DataSheet_3_Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection.zip

Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.</p

Image_1_Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection.jpeg

Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.</p

DataSheet_1_Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection.zip

Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.</p

DataSheet_2_Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection.zip

Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.</p

Carbohydrate-Based Label-Free Detection of <i>Escherichia coli</i> ORN 178 Using Electrochemical Impedance Spectroscopy

A label-free biosensor for <i>Escherichia coli</i> (<i>E. coli</i>) ORN 178 based on faradaic electrochemical impedance spectroscopy (EIS) was developed. α-Mannoside or β-galactoside was immobilized on a gold disk electrode using a self-assembled monolayer (SAM) via a spacer terminated in a thiol functionality. Impedance measurements (Nyquist plot) showed shifts due to the binding of <i>E. coli</i> ORN 178, which is specific for α-mannoside. No significant change in impedance was observed for <i>E. coli</i> ORN 208, which does not bind to α-mannoside. With increasing concentrations of <i>E. coli</i> ORN 178, electron-transfer resistance (<i>R</i>_et) increases before the sensor is saturated. After the Nyquist plot of <i>E. coli</i>/mixed SAM/gold electrode was modeled, a linear relationship between normalized <i>R</i>_et and the logarithmic value of <i>E. coli</i> concentrations was found in a range of bacterial concentration from 10² to 10³ CFU/mL. The combination of robust carbohydrate ligands with EIS provides a label-free, sensitive, specific, user-friendly, robust, and portable biosensing system that could potentially be used in a point-of-care or continuous environmental monitoring setting

Carbon Nanotube-Loaded Nafion Film Electrochemical Sensor for Metal Ions: Europium

A Nafion film loaded with novel catalyst-free multiwalled carbon nanotubes (MWCNTs) was used to modify a glassy carbon (GC) electrode to detect trace concentrations of metal ions, with europium ion (Eu³⁺) as a model. The interaction between the sidewalls of MWCNTs and the hydrophobic backbone of Nafion allows the MWCNTs to be dispersed in Nafion, which was then coated as a thin film on the GC electrode surface. The electrochemical response to Eu³⁺ was found to be ∼10 times improved by MWCNT concentrations between 0.5 and 2 mg/mL, which effectively expanded the electrode surface into the Nafion film and thereby reduced the diffusion distance of Eu³⁺ to the electrode surface. At low MWCNT concentrations of 0.25 and 0.5 mg/mL, no significant improvement in signal was obtained compared with Nafion alone. Scanning electron microscopy and electrochemical impedance spectroscopy were used to characterize the structure of the MWCNT–Nafion film, followed by electrochemical characterization with Eu³⁺ via cyclic voltammetry and preconcentration voltammetry. Under the optimized conditions, a linear range of 1–100 nM with a calculated detection limit of 0.37 nM (signal/noise = 3) was obtained for determination of Eu³⁺ by Osteryoung square-wave voltammetry after a preconcentration time of 480 s

SAFA interacted with antiviral related RNAs in a time-dependent manner during viral infection.

(A) Scatter diagram showing differential RNA binding profiles of SAFA in THP-1 cells with VSV infection for 6 hours or 24 hours. (B) Pie chart showing the changes of RNAs interacted with SAFA in RIP-seq upon VSV infection (left); pie chart showing the distribution profile of RNAs with increased interaction with SAFA after VSV infection (right). (C) GO term enrichment analysis of RNAs interacted with SAFA in RIP-seq. (D) Heatmap (log RPKM+1) showing RIP-seq signal for the indicated RNAs. (E) Line graph showing time-dependent RNA binding manner of indicated genes with VSV infection for indicated times. The cells were infected by VSV at 0.1 MOI. Data were pooled from two independent experiments (A-D). Data were pooled from three experiments (E).</p

Primers for ATAC-qRT-PCR.

(DOCX)</p

SAFA deficiency decreased the chromatin accessibility of antiviral immune genes.

(A) Models depicting the ATAC-seq and RNA-seq in Wild-type (WT) and SAFA−/− THP-1 cells with VSV infection(upper), and immunoblotting results showing the knockout of SAFA in THP-1 cells (lower). (B) Feature distribution of ATAC-seq profile after VSV infection in WT and SAFA−/− THP-1 cells. (C) Line graph showing SAFA in regulation of VSV induced accessible locus and insensitive locus. (D) Violin graph showing ISGs affected by SAFA depletion in ATAC-seq. (E) Genome browser views of ATAC-seq signal for the indicated genes. (F) WT and SAFA−/− THP-1 cells were infected with VSV infection for indicated times, and ATAC-qPCR showed the chromatin accessibility of indicated genes. (G) GO term enrichment analysis of genes significantly affected by SAFA depletion in RNA-seq. (H) Counting Kit-8 (CCK-8) assay to evaluate the cell viability at indicated time points infected by VSV at 0.1 MOI in both HEK293T cells and THP-1 cells. *p p p p (TIF)</p

RNA product interacted with SAFA mediated specific chromatin remodeling during viral infection.

(A) Models depicting the experiment design of knocking down RNA by CRISPR-Cas13d system and further detecting the chromatin accessibility with ATAC-qPCR after VSV infection. (B) Histogram showing the knockdown efficiency of crRNA of indicated RNAs after VSV infection for 18 hours. (C) ATAC-qPCR results showing the chromatin accessibility of indicated genes after the related RNA knockdown with or without VSV infection for 18 hours. Empty vector (EV) was used as control. *p p p < 0.001 (Student’s t test, B and C). The cells were infected by VSV at 0.1 MOI. Data were pooled from three independent experiments (B and C). Error bars, SEM. n = 3 cultures.</p