scholarly journals Alteration of L-Dopa decarboxylase expression in SARS-CoV-2 infection and its association with the interferon-inducible ACE2 isoform

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253458
Author(s):  
George Mpekoulis ◽  
Efseveia Frakolaki ◽  
Styliani Taka ◽  
Anastasios Ioannidis ◽  
Alice G. Vassiliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Infections ◽  
Dopa Decarboxylase ◽  
Nasopharyngeal Swab ◽  
Specific Cell ◽  
Mrna Levels ◽  
Host Gene Expression ◽  
Mediated Effects ◽  
Nasopharyngeal Tissue ◽  
Infected Cells

L-Dopa decarboxylase (DDC) is the most significantly co-expressed gene with ACE2, which encodes for the SARS-CoV-2 receptor angiotensin-converting enzyme 2 and the interferon-inducible truncated isoform dACE2. Our group previously showed the importance of DDC in viral infections. We hereby aimed to investigate DDC expression in COVID-19 patients and cultured SARS-CoV-2-infected cells, also in association with ACE2 and dACE2. We concurrently evaluated the expression of the viral infection- and interferon-stimulated gene ISG56 and the immune-modulatory, hypoxia-regulated gene EPO. Viral load and mRNA levels of DDC, ACE2, dACE2, ISG56 and EPO were quantified by RT-qPCR in nasopharyngeal swab samples from COVID-19 patients, showing no or mild symptoms, and from non-infected individuals. Samples from influenza-infected patients were analyzed in comparison. SARS-CoV-2-mediated effects in host gene expression were validated in cultured virus-permissive epithelial cells. We found substantially higher gene expression of DDC in COVID-19 patients (7.6-fold; p = 1.2e-13) but not in influenza-infected ones, compared to non-infected subjects. dACE2 was more elevated (2.9-fold; p = 1.02e-16) than ACE2 (1.7-fold; p = 0.0005) in SARS-CoV-2-infected individuals. ISG56 (2.5-fold; p = 3.01e-6) and EPO (2.6-fold; p = 2.1e-13) were also increased. Detected differences were not attributed to enrichment of specific cell populations in nasopharyngeal tissue. While SARS-CoV-2 virus load was positively associated with ACE2 expression (r≥0.8, p<0.001), it negatively correlated with DDC, dACE2 (r≤−0.7, p<0.001) and EPO (r≤−0.5, p<0.05). Moreover, a statistically significant correlation between DDC and dACE2 expression was observed in nasopharyngeal swab and whole blood samples of both COVID-19 and non-infected individuals (r≥0.7). In VeroE6 cells, SARS-CoV-2 negatively affected DDC, ACE2, dACE2 and EPO mRNA levels, and induced cell death, while ISG56 was enhanced at early hours post-infection. Thus, the regulation of DDC, dACE2 and EPO expression in the SARS-CoV-2-infected nasopharyngeal tissue is possibly related with an orchestrated antiviral response of the infected host as the virus suppresses these genes to favor its propagation.

scholarly journals Dysregulation of Cyclin E Gene Expression in Human Cytomegalovirus-Infected Cells Requires Viral Early Gene Expression and Is Associated with Changes in the Rb-Related Protein p130

2000 ◽  
Vol 74 (9) ◽  
pp. 4192-4206 ◽  
Author(s):  
Anita K. McElroy ◽  
Roopashree S. Dwarakanath ◽  
Deborah H. Spector
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Human Cytomegalovirus ◽  
Cyclin E ◽  
Early Gene ◽  
Immediate Early ◽  
Mrna Levels ◽  
Early Gene Expression ◽  
Cell Extracts ◽  
Infected Cells

