relocalization of normally endosomal IFITM3 to the plasma membrane resulted in loss of antiviral activity. rs12252-C, a naturally occurring variant of IFITM3 that may associate with severe influenza in humans, restricted CHIKV, MAYV, and influenza A virus infection as efficiently as wild-type IFITM3. Antivirally active IFITM variants displayed reduced cell surface levels in CHIKV-infected cells involving a posttranscriptional process mediated by one or several nonstructural protein(s) of CHIKV. Finally, IFITM3-imposed reduction of specific infectivity of nascent particles provides a rationale for the necessity of a virus-encoded counteraction strategy against this restriction factor.
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Minakshi, Rinki. "Interferon-Induced Transmembrane Protein: A Moonlighting Protein Against SARS-CoV-2 Infection or in Support of Invasive Ductal Breast Carcinoma?" Asian Pacific Journal of Cancer Care 5, S1 (September 15, 2020): 241–42. http://dx.doi.org/10.31557/apjcc.2020.5.s1.241-242.
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The interferon-induced transmembrane proteins (IFITMs), widely acting against invading viruses are ubiquitously expressed on the cellular membranes, were previously known for their prominent role in tumorigenesis. Studies productively showed that the entry restriction on SARS-CoV spike glycoprotein agreeably involved the action of frontier IFITM1, 2 and 3. On the contrary, overexpression of IFITM3 has been reported in Invasive ductal breast carcinoma (IDC) tissue specimens where lentivirus-delivered shRNA resulted in targeted silencing of IFITM3 mRNA expression. Despite acting protective against virus infection, expression of IFITM favors cancer migration as seen in IDC. The existence of such a phenomenon wherein a choice is made by the selection pressure on IFITM allele frequency in human population between opposing roles of the protein, needs to be untangled.
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Dimech, Christina, and Bhushan Nagar. "Towards a structural characterization of the IFIT antiviral complex." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C246. http://dx.doi.org/10.1107/s2053273314097538.
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Our first line of defense against viral pathogens is the innate immune system. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defense through the formation of the IFIT `Interactome', a multiprotein complex made up of IFIT1, IFIT2, IFIT3 and several other host factors1. Through IFIT1, this complex has the ability to distinguish self from non-self nucleic acids such as virus-derived RNA bearing 5´-triphosphate or viral mRNA lacking 2´-O methylation on the first two nucleotides1,2. We have limited information on the architecture of this complex, its role in innate immunity, and its activity downstream of RNA binding remain unclear. To better understand the mechanisms of Interactome formation, we are investigating the structure of its core, namely the IFIT1-IFIT2-IFIT3 complex. Since it is challenging to crystallize the complex as a whole, likely due to its size and heterogeneity, we are also targeting the structure of individual components and co-crystals of interacting domains. A crystal structure of human IFIT2 is available, and our lab has solved the structure of N-terminal human IFIT1 and, more recently, N-terminal IFIT3. In this study, we aim to characterize the interaction between IFIT1 and IFIT2, and between IFIT3 and IFIT2, through gel-filtration binding assays, in vitro pull-downs and deletion mutations. Preliminary results on the expression and purification of IFIT2-deletion mutants will be presented, as well as purification of IFIT subcomplexes. Understanding the molecular mechanisms behind IFIT-mediated virus elimination will help us unravel the complexities of these interactions and significantly advance our fundamental knowledge of innate immunity, paving the way for designing novel immunotherapeutics, which could potentially complement anti-cancer strategies that rely on oncolytic RNA viruses.
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Hickford, D., A. Pask, G. Shaw, and M. B. Renfree. "264. Primordial germ cell specification in a marsupial, the tammar wallaby." Reproduction, Fertility and Development 20, no. 9 (2008): 64. http://dx.doi.org/10.1071/srb08abs264.
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Primordial germ cells (PGCs) are the precursors of the gametes. In the mouse, PGCs are specified within the proximal epiblast in response to signals from the extraembryonic membranes during early gastrulation. Epiblast cells competent to form PGCs express Ifitm3. A subset of these cells then express Blimp1, a marker of PGC precursors. Once lineage-restricted, PGCs express Stella. Germ cells entering the gonads express VASA protein, which is a component of the germ plasm in animals in which germ cells are specified by the inheritance of maternal determinatives. Almost all of the research on mammalian PGC specification has used the mouse as a model and it is tacitly assumed that findings in the mouse will apply to mammals in general. We are using the tammar wallaby as a marsupial model for PGC specification. Eutherians and marsupials diverged 125–148 million years ago, so comparisons between the two will provide insights into the evolution of the control of mammalian PGC specification. There are IFITM clusters in both the human (chromosome 11) and mouse (chromosome 7). In the mouse, IFITM1, 2 and 3 are expressed in PGCs, whereas IFITM4 and 5 are not (1). Only one IFITM member, IFITM5, is annotated in the opossum Ensemble database. We have cloned one tammar IFITM member and identified at least one other putative member in the tammar trace archive database. We have also cloned tammar BLIMP1 and VASA, both of which show high sequence conservation with other mammals. RT–PCR profiles for both genes during tammar gastrulation are similar to those for the mouse. In contrast, no marsupial STELLA orthologueue has been identified in either the opossum or tammar genomes. These findings suggest that some but not all of the signals and mechanisms involved in eutherian PGC specification are also applicable to marsupials. (1) Lange UC, Saitou M, Western P, Barton SC and Surani MA (2003) BMC Dev. Biol. Epub 2003 Mar 19
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Confort, Marie-Pierre, Maëva Duboeuf, Adrien Thiesson, Léa Pons, Federico Marziali, Sophie Desloire, Maxime Ratinier, Andrea Cimarelli, and Frédérick Arnaud. "IFITMs from Naturally Infected Animal Species Exhibit Distinct Restriction Capacities against Toscana and Rift Valley Fever Viruses." Viruses 15, no. 2 (January 22, 2023): 306. http://dx.doi.org/10.3390/v15020306.
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Rift Valley Fever virus (RVFV) and Toscana virus (TOSV) are two pathogenic arthropod-borne viruses responsible for zoonotic infections in both humans and animals; as such, they represent a growing threat to public and veterinary health. Interferon-induced transmembrane (IFITM) proteins are broad inhibitors of a large panel of viruses belonging to various families and genera. However, little is known on the interplay between RVFV, TOSV, and the IFITM proteins derived from their naturally infected host species. In this study, we investigated the ability of human, bovine, and camel IFITMs to restrict RVFV and TOSV infection. Our results indicated that TOSV was extremely sensitive to inhibition by all the animal IFITMs tested, while RVFV was inhibited by human IFITM-2 and IFITM-3, but not IFITM-1,and exhibited a more heterogeneous resistance phenotype towards the individual bovine and camel IFITMs tested. Overall, our findings shed some light on the complex and differential interplay between two zoonotic viruses and IFITMs from their naturally infected animal species.
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Campbell, Robert A., Jesse W. Rowley, Andrew S. Weyrich, and Matthew T. Rondina. "Surface Ifitms on Megakaryocytes and Platelets Regulate Fibrinogen Endocytosis Under Inflammatory Conditions." Blood 126, no. 23 (December 3, 2015): 1034. http://dx.doi.org/10.1182/blood.v126.23.1034.1034.
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Abstract Background IFITM proteins (IFITM-1, -2, and -3) mediate cellular resistance to influenza, dengue, and other viruses. IFITM expression on human platelets has not been previously recognized. Our laboratory recently demonstrated that IFITMs are robustly expressed by human platelets and megakaryocytes after stimulation by pathogens and inflammatory mediators and restrict viral infection. IFITMs, which are interferon inducible, also mediate clathrin localization and associated protein endocytosis. Nevertheless, whether IFITMs regulate protein endocytosis by platelets and megakaryocytes remains unknown. Aims We investigated IFITM expression on murine megakaryocytes and platelets and determined whether IFITMs regulate fibrinogen endocytosis under basal and inflammatory conditions. Methods We examined the expression of IFITMs and clathrin in bone-marrow derived murine megakaryocytes and platelets under basal conditions and following interferon-beta (IFN-β) stimulation. To determine whether upregulation of IFITM causes increased fibrinogen endocytosis, megakaryocytes were stimulated ex vivo with IFN-β and treated with labeled fibrinogen. Endocytosis of labeled fibrinogen was then measured by immunocytochemistry and flow cytometry. To determine whether this response also occurred in vivo, C57Bl/6 mice were injected intraperitoneally (IP) with 50,000 units of IFN-β over four days. On the fourth day, 100 μg of labeled fibrinogen was injected into the tail vein and the amount of endocytosed, labeled fibrinogen in platelets was determined the next day via flow cytometry. Parallel experiments were performed in age and gender matched IFITM-/- mice. Results Bone-marrow derived murine megakaryocytes and platelets basally express IFITMs. Upon IFN-β stimulation, IFITM and clathrin expression significantly increased (p<0.05). Fibrinogen endocytosis by murine megakaryocytes occurred under resting conditions and appeared to be punctate and granular in nature. Upon IFN-b stimulation, fibrinogen endocytosis in megakaryocytes significantly increased compared to unstimulated conditions (p<0.004). The increase in endocytosis appeared independent of changes in αIIbβ3 expression as IFN-β stimulation did not change αIIbβ3 surface protein. Fibrinogen endocytosis after IFN-β stimulation did not increase in megakaryocytes from IFITM-/- mice, suggesting that IFITMs regulate fibrinogen uptake under these conditions. We next determined if fibrinogen endocytosis occurred in platelets isolated from IFITM-/- mice. Platelet counts and activation indices (assessed by JonA staining) were similar in C57Bl/6 mice (WT) and IFITM-/- mice. Nevertheless, the injection of IFN-β IP results in significant increases in fibrinogen endocytosis by platelets in vivo in WT but not IFITM-/- mice (p<0.02). Summary/Conclusions These findings suggest IFITMs, in addition to their anti-viral roles, mediate fibrinogen endocytosis. Further, in settings where inflammatory stimuli such as interferons are increased, enhanced IFITM expression may promote upregulation of fibrinogen endocytosis by platelets and megakaryocytes. Disclosures No relevant conflicts of interest to declare.
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Smith, S. E., M. S. Gibson, R. S. Wash, F. Ferrara, E. Wright, N. Temperton, P. Kellam, and M. Fife. "Chicken Interferon-Inducible Transmembrane Protein 3 Restricts Influenza Viruses and LyssavirusesIn Vitro." Journal of Virology 87, no. 23 (September 25, 2013): 12957–66. http://dx.doi.org/10.1128/jvi.01443-13.
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Interferon-inducible transmembrane protein 3 (IFITM3) is an effector protein of the innate immune system. It confers potent, cell-intrinsic resistance to infection by diverse enveloped viruses bothin vitroandin vivo, including influenza viruses, West Nile virus, and dengue virus. IFITM3 prevents cytosolic entry of these viruses by blocking complete virus envelope fusion with cell endosome membranes. Although the IFITM locus, which includesIFITM1, -2, -3, and -5, is present in mammalian species, this locus has not been unambiguously identified or functionally characterized in avian species. Here, we show that the IFITM locus exists in chickens and is syntenic with the IFITM locus in mammals. The chicken IFITM3 protein restricts cell infection by influenza A viruses and lyssaviruses to a similar level as its human orthologue. Furthermore, we show that chicken IFITM3 is functional in chicken cells and that knockdown of constitutive expression in chicken fibroblasts results in enhanced infection by influenza A virus. ChickenIFITM2and -3are constitutively expressed in all tissues examined, whereasIFITM1is only expressed in the bursa of Fabricius, gastrointestinal tract, cecal tonsil, and trachea. Despite being highly divergent at the amino acid level, IFITM3 proteins of birds and mammals can restrict replication of viruses that are able to infect different host species, suggesting IFITM proteins may provide a crucial barrier for zoonotic infections.
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Mudhasani, R., J. P. Tran, C. Retterer, S. R. Radoshitzky, K. P. Kota, L. A. Altamura, J. M. Smith, et al. "IFITM-2 and IFITM-3 but Not IFITM-1 Restrict Rift Valley Fever Virus." Journal of Virology 87, no. 15 (May 29, 2013): 8451–64. http://dx.doi.org/10.1128/jvi.03382-12.
