Data from: SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages
Data files
Jul 08, 2026 version files 2.39 MB
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Dryad_Submission_Files.zip
2.35 MB
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README.md
38.77 KB
Abstract
Nearly 20% of SARS-CoV-2 infections result in ICU admission, often driven by an imbalance between antiviral responses and inflammatory signaling, leading to uncontrolled cytokine secretion. The SARS-CoV-2 nucleocapsid (N) protein is a known immune antagonist, but its role in macrophage-driven cytokine storms is unclear. We demonstrate that N functions in a stimulus-specific manner, specifically amplifying extracellular and dampening intracellular RNA sensing. Moreover, we show that this is a conserved feature of pathogenic betacoronaviruses through distinct mechanisms. Our interaction networks with SARS-CoV-2 variant N proteins suggest the Delta variant N drives inflammation through interactions with several proteins, most notably cGAS. Profiling of secreted cytokines revealed that the N proteins disrupt the secretome in a variant-specific manner. Most notably, we found that supernatants from the Delta variant N-expressing macrophages dramatically disrupt heart endothelial barriers, implicating N in COVID-19-associated cardiac complications. Our findings highlight N-mediated immune imbalance as a driver of severe COVID-19 and identify N as a promising therapeutic target to mitigate hyperinflammation.
Transcriptomic and functional datasets of SARS-CoV-2 nucleocapsid–mediated modulation of innate immune responses in human macrophage-like cells
Description
This dataset contains processed data supporting the findings of the manuscript: SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages
All data are organized by figure and panel as presented in the manuscript. Each file corresponds to a specific dataset used to generate a figure or supplementary figure.
File Organization
All data can be downloaded from Dryad_Submission_Files.zip
Data are organized into folders by figure:
- Figure 1/ – Data corresponding to Figure 1
- Figure 2/ – Data corresponding to Figure 2
- Figure 3/ – Data corresponding to Figure 3
- Figure 4/ – Data corresponding to Figure 4
- Figure 5/ – Data corresponding to Figure 5
- Figure 6/ – Data corresponding to Figure 6
- Supplementary Figures/ – Data corresponding to supplementary figures
Each file is named according to the format:
FigX_Panel_Assay_Condition_Analyte.csv
Examples:
- Fig1_A_qPCR_WA1_IRT.csv
- Fig3_A_RNAseq_TLR78stim_TFprediction.csv
- Fig6_C_cytokines_Nexpression_log2FCdampened.csv
Data Types
The dataset includes:
- Processed data – Normalized, transformed, or statistically analyzed data used for figure generation
File Descriptions
Fig1_A_qPCR_WA1_IRT.csv
Description: Relative expression levels of inflammation-related transcripts (IRT) during infection with SARS-CoV-2 WA1.
Columns:
- ...1 – Gene symbol of the transcripts analyzed
- Parental, ...3, ...4 – Fold change of the indicated transcripts in parental THP-1 macrophage-like cells
- CD169, ...6, ...7 – Fold change of the indicated transcripts in parental THP-1 macrophage-like cells expressing CD169
- CD169+ACE2, ...9, ...10 – Fold change of the indicated transcripts in parental THP-1 macrophage-like cells expressing CD169 and ACE2
Fig1_B_qPCR_VLP_TNF.csv
Description: Relative expression levels of TNF during incubation with VLPs and CL097.
Columns:
- ...1 – Indication of the cell line used
- CL097, ...3, ...4 – Fold change of TNF expression in the indicated cells during CL097 stimulation
- CD169, ...6, ...7 – Fold change of TNF expression in the indicated cells during CL097 stimulation and VLP incubation
Fig1_C_qPCR_VLP_IFNB1.csv
Description: Relative expression levels of IFNB1 during incubation with VLPs and CL097.
