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Background/Objectives: COVID-19 still represents a lifethreatening disease in individuals with a specific genetic background. We successfully applied a new Machine Learning method on WES data to extract a set of coding variants relevant for COVID- 19 severity. We aim to identify personalized add-on therapy. Method(s): A subset of identified variants, "actionable" by repurposed drugs, were functionally tested by in vitro and in vivo experiments. Result(s): Males with either rare loss of function variants in the TLR7 gene or L412F polymorphism in the TLR3 gene benefit from IFN-gamma, which is specifically defective in activated PBMCs, restoring innate immunity. Females heterozygous for rare variants in the ADAMTS13 gene and males with D603N homozygous polymorphism in the SELP gene benefit from Caplacizumab, which reduces vWF aggregation and thrombus formation. Males with either the low-frequency gain of function variant T201M in CYP19A1 gene or with poly-Q repeats >=23 in the AR gene benefit from Letrozole, an aromatase inhibitor, which restores normal testosterone levels, reducing inflammation and which rescues male golden hamsters from severe COVID-19. Conclusion(s): By adding these commonly used drugs to standard of care of selected patients, the rate of intubation is expected to decrease consistently, especially in patients with high penetrance rare genetic markers, mitigating the effect of the pandemic with a significant impact on the healthcare system.
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Background: Vaccination plays a major role in controlling SARS-CoV2 infection but faces the issue of short-term protection. Beyond the generation of Abs, induction of memory CD8+T cells with stem cell-like (Tscm) properties is essential for long-term immunity to viruses. We have designed a sub-unit CD40.CoV-2 vaccine which targets Spike (S) and nucleocapsid (N) regions from SARS-CoV-2 to antigen presenting cells with comparable immunogenicity and protective effect than mRNA BNT162b2 (Pfizer-BioNTech) in preclinical models (Coleon S. EBioMed 2022). We hypothesized that CD40.CoV2 vaccine will elicit CD8+ Tscm cells. Method(s): CD40.CoV2 vaccine is a fully humanized mAb fused to RBD (aa 318-541) and N (aa 276-411). Humanized (hu) NSG mice (HIS-mice) (n=6/ group) received: i) CD40.CoV2 (10 mug equal to 1.3 mug of RBD, i.p.) +/- poly-ICLC (TLR3 agonist;50mug) or ii) BNT162b2 (1mug, i.m.);iii) IgG4.CoV2 (10mug, i.p.) as non-CD40-targeting control. Phenotype and function of splenic S and N-specific T cells were assessed at W5. Result(s): The CD40.CoV2 vaccine +/- poly-CLC induced significant S and N-specific Th1 huCD4+, cytokines-secreting huCD8+ T cells and RBD-specific IgG-switched huB cells as compared to mock injections and non-targeted IgG4.CoV2. CD40.CoV-2 vaccine +/- adjuvant induced higher frequencies of huCD8+ Tscm (CD95+ CD45RA+ CD62L+ ;median, (IQR) 22.4% (12.3-27.4) and 23% (20.7-29.1) +/- adjuvant, respectively) and central memory (TCM;CD45RA- CD62L+) CD8+ T cells (2.7% (2.3-6.2) and 5.1% (3.8-7.8) +/- adjuvant, respectively). In contrast, BNT162b2 induced predominantly effector memory (TEM, CD45RA- CD62L- ;median, (IQR) 63.1% (47.3-72.3)) but not Tscm (1.6% (0.9-6.6)) (figure). CD40.CoV-2 induced huCD8+ Tscm cells exhibit ;i) a higher proliferation index than TCM and TEM;ii) a functional profile secreting TNF and IFNgamma after restimulation with RBD or N peptides;cardinal features of Tscm cells. Conclusion(s): The CD40.SARS.CoV2, but not BNT162b2 vaccine, stimulates selective enrichment in S-and N-specific CD8+ Tscm cells that support longlasting anti-viral immunity. CD40.CoV2 sub-unit is under clinical development as a booster vaccine aimed to maintain durable anti-viral T and humoral responses. (Figure Presented).