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Kumar, Parimal, Trevor R. Sweeney, Maxim A. Skabkin, Olga V. Skabkina, Christopher U. T. Hellen, and Tatyana V. Pestova. "Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp- mRNAs." Nucleic Acids Research 42, no. 5 (December 25, 2013): 3228–45. http://dx.doi.org/10.1093/nar/gkt1321.
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AbstractRibosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA’s 5′-terminal ‘cap’. The minimal ‘cap0’ consists of N7-methylguanosine linked to the first nucleotide via a 5′-5′ triphosphate (ppp) bridge. Cap0 is further modified by 2′-O-methylation of the next two riboses, yielding ‘cap1’ (m7GpppNmN) and ‘cap2’ (m7GpppNmNm). However, some viral RNAs lack 2′-O-methylation, whereas others contain only ppp- at their 5′-end. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed effectors of innate immunity that inhibit viral replication by incompletely understood mechanisms. Here, we investigated the ability of IFIT family members to interact with cap1-, cap0- and 5′ppp- mRNAs and inhibit their translation. IFIT1 and IFIT1B showed very high affinity to cap-proximal regions of cap0-mRNAs (K1/2,app ∼9 to 23 nM). The 2′-O-methylation abrogated IFIT1/mRNA interaction, whereas IFIT1B retained the ability to bind cap1-mRNA, albeit with reduced affinity (K1/2,app ∼450 nM). The 5′-terminal regions of 5′ppp-mRNAs were recognized by IFIT5 (K1/2,app ∼400 nM). The activity of individual IFITs in inhibiting initiation on a specific mRNA was determined by their ability to interact with its 5′-terminal region: IFIT1 and IFIT1B efficiently outcompeted eIF4F and abrogated initiation on cap0-mRNAs, whereas inhibition on cap1- and 5′ppp- mRNAs by IFIT1B and IFIT5 was weaker and required higher protein concentrations.
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Franco, Justin H., Saurabh Chattopadhyay, and Zhixing K. Pan. "How Different Pathologies Are Affected by IFIT Expression." Viruses 15, no. 2 (January 25, 2023): 342. http://dx.doi.org/10.3390/v15020342.
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The type-I interferon (IFN) system represents the first line of defense against viral pathogens. Recognition of the virus initiates complex signaling pathways that result in the transcriptional induction of IFNs, which are then secreted. Secreted IFNs stimulate nearby cells and result in the production of numerous proinflammatory cytokines and antiviral factors. Of particular note, IFN-induced tetratricopeptide repeat (IFIT) proteins have been thoroughly studied because of their antiviral activity against different viral pathogens. Although classically studied as an antiviral protein, IFIT expression has recently been investigated in the context of nonviral pathologies, such as cancer and sepsis. In oral squamous cell carcinoma (OSCC), IFIT1 and IFIT3 promote metastasis, while IFIT2 exhibits the opposite effect. The role of IFIT proteins during bacterial/fungal sepsis is still under investigation, with studies showing conflicting roles for IFIT2 in disease severity. In the setting of viral sepsis, IFIT proteins play a key role in clearing viral infection. As a result, many viral pathogens, such as SARS-CoV-2, employ mechanisms to inhibit the type-I IFN system and promote viral replication. In cancers that are characterized by upregulated IFIT proteins, medications that decrease IFIT expression may reduce metastasis and improve survival rates. Likewise, in cases of viral sepsis, therapeutics that increase IFIT expression may improve viral clearance and reduce the risk of septic shock. By understanding the effect of IFIT proteins in different pathologies, novel therapeutics can be developed to halt disease progression.
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Steyn, Angela, Sarah Keep, Erica Bickerton, and Mark Fife. "The Characterization of chIFITMs in Avian Coronavirus Infection In Vivo, Ex Vivo and In Vitro." Genes 11, no. 8 (August 10, 2020): 918. http://dx.doi.org/10.3390/genes11080918.
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The coronaviruses are a large family of enveloped RNA viruses that commonly cause gastrointestinal or respiratory illnesses in the infected host. Avian coronavirus infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of chickens that can affect the kidneys and reproductive systems resulting in bird mortality and decreased reproductivity. The interferon-inducible transmembrane (IFITM) proteins are activated in response to viral infections and represent a class of cellular restriction factors that restrict the replication of many viral pathogens. Here, we characterize the relative mRNA expression of the chicken IFITM genes in response to IBV infection, in vivo, ex vivo and in vitro using the pathogenic M41-CK strain, the nephropathogenic QX strain and the nonpathogenic Beaudette strain. In vivo we demonstrate a significant upregulation of chIFITM1, 2, 3 and 5 in M41-CK- and QX-infected trachea two days post-infection. In vitro infection with Beaudette, M41-CK and QX results in a significant upregulation of chIFITM1, 2 and 3 at 24 h post-infection. We confirmed a differential innate response following infection with distinct IBV strains and believe that our data provide new insights into the possible role of chIFITMs in early IBV infection.
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Yánez, Diana C., Hemant Sahni, Susan Ross, Anisha Solanki, Ching-In Lau, Eleftheria Papaioannou, Alessandro Barbarulo, et al. "IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation." European Journal of Immunology 49, no. 1 (November 9, 2018): 66–78. http://dx.doi.org/10.1002/eji.201847692.
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Vishnubalaji, Radhakrishnan, Hibah Shaath, and Nehad M. Alajez. "Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response." Genes 11, no. 7 (July 7, 2020): 760. http://dx.doi.org/10.3390/genes11070760.
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The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated.
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Shaath, Hibah, Radhakrishnan Vishnubalaji, Eyad Elkord, and Nehad M. Alajez. "Single-Cell Transcriptome Analysis Highlights a Role for Neutrophils and Inflammatory Macrophages in the Pathogenesis of Severe COVID-19." Cells 9, no. 11 (October 29, 2020): 2374. http://dx.doi.org/10.3390/cells9112374.
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Cumulative data link cytokine storms with coronavirus disease 2019 (COVID-19) severity. The precise identification of immune cell subsets in bronchoalveolar lavage (BAL) and their correlation with COVID-19 disease severity are currently being unraveled. Herein, we employed iterative clustering and guide-gene selection 2 (ICGS2) as well as uniform manifold approximation and projection (UMAP) dimensionality reduction computational algorithms to decipher the complex immune and cellular composition of BAL, using publicly available datasets from a total of 68,873 single cells derived from two healthy subjects, three patients with mild COVID-19, and five patients with severe COVID-19. Our analysis revealed the presence of neutrophils and macrophage cluster-1 as a hallmark of severe COVID-19. Among the identified gene signatures, IFITM2, IFITM1, H3F3B, SAT1, and S100A8 gene signatures were highly associated with neutrophils, while CCL8, CCL3, CCL2, KLF6, and SPP1 were associated with macrophage cluster-1 in severe-COVID-19 patients. Interestingly, although macrophages were also present in healthy subjects and patients with mild COVID-19, they had different gene signatures, indicative of interstitial and cluster-0 macrophage (i.e., FABP4, APOC1, APOE, C1QB, and NURP1). Additionally, MALAT1, NEAT1, and SNGH25 were downregulated in patients with mild and severe COVID-19. Interferon signaling, FCγ receptor-mediated phagocytosis, IL17, and Tec kinase canonical pathways were enriched in patients with severe COVID-19, while PD-1 and PDL-1 pathways were suppressed. A number of upstream regulators (IFNG, PRL, TLR7, PRL, TGM2, TLR9, IL1B, TNF, NFkB, IL1A, STAT3, CCL5, and others) were also enriched in BAL cells from severe COVID-19-affected patients compared to those from patients with mild COVID-19. Further analyses revealed genes associated with the inflammatory response and chemotaxis of myeloid cells, phagocytes, and granulocytes, among the top activated functional categories in BAL from severe COVID-19-affected patients. Transcriptome data from another cohort of COVID-19-derived peripheral blood mononuclear cells (PBMCs) revealed the presence of several genes common to those found in BAL from patients with severe and mild COVID-19 (IFI27, IFITM3, IFI6, IFIT3, MX1, IFIT1, OASL, IFI30, OAS1) or to those seen only in BAL from severe-COVID-19 patients (S100A8, IFI44, IFI44L, CXCL8, CCR1, PLSCR1, EPSTI1, FPR1, OAS2, OAS3, IL1RN, TYMP, BCL2A1). Taken together, our data reveal the presence of neutrophils and macrophage cluster-1 as the main immune cell subsets associated with severe COVID-19 and identify their inflammatory and chemotactic gene signatures, also partially reflected systemically in the circulation, for possible diagnostic and therapeutic interventions.
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Skov, Vibe, Caroline Riley, Mads Thomassen, Lasse Kjær, Thomas Stauffer Larsen, Ole Weis Bjerrum, Torben A. Kruse, and Hans Carl Hasselbalch. "The Impact of Interferon on Interferon-Related Genes in Polycythemia Vera and Allied Neoplasms." Blood 132, Supplement 1 (November 29, 2018): 4328. http://dx.doi.org/10.1182/blood-2018-99-110602.
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Abstract Introduction: Using whole blood transcriptional profiling, we have previously shown deregulation of several interferon-stimulated genes (ISG) and deregulation of immune and inflammation genes in MPNs as well. Most lately, we have shown that deregulated HLA-genes are upregulated by interferon-alpha2 (IFN) treatment. Herein, we for the first time describe the landscape of ISGs during treatment with IFN, the aims being to describe if unique ISG transcriptional signatures might be elicited during IFN treatment with potential differences between subgroups. Methods: Eight patients with ET, 21 patients with PV, and 4 patients with PMF participated in the study. All patients received treatment with IFN, in the large majority in a dosage ranging from 45-90 ug x 1 sc/week. Gene expression microarray analysis of whole blood was performed before and after 3 months of treatment. Total RNA was purified from whole blood, amplified to biotin-labeled RNA, and hybridized to Affymetrix HG-U133 2.0 Plus chips recognizing 54,675 probe sets (38,500 genes). Results: We identified 6261, 10,008, and 2828 probe sets to be significantly differentially expressed in ET, PV, and PMF, respectively, in response to treatment with IFN (pvalue < 0.05). Twenty-one previously identified ISGs were investigated: Six genes involved the response to virus: ISG15, IFI35, IFI44, IFIH1, MX1, and OAS1, 2 transcriptional regulators: IFI16 and SP110, and 13 IFN-inducible genes: ADAR, CXCL10, IFI6, IFI27, IFI30, IFI44L, IFIT1, IFIT2, IFIT3, IFITM1, IFITM2, PSME1, and PYHIN1. Significant upregulation of 20, 21, and 18 ISGs was found in patients with ET, PV, and PMF, respectively. None of the 21 genes was significantly downregulated in any of the patient groups. The 6 genes involved in response to virus and the 2 transcriptional genes were significantly upregulated in all subgroups. In patients with ET all but one gene (CXCL10) of the 13 IFN-inducible genes were significantly upregulated. In patients with PV all 13 IFN-inducible genes were significantly upregulated and in PMF all but three (CXCL10, IFITM2, PUHIN1) IFN-inducible genes were significantly upregulated. No significant differences between subgroups were recorded (data not shown). Discussion and Conclusions: Eighteen genes were significantly upregulated compared to baseline values in all 3 MPN-subgroups. The CXCL10 gene was not significantly regulated in ET and PMF during IFN treatment but significantly upregulated in PV. CXCL10 is involved in the activation of neutrophils. Accordingly, impaired regulation of CXCL10 on exposure to IFN might compromise recruitment and activation of neutrophils. The excessively high expression levels of IFI27 after IFN are intriguing but might be explained by the reported high circulating levels of regulatory T cells (Tregs) after IFN. Thus, Tregs produce TGF-beta which stimulates IFI27. Indeed, TGF-beta was significantly upregulated in ET and PV but not in PMF, likely due to the low number of PMF patients. Surprisingly, we did not find any differences in ISG responses between MPNs. Indeed, taken into account that the MPNs depict a biological continuum from the early cancer stages (ET/PV) to the advanced "metastatic" myelofibrosis stage, different ISG signatures between the subtypes might be anticipated for several reasons. First, such differentiated signatures might exist merely reflecting the heterogeneity between subgroups in regard to "tumor burden". Second, differences in frequencies and functionality of immune cells between the subgroups as shown in most recent studies might impact the ISG signatures. Third, chronic inflammation, considered the driving force for clonal evolution in MPNs, has been shown to compromise cell responses to IFN, implying that PMF patients with the most pronounced inflammatory state might exhibit blunted ISG responses. However, the low number of PMF patients may account for the non-significant difference between ET/PV and PMF. In conclusion, except for 4 genes (CXCL10, IFITM1, IFITM2, and PYHIN1), our study has shown the ISGs to be significantly upregulated in all MPN- subtypes after 3 months of exposure to IFN. The reasons for the absence of upregulation of the above 4 genes are unknown but chronic inflammation and immune deregulation might be influential. Further transcriptional studies of ISGs during IFN treatment in larger study populations and with longer exposure times are needed to address these issues. Table. Table. Disclosures Hasselbalch: Novartis: Research Funding.