Columns:
- ...1 – Indication of the cell line used
- CL097, ...3, ...4 – Fold change of IFNB1 expression in the indicated cells during CL097 stimulation
- CD169, ...6, ...7 – Fold change of IFNB1 expression in the indicated cells during CL097 stimulation and VLP incubation
Fig1_D_qPCR_VLP_CCL4.csv
Description: Relative expression levels of CCL4 during incubation with VLPs and CL097.
Columns:
- ...1 – Indication of the cell line used
- CL097, ...3, ...4 – Fold change of CCL4 expression in the indicated cells during CL097 stimulation
- CD169, ...6, ...7 – Fold change of CCL4 expression in the indicated cells during CL097 stimulation and VLP incubation
Fig1_E_qPCR_VLP_CXCL10.csv
Description: Relative expression levels of CXCL10 during incubation with VLPs and CL097.
Columns:
- ...1 – Indication of the cell line used
- CL097, ...3, ...4 – Fold change of CXCL10 expression in the indicated cells during CL097 stimulation
- CD169, ...6, ...7 – Fold change of CXCL10 expression in the indicated cells during CL097 stimulation and VLP incubation
Fig1_F_qPCR_VLP_CXCL8.csv
Description: Relative expression levels of CXCL8 during incubation with VLPs and CL097.
Columns:
- ...1 – Indication of the cell line used
- CL097, ...3, ...4 – Fold change of CXCL8 expression in the indicated cells during CL097 stimulation
- CD169, ...6, ...7 – Fold change of CXCL8 expression in the indicated cells during CL097 stimulation and VLP incubation
Fig1_G_qPCR_Nexpression_IRT.csv
Description: Relative expression levels of inflammation-related transcripts (IRT) during expression of with SARS-CoV-2 Wuhan-Hu-1 nucleocapsid.
Columns:
- ...1 – Gene symbol of the transcripts analyzed
- Parental, ...3, ...4 – Fold change of the indicated transcripts in parental THP-1 macrophage-like cells
- Wuhan-Hu-1 N-expression, ...6, ...7 – Fold change of the indicated transcripts in THP-1 macrophage-like cells expressing N
Fig2_A_RNAseq_RLRstim_NDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to N-expressing cells and also shared between N-expressing cells and parental cells during RLR stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_A_RNAseq_RLRstim_parentalDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to parental cells during RLR stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_A_RNAseq_TLR3stim_NDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to N-expressing cells and also shared between N-expressing cells and parental cells during TLR3 stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_A_RNAseq_TLR3stim_parentalDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to parental cells during TLR3 stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_A_RNAseq_TLR78stim_NDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to N-expressing cells and also shared between N-expressing cells and parental cells during TLR7/8 stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_A_RNAseq_TLR78stim_parentalDEGs.csv
Description: Differentially expressed genes (DEGs) that are unique to parental cells during TLR7/8 stimulation.
Columns:
- genes – Gene symbols corresponding to each transcript analyzed
- logFC – Log2 fold change in gene expression between the specified experimental condition and control (e.g., treated vs untreated parental THP-1 macrophage-like cells)
- logCPM – Log2 counts per million (CPM), representing normalized gene expression levels across samples
- F – Moderated F-statistic from differential expression analysis, indicating overall significance of expression differences across conditions
- FDR – False discovery rate–adjusted p-value for differential expression (multiple testing corrected)
Fig2_B_RNAseq_RLRstim_log2FCshift.csv
Description: Shift in expression levels during N expression during RLR stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
- WT.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- WT.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- log.delFC - Difference in log2 fold change between N-expressing and WT cells (Δlog2FC = N.logFC − WT.logFC)
- delFC - Difference in linear fold change between N-expressing and WT cells
Fig2_B_RNAseq_TLR3stim_log2FCshift.csv
Description: Shift in expression levels during N expression during TLR3 stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
- WT.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- WT.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- log.delFC - Difference in log2 fold change between N-expressing and WT cells (Δlog2FC = N.logFC − WT.logFC)
- delFC - Difference in linear fold change between N-expressing and WT cells
Fig2_B_RNAseq_TLR78stim_log2FCshift.csv
Description: Shift in expression levels during N expression during TLR7/8 stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
- WT.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- WT.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- log.delFC - Difference in log2 fold change between N-expressing and WT cells (Δlog2FC = N.logFC − WT.logFC)
- delFC - Difference in linear fold change between N-expressing and WT cells
Fig2_C_RNAseq_RLRstim_GOTerms.csv
Description: Biological process gene ontology (GO) terms for the downshifted DEGs during RLR stimulation.