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As hyperbaric oxygen (HBO) has been shown to mitigate the COVID-19 symptoms, we were interested in studying whether HBO exposure affects expression of viral entry genes and innate immune genes in the air-liquid interface (ALI)-cultured human bronchial epithelial cells (HBECs) derived from normal individuals (NHBECs) and age-matched COPD patients (DHBECs), which were cultured under normoxia or daily exposure of 40-min hyperbaric oxygen (HBO) with 100% O2 at 2.5 ATA for 28 days in total. We found for the first time that HBO exposure differentially regulated mucociliary differentiation of HBECs by respectively decreasing and increasing expression of CGRP, MUC5AC, FOXJ1, NOTCH3 and HEYL in NHBECs and DHBECs, and respectively decreased and increased FOXO1 expression whereas increased and decreased NFE2L2 and NFKB1 expression in NHBECs and DHBECs, in association with respectively decreased and increased expression the SARS-CoV-2 entry genes ACE2 and 2 TMPRSS2 and the tight junction protein genes TJP1 and TJP2, and in association with respectively increased and decreased expression of the cell growth and inflammatory transcription factors SRF, c-FOS and TP63, as well as the TLR pathway genes TLR3, AKT1, IL-1B, IL-5, IL-6, IL-33, IRAK4 and NFKBIA in NHBECs and DHBECs. (Figure Presented).
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Introduction: In the natural conditions first and major target for respiratory viruses (RVs) are epithelial cells. Nonetheless, recently we have demonstrated that RVs are able to infect not only epithelium, but also Human Microvascular Lung Endothelial Cells (HMVEC-L) which increased network is observed during severe asthma due to increased angiogenesis. Furthermore, on the surface of HMVEC-L we observed intense expression of aminopeptidase N (AP-N)- an entry receptor for Human Coronavirus 229E (HCoV-229E). Due to the facts, that possibility of being infected by HCoV-229E should be considered and there is no research based on this model the aim of this study was to assess the vulnerability of HMVEC-L to HCoV-229E infection. Method(s): HMVEC-L was incubated with HCoV-229E (MOI 0,1;1,0;3,0) for 3 hours, 3x PBS washed and cultured for 120 hours. In relevant time points (5;24;48;72;96 and 120h) viral copy number and mRNA expression of inflammatory, anti-viral and receptor factors were evaluated in Real-Time PCR. Confocal microscopy (CM) and flow cytometry (FACS) were used to measure AP-N surface expression. Result(s): FACS and CM confirmed intense surface expression of AP-N on HMVEC-L. HCoV-229E efficiently infected HMVEC-L (604 945,5 +/-194 930,2 viral copies/mul) in 48h cultures (MOI 0,1) and induced relatively late (between 72- 96h) mRNA expression of RANTES (1181,12);IL-6 (89,6);IFN-beta (53,7);OAS-1 (64,3);PKR (11,4) and TLR-3 (42,4). Increased mRNA expression was also accompanied by protein release to the supernatants. Conclusion(s): HCoV-229E may efficiently infect HMVEC-L and induce delayed inflammatory and anti-viral response.
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Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging swine enteropathogenic coronavirus that causes severe diarrhea in neonatal piglets, leading to serious economic losses to the pig industries. At present, there are no effective control measures for SADS, making an urgent need to exploit effective antiviral therapies. Here, we confirmed that Aloe extract (Ae) can strongly inhibit SADS-CoV in Vero and IPI-FX cells in vitro. Furthermore, we detected that Emodin from Ae had anti-SADS-CoV activity in cells but did not impair SADS-CoV infectivity directly. The time-of-addition assay showed that Emodin inhibits SADS-CoV infection at the whole stages of the viral replication cycle. Notably, we found that Emodin can significantly reduce virus particles attaching to the cell surface and induce TLR3 (p < 0.001), IFN-λ3 (p < 0.01), and ISG15 (p < 0.01) expressions in IPI-FX cells, indicating that the anti-SADS-CoV activity of Emodin might be due to blocking viral attachment and the activation of TLR3-IFN-λ3-ISG15 signaling axis. These results suggest that Emodin has the potential value for the development of anti-SADS-CoV drugs.