ABSTRACT We have previously shown that many cell cycle regulatory gene products are markedly affected by infection of primary fibroblasts with human cytomegalovirus (HCMV) (F. M. Jault, J. M. Jault, F. Ruchti, E. A. Fortunato, C. Clark, J. Corbeil, D. D. Richman, and D. H. Spector, J. Virol. 69:6697–6704, 1995). One of these proteins, cyclin E, is a key determinant of cell cycle progression during G1, and its mRNA levels are significantly increased in HCMV-infected fibroblasts (B. S. Salvant, E. A. Fortunato, and D. H. Spector, J. Virol. 72:3729–3741, 1998). To determine the molecular basis of this effect, we have examined the events that occur at the endogenous cyclin E promoter during the course of infection. In vivo dimethyl sulfate footprinting of the cyclin E promoter revealed several regions of protection and hypersensitivity that were unique to infected cells. In accord with this observation, we find that the virus-induced cyclin E transcripts initiate downstream of the start site identified in mock-infected cells, in regions where these newly appearing protected and hypersensitive sites occur. Viral gene expression is required for this induction. However, the viral immediate-early proteins IE1-72 and IE2-86, either alone or in combination, cannot induce expression of the endogenous cyclin E. The virus must progress past the immediate-early phase and express an early gene product(s) for activation of cyclin E expression. Moreover, IE1-72 does not appear to be required, as infection of cells with an HCMV mutant containing a deletion in the IE1-72 gene leads to full upregulation of cyclin E expression. Using electrophoretic mobility shift assays with infected cell extracts and a region of the cyclin E promoter that includes two previously defined E2F sites as the probe, we detected the appearance of an infection-specific banding pattern. One of the infection-specific bands contained the proteins E2F-4, DP-1, and p130, which were maintained in the infected cells as uniquely phosphorylated species. These results suggest that an altered E2F-4–DP-1–p130 complex along with viral early gene expression may play a role in the transcriptional regulation of cyclin E mRNA during HCMV infection.

scholarly journals TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo

2020 ◽  
Author(s):  
Yating Liu ◽  
Anthony D. Fischer ◽  
Celine L. St. Pierre ◽  
Juan F. Macias-Velasco ◽  
Heather A. Lawson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Regulation ◽  
Transcript Abundance ◽  
Cell Types ◽  
Regulatory Elements ◽  
Model Organisms ◽  
Specific Cell ◽  
Translation Efficiency ◽  
Mrna Levels

AbstractThe alteration of gene expression due to variations in the sequences of transcriptional regulatory elements has been a focus of substantial inquiry in humans and model organisms. However, less is known about the extent to which natural variation contributes to post-transcriptional regulation. Allelic Expression Imbalance (AEI) is a classical approach for studying the association of specific haplotypes with relative changes in transcript abundance. Here, we piloted a new TRAP based approach to associate genetic variation with transcript occupancy on ribosomes in specific cell types, to determine if it will allow examination of Allelic Translation Imbalance (ATI), and Allelic Translation Efficiency Imbalance, using as a test case mouse astrocytes in vivo. We show that most changes of the mRNA levels on ribosomes were reflected in transcript abundance, though ∼1.5% of transcripts have variants that clearly alter loading onto ribosomes orthogonally to transcript levels. These variants were often in conserved residues and altered sequences known to regulate translation such as upstream ORFs, PolyA sites, and predicted miRNA binding sites. Such variants were also common in transcripts showing altered abundance, suggesting some genetic regulation of gene expression may function through post-transcriptional mechanisms. Overall, our work shows that naturally occurring genetic variants can impact ribosome occupancy in astrocytes in vivo and suggests that mechanisms may also play a role in genetic contributions to disease.

scholarly journals Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1431 ◽  
Author(s):  
Yvonne Drechsler ◽  
Elton J. R. Vasconcelos ◽  
Lisa M. Griggs ◽  
Pedro P. P. V. Diniz ◽  
Ellen Collisson
Keyword(s):  
Gene Expression ◽  
Viral Infections ◽  
Ex Vivo ◽  
Host Gene ◽  
Host Responses ◽  
Host Gene Expression ◽  
Feline Infectious Peritonitis ◽  
Host Immune Responses ◽  
Individual Host ◽  
Feline Coronavirus

