Exploration of potential mechanism of SARS-CoV-2 induced immune inflammatory response leading to progression of atherosclerosis and prediction of traditional Chinese medicine for preventing and treating based on bioinformatics.

Objective To explore the core targets and important pathways of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) induced atherosclerosis (AS) progression from the perspective of immune inflammation, so as to predict the potential prevention and treatment of traditional Chinese medicine (TCM). Methods Microarray data were obtained from the Gene Expression Omnibus (GEO) database for coronavirus disease 2019 (COVID-19) patients and AS patients, and the "limmar" and "Venn" packages were used to screen out the common differentially expressed genes (DEGs) genes in both diseases. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed on the common DEGs to annotate their functions and important pathways. The two gene sets were scored for immune cells and immune function to assess the level of immune cell infiltration. The protein-protein interaction (PPI) network was constructed by STRING database, and the CytoHubba plug-in of Cytoscape was used to identify the hub genes. Two external validation datasets were introduced to validate the hub genes and obtain the core genes. Immuno-infiltration analysis and gene set enrichment analysis (GSEA) were performed on the core genes respectively. Finally the potential TCM regulating the core genes were predicted by Coremine Medical database. Results A total of 7898 genes related to COVID-19, 471 genes related to AS progression;And 51 common DEGs, including 32 highly expressed genes and 19 low expressed genes were obtained. GO and KEGG analysis showed that common DEGs, which were mainly localized in cypermethrin-encapsulated vesicles, platelet alpha particles, phagocytic vesicle membranes and vesicles, were involved in many biological processes such as myeloid differentiation factor 88 (MyD88)-dependent Toll-like receptor signaling pathway transduction, interleukin-8 (IL-8) production and positive regulation, IL-6 production and positive regulation to play a role in regulating nicotinamide adenine dinucleotide phosphate oxidase activity, Toll-like receptor binding and lipopeptide and glycosaminoglycan binding through many biological pathways, including Toll-like receptor signaling pathways, neutrophil extracellular trap formation, complement and coagulation cascade reactions. The results of immune infiltration analysis demonstrated the state of immune microenvironment of COVID-19 and AS. A total of 5 hub genes were obtained after screening, among which Toll-like receptor 2 (TLR2), cluster of differentiation 163 (CD163) and complement C1q subcomponent subunit B (C1QB) genes passed external validation as core genes. The core genes showed strong correlation with immune process and inflammatory response in both immune infiltration analysis and GSEA enrichment analysis. A total of 35 TCMs, including Chuanxiong (Chuanxiong Rhizoma), Taoren (Persicae Semen), Danggui (Angelicae Sinensis Radix), Huangqin (Scutellariae Radix), Pugongying (Taraxaci Herba), Taizishen (Pseudostellariae Radix), Huangjing (Polygonati Rhizoma), could be used as potential therapeutic agents. Conclusion TLR2, CD163 and C1QB were the core molecules of SARS-CoV-2-mediated immune inflammatory response promoting AS progression, and targeting predicted herbs were potential drugs to slow down AS progression in COVID-19 patients.Copyright © 2023 Editorial Office of Chinese Traditional and Herbal Drugs. All rights reserved.

Surfactant Protein B Reduces Respiratory Viral Infectivity in Human Lungs

Purpose of Study: COVID pneumonia caused by SARS-CoV-2 can result in a depletion of surfactant & lung injury, which resembles neonatal respiratory distress syndrome. Exogenous surfactant has shown promise as a therapeutic option in intubated hospitalized patients. Our preliminary data in human lung organoids (LOs) with a deficiency of surfactant protein B (SP-B) showed an increased viral load compared to normal LOs. Single cell RNA sequencing (scRNAseq) revealed that SP-B-deficient cells showed increased viral entry genes (ACE2 receptor) & dysregulated inflammatory markers emanating from the lung cells themselves. Our objective was to determine: (1) cell-specific transcriptional differences between normal & SP-B deficient human lung cells after infection with SARS-CoV-2 and (2) a therapeutic role of SP-B protein & surfactant in COVID-19 pneumonia. Methods Used: We used normal and SP-B mutant (homozygous, frameshift, loss of function mutation p.Pro133GlnfsTer95, previously known as 121ins2) human induced pluripotent stem cells (hiPSC) and differentiated them into 3D proximal lung organoids. The organoids were infected with the delta variant of SARS-CoV-2 for 24 hours at an MOI of 1. Infected and uninfected organoids were fixed in trizol in triplicate and underwent processing for bulk RNA sequencing. We tested for differentially expressed genes using the program DEseq. We also plated normal iPSC derived lung organoids as a monolayer and pre-treated them with 1mg/ml of Poractant alfa or 5 uM of recombinant SP-B protein. The delta strain of SARS-CoV-2 was added to the 96 wells at an MOI of 0.1 for one hour with shaking, then an overlay with DMEM/CMC/FBS was added and left on for 23 hours. The plate was fixed and stained for nucleocapsid (NC) protein. Summary of Results: Bioinformatic analysis of the bulk RNA sequencing data showed an increase in the multiple cytokines and chemokines in the SP-B mutant LOs compared to control. We also saw differential gene expression patterns in the SP-B mutant LOs including a reduction in SFTPC, FOXA2, and NKX2-1 and an increase in IL1A, VEGFA, PPARG and SMAD3. In the exogenous surfactant experiments, there was a decrease in total expression of viral NC in the Poractant alfa & rSP-B-treated cells compared to SARS-CoV-2 infection alone (p<0.001). Conclusion(s): Surfactant modulates the viral load of SARS-CoV-2 infection in the human lung. Deficiency in SP-B results in the dysregulation of the lung epithelial inflammatory signaling pathways resulting in worsening infections.