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Russo, Max, Sara T. Humes, Ariana M. Figueroa, Abderrahmane Tagmount, Ping Zhang, Alex Loguinov, John A. Lednicky, Tara Sabo-Attwood, Chris D. Vulpe, and Bin Liu. "Organochlorine Pesticide Dieldrin Suppresses Cellular Interferon-Related Antiviral Gene Expression." Toxicological Sciences 182, no. 2 (May 29, 2021): 260–74. http://dx.doi.org/10.1093/toxsci/kfab064.
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Abstract Organochlorine pesticides (OCPs) are persistent pollutants linked to diverse adverse health outcomes. Environmental exposure to OCPs has been suggested to negatively impact the immune system but their effects on cellular antiviral responses remain unknown. Transcriptomic analysis of N27 rat dopaminergic neuronal cells unexpectedly detected high level expression of genes in the interferon (IFN)-related antiviral response pathways including the IFN-induced protein with tetratricopeptide repeats 1 and 2 (Ifit1/2) and the MX Dynamin Like GTPases Mx1 and Mx2. Interestingly, treatment of N27 cells with dieldrin markedly downregulated the expression of many of these genes. Dieldrin exterted a similar effect in inhibiting IFIT2 and MX1 gene expression in human SH-SY5Y neuronal cells induced by an RNA viral mimic, polyinosinic: polycytidylic acid (poly I:C) and IFIT2/3 gene expression in human pulmonary epithelial cells exposed to human influenza H1N1 virus. Mechanistically, dieldrin induced a rapid rise in levels of intracellular reactive oxygen species (iROS) and a decrease in intracellular glutathione (GSH) levels in SH-SY5Y cells. Treatment with N-acetylcysteine, an antioxidant and GSH biosynthesis precursor, effectively blocked both dieldrin-induced increases in iROS and its inhibition of poly I:C-induced upregulation of IFIT and MX gene expression, suggesting a role for intracellular oxidative status in dieldrin’s modulation of antiviral gene expression. This study demonstrates that dieldrin modulates key genes of the cellular innate immune responses that are normally involved in the host’s cellular defense against viral infections. Our findings have potential relevance to understanding the organismal effects of environmentally persistent organochlorine contaminants on the mammalian cellular immune system.
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Zhang, Jiao, Si-yu Shao, Li-zu Li, Di Liu, and Xiu-qin Yang. "Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5." Canadian Journal of Animal Science 95, no. 4 (December 2015): 551–56. http://dx.doi.org/10.4141/cjas-2015-009.
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Zhang, J., Shao, S.-y., Li, L.-z., Liu, D. and Yang, X.-q. 2015. Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5. Can. J. Anim. Sci. 95: 551–556. Interferon-induced protein with tetratricopeptide repeats (IFIT) family members play important roles in host defense against viral infection. In the present study, the complete coding sequence (CDS) of porcine IFIT5 gene was cloned using molecular biology techniques, and the genomic structure was determined using the bioinformatic method. The porcine IFIT5 is located on chromosome 14 containing 2 exons. Quantitative real-time PCR revealed that the transcripts of IFIT5 gene were unevenly distributed in all tissues studied, including heart, bladder, liver, large intestine, spleen, small intestine, lung, kidney, stomach, muscle, and lymph. Only one synonymous single nucleotide polymorphism was found in the complete CDS except for the first five nucleotides. IFIT5 is induced by poly(I:C) in a dose- and time-dependent manner, as revealed by using dual-luciferase analysis and reverse transcription-quantitative PCR methods. Furthermore, ectopic expression of porcine IFIT5 had no effect on the activation of interferon regulatory factor 3 (IRF3) significantly (P>0.05), suggesting it might not be a regulator of IRF3 signaling pathway.
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Sun, Fang, Zhiqiang Xia, Yuewen Han, Minjun Gao, Luyao Wang, Yingliang Wu, Jean-Marc Sabatier, Lixia Miao, and Zhijian Cao. "Topology, Antiviral Functional Residues and Mechanism of IFITM1." Viruses 12, no. 3 (March 8, 2020): 295. http://dx.doi.org/10.3390/v12030295.
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Interferon-inducible transmembrane proteins (IFITM1/2/3) have been reported to suppress the entry of a wide range of viruses. However, their antiviral functional residues and specific mechanisms are still unclear. Here, we firstly resolved the topology of IFITM1 on the plasma membrane where N-terminus points into the cytoplasm and C-terminus resides extracellularly. Further, KRRK basic residues of IFITM1 locating at 62–67 of the conserved intracellular loop (CIL) were found to play a key role in the restriction on the Zika virus (ZIKV) and dengue virus (DENV). Similarly, KRRK basic residues of IFITM2/3 also contributed to suppressing ZIKV replication. Finally, IFITM1 was revealed to be capable of restricting the release of ZIKV particles from endosome to cytosol so as to impede the entry of ZIKV into host cells, which was tightly related with the inhibition of IFITM1 on the acidification of organelles. Overall, our study provided topology, antiviral functional residues and the mechanism of interferon-inducible transmembrane proteins.
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Kummer, Susann, Ori Avinoam, and Hans-Georg Kräusslich. "IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells." Viruses 11, no. 6 (June 12, 2019): 548. http://dx.doi.org/10.3390/v11060548.
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Interferon-induced transmembrane proteins (IFITMs) have been shown to strongly affect influenza A virus (IAV) infectivity in tissue culture. Moreover, polymorphisms in IFITM3 have been associated with the severity of the disease in humans. IFITM3 appears to act early in the infection, but its mechanism of action and potential interactions with incoming IAV structures are not yet defined. Here, we visualized endogenous IFITM3 interactions with IAV in the human lung epithelial cell line A549 and in primary human airway epithelial cells employing stimulated emission depletion super-resolution microscopy. By applying an iterative approach for the cluster definition and computational cluster analysis, we found that IFITM3 reorganizes into clusters as IAV infection progresses. IFITM3 cluster formation started at 2-3 h post infection and increased over time to finally coat IAV-containing endosomal vesicles. This IAV-induced phenotype was due to the endosomal recruitment of IFITM3 rather than to an overall increase in the IFITM3 abundance. While the IAV-induced IFITM3 clustering and localization to endosomal vesicles was comparable in primary human airway epithelial cells and the human lung epithelial cell line A549, the endogenous IFITM3 signal was higher in primary cells. Moreover, we observed IFITM3 signals adjacent to IAV-containing recycling endosomes.
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Tirumurugaan, Krishnaswamy, Rahul Pawar, Gopal Dhinakar Raj, Arthanari Thangavelu, John Hammond, and Satya Parida. "RNAseq Reveals the Contribution of Interferon Stimulated Genes to the Increased Host Defense and Decreased PPR Viral Replication in Cattle." Viruses 12, no. 4 (April 20, 2020): 463. http://dx.doi.org/10.3390/v12040463.
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Peste des petits ruminants virus (PPRV) is known to replicate in a wide variety of ruminants causing very species-specific clinical symptoms. Small ruminants (goats and sheep) are susceptible to disease while domesticated cattle and buffalo are dead-end hosts and do not display clinical symptoms. Understanding the host factors that influence differential pathogenesis and disease susceptibility could help the development of better diagnostics and control measures. To study this, we generated transcriptome data from goat and cattle peripheral blood mononuclear cells (PBMC) experimentally infected with PPRV in-vitro. After identifying differentially expressed genes, we further analyzed these immune related pathway genes using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and selected candidate genes were validated using in-vitro experiments. Upon PPRV infection, we identified 12 and 22 immune related genes that were differentially expressed in goat and cattle respectively. In both species, this included the interferon stimulated genes (ISGs) IFI44, IFI6, IFIT1, IFIT2, IFIT3, ISG15, Mx1, Mx2, OAS1X, RSAD2, IRF7, DDX58 and DHX58 that were transcribed significantly higher in cattle. PPRV replication in goat PBMCs significantly increased the expression of phosphodiesterase 12 (PDE12), a 2′,5′-oligoadenylate degrading enzyme that contributes to the reduced modulation of interferon-regulated gene targets. Finally, a model is proposed for the differential susceptibility between large and small ruminants based on the expression levels of type-I interferons, ISGs and effector molecules.
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Dinwiddie, Darrell, Walter Dehority, Kurt C. Schwalm, Raymond J. Langley, Stephen A. Young, and Joshua L. Kennedy. "2249." Journal of Clinical and Translational Science 1, S1 (September 2017): 59. http://dx.doi.org/10.1017/cts.2017.213.
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OBJECTIVES/SPECIFIC AIMS: Respiratory viruses cause enormous medical burden, yet many of the specific virus and host genetic factors that impact pathogenesis are still largely unknown or poorly understood. To better understand the drivers of both acute clinical pathogenesis and long-term impacts, such as the development of asthma, we investigated the host response to respiratory syncytial virus (RSV) infections in pediatric patients. METHODS/STUDY POPULATION: We collected nasopharyngeal swabs from 32 pediatric patients with acute RSV infection. The swabs represented a mixed cell population including epithelial and immune cells at the active site of infection. Unbiased RNA sequencing with ribosomal RNA depletion allowed the simultaneous detection of host gene expression and RSV infection. We sequenced samples 2×75 bp on an Illumina NextSeq 500. Sequences were mapped to the human genome using the TopHat 2 aligner and FPKM estimation of reference genes and transcripts and assembly of novel transcripts were conducted with Cufflinks 2. RESULTS/ANTICIPATED RESULTS: During acute RSV infection we identified 7343 genes that were significantly expressed. Pathway analysis using KEGG revealed significant upregulation of pathways involved in innate immune response infection, ribosome function, oxidative phosphorylation, spliceosome and autoimmune disorders. We found high levels of innate immune response genes including CXCL8, IFITM1, IFITM2, IFITM3, IL1RN, and ISG15. In comparing RSV subtype A to RSV B we found significant differential expression of multiple noncoding RNAs. DISCUSSION/SIGNIFICANCE OF IMPACT: Examination of the host gene response during acute RSV infections, yielded important insight into the mechanisms that cause clinical pathogenesis and may provide understanding of the mechanisms that lead to known long-term impacts, such as the development of asthma. Together, this data may be used to guide clinical treatment and management decisions for children with severe RSV infections.
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Guo, Y., N. Jahmat, T. Van Shaik, M. Chanrot, J. F. Valarcher, G. Charpigny, E. Bongcam-Rudloff, G. Andersson, and P. Humblot. "124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION." Reproduction, Fertility and Development 29, no. 1 (2017): 170. http://dx.doi.org/10.1071/rdv29n1ab124.