Feline coronavirus is a highly contagious virus potentially resulting in feline infectious peritonitis (FIP), while the pathogenesis of FIP remains not well understood, particularly in the events leading to the disease. A predominant theory is that the pathogenic FIPV arises from a mutation, so that it could replicate not only in enterocytes of the intestines but also in monocytes, subsequently systemically transporting the virus. The immune status and genetics of affected cats certainly play an important role in the pathogenesis. Considering the importance of genetics and host immune responses in viral infections, the goal of this study was to elucidate host gene expression in macrophages using RNA sequencing. Macrophages from healthy male cats infected with FIPV 79-1146 ex vivo displayed a differential host gene expression. Despite the virus uptake, aligned viral reads did not increase from 2 to 17 h. The overlap of host gene expression among macrophages from different cats was limited, even though viral transcripts were detected in the cells. Interestingly, some of the downregulated genes in all macrophages were involved in immune signaling, while some upregulated genes common for all cats were found to be inhibiting immune activation. Our results highlight individual host responses playing an important role, consistent with the fact that few cats develop feline infectious peritonitis despite a common presence of enteric FCoV.

scholarly journals Comparative Study of SARS-CoV-2, SARS-CoV-1, MERS-CoV, HCoV-229E and Influenza Host Gene Expression in Asthma: Importance of Sex, Disease Severity, and Epithelial Heterogeneity

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1081
Author(s):  
Mackenzie E. Coden ◽  
Lucas F. Loffredo ◽  
Hiam Abdala-Valencia ◽  
Sergejs Berdnikovs
Keyword(s):  
Gene Expression ◽  
Viral Entry ◽  
Viral Infections ◽  
Differential Susceptibility ◽  
Asthma Severity ◽  
Host Gene Expression ◽  
Ciliated Cells ◽  
Human Coronavirus ◽  
Potential Factors ◽  
Viral Receptors

Epithelial characteristics underlying the differential susceptibility of chronic asthma to SARS-CoV-2 (COVID-19) and other viral infections are currently unclear. By revisiting transcriptomic data from patients with Th2 low versus Th2 high asthma, as well as mild, moderate, and severe asthmatics, we characterized the changes in expression of human coronavirus and influenza viral entry genes relative to sex, airway location, and disease endotype. We found sexual dimorphism in the expression of SARS-CoV-2-related genes ACE2, TMPRSS2, TMPRSS4, and SLC6A19. ACE2 receptor downregulation occurred specifically in females in Th2 high asthma, while proteases broadly assisting coronavirus and influenza viral entry, TMPRSS2, and TMPRSS4, were highly upregulated in both sexes. Overall, changes in SARS-CoV-2-related gene expression were specific to the Th2 high molecular endotype of asthma and different by asthma severity and airway location. The downregulation of ACE2 (COVID-19, SARS) and ANPEP (HCoV-229E) viral receptors wascorrelated with loss of club and ciliated cells in Th2 high asthma. Meanwhile, the increase in DPP4 (MERS-CoV), ST3GAL4, and ST6GAL1 (influenza) was associated with increased goblet and basal activated cells. Overall, this study elucidates sex, airway location, disease endotype, and changes in epithelial heterogeneity as potential factors underlying asthmatic susceptibility, or lack thereof, to SARS-CoV-2.

scholarly journals 1218. Comparing the Diagnostic Accuracy of Clinician Judgement to a Novel Host Response Diagnostic for Acute Respiratory Illness

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S630-S630
Author(s):  
Ian S Jaffe ◽  
Anja K Jaehne ◽  
Eugenia Quackenbush ◽  
Micah T McClain ◽  
Geoffrey S Ginsburg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Diagnostic Accuracy ◽  
Bacterial Infections ◽  
Viral Infections ◽  
Treatment Plan ◽  
Respiratory Illness ◽  
Host Gene ◽  
Host Gene Expression ◽  
Net Benefit ◽  
Material Support