Differentially-regulated miRNAs in COVID-19: A systematic review.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for coronavirus disease of 2019 (COVID-19) that infected more than 760 million people worldwide with over 6.8 million deaths to date. COVID-19 is one of the most challenging diseases of our times due to the nature of its spread, its effect on multiple organs, and an inability to predict disease prognosis, ranging from being completely asymptomatic to death. Upon infection, SARS-CoV-2 alters the host immune response by changing host-transcriptional machinery. MicroRNAs (miRNAs) are regarded as post-transcriptional regulators of gene expression that can be perturbed by invading viruses. Several in vitro and in vivo studies have reported such dysregulation of host miRNA expression upon SARS-CoV-2 infection. Some of this could occur as an anti-viral response of the host to the viral infection. Viruses themselves can counteract that response by mounting their own pro-viral response that facilitates virus infection, an aspect which may cause pathogenesis. Thus, miRNAs could serve as possible disease biomarkers in infected people. In the current review, we have summarised and analysed the existing data about miRNA dysregulation in patients infected with SARS-CoV-2 to determine their concordance between studies, and identified those that could serve as potential biomarkers during infection, disease progression, and death, even in people with other co-morbidities. Having such biomarkers can be vital in not only predicting COVID-19 prognosis, but also the development of novel miRNA-based anti-virals and therapeutics which can become invaluable in case of the emergence of new viral variants with pandemic potential in the future.

Transcriptome Profiling in Autoimmune Diseases

Autoimmune diseases are a group of different inflammatory disorders characterized by systemic or localized inflammation, affecting approximately 0.1–1% of the general population. Several studies suggest that genetic risk loci are shared between different autoimmune diseases and pathogenic mechanisms may also be shared. The strategy of performing differential gene expression profiles in autoimmune disorders has unveiled new transcripts that may be shared among these disorders. Microarray technology and bioinformatics offer the most comprehensive molecular evaluations and it is widely used to understand the changes in gene expression in specific organs or in peripheral blood cells. The major goal of transcriptome studies is the identification of specific biomarkers for different diseases. It is believed that such knowledge will contribute to the development of new drugs, new strategies for early diagnosis, avoiding tissue autoimmune destruction, or even preventing the development of autoimmune disease. In this review, we primarily focused on the transcription profiles of three typical autoimmune disorders, including type 1 diabetes mellitus (destruction of pancreatic islet beta cells), systemic lupus erythematosus (immune complex systemic disorder affecting several organs and tissues), and multiple sclerosis (inflammatory and demyelinating disease of the nervous system). © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2014, 2022.

Genomic regulatory network of human olfactory neuroepithelial cells infected with novel coronavirus (SARS-COV-2).