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Background: Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder characterized by abdominal pain and changes in intestinal movements in the absence of structural or biochemical abnormalities. In spite of the high prevalence its etiology is unknown and there are no specific diagnostic laboratory tests. Material and Methods: In a case/control study, 36 biopsy samples taken from of irritable bowel syndrome patients and 30 biopsy samples as control were obtained. expression of TLR 3, TLR 9 and RIG 1 in Macrophages, Lymphocytes and Plasma cells in terms of percentage and color intensity were evaluated by Immunohistochemistry. The obtained data were statistically analyzed using Mann Whitney u, chi-square methods.
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Introduction and Rationale: No targeted therapies exist that improve the outcomes of patients with Acute Respiratory Distress Syndrome (ARDS), in part to the multifactorial etiology of this devastating disease. Infectious agents remain the most common initiating insults, and besides SARS-CoV-2, Influenza-A virus (IAV) is responsible for more ARDS cases and deaths than any other agent. In fact, IAV increases the risk of mortality in ARDS patients three-fold, and accounts for almost half of all ARDS deaths. We recently identified TREK-1 potassium channels on epithelial cells as important regulators of alveolar inflammation and barrier function, two hallmarks of ARDS, and found that pharmacological activation of TREK-1 protects against hyperoxia-induced lung injury. However, whether TREK-1 channels convey similar protection in a clinically more relevant IAVinduced lung injury model, remains unknown. Methods: We infected adult C57BL/6 wildtype mice intra-tracheally (i.t.) with IAV (PR8 strain;TCID50 400), followed by once-daily i.t. injections (days 5, 6 and 7 post-IAV) with the novel TREK-1 activating compounds ML335 (60mcg/kg), BL1249 (100mcg/kg), or a vehicle control, to create a clinically-relevant treatment model. To evaluate the role of epithelial cells in this model, we infected primary human alveolar epithelial cells (HAEC) with IAV (0.01 pfu) for 24 hours. Endpoint analysis consistent in quantification of quasi-static lung compliance;BAL fluid total protein, cell counts, and ROS concentrations;cytokine levels in BAL fluid and cell supernatants;and HAEC viability (XTT assay). In addition, we measured alterations in epithelial potassium currents (fluorometric FLIPR assays) and in IAV-induced signaling cascades (real-time PCR) following IAV infection and treatment with our TREK-1 activators. Results: Oncedaily treatment of mice with the TREK-1 activating compounds ML335 or BL1249 following IAV infection improved lung compliance, and BAL fluid total protein levels, cell counts, IL-6, CXCL-10, MIP-1alpha, and TNF-alpha concentrations, but not ROS, CCL-2 or IL-10 levels. In HAEC, TREK-1 activation improved IAV-induced IL-6, CXCL-10, and CCL-2 levels, while MIP-1alpha, TNF-alpha and IL-10 levels remained unchanged. XTT assays confirmed that in our model IAV infection did not cause significant cell death. Interestingly, IAV infection decreased HAEC potassium currents, which could be counteracted by TREK-1 activation and cell hyperpolarization. Finally, TREK-1 activationmediated cell hyperpolarization inhibited TLR4- and TNFSF13-mediated downstream signaling in IAV-infected HAEC, whereas NFkB, RIG1, TLR3, and TLR7 signaling was not affected. Conclusions: TREK-1 potassium channel activation may represent a novel approach to protect against IAV-induced acute lung injury.