Abstract Background Discriminating bacterial and viral infections remains clinically challenging. The resulting antibacterial misuse contributes to antimicrobial resistance. Host gene expression-based tests are a promising strategy to discriminate of bacterial and viral infections, but their potential clinical utility has not yet been evaluated. Methods A host gene expression biosignature was measured using either qRT-PCR or microarray in 683 ED subjects with suspected infection. Based on chart reviews, we recorded clinical diagnosis as defined both by the provider assessment and by the provider treatment plan. The biosignature, diagnosis, treatment plan, and procalcitonin were compared to clinical adjudication as the reference standard. With this as a baseline, we then calculated average weighted accuracy (AWA) and change in overall net benefit (∆NB), weighting bacterial false negatives four times more seriously than false positives. Results Gene expression correctly classified the three possible disease etiologies (bacterial, viral, or non-infectious) 76.1% of the time, outperforming provider diagnosis, provider treatment, and procalcitonin (Table 1). Overall accuracy was higher in subjects with bacterial infections (n=278, 83.8% accurate) compared to those with viral (n=234, 76.5%) and non-infectious (n=171, 63.2%) etiologies. Due to a strong sensitivity bias to treat bacterial infections at the expense of diagnostic accuracy and specificity, the provider diagnosis was overall more accurate than the corresponding treatment plan (71.4% accuracy vs. 68.1%), resulting in inappropriate antibiotic use in 41.0% of cases where antibiotics were prescribed. The gene expression test had significantly higher AWA for the diagnosis of bacterial infection than both procalcitonin and provider treatment (82.4% vs. 70.3% and 74.4%, respectively; p &lt; 0.0001). Consequently, the host gene expression test had greater net benefit than provider treatment (∆NBbact = 9.9%), provider diagnosis (∆NBbact = 4.4%), and procalcitonin (∆NBbact = 27.1%). Table 1: Summary of provider, procalcitonin, and host gene expression test performance in a cohort of 683 subjects. Conclusion Host gene expression-based tests to distinguish bacterial and viral infection can facilitate more appropriate treatment, leading to improved patient outcomes and mitigating the antibiotic resistance crisis. Disclosures Geoffrey S. Ginsburg, MD PhD, Predigen, Inc (Shareholder, Other Financial or Material Support) Ephraim L. Tsalik, MD, MHS, PhD, Predigen (Shareholder, Other Financial or Material Support, Founder)

scholarly journals Zika, chikungunya, and dengue viral infections in human peripheral blood mononuclear cells: cell susceptibility and gene expression

2020 ◽  
Vol 29 (2) ◽  
pp. 129-35
Author(s):  
Ahmad Husein Alkaff ◽  
Benediktus Yohan ◽  
Usman Sumo Friend Tambunan ◽  
R. Tedjo Sasmono
Keyword(s):  
Gene Expression ◽  
Peripheral Blood Mononuclear Cells ◽  
Mononuclear Cells ◽  
Viral Infections ◽  
Human Peripheral Blood ◽  
Denv Infection ◽  
Peripheral Blood Mononuclear ◽  
Tnf Α ◽  
Blood Mononuclear Cells ◽  
Infected Cells

