scholarly journals Self-assembling short immunostimulatory duplex RNAs with broad spectrum antiviral activity

2021 ◽  
Author(s):  
Longlong Si ◽  
Haiqing Bai ◽  
Crystal Yuri Oh ◽  
Tian Zhang ◽  
Amanda Jiang ◽  
...  

The current COVID-19 pandemic highlights the need for broad-spectrum antiviral therapeutics. Here we describe a new class of self-assembling immunostimulatory short duplex RNAs that potently induce production of type I and type III interferon (IFN-I and IFN-III), in a wide range of human cell types. These RNAs require a minimum of 20 base pairs, lack any sequence or structural characteristics of known immunostimulatory RNAs, and instead require a unique conserved sequence motif (sense strand: 5'-C, antisense strand: 3'-GGG) that mediates end-to-end dimer self-assembly of these RNAs by Hoogsteen G-G base-pairing. The presence of terminal hydroxyl or monophosphate groups, blunt or overhanging ends, or terminal RNA or DNA bases did not affect their ability to induce IFN. Unlike previously described immunostimulatory siRNAs, their activity is independent of TLR7/8, but requires the RIG-I/IRF3 pathway that induces a more restricted antiviral response with a lower proinflammatory signature compared with poly(I:C). Immune stimulation mediated by these duplex RNAs results in broad spectrum inhibition of infections by many respiratory viruses with pandemic potential, including SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza A, as well as the common cold virus HCoV-NL63 in both cell lines and human Lung Chips that mimic organ-level lung pathophysiology. These short dsRNAs can be manufactured easily, and thus potentially could be harnessed to produce broad-spectrum antiviral therapeutics at low cost.

2019 ◽  
Vol 216 (3) ◽  
pp. 621-637 ◽  
Author(s):  
Alice E. Denton ◽  
Silvia Innocentin ◽  
Edward J. Carr ◽  
Barry M. Bradford ◽  
Fanny Lafouresse ◽  
...  

Ectopic lymphoid structures form in a wide range of inflammatory conditions, including infection, autoimmune disease, and cancer. In the context of infection, this response can be beneficial for the host: influenza A virus infection–induced pulmonary ectopic germinal centers give rise to more broadly cross-reactive antibody responses, thereby generating cross-strain protection. However, despite the ubiquity of ectopic lymphoid structures and their role in both health and disease, little is known about the mechanisms by which inflammation is able to convert a peripheral tissue into one that resembles a secondary lymphoid organ. Here, we show that type I IFN produced after viral infection can induce CXCL13 expression in a phenotypically distinct population of lung fibroblasts, driving CXCR5-dependent recruitment of B cells and initiating ectopic germinal center formation. This identifies type I IFN as a novel inducer of CXCL13, which, in combination with other stimuli, can promote lung remodeling, converting a nonlymphoid tissue into one permissive to functional tertiary lymphoid structure formation.


2020 ◽  
Vol 25 (1) ◽  
pp. 4-10
Author(s):  
Marina G. Avdeeva ◽  
Ol’ga R. Gafurova ◽  
Natalia V. Kolesnikova ◽  
Yekaterina V. Kolesnikova

Background: The physiological course of pregnancy is largely determined by immunological processes, the violation of which in the perinatal period can cause various congenital pathologies. The course of influenza during pregnancy largely depends on the level of physiological adjustment of the immune response. It is known that in severe cases of influenza A (H1N1), excessive production of a number of pro-inflammatory cytokines, the cytokine storm, is observed, with the development of endothelial necrosis. Aim: To determine the nature of the cytokine response to influenza A (H1N1) against the background of pregnancy and to clarify its relationship with the development of intrauterine neonatal pathology. Materials and methods: A total of 94 pregnant women were treated at the special clinical infectious diseases hospital of the Ministry of Health of the Krasnodar Region for influenza A (H1N1) during the epidemic recovery from December 2015 to February 2016. The diagnosis of influenza is confirmed by the isolation of RNA of influenza A (H1N1) virus by PCR in a nasopharyngeal scraping. Influenza occurred in the first trimester in 20 (21.3%), in the second trimester in 36 (38.3%) and in the third trimester in 38 (40.4%) women. The outcomes of pregnancy were traced, and a retrospective analysis of 91 neonatal observation cards in the maternity hospital was conducted. The comparison groups were as follows: 25 women with physiological pregnancy, 16 pregnant women with chronic placental insufficiency and intrauterine infection, and a control group of 20 healthy, non-pregnant women of reproductive age. The levels of IL-2, IL-4, IL-10, IFN-, and IFN- cytokines in blood serum were studied using the enzyme immunoassay with Vector-Best reagent kits (Novosibirsk) at a sensitivity of 1 pg/ml. The study of cytokine status was conducted at the height of the flu on the first day of admission to the hospital. Results: In pregnant women with influenza compared with physiological pregnancy, there are considerable decreases in the levels of IL-4 and IL-10, whereas IFN- and IFN- do not change significantly but have a wide range of indicators. Against the background of altered immunoreactivity in pregnancy, the immunosuppressive effects of the influenza virus, in blocking the production of type I interferons, exert a more pronounced negative effect. In pregnant women with influenza and those with chronic placental insufficiency combined with intrauterine infection, unidirectional changes in the levels of IL-4 and IL-10 against physiological pregnancy were detected. The level of IFN- in chronic placental insufficiency combined with intrauterine infection was significantly higher than the figures reported by other groups. The level of IFN- in chronic fetoplacental insufficiency and intrauterine infection was reduced. A significant increase in the IFN-/IL4 coefficient was associated with the development of intrauterine infection of the fetus. The level of IFN- was maximally reduced in women with influenza in the first trimester of pregnancy, whose newborns subsequently had developmental defects in the cardiovascular system. A decrease in the level of IFN- may reflect the onset of failure of the compensatory mechanisms of immunological regulation of pregnancy. Conclusion: Determination of the level of interleukins in the acute period of influenza in pregnant women makes it possible to assess the threat of development of the pathology of newborns. The determination of the levels of IL-4, IFN-, and IFN- is of diagnostic value. A high risk of intrauterine infection can be predicted with an increase in the IFN-/IL-4 coefficient. Prognostically unfavorable for the development of newborn malformations is a decrease in the level of IFN- in the development of influenza in women who are in early gestation.