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Background The translatability of the dual-endothelin1/VEGFsp receptor (DEspR) in human was first described in 2016 and its functionality is largely unknown since DEspR is not expressed in healthy human tissues except for kidney tissue and certain tumors. Recently, DEspR expression was reported on human neutrophil subsets of acute respiratory distress syndrome (ARDS) and COVID19-ADRS patients. DEspR+ neutrophil levels correlated with disease severity and mortality which may root in their delayed apoptosis and facilitated formation of neutrophil extracellular traps. Neutrophils play a major role in inflammation of chronic respiratory diseases and altered levels of DEspR ligands ET-1 and VEGF are found in COPD and asthma phenotypes. Here, we investigated the DEspR expression on human leukocyte populations of asthmatics, COPD patients and healthy smokers as well as on the human promyelocytic leucaemic cell line HL-60. Methods DEspR expression was measured on undifferentiated, promyelocytic HL-60 cells and after differentiation towards a neutrophilic phenotype using 1.25% DMSO. Expression was also measured after stimulation with 50 μg/mL poly I:C or 100 ng/mL LPS. Whole blood cells of COPD patients (step III, IV), healthy smokers and asthmatics (step III) were stained directly after blood draw or after stimulation with 50 μg/mL poly I:C or 100 ng/mL LPS. HL-60 and whole blood leukocytes were stained with Annexin V, 7AAD, DEspR (rhIgG4, clone 6g8), CD11b, CD14 and CD16a. Results Undifferentiated CD11b-, CD14- CD16a- and differentiated CD11b+, CD14-, CD16a- HL-60 cells did not express DEspR, neither with or without inflammatory stimulation. DespR was not expressed on whole blood leukocytes at baseline level (mean±SD: 0.15±0.26 to 0.91±0.60%) but poly I:C induced DEspR expression on neutrophils (34.10±18.52%), monocytes (29.16±20.00%), lymphocytes (9.67±6.11%) and eosinophils (6.14±4.39%). The distribution of DEspR+ cells upon poly I:C stimulation was not significantly altered among different disease types, however, healthy smokers showed a trend to higher DEspR levels. The median fluorescence intensity was not significantly altered among disease types but among the cell populations. Conclusion First experiments demonstrated that DEspR expression can be induced on leukocytes upon inflammatory stimulation. In contrast to previous results of us, LPS did not induce DEspR expression which might be related to differences in the age and disease severity of investigated patients. Interestingly, poly I:C induced a strong DEspR expression indicating a toll-like receptor 3 related mechanism. The sample size needs to be increased to confirm these first results and to investigate the underlying mechanism in detail.
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Context: The SARS-CoV-2 virus is the cause of the COVID-19 pandemic, which is a severe public health crisis worldwide. Aims: To analyze the SARS-CoV-2 isolates of Surabaya and predict ORF1ab polyprotein epitopes through the bioinformatics approach for vaccine candidate development. Methods: Three genomic sequences of Surabaya isolates were obtained from the GISAID, NCBI and PDB Gen-bank databases and MEGA-11 software were used to understand the transformations in the isolates. The IEDB and VaxiJen, AllerTop, and ToxinPred web servers were used to predict B-cell epitopes and analyze their antigenicity, non-allergenicity, non-toxicity, respectively. Moreover, these epitopes were linked by EAAAK for 3D modeling, refinement, and validation through Swiss- Model, Galaxy Refine, and RAMPAGE web tools. Results: The Surabaya isolates, RSDS-RCVTD-UNAIR-49-A, 54-A, and 42-A, had 10, 20, and 16 mutations in nucleotides and depicted a phylogenetically close relationship to isolates of Egypt, Pakistan, and Bangladesh, respectively. A total of 71 sequential Orf1ab B-cell epitopes were predicted, and only three peptides were found to be antigenic, non-allergenic, and non-toxic. These epitopes were linked with the EAAAK linker to develop a 3D refined and validated structure. This construct was docked with TLR-3 receptor by the Cluspro webserver and found a high affinity of ORF1ab+TLR3 due to 15 hydrogen bonds. The construct demonstrated good humoral and cellular immune responses in the C-ImmSim server, and cloning in the expression vector pET28a (+) yielded a colon of 846bp. Conclusions: ORF1ab B-cell epitopes could be useful for developing effective vaccines to combat SARS-CoV-2 infection.