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Lipopolysaccharide (LPS) is a component of the outer membrane of gram-negative bacteria and is involved in postpartum uterine infection in cattle. Lipopolysaccharide causes inflammation of the endometrium and the activation of immune and pro-inflammatory pathways in uterine cells has been well documented. This study was performed to investigate the effects of LPS on epithelial cells from whole-genome information, and this abstract focuses on genes and pathways involved in the regulation of implantation. Following in vitro culture of bovine endometrial epithelial cells (bEEC), passage 4 epithelial cell samples from 3 cows were exposed to 0, 2, and 8 µg mL−1 LPS (Sigma L2630, Escherichia coli O111:B4, Sigma Chemical Co., St. Louis, MO, USA) for 24 h. At time 0 and at 24 h for each LPS dosage, RNA was extracted by using the All prep DNA/RNA Universal kit (Qiagen, Valencia, CA, USA). Samples were analysed by RNA sequencing performed in the SciLife Laboratory in Uppsala. Differentially expressed genes (DEG) were identified by using Ensemble genes as a reference. No DEG were found between 2 and 8 µg mL−1 LPS-treated samples and at 24 h 2035 DEG were identified (Benjamini-Hochberg adjusted P-value < 0.05) between controls and samples treated with 2 µg mL−1 LPS. Gene ontology analysis did show that DEG were associated to immune response (up), response to stress and external stimuli (up), catalytic activity (up), cell cycle, anatomical structures especially cell membrane, and adhesion (down) pathways. In the latest, numerous specific genes in relation with implantation were highly deregulated. This includes down-regulation of 8 members of the cadherin superfamily. On the contrary, 4 members of the mucin family were strongly up-regulated by LPS (MUC1, MUC13, MUC16, F1MUC1). Molecules such as plakophilins and desmogleins involved in desmosomes, in tight junctions, and in the control of cell adhesion were also deregulated. Specific changes occurred in immune response related with implantation [strong up-regulation of the immunoglobulin superfamily members such ICAM1 (or CD54) and down-regulation of ALCAM]. A set of 10 molecules belonging to the family of integrins and their binding partners were also deregulated [for instance, down-regulation of osteopontin (SPP1)]. In addition, LPS deregulated a large set of genes binding the above molecules (such as galectins LGALS1, S3, S9) and more than 20 transcripts coding for cytokines and their receptors. A large series of interferon-induced genes (IFITS) and genes coding for interferon-induced trans membrane proteins (IFITM) were highly up-regulated by LPS. This may be of functional importance due to the fact that all those genes are normally up-regulated by interferon tau from embryonic origin. The above results show that the function of endometrial epithelial cells is profoundly affected by LPS and that most of the key signals involved in implantation are deregulated. It is likely that these LPS-induced changes strongly perturb lately endometrial responsiveness to embryos at the time of implantation. Research was done with the financial support of FP7 project “Prolific” and RMUTSV (Thailand).
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Morodomi, Yosuke, Roberto Aiolfi, Eric Won, Sachiko Kanaji, Paul Schimmel, Zaverio M. Ruggeri, and Taisuke Kanaji. "Sca-1 As a Marker of Stress-Induced Thrombopoiesis in Mice." Blood 134, Supplement_1 (November 13, 2019): 1068. http://dx.doi.org/10.1182/blood-2019-127446.
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Introduction: It has been shown that megakaryocytes (MKs) can develop from a subset of MK-biased hematopoietic stem cells (HSCs). We also demonstrated that an active form of tyrosyl tRNA synthetase (YRS) has ex-translational activities that stimulate rapid platelet production in thrombocytopenic mice. Remarkably, YRS stimulates the development of MKs expressing the stem cell marker, Sca-1, and the monocyte/macrophage marker, F4/80. Thus, we hypothesized that YRS treatment mimics stress-induced megakaryopoiesis and Sca-1 may be a marker for MKs/platelets derived from MK-biased HSCs under inflammatory stress conditions. Accordingly, YRS does not induce Sca-1+ MKs in type I interferon (IFN-I) receptor knockout mice, suggesting a role of IFNs in the induction of Sca1+ MKs. Methods: We used a transgenic mouse strain expressing EGFP under the transcriptional regulatory elements of the Sca-1 gene (Sca-1-EGFP Tg) as a sensitive marker of Sca-1+ MKs. To compare transcriptional profiles, we sorted from mouse bone marrow (BM) EGFP+F4/80+CD41+mGPIbα+ and EGFP-F4/80-CD41+mGPIbα+ cells - representing Sca-1+ MKs and Sca-1- (conventional) MKs, respectively - and performed RNA-Seq analysis. To investigate the mechanism of Sca-1+ MK induction, mouse BM cells were treated with a synthetic TLR7 agonist and MKs were analyzed by flow cytometry. To elucidate the role of Sca-1+ MKs in thrombopoiesis, we infected Sca-1-EGFP Tg mice with lymphocytic choriomeningitis virus (LCMV) Armstrong strain, and analyzed the percentage of EGFP+ platelets and expression of IFN-stimulated genes. Results: We found that expression of MK-specific mRNAs is ~10-fold higher in Sca1+ than Sca1- MKs. As shown in Figure 1A, Sca1+ MKs highly expressed myeloid-related genes (Mpo, Elane, and Ctsg) and stem cell-related genes (Cd34 and Kit); in contrast, Sca1- MKs highly expressed erythroid lineage genes, consistent with origin from a common megakaryocyte-erythroid progenitor (MEP). Expression of IFN-stimulated genes, such as Ifitm1/2/3, is upregulated in Sca-1+ MKs, suggesting the involvement of IFN-I signaling in Sca-1+ MK induction. TLR7 typically recognizes single-stranded viral RNA and stimulates IFN-I production. When Sca-1-EGFP Tg BM cells were cultured in the presence of Gardiquimoid (1 µg/ml), a synthetic TLR7 agonist, Sca1- MKs were reduced and Sca1+ MKs were markedly increased compared to control vehicle treatment (9442 ± 1465 vs 4201 ± 1100). Notably, the proportion of high-ploidy cells was greater in Sca1+ thanSca1- MKs. Moreover, when Sca-1-EGFP Tg mice were infected with LCMV, which cause IFN-I-dependent thrombocytopenia, the percentage of EGFP+ platelets was markedly increased on day 3 (40.0 ± 3.7%) and peaked at day 7 (89.2 ± 5.4%) post-infection as compared to before (3.0 ± 1.0%) (Figure 1B), with 100-fold increase in the EGFP mean fluorescence intensity. Expression of Ifitm3 in platelets was also increased at day 10 post-infection. These results are consistent with our original hypothesis that YRS mimics inflammatory stress conditions and Sca1+ MKs are induced as a consequence of TLRs activation and IFN-I signaling. Conclusions: Our findings indicate that TLR7 activation and IFN-I signaling shift MK generation from Sca-1- to Sca-1+ progenitors, which rapidly develop to high-ploidy Sca-1+ MKs that may accelerate recovery from thrombocytopenia. Accordingly, under inflammatory stress conditions, such as viral infection, the majority of circulating platelets originate was from Sca-1+ MKs. The high expression of Ifitm proteins, which are known to inhibit cellular entry by viruses, in Sca-1+ MKs/platelets may contribute to their role in host defense. Disclosures Aiolfi: MERU-VasImmune, Inc: Other: Stock option. Kanaji:MERU-VasImmune, Inc: Other: Stock option. Schimmel:aTyr Pharma: Consultancy, Equity Ownership, Patents & Royalties. Ruggeri:MERU-VasImmune Inc.: Equity Ownership, Other: CEO and Founder. Kanaji:MERU-VasImmune, Inc: Other: Stock option.
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Fricke, Thomas, Sarah Schlagowski, Shanchuan Liu, Xiaoliang Yang, Uwe Fiebig, Artur Kaul, Armin Ensser, and Alexander S. Hahn. "Comparison of a Genotype 1 and a Genotype 2 Macaque Foamy Virus env Gene Indicates Distinct Infectivity and Cell-Cell Fusion but Similar Tropism and Restriction of Cell Entry by Interferon-Induced Transmembrane Proteins." Viruses 15, no. 2 (January 17, 2023): 262. http://dx.doi.org/10.3390/v15020262.
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Foamy viruses (FVs) are naturally found in many different animals and also in primates with the notable exception of humans, but zoonotic infections are common. In several species, two different envelope (env) gene sequence clades or genotypes exist. We constructed a simian FV (SFV) clone containing a reporter gene cassette. In this background, we compared the env genes of the SFVmmu-DPZ9524 (genotype 1) and of the SFVmmu_R289hybAGM (genotype 2) isolates. SFVmmu_R289hybAGM env-driven infection was largely resistant to neutralization by SFVmmu-DPZ9524-neutralizing sera. While SFVmmu_R289hybAGM env consistently effected higher infectivity and cell-cell fusion, we found no differences in the cell tropism conferred by either env across a range of different cells. Infection by both viruses was weakly and non-significantly enhanced by simultaneous knockout of interferon-induced transmembrane proteins (IFITMs) 1, 2, and 3 in A549 cells, irrespective of prior interferon stimulation. Infection was modestly reduced by recombinant overexpression of IFITM3, suggesting that the SFV entry step might be weakly restricted by IFITM3 under some conditions. Overall, our results suggest that the different env gene clades in macaque foamy viruses induce genotype-specific neutralizing antibodies without exhibiting overt differences in cell tropism, but individual env genes may differ significantly with regard to fitness.
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Zhen, Jing, Zhe Song, WenJie Su, Qing-Cui Zeng, JiaCen Li, and Qin Sun. "Integrated analysis of RNA-binding proteins in thyroid cancer." PLOS ONE 16, no. 3 (March 12, 2021): e0247836. http://dx.doi.org/10.1371/journal.pone.0247836.
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Recently, the incidence of thyroid cancer (THCA) has been on the rise. RNA binding proteins (RBPs) and their abnormal expression are closely related to the emergence and pathogenesis of tumor diseases. In this study, we obtained gene expression data and corresponding clinical information from the TCGA database. A total of 162 aberrantly expressed RBPs were obtained, comprising 92 up-regulated and 70 down-regulated RBPs. Then, we performed a functional enrichment analysis and constructed a PPI network. Through univariate Cox regression analysis of key genes and found that NOLC1 (p = 0.036), RPS27L (p = 0.011), TDRD9 (p = 0.016), TDRD6 (p = 0.002), IFIT2 (p = 0.037), and IFIT3 (p = 0.02) were significantly related to the prognosis. Through the online website Kaplan-Meier plotter and multivariate Cox analysis, we identified 2 RBP-coding genes (RPS27L and IFIT3) to construct a predictive model in the entire TCGA dataset and then validate in two subsets. In-depth analysis revealed that the data gave by this model, the patient’s high-risk score is very closely related to the overall survival rate difference (p = 0.038). Further, we investigated the correlation between the model and the clinic, and the results indicated that the high-risk was in the male group (p = 0.011) and the T3-4 group (p = 0.046) was associated with a poor prognosis. On the whole, the conclusions of our research this time can make it possible to find more insights into the research on the pathogenesis of THCA, this could be beneficial for individualized treatment and medical decision making.
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Yount, Jacob S., Ashley Zani, and Adam D. Kenney. "Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice." Journal of Immunology 208, no. 1_Supplement (May 1, 2022): 51.17. http://dx.doi.org/10.4049/jimmunol.208.supp.51.17.
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Abstract Interferon-induced transmembrane protein 3 (IFITM3) is a host antiviral protein that alters cell membranes to block fusion of viruses. Published reports have identified conflicting pro- and anti-viral effects of IFITM3 on SARS-CoV-2 in cultured cells, and its impact on viral pathology in vivo remains unclear. Here, we show that IFITM3 knockout (KO) mice infected with mouse-adapted SARS-CoV-2 experienced extreme weight loss and lethality, while wild type (WT) mice lost only 10% of their body weight and recovered. KO mice had higher lung viral titers and increases in lung inflammatory cytokine levels, CD45-positive immune cell infiltration, and histopathology, compared to WT mice. Mechanistically, we observed disseminated viral antigen staining throughout the lung tissue and pulmonary vasculature in KO mice, while staining was observed in confined regions in WT lungs. Global transcriptomic analysis of infected lungs identified upregulation of gene signatures associated with interferons, inflammation, and angiogenesis in KO versus WT animals, highlighting changes in lung gene expression programs that precede severe lung pathology and fatality. Corroborating the protective effect of IFITM3 in vivo, K18-hACE2/IFITM3 KO mice infected with non-adapted SARS-CoV-2 showed enhanced, rapid weight loss and early death compared to control mice. Increased heart infection was observed in both mouse models in the absence of IFITM3, indicating that IFITM3 constrains extrapulmonary dissemination of SARS-CoV-2. Our results establish IFITM3 KO mice as a new animal model for studying severe SARS-CoV-2 infection, and overall demonstrate that IFITM3 is protective in SARS-CoV-2 infections of mice. Supported by grants from the NIH (R01 AI130110, R21 AI151230, R01 HL154001, R21 AI142256, and U54 CA260582)
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Pellagatti, Andrea, Mario Cazzola, Aristoteles Giagounidis, Luca Malcovati, Matteo G. Della Porta, Martin Jädersten, Sally Killick, et al. "Expression Profiling of CD34+ Cells in Patients with Myelodysplastic Syndromes: Involvement of Interferon-Stimulated Genes and Correlation to FAB Subtype and Karyotype." Blood 108, no. 11 (November 16, 2006): 2626. http://dx.doi.org/10.1182/blood.v108.11.2626.2626.