2020 ◽  
Author(s):  
Phuc-Chau Do ◽  
Trung H. Nguyen ◽  
Uyen T.M. Vo ◽  
Ly Le

AbstractInfluenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed an in silico protocol called iBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structure of available broad-spectrum Abs or Fabs against a wide range of H1N1 influenza A virus. As a result, the proposed Fab model followed iBRAB has good binding affinity over 27 selected HA of different strains of H1 influenza A virus, including wild-type and mutated ones. The examination also took by computational tools to fasten the procedure. This protocol could be applied for a fast designed therapeutic vaccine against different types of threats.


2019 ◽  
Vol 217 (3) ◽  
Author(s):  
Hector Huerga Encabo ◽  
Laia Traveset ◽  
Jordi Argilaguet ◽  
Ana Angulo ◽  
Estanislao Nistal-Villán ◽  
...  

Type I interferon (IFN-I) provides effective antiviral immunity but can exacerbate harmful inflammatory reactions and cause hematopoietic stem cell (HSC) exhaustion; therefore, IFN-I expression must be tightly controlled. While signaling mechanisms that limit IFN-I induction and function have been extensively studied, less is known about transcriptional repressors acting directly on IFN-I regulatory regions. We show that NFAT5, an activator of macrophage pro-inflammatory responses, represses Toll-like receptor 3 and virus-induced expression of IFN-I in macrophages and dendritic cells. Mice lacking NFAT5 exhibit increased IFN-I production and better control of viral burden upon LCMV infection but show exacerbated HSC activation under systemic poly(I:C)-induced inflammation. We identify IFNβ as a primary target repressed by NFAT5, which opposes the master IFN-I inducer IRF3 by binding to an evolutionarily conserved sequence in the IFNB1 enhanceosome that overlaps a key IRF site. These findings illustrate how IFN-I responses are balanced by simultaneously opposing transcription factors.


2015 ◽  
Vol 112 (30) ◽  
pp. E4007-E4016 ◽  
Author(s):  
Stefan Mockenhaupt ◽  
Stefanie Grosse ◽  
Daniel Rupp ◽  
Ralf Bartenschlager ◽  
Dirk Grimm

Exogenous RNAi triggers such as shRNAs ideally exert their activities exclusively via the antisense strand that binds and silences designated target mRNAs. However, in principle, the sense strand also possesses silencing capacity that may contribute to adverse RNAi side effects including off-target gene regulation. Here, we address this concern with a novel strategy that reduces sense strand activity of vector-encoded shRNAs via codelivery of inhibitory tough decoy (TuD) RNAs. Using various shRNAs for proof of concept, we validate that coexpression of TuDs can sequester and inactivate shRNA sense strands in human cells selectively without affecting desired antisense activities from the same shRNAs. Moreover, we show how coexpressed TuDs can alleviate shRNA-mediated perturbation of global gene expression by specifically de-repressing off-target transcripts carrying seed matches to the shRNA sense strand. Our combination of shRNA and TuD in a single bicistronic gene transfer vector derived from Adeno-associated virus (AAV) enables a wide range of applications, including gene therapies. To this end, we engineered our constructs in a modular fashion and identified simple hairpin design rules permitting adaptation to preexisting or new shRNAs. Finally, we demonstrate the power of our vectors for combinatorial RNAi strategies by showing robust suppression of hepatitis C virus (HCV) with an AAV expressing a bifunctional TuD against an anti-HCV shRNA sense strand and an HCV-related cellular miRNA. The data and tools reported here represent an important step toward the next generation of RNAi triggers with increased specificity and thus ultimately safety in humans.


PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0239112
Author(s):  
Phuc-Chau Do ◽  
Trung H. Nguyen ◽  
Uyen H. M. Vo ◽  
Ly Le

Influenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed an in silico protocol called iBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structures of available broad-spectrum Abs or Fabs against a wide range of H1N1 influenza A virus. As a result, the proposed Fab model followed iBRAB has good binding affinity over 27 selected HA of different strains of H1 influenza A virus, including wild-type and mutated ones. The examination also took by computational tools to fasten the procedure. This protocol could be applied for a fast-designed therapeutic vaccine against different types of threats.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ya-Lang Huang ◽  
Ming-Ting Huang ◽  
Pei-Shan Sung ◽  
Teh-Ying Chou ◽  
Ruey-Bing Yang ◽  
...  

AbstractHuman C-type lectin member 18A (CLEC18A) is ubiquitously expressed in human, and highest expression levels are found in human myeloid cells and liver. In contrast, mouse CLEC18A (mCLEC18A) is only expressed in brain, kidney and heart. However, the biological functions of CLEC18A are still unclear. We have shown that a single amino acid change (S339 →R339) in CTLD domain has profound effect in their binding to polysaccharides and house dust mite allergens. In this study, we further demonstrate that CLEC18A and its mutant CLEC18A(S339R) associate with TLR3 in endosome and bind poly (I:C) specifically. Compared to TLR3 alone, binding affinity to poly (I:C) is further increased in TLR3-CLEC18A and TLR3-CLEC18A(S339R) complexes. Moreover, CLEC18A and CLEC18A(S339R) enhance the production of type I and type III interferons (IFNs), but not proinflammatory cytokines, in response to poly (I:C) or H5N1 influenza A virus (IAV) infection. Compared to wild type (WT) mice, ROSA-CLEC18A and ROSA-CLEC18A(S339R) mice generate higher amounts of interferons and are more resistant to H5N1 IAV infection. Thus, CLEC18A is a TLR3 co-receptor, and may contribute to the differential immune responses to poly (I:C) and IAV infection between human and mouse.


2004 ◽  
Vol 69 (3) ◽  
pp. 535-563 ◽  
Author(s):  
Karel Bezouška

The superfamily of C-type animal lectins is defined by a sequence motif of the carbohydrate- recognition domains (CRDs) and comprises seven groups of molecules. The soluble proteins are group I proteoglycans, group III collectins, and group VII containing the isolated CRDs. Type I membrane proteins include group IV selectins and group VI macrophage receptors and related molecules. Type II membrane proteins are group II hepatic lectins and group V natural killer cell receptors. The latter group has recently attracted considerable attention of the biomedical community. These receptors are arranged at the surface of lymphocytes as homo- or heterodimers composed of two polypeptides consisting of N-terminal peptide tails responsible for signaling, transmembrane domain, neck regions of varying length, and C-terminal lectin-like domains (CTLDs). Since this group is evolutionarily most distant from the rest of C-type animal lectins, the sequence of the C-terminal ligand-binding domain has diversified to accommodate other ligands than calcium or carbohydrates. These domains are referred to as natural killer domains (NKDs) forming a large percentage of CTLDs in vertebrates. Here are summarized the data indicating that calcium, carbohydrates, peptides, and large proteins such as major histocompatibility complex (MHC) class I can all be ligands for NKDs. The wide range of ligands that can be recognized by NKDs includes some new, unexpected compounds such as signal peptide-derived fragments, heat shock proteins, or oxidized lipids. The biological importance of this extended range of recognition abilities is also discussed. A review with 134 references.


mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Wenjun Shao ◽  
Morgan N. Price ◽  
Adam M. Deutschbauer ◽  
Margaret F. Romine ◽  
Adam P. Arkin

ABSTRACT Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5′-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function. IMPORTANCE The first step of gene expression is the initiation of transcription from promoters, which have been traditionally thought to be located upstream of genes. Recently, studies showed that in diverse bacteria, promoters are often located inside genes. It has not been clear if these unexpected promoters are important to the organism or if they result from transcriptional noise. Here, we identify and examine promoters in eight related bacterial species. Promoters that lie within genes on the sense strand are often conserved as locations and in their sequences. Furthermore, these promoters often affect the bacterium’s growth. Thus, many of these unexpected promoters are likely functional. Fewer promoters that lie within genes on the antisense strand are conserved, but the conserved ones seem to drive the expression of nearby genes.


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