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Background: The number of cases of SARS-CoV-2 infection after BNT162b2 mRNA vaccination is significantly higher in elderly people, which has been associated to lower frequencies of SARS-CoV-2 neutralizing antibodies. Our objective was to investigate the differences in the cellular response in old and young people after the SARS-CoV-2 vaccination. Methods: Young (24-53 years, n=20) and old (70-76 years, n=20) healthy subjects vaccinated with BNT162b2 SARS-CoV-2 mRNA vaccine were studied before vaccination, two weeks after the first dose and two months after the second dose. SARS-CoV-2 (spike) specific T cell response, TLR-4 dependent monocyte response and TLR-3 dependent myeloid dendritic cell (DC) response and DC, monocyte and T-cell immunophenotype, were studied by multiparametric flow cytometry. TLR-9 dependent interferon-α (IFNα) production by PBMCs was measured by ELISA and thymic function assayed by sj/β TREC ratio using droplet digital PCR. Results: The SARS-CoV-2 specific T cell response was lower and less polyfunctional in old people. Most of the differences in CD4+ and CD8+ T cell subsets were found in degranulation (CD107a), cytokine (IFN-γ) and cytotoxic (perforin) profile (eg, Memory CD8+ perforin+;p=0.0016). The lower SARS-CoV-2 specific T cell response was associated with lower thymic function levels (eg, Memory CD4+ perforin+, r=0.631;p=0.0001). The vaccination induced a higher activation and proliferation (eg, CM CD4 HLA-DR+ p=0.002, Ki67+ p=0.019) of T cells in young people than in old ones, in addition to a higher level of homing makers to different tissues and inflammatory sites (eg, CD1c mDC integrin β7+ p=0.001, intermediate monocytes CCR2+ p=0.0003) in DCs and monocytes. Moreover, after the vaccination, old subjects showed a higher production of proinflammatory cytokines by monocytes in response to LPS (eg, IL6+;p=0.015), while young people showed a higher production of IFNα by plasmacytoid DCs after CpG-A stimulation (p=0.0009). Conclusion: The magnitude and polyfunctionality of SARS-CoV-2 specific T cell response is lower in old people, associated to a lower thymic function. In old people, the vaccination induced less immune activation and homing and the myeloid TLR-dependent response is directed towards a proinflammatory response, while in young people prevails IFNα production, related to a more effective antiviral response. These results support the additional boosting strategies in this vulnerable population.
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Coronavirus disease 2019 (COVID-19) is caused by pathogenic and highly transmissible Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a single stranded RNA virus. It rapidly emerged from an epidemic to a global pandemic form spreading in alarming levels. The pathogenesis involving spike protein which is present on the viral surface, plays a key role in host attachment and penetration. SARS-CoV-2 infection significantly affects respiratory system, but may involve other systems including haematopoietic system and homeostasis. Aim of the review article is to discuss spectrum of haematological changes in the blood counts, coagulation, peripheral blood and bone marrow in COVID-19 for complete understanding the disease process, the knowledge of which is helpful in early diagnosis and management of these patients. An extensive immune profiling of B and T cell population with analysis of spectrum of immune changes during the period of infection were also discussed. In COVID-19, changes in laboratory parameters and hematologic abnormalities have been reported and its association with early diagnosis, disease prognosis and severity has been repeatedly discussed in the literature. Changes in laboratory investigations help in risk stratification and early intervention. The most common laboratory finding in COVID-19 is lymphopenia. COVID-19 patients presented with coagulopathy is at high risk of morbidity and mortality. In severe COVID-19 patients, bone marrow aspirate shows histiocytic proliferation with hemophagocytosis. To understand the correlations between immune responses and severity of COVID-19, immune profiling of B and T cell population was compared with extensive clinical data. A deep understanding of the laboratory findings and haematological abnormalities associated with SARS-CoV-2 infection would help to raise disease suspicion in absence of Real time polymerase chain reaction or antibody results. Also the blood counts along with the morphological changes in peripheral blood would be helpful in prompt screening, diagnosis, prognosis and management of COVID-19 patients.