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Abstract The myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic malignancies. We have used Affymetrix microarray technology to determine the gene expression profiles in CD34+ cells of 84 MDS patients (25 RA, 28 RARS and 31 RAEB) and 16 healthy controls. Twenty-five of 84 patients had a del(5q). CD34+ cells were isolated from bone marrow samples using MACS magnetic columns. Extracted total RNA was amplified using the Two-Cycle Target Labelling kit (Affymetrix) and samples were hybridized to Affymetrix U133 Plus2.0 chips (representing 39,000 human genes). Cell intensity calculation and scaling was performed using GeneChip Operating Software and data analysis using GeneSpring 7.3. The expression profiles of MDS CD34+ cells showed many similarities to reported interferon-γ induced gene expression in normal CD34+ cells. Indeed the two most up-regulated genes, IFIT1 and IFITM1, are interferon-stimulated genes. IFIT1 and IFITM1 were up-regulated by >2-fold in 58/84 and 53/84 MDS patients respectively. Genes down-regulated by >2-fold in the majority of MDS patients include the putative tumor suppressor gene Gravin/AKAP12, ARPP-21, CD24 and MME. The association of distinct gene expression profiles with specific FAB and cytogenetic groups was determined using data from 55 MDS patients as a training set. Hierarchical clustering performed using 457 significantly different genes between different FAB subtypes showed that MDS patients with RARS constitute a homogeneous group, while MDS patients with RA and RAEB show more overlap. CD34+ cells from patients with RARS showed up-regulation of mitochondrial-related genes, and in particular of those of heme synthesis (e.g. ALAS2). Statistical analysis showed that 889 probe-sets could discriminate MDS patients with a del(5q) from those without a del(5q). MDS patients with the del(5q) showed distinctive down-regulation of genes mapping to chromosome 5q, and up-regulation of the histone HIST1 gene cluster at chromosome 6p21 and of genes related to the actin cytoskeleton. In order to identify genes differentially expressed between early and advanced MDS, a comparison was made between the 18 patients with RA and the nine MDS patients with RAEBII. 762 significantly different probe sets were identified that could group together MDS patients with RAEBII. The most significant genes identified include CASP3 and FLT3, and represent potential prognostic markers or markers of disease progression. The remaining 29 MDS patients were used as a test set for class prediction using support vector machines. The FAB subtype was correctly predicted for 83% of the test samples. The presence or absence of a del(5q) was predicted correctly for 93% of the test samples. Finally, 94% of the test samples were predicted correctly as RA or RAEBII. This study provides important and new insights into the pathophysiology of MDS.
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Kim, Yong-Chan, and Byung-Hoon Jeong. "Phylogenetic and topological analyses of the bovine interferon-induced transmembrane protein (IFITM3)." Acta Veterinaria Hungarica 69, no. 1 (June 5, 2021): 14–22. http://dx.doi.org/10.1556/004.2021.00010.
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AbstractInterferon-induced transmembrane protein 3 (IFITM3) plays a pivotal role in antiviral capacity in several species. However, to date, investigations of the IFITM3 protein in cattle have been rare. According to recent studies, interspecific differences in the IFITM3 protein result in several unique features of the IFITM3 protein relative to primates and birds. Thus, in the present study, we investigated the bovine IFITM3 protein based on nucleotide and amino acid sequences to find its distinct features. We found that the bovine IFITM3 gene showed a significantly different length and homology relative to other species, including primates, rodents and birds. Phylogenetic analyses indicated that the bovine IFITM3 gene and IFITM3 protein showed closer evolutionary distance with primates than with rodents. However, cattle showed an independent clade among primates, rodents and birds. Multiple sequence alignment of the IFITM3 protein indicated that the bovine IFITM3 protein contains 36 bovine-specific amino acids. Notably, the bovine IFITM3 protein was predicted to prefer inside-to-outside topology of intramembrane domain 1 (IMD1) and inside-to-outside topology of transmembrane domain 2 by TMpred and three membrane embedding domains according to the SOSUI system.
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Zhang, Jing, Xin Xu, Huiling Zhu, Yang Wang, Yongqing Hou, and Yulan Liu. "Dietary fish oil supplementation alters liver gene expressions to protect against LPS-induced liver injury in weanling piglets." Innate Immunity 25, no. 1 (January 2019): 60–72. http://dx.doi.org/10.1177/1753425918821420.
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Here, the potential mechanisms of the protective effects of fish oil against LPS-induced liver injury in a piglet model were investigated by using RNA sequencing. Twenty-four piglets were used in a 2 × 2 factorial design, and the main factors included diet (5% corn oil or 5% fish oil) and immunological challenge (LPS or saline, on d 19). All piglets were slaughtered at 4 h after challenge, and liver samples were collected. Fish oil improved liver morphology and reduced TNF-α, IL-1β and IL-6 productions after LPS challenge. RNA sequencing analysis showed fish oil had significant effect on the expressions of genes involved in immune response during LPS-induced inflammation. Selected gene expression changes were validated using quantitative RT-PCR. Fish oil reduced the expressions of pro-inflammatory genes IL1R1, IL1RAP, CEBPB and CRP, and increased that of anti-inflammatory genes IL-18BP, NFKBIA, IFIT1, IFIT2 and ATF3. Moreover, fish oil restored the expressions of some lipid metabolism-related genes, such as ACAA1, ACACA, ACADS and ACADM, which were only decreased in pigs fed a corn oil diet after LPS challenge. Our RNA sequencing reveals novel gene-nutrient interactions following fish oil supplementation and evoked inflammation, which add to the current understanding of the benefits of n-3 polyunsaturated fatty acids against liver injury.
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Young, D. F., J. Andrejeva, X. Li, F. Inesta-Vaquera, C. Dong, V. H. Cowling, S. Goodbourn, and R. E. Randall. "Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family." Journal of Virology 90, no. 20 (August 10, 2016): 9446–56. http://dx.doi.org/10.1128/jvi.01056-16.
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ABSTRACTWe have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. The IFIT1 sensitivity of PIV5 was not rescued by coinfection with an IFIT1-resistant virus (PIV3), demonstrating that PIV3 does not specifically inhibit the antiviral activity of IFIT1 and that the inhibition of PIV5 mRNAs is regulated bycis-acting elements. We developed anin vitrotranslation system using purified human IFIT1 to further investigate the mechanism of action of IFIT1. While the translations of PIV2, PIV5, and MuV mRNAs were directly inhibited by IFIT1, the translations of PIV3, SeV, and CDV mRNAs were not. Using purified human mRNA-capping enzymes, we show biochemically that efficient inhibition by IFIT1 is dependent upon a 5′ guanosine nucleoside cap (which need not be N7 methylated) and that this sensitivity is partly abrogated by 2′O methylation of the cap 1 ribose. Intriguingly, PIV5 M mRNA, in contrast to NP mRNA, remained sensitive to inhibition by IFIT1 followingin vitro2′O methylation, suggesting that other structural features of mRNAs may influence their sensitivity to IFIT1. Thus, surprisingly, the viral polymerases (which have 2′-O-methyltransferase activity) of rubulaviruses do not protect these viruses from inhibition by IFIT1. Possible biological consequences of this are discussed.IMPORTANCEParamyxoviruses cause a wide variety of diseases, and yet most of their genes encode structural proteins and proteins involved in their replication cycle. Thus, the amount of genetic information that determines the type of disease that paramyxoviruses cause is relatively small. One factor that will influence disease outcomes is how they interact with innate host cell defenses, including the interferon (IFN) system. Here we show that different paramyxoviruses interact in distinct ways with cells in a preexisting IFN-induced antiviral state. Strikingly, all the rubulaviruses tested were sensitive to the antiviral action of ISG56/IFIT1, while all the other paramyxoviruses tested were resistant. We developed novelin vitrobiochemical assays to investigate the mechanism of action of IFIT1, demonstrating that the mRNAs of rubulaviruses can be directly inhibited by IFIT1 and that this is at least partially because their mRNAs are not correctly methylated.
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Maletzko, Antonia, Jana Key, Ilka Wittig, Suzana Gispert, Gabriele Koepf, Júlia Canet-Pons, Sylvia Torres-Odio, A. Phillip West, and Georg Auburger. "Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse." neurogenetics 22, no. 4 (August 3, 2021): 297–312. http://dx.doi.org/10.1007/s10048-021-00657-2.
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AbstractMitochondrial dysfunction may activate innate immunity, e.g. upon abnormal handling of mitochondrial DNA in TFAM mutants or in altered mitophagy. Recent reports showed that also deletion of mitochondrial matrix peptidase ClpP in mice triggers transcriptional upregulation of inflammatory factors. Here, we studied ClpP-null mouse brain at two ages and mouse embryonal fibroblasts, to identify which signaling pathways are responsible, employing mass spectrometry, subcellular fractionation, immunoblots, and reverse transcriptase polymerase chain reaction. Several mitochondrial unfolded protein response factors showed accumulation and altered migration in blue-native gels, prominently the co-chaperone DNAJA3. Its mitochondrial dysregulation increased also its extra-mitochondrial abundance in the nucleus, a relevant observation given that DNAJA3 modulates innate immunity. Similar observations were made for STAT1, a putative DNAJA3 interactor. Elevated expression was observed not only for the transcription factors Stat1/2, but also for two interferon-stimulated genes (Ifi44, Gbp3). Inflammatory responses were strongest for the RLR pattern recognition receptors (Ddx58, Ifih1, Oasl2, Trim25) and several cytosolic nucleic acid sensors (Ifit1, Ifit3, Oas1b, Ifi204, Mnda). The consistent dysregulation of these factors from an early age might influence also human Perrault syndrome, where ClpP loss-of-function leads to early infertility and deafness, with subsequent widespread neurodegeneration.
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Padariya, Monikaben, Alicja Sznarkowska, Sachin Kote, Maria Gómez-Herranz, Sara Mikac, Magdalena Pilch, Javier Alfaro, Robin Fahraeus, Ted Hupp, and Umesh Kalathiya. "Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes." Biomolecules 11, no. 5 (April 22, 2021): 622. http://dx.doi.org/10.3390/biom11050622.
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Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Nikpour, Maryam, Andrea Pellagatti, Martin Jädersten, Ann-Mari Forsblom, James S. Wainscoat, Jacqueline Boultwood, and Eva Hellström-Lindberg. "Gene Expression Profiling of Day 7 Erythroblasts from RARS Before and after Treatment with G-CSF." Blood 110, no. 11 (November 16, 2007): 2427. http://dx.doi.org/10.1182/blood.v110.11.2427.2427.
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Abstract Refractory Anemia with Ringed Sideroblasts (RARS) is characterized by severe ineffective erythropoesis, cytochrome c release, and mitochondrial iron overload. (Tehranchi, 2003). Granulocyte-CSF inhibit erythroid apoptosis in vitro as well as in vivo (Tehranchi 2005) The molecular mechanisms underlying the erythroid apoptosis in RARS and the effects of G-CSF were studied by gene expression profiling of erythroblasts from 8 healthy controls and 6 RARS patients. CD34+ selected marrow cells were cultured for 7 days in Iscove’s medium with 15% BIT9500. At day 7 an aliquot of RARS cells were treated with G-CSF (100ng/ml) for 4 hours. The gene expression profiles were determined using Affymetrix, U133 Plus2.0 chips (Pellagatti, 2006). Statistical analysis showed that 1426 probe-sets were significantly differentially expressed (P<0.01) between untreated and G-CSF treated RARS samples, and healthy controls. Hierarchical clustering separated these groups into distinct clusters. 22 genes were significantly up-regulated by ≥2-fold in all RARS samples and included CCND2, DLK1, PPM1A and TBC1D8. 35 genes were significantly down-regulated by ≥2-fold, including LRIG1, ABCB7 and MLL3. RARS erythroblasts showed dysregulation of several genes involved in proliferation, apoptosis and iron transport. For instance CCND2 and TBC1D8, positive regulators of proliferation, were up-regulated in RARS, whereas LRIG1, a negative regulator of proliferation, was down-regulated. PPM1A, whose function leads to G2/M cell cycle arrest and apoptosis via p53 activation, was also up-regulated. ABCB7, involved in the transfer of iron from mitochondria to cytosol and in maturation of cytosolic Fe/S enzymes, and mutated in X-linked sideroblastic anemia with ataxia, was significantly down-regulated in RARS. Several dysregulated genes in RARS were restored to the range of normal expression after G-CSF treatment. Of these, MFN2, which was down-regulated in RARS, maintains mitochondrial membrane stability, and restores mitochondrial membrane potential and cell respiration. A normalization of MFN2 is thus consistent with the observed inhibitory effect on cytochrome c release. Several dysregulated genes including BAX, FLIP and BAG1 were not altered by G-CSF treatment, indicating that G-CSF does not exert an unspecific anti-apoptotic effect through the Bcl2 family proteins. Only one, BCLAF1, a transcriptional repressor and pro-apoptotic member of BCL2 family was upregulated in RARS erythroblasts and down-regulated by G-CSF. G-CSF treatment down-regulated also the expression of interferon induced genes including IFIT1, IFIH1, IFI44, IFIT2, IFIT3, IRF7, IFRG28 and IFI78, several of which were previously shown to be upregulated in RARS CD34+ cells (Pellagatti, 2006). Since G-CSF specifically supports erythroblast survival in RARS through inhibition of mitochondria-mediated apoptosis, our findings may lead to further understanding of the molecular mechanisms in RARS and to the identification of candidate genes in this disease. Figure Figure
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Kim, Yong-Chan, Min-Ju Jeong, and Byung-Hoon Jeong. "Regulatory Single Nucleotide Polymorphism of the Bovine IFITM3 Gene Induces Differential Transcriptional Capacities of Hanwoo and Holstein Cattle." Genes 12, no. 11 (October 21, 2021): 1662. http://dx.doi.org/10.3390/genes12111662.