Objective To explore the genomic changes of human olfactory neuroepithelial cells after the novel coronavirus (SARS-COV-2) infecting the human body, and establish a protein-protein interaction (PPI) network of differentially expressed genes (DEGs), in order to understand the impact of SARS-COV-2 infection on human olfactory neuroepithelial cells, and provide reference for the prevention and treatment of new coronavirus pneumonia. Methods The public dataset GSE151973 was analyzed by NetworkAnalyst. DEGs were selected by conducting Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis. PPI network, DEGs-microRNA regulatory network, transcription factor-DEGs regulatory network, environmental chemicals-DEGs regulatory network, and drug-DEGs regulatory network were created and visualized by using Cytoscape 3.7.2. Results After SAR-COV-2 invading human olfactory neuroepithelial cells, part of the gene expression profile was significantly up-regulated or down-regulated. A total of 568 DEGs were found, including 550 up-regulated genes (96.8%) and 18 down-regulated genes (3.2%). DEGs were mainly involved in biological processes such as endothelial development and angiogenesis of the olfactory epithelium, and the expression of molecular functions such as the binding of the N-terminal myristylation domain. PPI network suggested that RTP1 and RTP2 were core proteins. MAZ was the most influential transcription factor. Hsa-mir-26b-5p had the most obvious interaction with DEGs regulation. Environmental chemical valproic acid and drug ethanol had the most influence on the regulation of DEG. Conclusion The gene expression of olfactory neuroepithelial cells is significantly up-regulated or down-regulated after infection with SAR-COV-2. SARS-CoV-2 may inhibit the proliferation and differentiation of muscle satellite cells by inhibiting the function of PAX7. RTP1 and RTP2 may resist SARS-CoV-2 by promoting the ability of olfactory receptors to coat the membrane and enhancing the ability of olfactory receptors to respond to odorant ligands. MAZ may regulate DEGs by affecting cell growth and proliferation. Micro RNA, environmental chemicals and drugs also play an important role in the anti-SAR-COV-2 infection process of human olfactory neuroepithelial cells.Copyright © 2022 Editorial Department of Journal of Shanghai Second Medical University. All rights reserved.

FYN, SARS-CoV-2, and IFITM3 in the neurobiology of Alzheimer's disease

Introduction: (IFITM3) is an innate immune protein that has been identified as a novel gamma-secretase (gammas) modulator. FYN is a kinase that stabilizes IFITM3 on the membrane, primes APP for amyloidogenic gammas processing and mediates tau oligomerization. The purpose of this study is to explore the role of FYN and IFITM3 in AD and COVID-19, expanding on previous research from our group. Method(s): A 520 gene signature containing FYN and IFITM3 (termed Ia) was extracted from a previously published meta-analysis of Alzheimer's disease (AD) bulk- and single nuclei sequencing data. Exploratory analyses involved meta-analysis of bulk and single cell RNA data for IFITM3 and FYN differential expression per CNS site and cellular type. Confirmatory analyses, gene set enrichment analysis (GSEA) on Ia was performed to detect overlapping enriched biological networks between COVID-19 with AD. Result(s): Bulk RNA data analysis revealed that IFITM3 and FYN were overexpressed in two CNS regions in AD vs. Controls: the temporal cortex Wilcoxon p-value=1.3e-6) and the parahippocampal cortex Wilcoxon p-value=0.012). Correspondingly, single cell RNA analysis of IFITM3 and FYN revealed that it was differentially expressed in neurons, glial and endothelial cells donated b AD patients, when compared to controls. Discussion(s): IFITM3 and FYN were found as interactors within biological networks overlapping between AD and SARS-CoV-2 infection. Within the context of SARS-CoV-2 induced tau aggregation and interactions between tau and Ab1-42, the FYN - IFITM3 regulome may outline an important innate immunity element responsive to viral infection and IFN-I signaling in both AD and COVID-19.Copyright © 2021 The Authors

Viral and Host Small RNA Response to SARS-CoV-2 Infection

After two years into the pandemic of the coronavirus disease 2019 (COVID-19), it remains unclear how the host RNA interference (RNAi) pathway and host miRNAs regulate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and impact the development of COVID-19. In this study, we profiled small RNAs in SARS-CoV-2-infected human ACE2-expressing HEK293T cells and observed dysregulated host small RNA groups, including specific host miRNAs that are altered in response to SARS-CoV-2 infection. By comparing dysregulated miRNAs in different SARS-CoV-2-infected samples, we identified miRNA-210-3p, miRNA-30-5p, and miR-146a/b as key host miRNAs that may be involved in SARS-CoV-2 infection. Furthermore, by comparing virally derived small RNAs (vsmRNAs) in different SARS-CoV-2-infected samples, we observed multiple hot spots in the viral genome that are prone to generating vsmRNAs, and their biogenesis can be dependent on the antiviral isoform of Dicer. Moreover, we investigated the biogenesis of a recently identified SARS-CoV-2 viral miRNA encoded by ORF7a and found that it is differentially expressed in different infected cell lines or in the same cell line with different viral doses. Our results demonstrate the involvement of both host small RNAs and vsmRNAs in SARS-CoV-2 infection and identify these small RNAs as potential targets for anti-COVID-19 therapeutic development. © 2022 by the authors.