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Background. Covid-19 has accelerated global demand for easily distributed vaccines. Furthermore, as variant SARS-CoV-2 strains that circumvent antibody responses emerge, cross-protective vaccines provide substantial public health benefits. Vaxart is developing a shelf stable oral tablet vaccine that incorporates both the spike (S) and the more conserved nucleocapsid (N) proteins. Vaxart's vaccine platform uses a non-replicating adenovirus and a TLR3 agonist as an adjuvant. Methods. In an open-label phase 1 clinical study, 35 healthy subjects received either a single low (1x1010 IU;n=15) or high (5x1010 IU;n=15) dose of the vaccine candidate VXA-CoV2-1 with a small cohort receiving 2 low doses. PBMCs were taken at pre- and 7 days post-vaccination and restimulated with S and N peptides from SARSCoV-2 or the 4 human endemic coronaviruses (HCoV). Cells were stained for CD4/ CD8/CD107a (surface) and IFNγ/TNFα (intracellular). Subjects that received an intramuscular (i.m.) mRNA vaccine had PBMCs taken at the same timepoints and were compared in the same assay. Results. The study's results indicate that the VXA-CoV2-1 tablet was well tolerated. The majority of subjects had an increase in S-specific anti-viral CD8+ T cell responses. 19/26 (73%) subjects had a measurable CD8+ T cell response on day 8 above baseline, on average 1.5-4.6%. In a comparator experiment with the 2 SARS-CoV-2 i.m. mRNA vaccines, VXA-CoV2-1 outperformed other vaccine candidates with a >3.5-fold increase in S specific antiviral CD8 T cell responses. T cell responses specific to the 4 endemic HCoV were increased by 0.6% in subjects given VXA-CoV2-1. Conclusion. Here we describe a room temperature stable tablet that induces SARS-CoV-2 S specific CD8 T cells of high magnitude after one dose in humans. Overall, the level of antiviral SARS-CoV-2 specific T cells, particularly IFNg-producing CD8s, induced following oral immunization with VXA-CoV2-1 are of higher magnitude than the mRNA vaccines currently in use against COVID-19. T cell responses against 4 endemic HCoV were also induced. Because T cells may be important in protecting against death and severe infection, these results suggest that VXA-CoV2-1 could be cross-protective against a wide array of emerging pandemic coronaviruses.
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It is difficult to assign a precise frequency of infections that defines an increased susceptibility to infections reflecting an impaired immune response given the majority of patients with intact immune systems still contract multiple upper respiratory infections each year, usually of viral origin. In fact, the average child may experience up to six to eight upper respiratory infections each year. The frequency of these infections may be related to environmental exposures but also may be triggered by genetic susceptibility. As an example, respiratory disease complicates the management of several inherited metabolic diseases, either at presentation or as late-onset features. More recently, children of all ages have been shown to contract COVID-19;however, children with underlying medical conditions are at increased risk. COVID-19 has been known for almost a year now, with several studies identifying genetic risk factors are associated with severe COVID-19. In the context of a health system wide genomic medicine program “Genomic Answers for Kids” at Children’s Mercy, Kansas City, we performed a retrospective analysis of rare variants predicted to be deleterious at 12 known loci known to govern TLR3- and IRF7- dependant type I Interferon immunity of all patients/families (>2000) tested for suspected genetic disorders. We bioinformatically extracted all rare variants in those 12 genes linked to type I interferon pathway from our internal warehouse. From those, ~340 variants were further analyzed based on inheritance, minor allele frequency in population datasets, and in silico prediction. The vast majority of this subgroup of GA4 K patients were referred for a suspected neurological disorder with or without multiple congenital anomalies (~75%). Only 15% were referred for metabolic disorders. Of those, 50% have a known genetic diagnosis unrelated to Immune deficiency. Of the selected index cases, the medical records, and if available the outpatient records, were reviewed to document the occurrence of recurrent infection and/or COVID-19. Preliminary data showed 46 “extremely” rare variants were detected in 37 GA4 K patients;6/37 (16%) have ≥2 in 1–12 genes, one GA4 K patient has 4 “extremely” rare variants in IRF7, and 3/37 GA4 K patients are deceased (~1%). Moreover, a novel disease gene was uncovered in a