BACKGROUND Infections of Zika (ZIKV), dengue (DENV), and chikungunya viruses (CHIKV) are presented with similar clinical symptoms; these often lead to misdiagnosis. Viremia levels and host immune responses may contribute to disease severity. This study was aimed to characterize the ability of ZIKV, CHIKV, and DENV to infect human peripheral blood mononuclear cells (PBMCs) and assess the expression of tumor necrosis factor (TNF)-α, interleukin (IL)-10, and interferon gamma-induced protein (IP)- 10 genes in response to the viral infections.  METHODS PBMCs were isolated from healthy donors using gradient centrifugation. Cells were infected with Indonesian isolates of ZIKV, CHIKV, and DENV for 48 hours. Plaque assays were performed to measure viable virus titers, while viral genomic RNA and the gene expression of TNF-α, IL-10, and IP-10 were determined using real-time quantitative reverse transcription-polymerase chain reaction.  RESULTS The susceptibility of PBMCs to ZIKV, CHIKV, and DENV infection was observed, and the viable virus titer and viral genome quantity were found to be significantly higher in ZIKV and CHIKV. All viruses induced the expression of immune-related proteins. The TNF-α gene was upregulated by all viruses to relatively similar levels. IL-10 expression was highest in response to ZIKV, followed by CHIKV. In contrast, IP-10 expression was highly upregulated in DENV-infected cells and only moderately expressed in ZIKV- and CHIKV-infected cells.  CONCLUSIONS ZIKV, CHIKV, and DENV clinical isolates infected PBMCs with different levels of virus infectivity. The gene expression of IL-10 was highly upregulated in ZIKV infection and IP-10 in DENV infection.

scholarly journals Complex regulation of human NKG2D-DAP10 cell surface expression: opposing roles of the γc cytokines and TGF-β1

Blood ◽  
2011 ◽  
Vol 118 (11) ◽  
pp. 3019-3027 ◽  
Author(s):  
Yuk Pheel Park ◽  
Seung-Chul Choi ◽  
Patricia Kiesler ◽  
Aleksandra Gil-Krzewska ◽  
Francisco Borrego ◽  
...  
Keyword(s):  
Nk Cells ◽  
Rna Polymerase Ii ◽  
Viral Infections ◽  
Adaptor Protein ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Mrna Levels ◽  
Mediated Effects ◽  
Complex Regulation ◽  
Tgf Β1

Abstract Natural killer (NK) cells help protect the host against viral infections and tumors. NKG2D is a vital activating receptor, also expressed on subsets of T cells, whose ligands are up-regulated by cells in stress. Ligation of NKG2D leads to phosphorylation of the associated DAP10 adaptor protein, thereby activating immune cells. Understanding how the expression of NKG2D-DAP10 is regulated has implications for immunotherapy. We show that IL-2 and TGF-β1 oppositely regulate NKG2D-DAP10 expression by NK cells. IL-2 stimulation increases NKG2D surface expression despite a decrease in NKG2D mRNA levels. Stimulation with IL-2 results in a small increase of DAP10 mRNA and a large up-regulation of DAP10 protein synthesis, indicating that IL-2–mediated effects are mostly posttranscriptional. Newly synthesized DAP10 undergoes glycosylation that is required for DAP10 association with NKG2D and stabilization of NKG2D expression. TGF-β1 has an opposite and dominant effect to IL-2. TGF-β1 treatment decreases DAP10, as its presence inhibits the association of RNA polymerase II with the DAP10 promoter, but not NKG2D mRNA levels. This leads to the down-regulation of DAP10 expression and, as a consequence, NKG2D protein as well. Finally, we show that other γc cytokines act similarly to IL-2 in up-regulating DAP10 expression and NKG2D-DAP10 surface expression.

scholarly journals The Endonucleolytic RNA Cleavage Function of nsp1 of Middle East Respiratory Syndrome Coronavirus Promotes the Production of Infectious Virus Particles in Specific Human Cell Lines

2018 ◽  
Vol 92 (21) ◽  
Author(s):  
Keisuke Nakagawa ◽  
Krishna Narayanan ◽  
Masami Wada ◽  
Vsevolod L. Popov ◽  
Maria Cajimat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Virus Replication ◽  
Virus Assembly ◽  
Host Gene ◽  
Wild Type Virus ◽  
Rna Cleavage ◽  
Host Gene Expression ◽  
Biological Functions ◽  
Wild Type ◽  
Infected Cells