Longitudinal profiling of the peripheral blood transcriptome identifies risk of Major Cardiac Events after Hospitalization for COVID-19

Introduction: SARS-CoV-2 infection has profound effects on endothelial and immune cell function and coagulation, and better understanding of these events in COVID-19 would allow for targeted cardiovascular treatment and followup. Method(s): Longitudinal observational study of patients with PCR-confirmed SARS-CoV-2 infection admitted to hospital at two UK sites. Patients were enrolled within 96 hours of admission, with sampling up to day 29. RNAstabilised whole blood was processed for mRNA sequencing. Gene expression levels were compared between patients who did and did not suffer a major cardiac event (MACE) from admission to 1-year post-hospitalization. Result(s): At day 1, in acute COVID-19, no differences in gene expression were observed between those with (n=23) and without (n=140) a MACE. However, 93 significant differentially expressed genes (DEGs;adjusted pvalue<0.05;Wald test with Benjamini-Hochberg correction) were identified at day 29 between patients who suffered a MACE (n=16) or not (n=85) post-hospitalization. Neutrophil elastase (ELANE), tissue factor pathways inhibitor (TFPI) and integrin subunit alpha-2 (ITGA2B) were significantly elevated in patients who suffered a MACE. Significantly enriched pathways associated with cardiovascular events included type I interferon signalling and neutrophil chemotaxis. Conclusion(s): COVID-19 patients who experienced a MACE demonstrated significant changes in peripheral blood transcriptome 29 days after hospital admission. Significant DEGs were related to neutrophil activity, coagulation and interferon signalling, suggesting a relationship between these pathways and increased cardiovascular risk.

Genomic regulatory network of human olfactory neuroepithelial cells infected with novel coronavirus (SARS-COV-2)

Objective To explore the genomic changes of human olfactory neuroepithelial cells after the novel coronavirus (SARS-COV-2) infecting the human body, and establish a protein-protein interaction (PPI) network of differentially expressed genes (DEGs), in order to understand the impact of SARS-COV-2 infection on human olfactory neuroepithelial cells, and provide reference for the prevention and treatment of new coronavirus pneumonia. Methods The public dataset GSE151973 was analyzed by NetworkAnalyst. DEGs were selected by conducting Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis. PPI network, DEGs-microRNA regulatory network, transcription factor-DEGs regulatory network, environmental chemicals-DEGs regulatory network, and drug-DEGs regulatory network were created and visualized by using Cytoscape 3.7.2. Results After SAR-COV-2 invading human olfactory neuroepithelial cells, part of the gene expression profile was significantly up-regulated or down-regulated. A total of 568 DEGs were found, including 550 up-regulated genes (96.8%) and 18 down-regulated genes (3.2%). DEGs were mainly involved in biological processes such as endothelial development and angiogenesis of the olfactory epithelium, and the expression of molecular functions such as the binding of the N-terminal myristylation domain. PPI network suggested that RTP1 and RTP2 were core proteins. MAZ was the most influential transcription factor. Hsa-mir-26b-5p had the most obvious interaction with DEGs regulation. Environmental chemical valproic acid and drug ethanol had the most influence on the regulation of DEG. Conclusion The gene expression of olfactory neuroepithelial cells is significantly up-regulated or down-regulated after infection with SAR-COV-2. SARS-CoV-2 may inhibit the proliferation and differentiation of muscle satellite cells by inhibiting the function of PAX7. RTP1 and RTP2 may resist SARS-CoV-2 by promoting the ability of olfactory receptors to coat the membrane and enhancing the ability of olfactory receptors to respond to odorant ligands. MAZ may regulate DEGs by affecting cell growth and proliferation. Micro RNA, environmental chemicals and drugs also play an important role in the anti-SAR-COV-2 infection process of human olfactory neuroepithelial cells.

Bioinformatics and system biology approach to identify the influences of COVID-19 on primary sjogren's syndrome patients