previously undiagnosed family, of which we identified an additional two affected individuals from an international collaboration. Finally, in a family with apparently dominant transmission of tumid lupus we observe putative causal variant in gene UNC93B1 – linking chronic inflammatory disorder (with known type I interferon association) to mutations predisposing to COVID-19. Recurrent or persistent infection is usually a manifestation of primary immunodeficiency. While most children with recurrent infections have a normal immunity, it is important to remember a subset of patients have an unrecognized genetic susceptibility to infection. Further analysis and monitoring are on-going. As we are continuing to struggle with the COVID-19 pandemic, combined with flu season, understanding precisely who may be at higher risk of infection and complications is critical and could play an important role in ongoing efforts to in disease prevention and the development of better treatment protocols
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Aim: The Sars Corona Virus (SARS CoV) belongs to the Nidovirales order, the Coronaviridae family, and the genus Coronavirus. The SARS CoV has enveloped, linear, positive sense and single-stranded RNA. The disease caused by SARS-CoV 2 as named as COVID-19. Toll-like receptors (TLRs) initiate signaling cascades leading to the activation of the innate immune system. TLR3 activates antiviral immune responses through the production of inflammatory cytokines and type I interferons. In this study we aimed to investigate TLR 3 c.1377C/T and -7C/A polymorphisms in COVID-19 infection. Methods: In this study, we investigated the frequencies of TLR3 (c.1377C/T and -7 C/A) polymorphisms in 150 COVID-19 patients and 171 healthy adults as controls in Sivas Cumhuriyet University. Firstly, DNA was isolated using phenol-chloroform methods. Then we performed polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP). We also investigated whether these polymorphisms were related to the severity of COVID-19 disease. Results: We found that both TLR3 polymorphisms were associated with COVID-19 disease. TLR3 c.1377C/T TT genotype frequencies were found statistically significant between patients and controls (p=0.019). In TLR3 -7C/A polymorphism we found statistically significant difference in A allele frequencies (p=0.03). There is an also statistically significant difference in distribution of TLR3 -7C/A CT genotype frequency between patients and controls (p=0.04). However, there is no statistically significant association between severe/non-severe and two TLR3 polymorphisms. Conclusion: Our findings suggest that TLR3 c.1377C/T and -7C/A polymorphisms may be important on susceptibility or clinical course of COVID-19.
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The proceedings contain 108 papers. The topics discussed include: toll-like receptor 3 c.1377C/T and -7C/A polymorphisms in COVID-19 infection;a cleft palate with 49, XXXXY karyotype: A case report;a case with atypical autism and hereditary motor sensory neuropathy;investigation of genetic etiology in gastrointestinal cancer patients with next generation sequencing method;a rare disease associated with the CDK13 gene: CHHDFIDD;a case report of pericentric inversion, inv (21) (p12;q22) in repeated pregnancy loss;a case of rare CYP26B1-related craniosynostosis in a Turkish female patient;a novel homozygous mutation in CYP11A1 gene in 46, XX patient with P450scc deficiency;and a novel homozygous variant in SUOX gene causes classic isolated sulfite oxidase deficiency: a case report.
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Introduction: After spring 2020, a series of reports from Europe and USA described clusters of children, presenting life-threatening multisystem inflammatory syndrome in children (MIS-C), associated with antecedent exposure to SARS-CoV-2 (1). In patients with life threatening COVID-19 3.5% were found to have inborn errors in type I IFN signalling pathway (2). A case series of 4 young patients with severe COVID-19 reported rare loss-of-function variants in the TLR7 gene associated with impaired type I IFN responses (3). Clinically, MIS-C shares features with secondary hemophagocytic lymphohistiocytosis (HLH) and Kawasaki disease (KD), which were also associated with possible infectious trigger and might share a common genetic cause (4). Objectives: We analysed whether MIS-C patients have an underlying presence of genetic variants in exomes associated with inborn errors of type I IFN immunity, HLH, KD and presence of variants in TLR7 gene. Methods: Blood was drawn from 17 MIS-C patients upon submission into the hospital, DNA from peripheral blood was isolated