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Interferon-induced transmembrane protein 3 (IFITM3), a crucial effector of the host’s innate immune system, prohibits an extensive range of viruses. Previous studies have reported that single nucleotide polymorphisms (SNPs) of the IFITM3 gene are associated with the expression level and length of the IFITM3 protein and can impact susceptibility to infectious viruses and the severity of infection with these viruses. However, there have been no studies on polymorphisms of the bovine IFITM3 gene. In the present study, we finely mapped the bovine IFITM3 gene and annotated the identified polymorphisms. We investigated polymorphisms of the bovine IFITM3 gene in 108 Hanwoo and 113 Holstein cattle using direct sequencing and analyzed genotype, allele, and haplotype frequencies and linkage disequilibrium (LD) between the IFITM3 genes of the two cattle breeds. In addition, we analyzed transcription factor-binding sites and transcriptional capacity using PROMO and luciferase assays, respectively. Furthermore, we analyzed the effect of a nonsynonymous SNP of the IFITM3 gene using PolyPhen-2, PANTHER, and PROVEAN. We identified 23 polymorphisms in the bovine IFITM3 gene and found significantly different genotype, allele, and haplotype frequency distributions and LD scores between polymorphisms of the bovine IFITM3 gene in Hanwoo and Holstein cattle. In addition, the ability to bind the transcription factor Nkx2-1 and transcriptional capacities were significantly different depending on the c.-193T > C allele. Furthermore, nonsynonymous SNP (F121L) was predicted to be benign. To the best of our knowledge, this is the first genetic study of bovine IFITM3 polymorphisms.
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Regmi, Prabha, Kuo-Chu Lai, Chung-Ji Liu, and Te-Chang Lee. "SAHA Overcomes 5-FU Resistance in IFIT2-Depleted Oral Squamous Cell Carcinoma Cells." Cancers 12, no. 12 (November 26, 2020): 3527. http://dx.doi.org/10.3390/cancers12123527.
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Interferon-induced protein with tetratricopeptide repeats 2 (IFIT2) is a member of the interferon-stimulated gene family that contains tetratricopeptide repeats (TPRs), which mediate protein–protein interactions in various biological systems. We previously showed the depletion of IFIT2 enhanced cell migration and metastatic activity in oral squamous cell carcinoma (OSCC) cells via the activation of atypical PKC signaling. In this study, we found that IFIT2-knockdown cells displayed higher resistance to 5-fluorouracil (5-FU) than control cells. The comet assay and annexin V analysis showed decreased DNA damage and cell death in IFIT2-knockdown cells compared to control cells treated with 5-FU. Cell cycle progression was also perturbed by 5-FU treatment, with the accumulation of IFIT2-depleted cells in S phase in a time-dependent manner. We further observed the overexpression of thymidylate synthase (TS) and thymidine kinase (TK) in IFIT2-knockdown cells. Inhibition of TS alone or double inhibition of TS and TK1 using the siRNA technique increased susceptibility to 5-FU in IFIT2-knockdown cells. We further identified that suberanilohydroxamic acid (SAHA) treatment decreased the expression of TS in IFIT2-knockdown cells and demonstrated that pretreatment with SAHA sensitized IFIT2-knockdown cells to 5-FU in vitro and in vivo. In conclusion, IFIT2 knockdown enhances TS expression, which mediates 5-FU resistance, and SAHA pretreatment suppresses TS expression and hence sensitizes cells to 5-FU. SAHA will be an effective strategy for the treatment of OSCC patients with 5-FU resistance.
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Park, Hyun Jung, In Sun Kuk, Jin Hoi Kim, Jae Hwan Kim, Sang Jin Song, Bum Chae Choi, Bokyoung Kim, Nam Hyung Kim, and Hyuk Song. "Characterisation of mouse interferon-induced transmembrane protein-1 gene expression in the mouse uterus during the oestrous cycle and pregnancy." Reproduction, Fertility and Development 23, no. 6 (2011): 798. http://dx.doi.org/10.1071/rd10086.
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During the oestrous cycle, pregnancy and parturition, the uterus undergoes marked morphological, physiological and functional changes. Amid these changes, the Wnt/β-catenin signalling pathway has been identified as having a crucial role in regulating associated biological events. Recently, based on results from a mouse embryo study, interferon-induced transmembrane protein 1 (Ifitm1) was reported as a downstream molecule of the Wnt/β-catenin signalling pathway. Differential expression patterns of the Ifitm1 gene during the oestrous cycle, pregnancy and parturition were identified in the present study. Quantitative real-time polymerase chain reaction data from uterine samples of mice induced start the oestrous cycle by injection of human chorionic gonadotropin (hCG) and revealed that Ifitm1 mRNA expression increased from late pro-oestrus to metoestrus, and decreased during dioestrus and early pro-oestrus. During pregnancy, Ifitm1 gene expression was minimal until parturition, but increased markedly 2 days after parturition. This significant elevation in Ifitm1 gene expression at post partum stage was identical to Ifitm1 expression after the induction of abortion by injection of prostaglandin F2α. Interestingly, pregnant mare serum gonadotropin (PMSG) and oestrogen are also facilitates changes in Ifitm1 gene expression in an ovariectomised (OVX) mouse model. Expression of Ifitm1 mRNA was higher in response to PMSG than other hormones investigated. These results suggest that Ifitm1 may be involved in uteri physiology, although the mechanisms involved in the regulation of this gene expression and function in the uterus remain unknown. In the present study, differential expression patterns of the Ifitm1 gene were identified in the uteri of mice and the correlation between the patterns of Ifitm1 gene expression and Wnt/β-catenin signalling discussed.
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Chen, Lujun, Wensi Zhai, Xiao Zheng, Quanqin Xie, Qi Zhou, Min Tao, Yibei Zhu, Changping Wu, and Jingting Jiang. "Decreased IFIT2 Expression Promotes Gastric Cancer Progression and Predicts Poor Prognosis of the Patients." Cellular Physiology and Biochemistry 45, no. 1 (December 22, 2017): 15–25. http://dx.doi.org/10.1159/000486219.
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Background/Aims: The status of interferon (IFN) signaling pathway has been shown to be closely associated with the response of immune checkpoint blockade therapy against advanced human cancers. IFN-induced protein with tetratricopeptide repeats 2 (IFIT2), also known as IFN-stimulated gene 54 (ISG54), is one of the most highly responsive ISGs, which can inhibit the proliferation and migration of cancer cells, and regulate viral replication, resulting in anti-cancer and anti-viral effects. In the present study, we aimed to investigate the role of IFIT2 in human gastric cancer. Methods: Immunohistochemistry assay was used to investigate the correlation between the IFIT2 expression in cancer tissues and clinical parameters of gastric cancer patients. Knockdown of IFIT2 was performed using RNAi to assess the role of IFIT2 in the regulation of biological behaviors in human gastric cancer cell lines. Results: IFIT2 expression in gastric cancer tissues was significantly associated with tumor stage and postoperative prognoses of the patients. Moreover, decreased IFIT2 expression in human gastric cancer cell lines SGC-7901 and AGS significantly increased the cell viability, cell migration and the ratios of cells in S phase. Conclusion: Our present study demonstrated that the decreased IFIT2 expression could promote the gastric cancer progression and predict poor therapeutic outcomes of the patients.
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Shao, Huaming, Yong Zhang, Yishuai Liu, Yan Yang, Xiaozhu Tang, Jiajia Li, and Changxin Jia. "Establishment and Verification of a Gene Signature for Diagnosing Type 2 Diabetics by WGCNA, LASSO Analysis, and In Vitro Experiments." BioMed Research International 2022 (May 23, 2022): 1–34. http://dx.doi.org/10.1155/2022/4446342.
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Objective. The incidence and prevalence of type 2 diabetes are increasing with age. Nevertheless, there is lack of sensitive diagnostic tools and effective therapeutic regimens. We aimed to establish and verify a practical and valid diagnostic tool for this disease. Methods. WGCNA was presented on the expression profiling of type 2 diabetic and normal islets in combined GSE25724 and GSE38642 datasets. By LASSO Cox regression analyses, a gene signature was constructed based on the genes in diabetes-related modules. ROC curves were plotted for assessing the diagnostic efficacy. Correlations between the genes and immune cell infiltration and pathways were analyzed. BST2 and BTBD1 expression was verified in glucotoxicity-induced and normal islet β cells. The influence of BST2 on β cell dysfunction was investigated under si-BST2 transfection. Results. Totally, 14 coexpression modules were constructed, and red and cyan modules displayed the correlations to diabetes. The LASSO gene signature (BST2, BTBD1, IFIT1, IFIT3, and RTP4) was developed. The AUCs in the combined datasets and GSE20966 dataset were separately 0.914 and 0.910, confirming the excellent performance in diagnosing type 2 diabetes. Each gene in the model was distinctly correlated to immune cell infiltration and key signaling pathways (TGF-β and P53, etc.). The abnormal expression of BST2 and BTBD1 was confirmed in glucotoxicity-induced β cells. BST2 knockdown ameliorated β cell dysfunction and altered the activation of TGF-β and P53 pathways. Conclusion. Our findings propose a gene signature with high efficacy to diagnose type 2 diabetes, which could assist and improve early diagnosis and therapy.
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Abbas, Yazan M., Beatrice Theres Laudenbach, Saúl Martínez-Montero, Regina Cencic, Matthias Habjan, Andreas Pichlmair, Masad J. Damha, Jerry Pelletier, and Bhushan Nagar. "Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2′-O methylations." Proceedings of the National Academy of Sciences 114, no. 11 (March 1, 2017): E2106—E2115. http://dx.doi.org/10.1073/pnas.1612444114.
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IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to compete with the translation initiation factor eIF4F to specifically recognize foreign capped mRNAs, while remaining inactive against host mRNAs marked by ribose 2′-O methylation at the first cap-proximal nucleotide (N1). We report here several crystal structures of RNA-bound human IFIT1, including a 1.6-Å complex with capped RNA. IFIT1 forms a water-filled, positively charged RNA-binding tunnel with a separate hydrophobic extension that unexpectedly engages the cap in multiple conformations (synandanti) giving rise to a relatively plastic and nonspecific mode of binding, in stark contrast to eIF4E. Cap-proximal nucleotides encircled by the tunnel provide affinity to compete with eIF4F while allowing IFIT1 to select against N1 methylated mRNA. Gel-shift binding assays confirm that N1 methylation interferes with IFIT1 binding, but in an RNA-dependent manner, whereas translation assays reveal that N1 methylation alone is not sufficient to prevent mRNA recognition at high IFIT1 concentrations. Structural and functional analysis show that 2′-O methylation at N2, another abundant mRNA modification, is also detrimental for RNA binding, thus revealing a potentially synergistic role for it in self- versus nonself-mRNA discernment. Finally, structure-guided mutational analysis confirms the importance of RNA binding for IFIT1 restriction of a human coronavirus mutant lacking viral N1 methylation. Our structural and biochemical analysis sheds new light on the molecular basis for IFIT1 translational inhibition of capped viral RNA.