Background: Primary Sjogren's syndrome (pSS) is a chronic, systemic, inflammatory autoimmune disease in which existing studies have found the presence of pSS-specific antibodies anti-SSA/ Ro in acute infection with COVID-19.1 The emergence of this phenomenon makes us aware that in the context of the long-term epidemic of COVID-19, it is necessary to further study the molecular mechanisms of the high susceptibility of pSS patients to COVID-19. Method(s): The gene expression profiles of 8 COVID-19 datasets and 5 pSS datasets were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between COVID-19 and PSS were identified using the limma software package and Weighted Gene Co-expression Network Analysis (WGCNA). A Venn diagram was used to discover common upregulated DEGs. To explore the possible pathogenesis of both diseases, common signaling pathways were explored by enriching DEGs using Gene Ontology (GO) and the Kyoto Gene and Genome Encyclopedia (KEGG) pathway. Protein-protein interactions (PPIs) were established to identify hub genes and key modules. The analysis of key gene expression characteristics by The Connectivity Map was used to predict potentially effective drugs. Finally, the CIBERSORT method was used to comprehensively evaluate the immune infiltrates of patients with COVID-19 and PSS to study the mechanisms that may have a common immune response or immune cell infiltration. Result(s): A total of 82 upregulated DEGs were identified in both COVID-19 and PSS (Figure 1 A-E). Functional enrichment analysis illustrated the important role of enhanced signaling pathways in response to virus defense and interferon-alpha in both diseases (Figure 1F).Three key modules including 25 hub genes were identified (Figure 1G). The correlation analysis of immune cell infiltration showed the expression of B cells memory resting decreased and NK cells resting increased significantly in the two diseases (Figure 1H, I). Finally, estradiol in drug prediction outcomes has been shown to reduce susceptibility to COVID-19 and its severity through its involvement in regulating immune cells, while the most common manifestation of dry eye in pSS patients is strongly associated with low estrogen. Conclusion(s): High defense response to virus and response to interferon-alpha in pSS patients might be a crucial susceptible factor for COVID-19 and predictive drugs such as estradiol, suggested by susceptibility genes common to COVID-19 and pSS, may help in the clinical treatment of both diseases.

Identification of shared genes and possible therapeutic target between systemic lupus erythematosus and COVID-19

Background/purpose: Coronavirus disease 2019 (COVID-19) has led to a rapid increase in mortality worldwide. Systemic lupus erythematosus (SLE) was a high-risk factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) infection, Whereas the molecular mechanisms underlying SLE and CVOID-19 are not well understood. This study aims to discover the common molecular mechanisms and genetic biomarkers of SLE and COVID-19, providing new ideas for the treatment of COVID-19. Method(s): RNA sequencing data of peripheral blood mononuclear cells (PBMC) from 6 SLE datasets and 8 COVID-19 datasets were obtained from the GEO database. Highly related modular genes associated with COVID-19 and SLE were identified by weighted gene co-expression network analysis (WGCNA). The differentially expressed genes (DEGs) between patients and healthy controls (HCs) were identified by the limma package. Common shared DEGs from COVID-19 and SLE were identified. Cytoscape and MCODE plugin were utilized for exploring the protein-protein interaction network (PPI) and identifying shared hub genes. Potential biological functions and pathways were also explored from the common DEGs. For better analysis of detailed biological mechanisms, both xCell algorithm and the cMap in CLUE (https://clue.io/) were utilized for discovering immune cell infiltration and predicting potential drugs that negatively regulate the highly expressed genes. Result(s): With identified 498 up-regulated common DEGs in SLE and COVID-19 related genes, total 11 and 13 gene modules of SLE and COVID-19 were identified espectively After overlapping differential genes, the final intersection gene set contains 218 genes. The PPI, especially the functional subnet module consists of upregulated genes by MCODE showed a great deal IFN related genes involved in the regulation of immunity. GO biological processes also showed possible functions were defense response to virus and mitotic cell cycle. Moreover, changes of most immune cells were strongly consistent between SLE and COVID-19. CDK inhibitors identified may be more likely to inhibit two diseases. Conclusion(s): Our study examined in detail the common molecular mechanisms of SLE and COVID-19, in which cellular response to cytokine stimulus, like regulating IFN, which might be the key target of both diseases. CDK is associated with the progression of SLE and COVID-19, which may be the potential therapeutic drug for SLE patients with COVID-19 infection.

Genomic regulatory network of human olfactory neuroepithelial cells infected with novel coronavirus (SARS-COV-2)