Columns:
- Category - Gene Ontology (GO) category from which the term is derived (e.g., biological process, molecular function, cellular component)
- Term - GO identifier and descriptive name of the enriched biological term
- Count - Number of genes from the input list associated with the given GO term
- % - Percentage of genes in the input list that are associated with the given GO term
- PValue - Raw p-value indicating the statistical significance of enrichment for the GO term
- Genes - List of input genes that are associated with the given GO term
- List Total - Total number of genes in the input gene list used for enrichment analysis
- Pop Hits - Number of genes in the background population associated with the given GO term
- Pop Total - Total number of genes in the background population
- Fold Enrichment - Degree of enrichment calculated as the ratio of observed gene count to expected gene count for the GO term
- Bonferroni - Bonferroni-corrected p-value for multiple hypothesis testing
- Benjamini - Benjamini-Hochberg adjusted p-value controlling for false discovery rate
- FDR - False discovery rate–adjusted p-value indicating significance after multiple testing correction
Fig2_C_RNAseq_TLR3stim_GOTerms.csv
Description: Biological process gene ontology (GO) terms for the up shifted DEGs during TLR3 stimulation.
Columns:
- Category - Gene Ontology (GO) category from which the term is derived (e.g., biological process, molecular function, cellular component)
- Term - GO identifier and descriptive name of the enriched biological term
- Count - Number of genes from the input list associated with the given GO term
- % - Percentage of genes in the input list that are associated with the given GO term
- PValue - Raw p-value indicating the statistical significance of enrichment for the GO term
- Genes - List of input genes that are associated with the given GO term
- List Total - Total number of genes in the input gene list used for enrichment analysis
- Pop Hits - Number of genes in the background population associated with the given GO term
- Pop Total - Total number of genes in the background population
- Fold Enrichment - Degree of enrichment calculated as the ratio of observed gene count to expected gene count for the GO term
- Bonferroni - Bonferroni-corrected p-value for multiple hypothesis testing
- Benjamini - Benjamini-Hochberg adjusted p-value controlling for false discovery rate
- FDR - False discovery rate–adjusted p-value indicating significance after multiple testing correction
Fig2_C_RNAseq_TLR78stim_GOTerms.csv
Description: Biological process gene ontology (GO) terms for the up shifted DEGs during TLR7/8 stimulation.
Columns:
- Category - Gene Ontology (GO) category from which the term is derived (e.g., biological process, molecular function, cellular component)
- Term - GO identifier and descriptive name of the enriched biological term
- Count - Number of genes from the input list associated with the given GO term
- % - Percentage of genes in the input list that are associated with the given GO term
- PValue - Raw p-value indicating the statistical significance of enrichment for the GO term
- Genes - List of input genes that are associated with the given GO term
- List Total - Total number of genes in the input gene list used for enrichment analysis
- Pop Hits - Number of genes in the background population associated with the given GO term
- Pop Total - Total number of genes in the background population
- Fold Enrichment - Degree of enrichment calculated as the ratio of observed gene count to expected gene count for the GO term
- Bonferroni - Bonferroni-corrected p-value for multiple hypothesis testing
- Benjamini - Benjamini-Hochberg adjusted p-value controlling for false discovery rate
- FDR - False discovery rate–adjusted p-value indicating significance after multiple testing correction
Fig3_A_RNAseq_TLR78stim_TFprediction.csv
Description: Transcription factor prediction of N-shifted DEGs during TLR7/8 stimulation.