and whole exome sequencing was performed. Variants in the following genes were investigated: type I IFN immunity (TLR3, UNC93B1, TRAF3, TBK1, IRF3/9, IRF7, IFNAR1/2, STAT1/2, IKBKG, TRIF), HLH (AP3B1, CD27, FADD, FAS, FASLG, HPLH1, ITK, LYST, MAGT1, MYO5A, NLRC4, PRF1, RAB27A, RECQL4, SH2D1A, STX11, STXBP2, UNC13D, XIAP, TNFRSF9, CDC42), KD (ITPKC, CD40, FCGR2A, BLK, CASP3, TRX-CAT1-7, PGBD1, LTA, TSBP1, HLA-DQB1/2, HLA-DOB, IGHV1-69) and TLR7 genes. Analysis was focused on rare (GnomAD<0.01) exonic or splicing variants. Results: No common genetic denominators were found in analysed genes. Five rare variants were observed in four patients (4/17). According to ACMG classification variants of uncertain significance (VUS) were found in LYST (2), IKBKG (1), IRF3 (1) and NLRC4 (1) in heterozygous genotype. No clinical evidence was found in ClinVar database for any of the variants, except for one variant in LYST (c.3931A>G:p.M1311V) with uncertain significance for Chédiak-Higashi syndrome and medium prediction scores. Variants in LYST (c.5990C>G:p.A1997G), NLRC4 (c.772T>C:p.C258R) and IRF3 (c.325G>C: p.G109R) have high CADD, Mutation Taster, Polyphen and SIFT prediction scores. And IKBKG (c.325C>G:p.L109V) variant had medium prediction scores. Conclusion: Our findings suggest that MIS-C patients do not share a rare loss-of-function variant in type I IFN immunity genes, TLR7 gene or genes associated either with HLH or KD. Despite numerous clinical, immunological and genetic research of the MIS-C patients, the syndromes pathogenesis and etiologic cause remain elusive.
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BACKGROUND: Coronavirus disease 2019 is characterized by the elevation of a broad spectrum of inflammatory mediators associated with poor disease outcomes. We aimed at an in-silico analysis of regulatory microRNA and their transcription factors (TF) for these inflammatory genes that may help to devise potential therapeutic strategies in the future. METHODS: The cytokine regulating immune-expressed genes (CRIEG) were sorted from literature and the GEO microarray dataset. Their co-differentially expressed miRNA and transcription factors were predicted from publicly available databases. Enrichment analysis was done through mienturnet, MiEAA, Gene Ontology, and pathways predicted by KEGG and Reactome pathways. Finally, the functional and regulatory features were analyzed and visualized through Cytoscape. RESULTS: Sixteen CRIEG were observed to have a significant protein-protein interaction network. The ontological analysis revealed significantly enriched pathways for biological processes, molecular functions, and cellular components. The search performed in the miRNA database yielded ten miRNAs that are significantly involved in regulating these genes and their transcription factors. CONCLUSION: An in-silico representation of a network involving miRNAs, CRIEGs, and TF, which take part in the inflammatory response in COVID-19, has been elucidated. Thus, these regulatory factors may have potentially critical roles in the inflammatory response in COVID-19 and may be explored further to develop targeted therapeutic strategies and mechanistic validation.
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Senescent cells, which arise due to damage-associated signals, are apoptosis-resistant and can express a pro-inflammatory, tissue-destructive senescence-associated secretory phenotype (SASP). We recently reported that a component of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface protein, S1, can amplify the SASP of senescent cultured human cells and that a related mouse ß-coronavirus, mouse hepatitis virus (MHV), increases SASP factors and senescent cell burden in infected mice. Here, we show that SARS-CoV-2 induces senescence in human non-senescent cells and exacerbates the SASP in human senescent cells through Toll-like receptor-3 (TLR-3). TLR-3, which senses viral RNA, was increased in human senescent compared to non-senescent cells. Notably, genetically or pharmacologically inhibiting TLR-3 prevented senescence induction and SASP amplification by SARS-CoV-2 or Spike pseudotyped virus. While an artificial TLR-3 agonist alone was not sufficient to induce senescence, it amplified the SASP in senescent human cells. Consistent with these findings, lung p16INK4a+ senescent cell burden was higher in patients who died from acute SARS-CoV-2 infection than other causes. Our results suggest that induction of cellular senescence and SASP amplification through TLR-3 contribute to SARS-CoV-2 morbidity, indicating that clinical trials of senolytics and/or SASP/TLR-3 inhibitors for alleviating acute and long-term SARS-CoV-2 sequelae are warranted.