Objective To explore the genomic changes of human olfactory neuroepithelial cells after the novel coronavirus (SARS-COV-2) infecting the human body, and establish a protein-protein interaction (PPI) network of differentially expressed genes (DEGs), in order to understand the impact of SARS-COV-2 infection on human olfactory neuroepithelial cells, and provide reference for the prevention and treatment of new coronavirus pneumonia. Methods The public dataset GSE151973 was analyzed by NetworkAnalyst. DEGs were selected by conducting Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis. PPI network, DEGs-microRNA regulatory network, transcription factor-DEGs regulatory network, environmental chemicals-DEGs regulatory network, and drug-DEGs regulatory network were created and visualized by using Cytoscape 3.7.2. Results After SAR-COV-2 invading human olfactory neuroepithelial cells, part of the gene expression profile was significantly up-regulated or down-regulated. A total of 568 DEGs were found, including 550 up-regulated genes (96.8%) and 18 down-regulated genes (3.2%). DEGs were mainly involved in biological processes such as endothelial development and angiogenesis of the olfactory epithelium, and the expression of molecular functions such as the binding of the N-terminal myristylation domain. PPI network suggested that RTP1 and RTP2 were core proteins. MAZ was the most influential transcription factor. Hsa-mir-26b-5p had the most obvious interaction with DEGs regulation. Environmental chemical valproic acid and drug ethanol had the most influence on the regulation of DEG. Conclusion The gene expression of olfactory neuroepithelial cells is significantly up-regulated or down-regulated after infection with SAR-COV-2. SARS-CoV-2 may inhibit the proliferation and differentiation of muscle satellite cells by inhibiting the function of PAX7. RTP1 and RTP2 may resist SARS-CoV-2 by promoting the ability of olfactory receptors to coat the membrane and enhancing the ability of olfactory receptors to respond to odorant ligands. MAZ may regulate DEGs by affecting cell growth and proliferation. Micro RNA, environmental chemicals and drugs also play an important role in the anti-SAR-COV-2 infection process of human olfactory neuroepithelial cells. Copyright © 2022 Editorial Department of Journal of Shanghai Second Medical University. All rights reserved.

Exploring Feature Genes for Ischemic Stroke Based on Bioinformatics and Machine Learning

Background and Aims: This study aims to screen the feature genes of ischemic stroke (IS) by bioinformatics and machine learning (ML) and explore the possible pathophysiological mechanism of the genes in IS. Method(s): Two RNA sequencing datasets were downloaded from NCBI Gene Expression Omnibus (GEO) database. The GSE122709 dataset with a larger sample size was used as the training set and analyzed for differentially expressed genes (DEGs), while the GSE140275 dataset was used as the test set. The DEGs were further analyzed for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Disease Ontology (DO) enrichment analyses. Then, feature genes selection was performed by two ML algorithms. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of the ML algorithms. Result(s): A total of 378 DEGs (Fold Change>=2 and p value<=0.05) were identified. The GO and KEGG analyses demonstrated that the majority of DEGs were associated with inflammatory response, immune regulation and COVID-19. The DO analysis revealed that the DEGs were mainly linked to demyelinating disease and cancer. The TVP23C and B3GAT1 were identified as feature genes by ML algorithms, and the AUCs of them were closer to 1 both in the training and test set. It is found that B3GAT1 may be involved in brain injury of IS by regulating AMRA glutamate receptors. Conclusion(s): The integrated approach of bioinformatics and ML could be a novel approaches for screening feature genes, and the B3GAT1 gene may be a possible therapeutic target in IS.

Transcriptomic analyses unravel differential expression of genes involved in the N-glycosylation pathway of Phaeodactylum tricornutum ecotypes

Most of the biologics are glycoproteins. It is well-established that N-glycans harboured by proteins are involved in the protein half-life, bioactivity and immunogenicity. Currently, most of the biologics are produced in mammalian cells. However, microalgae emerged as a cheaper alternative biofactory. Among them, the diatom Phaeodactylum tricornutum benefits from numerous advantages and has been successfully used to produce biologics such as SARS-COV2 RBD and functional monoclonal antibodies (mAbs). These mAbs have been demonstrated to be glycosylated with oligomannosides that are similar to the mammalian ones and that result from processing steps occurring in the ER and the early Golgi apparatus. Surprisingly, these oligomannosides represent the major N-glycans population even if the diatom possesses glycoenzymes potentially involved in the biosynthesis of complex-type N-glycans in the Golgi apparatus. Therefore, it is essential to characterize the regulation of the P. tricornutum protein N-glycosylation pathway as well as the expression level of genes involved in the N-glycosylation of proteins. In the present work, we performed RNA-Seq analyses on different ecotypes of P. tricornutum and decode the differential expression of genes involved in the protein N-glycosylation pathway.

AKI in Patients With SARS-CoV-2 Is Significantly Associated With Mitochondrial Dysfunction and ER Stress