Columns:
- Term - Transcription factor and species from the TRRUST database associated with the enriched regulatory network
- Overlap - Number of genes from the input list that overlap with known target genes of the transcription factor, shown as (overlap count / total target genes)
- P-value - Raw p-value indicating the statistical significance of enrichment for the transcription factor’s target genes in the input list
- Adjusted P-value - Multiple testing–corrected p-value (e.g., Benjamini-Hochberg) for transcription factor enrichment
- Old P-value - Raw p-value from a previous or alternative version of the enrichment calculation
- Old Adjusted P-value - Multiple testing–corrected p-value corresponding to the old p-value calculation
- Odds Ratio - Measure of association indicating how strongly the transcription factor’s target genes are enriched in the input list compared to the background
- Combined Score - Composite score integrating the p-value and deviation from expected rank, used to prioritize transcription factor enrichment results
- Genes - List of input genes that overlap with known target genes of the transcription factor
Fig3_B_RNAseq_TLR3stim_TFprediction.csv
Description: Transcription factor prediction of N-shifted DEGs during TLR3 stimulation.
Columns:
- Term - Transcription factor and species from the TRRUST database associated with the enriched regulatory network
- Overlap - Number of genes from the input list that overlap with known target genes of the transcription factor, shown as (overlap count / total target genes)
- P-value - Raw p-value indicating the statistical significance of enrichment for the transcription factor’s target genes in the input list
- Adjusted P-value - Multiple testing–corrected p-value (e.g., Benjamini-Hochberg) for transcription factor enrichment
- Old P-value - Raw p-value from a previous or alternative version of the enrichment calculation
- Old Adjusted P-value - Multiple testing–corrected p-value corresponding to the old p-value calculation
- Odds Ratio - Measure of association indicating how strongly the transcription factor’s target genes are enriched in the input list compared to the background
- Combined Score - Composite score integrating the p-value and deviation from expected rank, used to prioritize transcription factor enrichment results
- Genes - List of input genes that overlap with known target genes of the transcription factor
Fig3_C_RNAseq_TLR78stim_TFtargetlog2FC.csv
Description: Expression levels of predicted transcription factor targets during TLR7/8 stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- wt.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- wt.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
Fig3_D_RNAseq_TLR3stim_TFtargetlog2FC.csv
Description: Expression levels of predicted transcription factor targets during TLR3 stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- wt.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- wt.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
Fig3_E_RNAseq_RLRstim_TFtargetlog2FC.csv
Description: Expression levels of predicted transcription factor targets during RLR stimulation.
Columns:
- genes - Gene symbols corresponding to each transcript analyzed
- wt.logFC - Log2 fold change in gene expression after stimulation in parental (wild-type) cells relative to their unstimulated control
- wt.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in parental (wild-type) cells
- N.logFC - Log2 fold change in gene expression after stimulation in N-expressing cells relative to their unstimulated control
- N.FDR - False discovery rate (FDR)–adjusted p-value for differential expression after stimulation in N-expressing cells
Fig4_A_qPCR_Variants_Ntranscript.csv
Description: Expression levels of nucleocapsid transcripts in CD169+ACE2 THP-1 macrophage-like cells infected with SARS-CoV-2 variants.
Columns:
- ...1 - Column was used just to indicate that the values were pertaining to N expression levels
- mock - CD169+ACE2 cells treated with inoculumn only, no virus.
- WA1 - CD169+ACE2 cells infected with the SARS-CoV-2 USA-WA1/2020 strain.
- Delta - CD169+ACE2 cells infected with the SARS-CoV-2 Delta variant.
- Omicron BA.1 - CD169+ACE2 cells infected with the SARS-CoV-2 Omicron BA.1 variant.
- Omicron BA.4 - CD169+ACE2 cells infected with the SARS-CoV-2 Omicron BA.4 variant.
- Omicron BA.5 - CD169+ACE2 cells infected with the SARS-CoV-2 Omicron BA.5 variant.