ABSTRACTMiddle East respiratory syndrome coronavirus (MERS-CoV) nsp1 suppresses host gene expression in expressed cells by inhibiting translation and inducing endonucleolytic cleavage of host mRNAs, the latter of which leads to mRNA decay. We examined the biological functions of nsp1 in infected cells and its role in virus replication by using wild-type MERS-CoV and two mutant viruses with specific mutations in the nsp1; one mutant lacked both biological functions, while the other lacked the RNA cleavage function but retained the translation inhibition function. In Vero cells, all three viruses replicated efficiently with similar replication kinetics, while wild-type virus induced stronger host translational suppression and host mRNA degradation than the mutants, demonstrating that nsp1 suppressed host gene expression in infected cells. The mutant viruses replicated less efficiently than wild-type virus in Huh-7 cells, HeLa-derived cells, and 293-derived cells, the latter two of which stably expressed a viral receptor protein. In 293-derived cells, the three viruses accumulated similar levels of nsp1 and major viral structural proteins and did not induceIFN-β andIFN-λ mRNAs; however, both mutants were unable to generate intracellular virus particles as efficiently as wild-type virus, leading to inefficient production of infectious viruses. These data strongly suggest that the endonucleolytic RNA cleavage function of the nsp1 promoted MERS-CoV assembly and/or budding in a 293-derived cell line. MERS-CoV nsp1 represents the first CoV gene 1 protein that plays an important role in virus assembly/budding and is the first identified viral protein whose RNA cleavage-inducing function promotes virus assembly/budding.IMPORTANCEMERS-CoV represents a high public health threat. Because CoV nsp1 is a major viral virulence factor, uncovering the biological functions of MERS-CoV nsp1 could contribute to our understanding of MERS-CoV pathogenicity and spur development of medical countermeasures. Expressed MERS-CoV nsp1 suppresses host gene expression, but its biological functions for virus replication and effects on host gene expression in infected cells are largely unexplored. We found that nsp1 suppressed host gene expression in infected cells. Our data further demonstrated that nsp1, which was not detected in virus particles, promoted virus assembly or budding in a 293-derived cell line, leading to efficient virus replication. These data suggest that nsp1 plays an important role in MERS-CoV replication and possibly affects virus-induced diseases by promoting virus particle production in infected hosts. Our data, which uncovered an unexpected novel biological function of nsp1 in virus replication, contribute to further understanding of the MERS-CoV replication strategies.

scholarly journals The hepatitis C viral nonstructural protein 5A stabilizes growth-regulatory human transcripts

2018 ◽  
Vol 46 (5) ◽  
pp. 2537-2547 ◽  
Author(s):  
Liang Guo ◽  
Suresh D Sharma ◽  
Jose D Debes ◽  
Daniel Beisang ◽  
Bernd Rattenbacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatitis C ◽  
Chronic Infection ◽  
Nonstructural Protein ◽  
Host Gene Expression ◽  
Subgenomic Replicon ◽  
Mrna Stabilization ◽  
Infected Cells ◽  
Nonstructural Protein 5A

AbstractNumerous mammalian proto-oncogene and other growth-regulatory transcripts are upregulated in malignancy due to abnormal mRNA stabilization. In hepatoma cells expressing a hepatitis C virus (HCV) subgenomic replicon, we found that the viral nonstructural protein 5A (NS5A), a protein known to bind to viral RNA, also bound specifically to human cellular transcripts that encode regulators of cell growth and apoptosis, and this binding correlated with transcript stabilization. An important subset of human NS5A-target transcripts contained GU-rich elements, sequences known to destabilize mRNA. We found that NS5A bound to GU-rich elements in vitro and in cells. Mutation of the NS5A zinc finger abrogated its GU-rich element-binding and mRNA stabilizing activities. Overall, we identified a molecular mechanism whereby HCV manipulates host gene expression by stabilizing host transcripts in a manner that would promote growth and prevent death of virus-infected cells, allowing the virus to establish chronic infection and lead to the development of hepatocellular carcinoma.

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