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Andrejeva, J., H. Norsted, M. Habjan, V. Thiel, S. Goodbourn, and R. E. Randall. "ISG56/IFIT1 is primarily responsible for interferon-induced changes to patterns of parainfluenza virus type 5 transcription and protein synthesis." Journal of General Virology 94, no. 1 (January 1, 2013): 59–68. http://dx.doi.org/10.1099/vir.0.046797-0.
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Interferon (IFN) induces an antiviral state in cells that results in alterations of the patterns and levels of parainfluenza virus type 5 (PIV5) transcripts and proteins. This study reports that IFN-stimulated gene 56/IFN-induced protein with tetratricopeptide repeats 1 (ISG56/IFIT1) is primarily responsible for these effects of IFN. It was shown that treating cells with IFN after infection resulted in an increase in virus transcription but an overall decrease in virus protein synthesis. As there was no obvious decrease in the overall levels of cellular protein synthesis in infected cells treated with IFN, these results suggested that ISG56/IFIT1 selectively inhibits the translation of viral mRNAs. This conclusion was supported by in vitro translation studies. Previous work has shown that ISG56/IFIT1 can restrict the replication of viruses lacking a 2′-O-methyltransferase activity, an enzyme that methylates the 2′-hydroxyl group of ribose sugars in the 5′-cap structures of mRNA. However, the data in the current study strongly suggested that PIV5 mRNAs are methylated at the 2′-hydroxyl group and thus that ISG56/IFIT1 selectively inhibits the translation of PIV5 mRNA by some as yet unrecognized mechanism. It was also shown that ISG56/IFIT1 is primarily responsible for the IFN-induced inhibition of PIV5.
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Smith, Jacqueline, Jean-Remy Sadeyen, Colin Butter, Pete Kaiser, and David W. Burt. "Analysis of the Early Immune Response to Infection by Infectious Bursal Disease Virus in Chickens Differing in Their Resistance to the Disease." Journal of Virology 89, no. 5 (December 10, 2014): 2469–82. http://dx.doi.org/10.1128/jvi.02828-14.
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ABSTRACTChicken whole-genome gene expression arrays were used to analyze the host response to infection by infectious bursal disease virus (IBDV). Spleen and bursal tissue were examined from control and infected birds at 2, 3, and 4 days postinfection from two lines that differ in their resistance to IBDV infection. The host response was evaluated over this period, and differences between susceptible and resistant chicken lines were examined. Antiviral genes, includingIFNA,IFNG,MX1,IFITM1,IFITM3, andIFITM5, were upregulated in response to infection. Evaluation of this gene expression data allowed us to predict several genes as candidates for involvement in resistance to IBDV.IMPORTANCEInfectious bursal disease (IBD) is of economic importance to the poultry industry and thus is also important for food security. Vaccines are available, but field strains of the virus are of increasing virulence. There is thus an urgent need to explore new control solutions, one of which would be to breed birds with greater resistance to IBD. This goal is perhaps uniquely achievable with poultry, of all farm animal species, since the genetics of 85% of the 60 billion chickens produced worldwide each year is under the control of essentially two breeding companies. In a comprehensive study, we attempt here to identify global transcriptomic differences in the target organ of the virus between chicken lines that differ in resistance and to predict candidate resistance genes.
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Magro, R., C. Saliba, L. Camilleri, C. Scerri, and A. Borg. "THU0235 VITAMIN D AND INTERFERON SIGNATURE GENE EXPRESSION IN SYSTEMIC LUPUS ERYTHEMATOSUS." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 344.3–345. http://dx.doi.org/10.1136/annrheumdis-2020-eular.934.
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Background:Vitamin D deficiency is more prevalent in patients with systemic lupus eythematosus (SLE) as a result of sun avoidance.1The potential negative impact of vitamin D deficiency on SLE disease activity has been shown in a number of studies.2The expression of the interferon signature genes in SLE correlates positively with disease activity, and these genes are thought to mediate the clinical manifestations of the disease.3Objectives:The aim of this study was to establish whether a relationship exists between serum 25-hydroxyvitamin D level and the interferon signature gene expression in whole blood of SLE patients.Methods:Informed consent was obtained from 92 SLE patients who were over the age of 18 and who fulfilled the SLICC classification criteria for SLE. The patients were interviewed and blood samples were taken. SLE disease activity was measured by SLE disease activity index-2K (SLEDAI-2K). RNA extraction was performed from whole blood. QuantiGene Plex technology was used to measure the expression of 12 interferon signature genes in the extracted RNA. The study was approved by the University Research Ethics Committee.Results:92.4% of the cohort studied were female. 58.7% were receiving vitamin D3 supplementation at a mean dose of 1031IU daily. 27.2% had vitamin D insufficiency (25-hydroxyvitamin D 21-29ng/ml) and 15.2% were vitamin D deficient (25-hydroxyvitamin D <20ng/ml). Mean serum 25-hydroxyvitamin D was 30.75ng/ml (standard deviation 9.53 ng/ml). Median SLEDAI-2K was 4 (range 0-12). Serum 25-hydroxyvitamin D had a significant negative correlation with body mass index (BMI) (R=-0.258, p=0.006) but there was no significant negative correlation with SLEDAI-2K or with the expression of the interferon signature genes. The expression of most interferon signatures genes measured (IFI35, OAS1, MX1, IFITM1, STAT2, IFIT3, IFIT1, STAT1, SOCS1) had a significant positive correlation with SLEDAI-2K.Conclusion:This study did not show a significant relationship between serum vitamin D level and disease activity. In keeping with this, there was no significant negative correlation between serum 25-hydroxyvitamin D and interferon signature gene expression. Further prospective studies and randomised controlled trials are required to study this relationship in greater depth.References:[1]Kamen DL, Cooper GS, Bouali H, Shaftman SR, Hollis BW, Gilkeson GS. Vitamin D deficiency in systemic lupus erythematosus. Autoimmun Rev. 2006; 5: 114-7.[2]Sahebari M, Nabavi N, Salehi M. Correlation between serum 25(OH)D values and lupus disease activity: an original article and a systematic review with meta-analysis focusing on serum VitD confounders.Lupus2014; 23: 1164-77.[3]Arasappan D, Tong W, Mummaneni P, Fang H, Amur S. Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells. BMC Med. 2011; 9: 65.Disclosure of Interests: :None declared
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Xu, Fengwen, Geng Wang, Fei Zhao, Yu Huang, Zhangling Fan, Shan Mei, Yu Xie, et al. "IFITM3 Inhibits SARS-CoV-2 Infection and Is Associated with COVID-19 Susceptibility." Viruses 14, no. 11 (November 18, 2022): 2553. http://dx.doi.org/10.3390/v14112553.
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SARS-CoV-2 has become a global threat to public health. Infected individuals can be asymptomatic or develop mild to severe symptoms, including pneumonia, respiratory distress, and death. This wide spectrum of clinical presentations of SARS-CoV-2 infection is believed in part due to the polymorphisms of key genetic factors in the population. In this study, we report that the interferon-induced antiviral factor IFITM3 inhibits SARS-CoV-2 infection by preventing SARS-CoV-2 spike-protein-mediated virus entry and cell-to-cell fusion. Analysis of a Chinese COVID-19 patient cohort demonstrates that the rs12252 CC genotype of IFITM3 is associated with SARS-CoV-2 infection risk in the studied cohort. These data suggest that individuals carrying the rs12252 C allele in the IFITM3 gene may be vulnerable to SARS-CoV-2 infection and thus may benefit from early medical intervention.
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Solstad, Abigail, Adam D. Kenney, Ashley Zani, Jacob S. Yount, and Emily A. Hemann. "Endogenous interferon-lambda signaling restricts virus replication and disease severity in a murine model of SARS-CoV-2 infection." Journal of Immunology 208, no. 1_Supplement (May 1, 2022): 125.08. http://dx.doi.org/10.4049/jimmunol.208.supp.125.08.
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Abstract Interferon-lambda (IFN-λ) is currently being investigated in a phase III clinical trial as a therapeutic against COVID-19. Exogenous IFN-λ restricts SARS-CoV-2 in vitro and in Balb/c and C57Bl/6 (WT) murine models of infection. However, roles of endogenously produced IFN-λ in SARS-CoV-2 pathogenesis are not currently known, and the overall mechanisms by which IFN-λ modulates the induction of protective immune responses in SARS-CoV-2 infections remains to be elucidated. We find that IFN-λ receptor deficient mice (Ifnlr1−/−) infected with mouse-adapted SARS-CoV-2 lose significantly more weight and have increased SARS-CoV-2 viral replication compared to WT through day 5 post infection. Intriguingly, Ifit3 and Ifitm3 are increased in the lungs of Ifnlr1−/− mice compared to WT following infection, despite similar IFN-α/β and IFN-λ mRNA levels, suggesting compensatory increases in type I IFN signaling are not driving the increased weight loss or ISG induction observed in Ifnlr1−/− mice. Global transcriptomics revealed induction of a suppressive immunoregulatory signature with increased IL-10 as a hallmark in Ifnlr1−/− lungs, suggesting IFN-λ is critically involved in regulating appropriate immune activation to limit SARS-CoV-2 pathogenesis. Histological analysis revealed a significant increase in CD45+ cells (but not neutrophils) in the lungs of Ifnlr1−/− mice compared to WT on day 5 post infection, and we identified increases in pathways associated with myeloid cell function and T cell activation in Ifnlr1−/− by comparative transcriptomics. Overall, broadening the understanding of how IFN-λ regulates SARS-CoV-2 infection, pathogenesis, and immunity will inform the utilization of IFN-λ as an immunotherapy and adjuvant. Supported by NIH Award K22 AI146141 to EAH.
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Nekhai, Sergei, Namita Kumari, Songping Wang, Sharmin Diaz, and Marina Jerebtsova. "Upregulation of Antiviral Factors That Inhibit HIV-1 Infection in Sickle Cell Disease." Blood 138, Supplement 1 (November 5, 2021): 960. http://dx.doi.org/10.1182/blood-2021-150883.
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Abstract Introduction Patients with Sickle cell disease (SCD) have lower risk for HIV-1 infection. We showed that ex vivo HIV-1 replication is blocked in SCD PBMCs in part because of the increased expression of ferroportin (FPN) and activation of SAMHD1, a host antiviral restriction factor. We hypothesized that rupture of sickling red blood cells releases sickle cell hemoglobin (HbS) that is phagocyted by macrophages leading to upregulation of innate antiviral response and inhibition of HIV-1 replication. We accessed changes in antiviral gene expression in PBMCs obtained from SCD patients compared to healthy controls. We also analyzed antiviral gene expression in macrophages treated with HbS compared to the HbA treatment. Methods The study was approved by Howard University review board (IRB) and all subjects consented to sample collection. Whole blood was collected from 9 SCA patients and 9 age and gender- matched healthy controls. PBMCs were activated with PHA (0.5 μg/ml) for 24-48 hrs followed by IL-2 (10 U/ml) for 24 hrs. Human THP-1 cells were differentiated into macrophages with PMA (25nM) for 72 hrs and treated with purified HbS or HbA (5µM). RNA strand-specific libraries were constructed using TruSeq Stranded Total RNA Gold kit (Illumina) and sequenced on an Illumina NextSeq 500 using 75 bp paired-end sequencing on two v2.5 150 cycle High-Output kits, generating 40-50 million paired-end reads per sample. The sequencing data were mapped using Dragen RNA and compared using Dragen differential expression software (Illumina). Ingenuity Pathway analysis (IPA, Qiagen) was used for pathway analysis. Results In activated SCD PBMCs compared to control PBMCs, 40432 genes were detected including 2230 differentially expressed genes (5.5%, 1.5-fold difference, 287 down and 1943 up) at 5% false discovery rate. In non-activated SCD PBMCs compared to control PBMCs, 33119 genes were detected including 5299 differentially expressed genes (16%, 923 down and 4376 up). In THP-1-differentiated macrophages treated with HbS versus HbA, 28362 genes were detected including 322 differentially expressed genes (1.1%, 187 down and 135 up). We focused our analysis on 61 genes including viral restriction factors and iron regulatory genes. In activated SCD PBMCs, four genes had highest upregulation: APOBEC3A (23-fold, p=2 x 10 -5), CH25H (11-fold, p=4 x 10 -5), heme oxygenase-1 (HMOX1, 13-fold, p=1.5 x 10 -12) and FPN (SLC40A1, 5-fold, p = 9 x 10 -8) (Fig.1). Several additional genes were upregulated with 1.5-3-fold increase and high significance including APOBEC3B, BRD4, CD40, CDKN1A (p21), GDR1, IFIT3, IFITM3 and SAMHD1. In non-activated SCD PBMCs, the most upregulated gene was PKR (EIF2AK2, 15-fold, p=1 x 10 -11) and genes with 1.5-3 fold upregulation included APOBEC3B, BST2, CPSF6, IFI16, IFITM3, ISG15, LGALS3BP, PML and RTF1 (Fig.1). Of these genes, only IFITM3 overlapped between activated and non-activated PBMCs. To test whether circulating HbS leads to the upregulation of antiviral response, we analyzed HbS-treated macrophages and found upregulation of several antiviral restriction factors (1.5-2.3 fold): IFIT3, LGALS3BP, MX2 and RTF1 (Fig.1). Unsupervised IPA showed upregulation of IRF-7 signaling pathway and down regulation of viral infection and replication (Fig.2). We validated the CH25 and HO-1 antiviral role in activated SCD PBMCs using small molecule inhibitors. We also confirmed overexpression of CH25H and HO-1 by western blot and ELISA. We observed higher levels of IRF7 in the activated SCD PBMCs confirming that it may play a role in the induction of antiviral response. Conclusion We propose that HbS released by hemolysis and uptaken by macrophages leads to the IRF-7-triggered induction of antiviral state in macrophages that will induced antiviral state in non-activated circulating PBMCs likely though the cytokines and interferons secretion known to be elevated in SCD patients. Upregulation of PKR (EIFAK2) levels in non-activated PBMCs strongly argue toward this possibility. Upon activation of PBMCs, additional factors are expressed including CH25H, HO-1, APOBEC3A and FPN that facilitated stronger and more robust anti-HIV-1 effect and block viral replication. Taken together, our study point to novel mechanism of upregulation of antiviral factors mediated by sickle cell hemoglobin that included induction of antiviral, heme- and iron- regulatory pathways. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
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Pinto, Amelia K., Graham D. Williams, Kristy J. Szretter, James P. White, José Luiz Proença-Módena, Gai Liu, Judith Olejnik, et al. "Human and Murine IFIT1 Proteins Do Not Restrict Infection of Negative-Sense RNA Viruses of the Orthomyxoviridae, Bunyaviridae, and Filoviridae Families." Journal of Virology 89, no. 18 (July 8, 2015): 9465–76. http://dx.doi.org/10.1128/jvi.00996-15.