Fig4_B_qPCR_Variants_IRT.csv
Description: Relative expression levels of inflammation-related transcripts (IRT) during infection with SARS-CoV-2 variants.
Columns:
- ...1 - Gene symbols corresponding to each transcript analyzed
- WA-1, ...3, ...4, ...5 - Expression values for WA-1–infected cells across replicates
- Delta, ...7, ...8, ...9 - Expression values for Delta-infected cells across replicates
- Omicron BA.1, ...11, ...12, ...13 - Expression values for Omicron BA.1–infected cells across replicates
- Omicron BA.4, ...15, ...16, ...17 - Expression values for Omicron BA.4–infected cells across replicates
- Omicron BA.5, ...19, ...20, ...21 - Expression values for Omicron BA.5–infected cells across replicates
Fig4_C_qPCR_Nexpression_TNF.csv
Description: Relative expression levels of TNF during TLR7/8 stimulation in THP-1 macrophage-like cells expressing different betacoronavirus nucleocapsids.
Columns:
- ...1 - Treatment conditions
- Parental, ...3, ...4, ...5 - Expression values for parental (control) cells not expressing any viral protein across replicates
- Wuhan, ...7, ...8, ...9 - Expression values for cells expressing SARS-CoV-2 Wuhan-Hu-1 nucleocapsid (N) protein across replicates
- Delta, ...11, ...12, ...13 - Expression values for cells expressing SARS-CoV-2 Delta variant nucleocapsid (N) protein across replicates
- Omicron BA.1, ...15, ...16, ...17 - Expression values for cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
- SARS1, ...19, ...20, ...21 - Expression values for cells expressing SARS-CoV-1 nucleocapsid (N) protein across replicates
- MERS, ...23, ...24, ...25 - Expression values for cells expressing MERS-CoV nucleocapsid (N) protein across replicates
Fig4_D_qPCR_Nexpression_CCL4.csv
Description: Relative expression levels of CCL4 during TLR7/8 stimulation in THP-1 macrophage-like cells expressing different betacoronavirus nucleocapsids.
Columns:
- ...1 - Treatment conditions
- Parental, ...3, ...4, ...5 - Expression values for parental (control) cells not expressing any viral protein across replicates
- Wuhan, ...7, ...8, ...9 - Expression values for cells expressing SARS-CoV-2 Wuhan-Hu-1 nucleocapsid (N) protein across replicates
- Delta, ...11, ...12, ...13 - Expression values for cells expressing SARS-CoV-2 Delta variant nucleocapsid (N) protein across replicates
- Omicron BA.1, ...15, ...16, ...17 - Expression values for cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
- SARS1, ...19, ...20, ...21 - Expression values for cells expressing SARS-CoV-1 nucleocapsid (N) protein across replicates
- MERS, ...23, ...24, ...25 - Expression values for cells expressing MERS-CoV nucleocapsid (N) protein across replicates
Fig4_E_qPCR_Nexpression_CXCL10.csv
Description: Relative expression levels of CXCL10 during TLR7/8 stimulation in THP-1 macrophage-like cells expressing different betacoronavirus nucleocapsids.
Columns:
- ...1 - Treatment conditions
- Parental, ...3, ...4, ...5 - Expression values for parental (control) cells not expressing any viral protein across replicates
- Wuhan, ...7, ...8, ...9 - Expression values for cells expressing SARS-CoV-2 Wuhan-Hu-1 nucleocapsid (N) protein across replicates
- Delta, ...11, ...12, ...13 - Expression values for cells expressing SARS-CoV-2 Delta variant nucleocapsid (N) protein across replicates
- Omicron BA.1, ...15, ...16, ...17 - Expression values for cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
- SARS1, ...19, ...20, ...21 - Expression values for cells expressing SARS-CoV-1 nucleocapsid (N) protein across replicates
- MERS, ...23, ...24, ...25 - Expression values for cells expressing MERS-CoV nucleocapsid (N) protein across replicates
Fig5_C_Proteomics_DeltavsOmicron_GOTerms.csv
Description: Gene Ontology (GO) analysis of nucleocapsid (N) interaction partners.