Background: AKI is a common complication of COVID-19. The peripheral blood molecular signatures are unknown and could unveil potential therapeutic targets. Method(s): We enrolled a prospective patient cohort of 283 patients with COVID-19 (Mar 24-Aug 26, 2020), with blood samples from Mount Sinai Biobank. We determined AKI severity using KDIGO criteria on admission parameters. 31 patients with severe AKI (AKI 2-3) were defined as cases. We then performed bulk peripheral RNA sequencing and fit a multivariate linear regression model adjusting for key covariates. We also performed cell-type deconvolution following to adjust for neutrophils, and whole blood cells. We considered a significant p-value (0.05) after Bonferroni correction and then used ingenuity pathway analysis (IPA) to analyze differentially expressed genes. Result(s): Patients who developed AKI were significantly older (67 vs. 60 yrs.) and had a greater prevalence of type 2 diabetes (37% vs 20%), and chronic kidney disease (20% vs 4%) vs. controls. Of the 18539 genes in the analysis, 1597 were upregulated and 1267 were downregulated after Bonferroni correction. Top canonical pathways (Fig 1) showed significantly downregulated genes including EIF2, eIF4, and p70S6K via activation of ATF6, a marker of ER stress. Potential mechanisms displayed by our analyses include upregulation of the NF-KB inhibitor and IL6 pathways. Genes involved in oxidative Phosphorylation and mitochondrial dysfunction were heavily downregulated and there was upregulation of markers of kidney cell necrosis. In contrast, upregulated genes CRK and TIMP2 have been previously implicated in kidney injury and progression. Downregulated mTOR pathway is responsible for the activation of the ER stress response via the eIF2/4 complex which is also supported by our finding of upregulated NRF2- transcriptional pathway. Conclusion(s): Transcriptomic analysis of AKI in COVID-19 revealed evidence of mitochondrial dysfunction driven by ER stress and immune-mediated pathways. Addressing these pathways could aide development of targeted therapies. (Figure Presented).

Urinary Transcriptomics Identified Inflammatory Signals Associated With COVID-19-Related AKI

Background: SARS-CoV-2, associated with COVID-19, can include dysfunction in many organs including the kidney. Early in the pandemic, a high incidence of acute kidney injury (AKI), with an associated increase in mortality, was observed, particularly in those with severe respiratory failure. Given the effect on the kidney and limited availability of biopsied tissue, we designed a non-invasive protocol to isolate and sequence renal cells from the urine of patients with COVID-19 to identify the cellular and molecular mechanisms of COVID-19-related AKI, and the impact of immunomodulatory treatment. Method(s): Three groups of hospitalized patients, AKI with and without COVID-19 and COVID-19 without AKI, were recruited at Michigan Medicine (N=48). We documented >90 clinical parameters, including serum creatinine trends, treatment exposure to IL-6 inhibitors, and patient outcomes. Urine samples near peak AKI were collected and immediately processed for single cell RNA sequencing (scRNAseq);profiles were generated on the 10x Genomics platform and clustered using Seurat. Differentially expressed gene profiles were generated in a cell type selective manner. Result(s): Urine scRNAseq profiles from 44,440 cells clustered into 5 major celltypes, based on cell marker assignment. Renal cells comprised 12% of the recovered cells. Comparing renal cells from COVID-19-related AKI group to either of the two other groups identified 129 up-regulated and 89 down-regulated genes in common (q<0.05). The COVID-19-related AKI renal cell profile was consistent with activation of one or more inflammatory cytokines including IFN-gamma, IL-6, and IL-1beta. Conversely, patients exposed to IL-6 inhibitors had a reduced expression of inflammatory marker genes. Conclusion(s): This study demonstrates the successful isolation and generation of cell type transcriptional profiles of renal cells in the urine of patients with COVID-19, with or without AKI, and non-COVID-19 AKI. Expression profiles in renal cells were consistent with intra-renal inflammatory activation in COVID-19-related AKI. Association of profiles with renal function and patient outcomes may identify predictive markers of COVID-19-related AKI and potential targets for therapeutic modulation.

2022 Annual Meeting of the Society for Glycobiology

The proceedings contain 195 papers. The topics discussed include: structural and mechanistic studies of C-mannosyltransferase;development of radical carbohydrate footprinting for glycan solvent accessible surface analysis;GlycoGrip: a glycocalyx-inspired lateral flow strip-based assay designed to detect betacoronaviruses;glycans as central regulators of the immunological pathways at the frontiers of microbial infections, chronic inflammation and autoimmunity;an atlas of the human O-Man glycoproteome reveals domain-specific modifications and substrate specificities of human mannosyltransferases;role of proteoglycans in determining muscle stem cell fate during pregnancy;transcriptomic analyses unravel differential expression of genes involved in the N-glycosylation pathway of phaeodactylum tricornutum ecotypes;immunoglobulin N-glycosylation discriminates acute Lyme disease from endemic healthy controls and mimic diseases ' a novel diagnostic and prognostic;spatiotemporal biosynthesis of paucimannosidic proteins via a noncanonical truncation pathway in human neutrophils;and specific N-glycans regulate the function of an extracellular adhesion complex during somatosensory dendrite patterning.