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ABSTRACTInterferon-induced protein with tetratricopeptide repeats 1 (IFIT1) is a host protein with reported cell-intrinsic antiviral activity against several RNA viruses. The proposed basis for the activity against negative-sense RNA viruses is the binding to exposed 5′-triphosphates (5′-ppp) on the genome of viral RNA. However, recent studies reported relatively low binding affinities of IFIT1 for 5′-ppp RNA, suggesting that IFIT1 may not interact efficiently with this moiety under physiological conditions. To evaluate the ability of IFIT1 to have an impact on negative-sense RNA viruses, we infectedIfit1−/−and wild-type control mice and primary cells with four negative-sense RNA viruses (influenza A virus [IAV], La Crosse virus [LACV], Oropouche virus [OROV], and Ebola virus) corresponding to three distinct families. Unexpectedly, a lack ofIfit1gene expression did not result in increased infection by any of these viruses in cell culture. Analogously, morbidity, mortality, and viral burdens in tissues were identical betweenIfit1−/−and control mice after infection with IAV, LACV, or OROV. Finally, deletion of the human IFIT1 protein in A549 cells did not affect IAV replication or infection, and reciprocally, ectopic expression of IFIT1 in HEK293T cells did not inhibit IAV infection. To explain the lack of antiviral activity against IAV, we measured the binding affinity of IFIT1 for RNA oligonucleotides resembling the 5′ ends of IAV gene segments. The affinity for 5′-ppp RNA was approximately 10-fold lower than that for non-2′-O-methylated (cap 0) RNA oligonucleotides. Based on this analysis, we conclude that IFIT1 is not a dominant restriction factor against negative-sense RNA viruses.IMPORTANCENegative-sense RNA viruses, including influenza virus and Ebola virus, have been responsible for some of the most deadly outbreaks in recent history. The host interferon response and induction of antiviral genes contribute to the control of infections by these viruses. IFIT1 is highly induced after virus infection and reportedly has antiviral activity against several RNA and DNA viruses. However, its role in restricting infection by negative-sense RNA viruses remains unclear. In this study, we evaluated the ability of IFIT1 to inhibit negative-sense RNA virus replication and pathogenesis bothin vitroandin vivo. Detailed cell culture and animal studies demonstrated that IFIT1 is not a dominant restriction factor against three different families of negative-sense RNA viruses.
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Watanabe, Naoki, Shouguo Gao, Sachiko Kajigaya, Carrie Diamond, Lemlem Alemu, Amanda Ombrello, and Neal S. Young. "Analysis of Deficiency of Adenosine Deaminase 2 Pathogenesis Based on Single Cell RNA Sequencing of Monocytes." Blood 134, Supplement_1 (November 13, 2019): 2317. http://dx.doi.org/10.1182/blood-2019-123859.
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Deficiency of adenosine deaminase 2 (DADA2) is a rare autosomal recessive disease caused by loss-of-function mutations in the ADA2 gene. DADA2 typically presents in childhood and is characterized by vasculopathy, stroke, inflammation, and immunodeficiency as well as hematologic manifestations, such as bone marrow failure and lymphoproliferation. The ADA2 protein is predominantly expressed in stimulated monocytes, dendritic cells and macrophages. ADA2 increases in the setting of inflammation and/or infection conditions. ADA2 has been reported to have a critical role in maintaining the balance between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophages. Macrophages of DADA2 patients are polarized towards M1 subset., DADA2 pathogenesis is not well characterized. To elucidate molecular mechanisms in DADA2 deficiency, we analyzed a gene expression profile of CD14+ monocytes derived from peripheral blood using single cell RNA sequencing (scRNA-seq). Blood was collected from DADA2 patients and age- and sex-matched healthy donors; all patients were studied in a registered research protocol (clinicaltrials.gov NCT00071045). Samples were obtained from 14 DADA2 patients and 6 healthy donors; median age of the DADA2 patients was 23 years old (range, 5 - 57 years). Among the 14 patients, 7 had hematological phenotypes: 5 lymphopenia, 3 neutropenia, 3 thrombocytopenia, and 2 with hypocellular bone marrow histology. Low serum immunoglobulins and cutaneous findings were frequent. Nine of the 14 patients had been treated with TNF inhibitors (etanercept and adalimumab). Mutations were distributed throughout the ADA2 gene; although two siblings had the same mutation, even they showed poor genotype-phenotype correlation. Monocytes were isolated by immunomagnetic positive selection with the EasySep™ positive CD14 selection kit Ⅱ, then subjected to scRNA-seq using Single Cell 3' Reagent Kits v2 (10X Genomics). Libraries for scRNA-seq were sequenced on the HiSeq-3000 instrument. Based on scRNA-seq data, we could classify monocytes into three populations by conventional flow cytometric criteria using cell surface protein expression imputed from scRNA-seq: CD14++CD16- classical, CD14++CD16+ intermediate, and CD14+CD16++ nonclassical monocytes (Figure A). CD16 expression was higher in DADA2 patients than in healthy donors (Figure B). A proportion of nonclassical monocytes among total monocytes were significantly higher in DADA2 patients compared to healthy donors (Figure C). On comparison of gene expression of each monocyte subtypes in DADA2 patients with that of healthy donors, there were 215, 237, and 267 differentially expressed upregulated genes in classical, intermediate, and nonclassical monocytes, respectively (at a threshold avg_logFC > 0.2). Approximately 35% of upregulated genes were overlapped among the three monocyte subtypes of DADA2 patients, including immune response genes such as IFITM1, IFITM2, IFITM3, and C3AR1 (Figure D). Common gene pathways were associated with immune function, such as interferon alpha/beta signaling and interferon gamma signaling. Specific genes to classical and intermediate monocytes were less than 10% of all the upregulated genes. Distinctively, the NF-κB pathway was upregulated in nonclassical monocytes, this might contribute to the pathogenesis of DADA2 as inflammatory disease. Overall, each monocyte subtype of DADA2 patients showed upregulation of immune response gene sets compared to controls. DADA2 patients have increased numbers of nonclassical monocytes which may contribute the immune dysregulation and increased inflammation observed in the disease. Figure Disclosures No relevant conflicts of interest to declare.
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Zimmerer, J. M., A. Lehman, A. Ruppert, T. Olencki, K. Kendra, M. J. Walker, and W. E. Carson. "Interferon-alpha-2b induced signal transduction and gene regulation in patient immune cells is not enhanced by a dose increase from 5 MU/m2 to 10 MU/m2." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 3026. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.3026.
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3026 Background: High dose interferon-alpha-2b (IFN-a) is employed as an adjuvant in melanoma patients who have had surgery for high-risk lesions. It mediates its anti-tumor effects via activation of the transcription factor STAT1 (signal transducer and activator of transcription) within host immune cells. We hypothesized that intermediate doses of IFN-a would be just as effective as higher doses in stimulating the activation of STAT1 and gene transcription in immune cells. Methods: Samples for analysis were obtained from patients with metastatic melanoma who were enrolled in a clinical trial of bevacizumab in combination with escalating doses of IFN-a (5 MU/m^2 and then 10 MU/m^2). Peripheral blood mononuclear cells (PBMCs) were procured before and 1 hour after the administration of IFN-a and analyzed for the presence of phosphorylated STAT1 (P-STAT1) and P-STAT2 by intracellular flow cytometric analysis and the induction of interferon stimulated gene (ISG) transcripts by Real Time PCR. Results: P-STAT1 in response to 5 MU/m^2 IFN-a was higher than that for the 10 MU/m^2 dose (p = 0.0617). The 5 MU/m^2 dose also led to a greater activation of STAT2 (p = 0.0388). The induction of interferon stimulated genes (ISGs; IFIT1, IFIT2, OAS3) within PBMCs was not enhanced following the increase in IFN-a dose to 10 MU/m^2 at 2 weeks although inhibitors of IFN-a-signaling (SOCS1 and SOCS3) were activated to a greater degree. In addition, microarray analysis was performed on 4 patients and revealed that only one of 36 interferon regulated genes was expressed to a greater extent following treatment with 10 MU/m^2 IFN-a as compared to 5 MU/m^2. Conclusions: These results suggest that 5 MU/m^2 of IFN-a are as effective as higher doses with respect to the induction of STAT signal transduction and ISGs within immune effector cells. No significant financial relationships to disclose.
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Kim, Yong-Chan, and Byung-Hoon Jeong. "Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level." Genes 12, no. 1 (December 30, 2020): 42. http://dx.doi.org/10.3390/genes12010042.
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Coronavirus disease 2019 (COVID-19) is a fatal pandemic disease that is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 13 December, 2020, over 70,000,000 cases and 1,500,000 deaths have been reported over a period of several months; however, the mechanism underlying the pathogenesis of COVID-19 has not been elucidated. To identify the novel risk genetic biomarker for COVID-19, we evaluated the correlation between the case fatality rate of COVID-19 and the genetic polymorphisms of several potential COVID-19-related genes, including interferon-induced transmembrane protein 3 (IFITM3), the angiotensin I converting enzyme 2 (ACE2) gene, transmembrane protease, serine 2 (TMPRSS2), interleukin 6 (IL6), leucine zipper transcription factor-like protein 1 (LZTFL1), and the ABO genes, in various ethnic groups. We obtained the number of COVID-19 cases and deaths from the World Health Organization (WHO) COVID-19 dashboard and calculated the case fatality rate of each ethnic group. In addition, we obtained the allele distribution of the polymorphisms of the IFITM3, ACE2, TMPRSS2, IL6, LZTFL1, and ABO genes from the 1000 Genomes Project and performed Log-linear regression analysis using SAS version 9.4. We found different COVID-19 case fatality rates in each ethnic group. Notably, we identified a strong correlation between the case fatality rate of COVID-19 and the allele frequency of the rs6598045 single nucleotide polymorphism (SNP) of the IFITM3 gene. To the best of our knowledge, this report is the first to describe a strong correlation between the COVID-19 case fatality rate and the rs6598045 SNP of the IFITM3 gene at the population-level.