Post Vaccination Transcriptomic Profiling in Sarcoidosis Yields Pathways Associated with Decreased Immune Response

Introduction/Background Sarcoidosis is a T cell mediated systemic disease of unknown etiology that results in granulomatous inflammation and multiorgan dysfunction. Individuals with sarcoidosis have been shown to be at increased risk for infection arguing the importance of vaccination as a primary prevention strategy. However, current knowledge as to how individuals with sarcoidosis respond to vaccination is limited. Furthermore, proteomic and transcriptomic profiling post vaccination will offer integrated insight into the immune mechanisms that drive sarcoidosis disease. Objective(s) The objective of this study is to determine the quantitative antibody response to COVID-19 vaccination to correlate to the unique proteomic and transcriptomic profiles underlying the immune response. Methods With local institutional review board approval, a prospective case control study was conducted to compare the proteomic and transcriptomic profiles of subjects with and without sarcoidosis before and after vaccination with the BNT162b2 mRNA vaccine. Recruited subjects included individuals -18 years who received two doses of the vaccine at the University of Illinois (UIC). Sixteen subjects with biopsy proven sarcoidosis were recruited, six of whom were not on any treatment while 10 were on immunosuppressive therapy, while 23 age-gender matched healthy controls were recruited. Blood was sampled prior to each vaccine dose as well as one and seven days after vaccination. Anti-spike protein IgG titers and serum cytokine profiles were quantified with ELISA while bulk RNA sequencing was performed on peripheral blood mononuclear cells (PBMCs). Results Sarcoidosis subjects had significantly less antibody production after two doses of the BNT162b2 mRNA vaccine than controls (p-val 0.0040). A multivariate regression analysis indicated that a sarcoidosis diagnosis (p-val 0.026) was significantly and independently predictive with lower follow up antibody titers, which was more pronounced if subjects were on immunosuppressive therapy (p-val 0.00013). Differential gene expression will compare temporal individual variation after vaccination and identify group differences to identify transcriptomic pathways associated with the diminished antibody response. Weighted gene co-expression analysis will identify likely expressed genes to determine distinct profiles that may be predictive of sarcoidosis disease. Conclusion Subjects with sarcoidosis mount a decreased antibody response to the BNT162b2 mRNA COVID-19 vaccine supporting a dysregulated immune response inherent to sarcoidosis pathogenesis. Correlated transcriptomic and proteomic profiling offers a unique opportunity to comprehensively study the genes and pathways underlying the immune response to vaccination in sarcoidosis.

Blood Transcriptomes of Kidney Recipients with Covid-19 Demonstrate Deficient Adaptive Immune Activation

Purpose: Kidney transplant recipients (KTRs) have poor outcomes compared to non-KTRs with acute COVID-19. To provide insight into management of immunosuppression (IS) during COVID-19, we studied immune signatures from the peripheral blood during and after COVID-19 infection from a multicenter KTR cohort. Method(s): Clinical data were collected by chart review. Paxgene blood RNA was polyA-selected and sequenced at enrollment Results: A total of 64 KTRs affected with COVID-19 were enrolled (31 Early cases (<4weeks from a positive SARS-CoV-2 PCR test) and 33 late cases). Out of the 64 patients, eight died and three encountered graft losses during follow-up. Among 31 early cases, we detected differentially expressed genes (nominal p-value < 0.01) in the blood transcriptome that were positively or negatively associated with the COVID-19 severity score (scale of 1 to 7 with increasing severity;Fig 1A). Enrichment analyses showed upregulation of neutrophil and innate immune pathways and downregulation of adaptive immune activation pathways with increasing severity score (Fig 1B). This observation was independent of lymphocyte count, despite reduction in immunosuppression (IS) in 75% of KTRs. Interestingly, compared with early cases, the blood transcriptome in late cases showed "normalization" of these enriched pathways after 4 weeks, suggesting return of adaptive immune system activation despite re-initiation of immunosuppression (Fig 1C). The latter analyses were adjusted for the severity score. Interestingly, similar pathway enrichment with worsening severity of COVID-19 was identifiable from a public dataset of non-KTRs (GSE152418), showing overlapped signatures for acute COVID-19 between KTRs and non-KTRs (overlap P<0.05) (Fig 1D). Conclusion(s): Blood transcriptome of COVID-KTRs shows marked decrease in adaptive immune system activation during acute COVID-19, even during IS reduction, which show recovery after acute illness. (Figure Presented).

RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.

OBJECTIVES: The characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients. METHODS: A ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data. RESULTS: Both groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients. CONCLUSION: A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.