Columns:
- Category - Gene Ontology (GO) category from which the term is derived (e.g., biological process, molecular function, cellular component) based on proteomics-identified proteins
- Term - GO identifier and descriptive name of the enriched biological term associated with the identified proteins
- Count - Number of proteins from the input dataset associated with the given GO term
- % - Percentage of proteins in the input dataset that are associated with the given GO term
- PValue - Raw p-value indicating the statistical significance of enrichment for the GO term
- Genes - List of proteins (gene symbols) from the dataset associated with the given GO term
- List Total - Total number of proteins in the input dataset used for enrichment analysis
- Pop Hits - Number of proteins in the background population associated with the given GO term
- Pop Total - Total number of proteins in the background population
- Fold Enrichment - Degree of enrichment calculated as the ratio of observed protein count to expected protein count for the GO term
- Bonferroni - Bonferroni-corrected p-value for multiple hypothesis testing
- Benjamini - Benjamini-Hochberg adjusted p-value controlling for false discovery rate
- FDR - False discovery rate–adjusted p-value indicating significance after multiple testing correction
Fig5_E_qPCR_cGASi_TNF.csv
Description: Relative expression levels of TNF during TLR7/8 stimulation with and without the presence of a cGAS inhibitor (G140) in THP-1 macrophage-like cells expressing different either Delta or Omicron BA.1 nucleocapsids.
Columns:
- ...1 - Indication of whether or not cGAS inhibitor is present
- THP-1, ...3, ...4, ...5, ...6, ...7, ...8, ...9 - Relative expression values for parental THP-1 macrophage-like cells (control condition) across replicates
- Delta, ...11, ...12, ...13, ...14, ...15, ...16, ...17 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Delta nucleocapsid (N) protein across replicates
- Omicron BA.1, ...19, ...20, ...21, ...22, ...23, ...24, ...25 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
Fig5_F_qPCR_cGASi_CCL4.csv
Description: Relative expression levels of CCL4 during TLR7/8 stimulation with and without the presence of a cGAS inhibitor (G140) in THP-1 macrophage-like cells expressing different either Delta or Omicron BA.1 nucleocapsids.
Columns:
- ...1 - Indication of whether or not cGAS inhibitor is present
- THP-1, ...3, ...4, ...5, ...6, ...7, ...8, ...9 - Relative expression values for parental THP-1 macrophage-like cells (control condition) across replicates
- Delta, ...11, ...12, ...13, ...14, ...15, ...16, ...17 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Delta nucleocapsid (N) protein across replicates
- Omicron BA.1, ...19, ...20, ...21, ...22, ...23, ...24, ...25 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
Fig5_G_qPCR_cGASi_CXCL10.csv
Description: Relative expression levels of CXCL10 during TLR7/8 stimulation with and without the presence of a cGAS inhibitor (G140) in THP-1 macrophage-like cells expressing different either Delta or Omicron BA.1 nucleocapsids.
Columns:
- ...1 - Indication of whether or not cGAS inhibitor is present
- THP-1, ...3, ...4, ...5, ...6, ...7, ...8, ...9 - Relative expression values for parental THP-1 macrophage-like cells (control condition) across replicates
- Delta, ...11, ...12, ...13, ...14, ...15, ...16, ...17 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Delta nucleocapsid (N) protein across replicates
- Omicron BA.1, ...19, ...20, ...21, ...22, ...23, ...24, ...25 - Relative expression values for THP-1 macrophage-like cells expressing SARS-CoV-2 Omicron BA.1 nucleocapsid (N) protein across replicates
Fig6_B_cytokines_Nexpression_log2FCstimulated.csv
Description: Log2 fold changes of cytokines in TLR7/8 stimulated compared to unstimulated cells across parental and N-expressing cell lines (specifically, cytokines that are significantly stimulated in parental cells).
Columns:
- Parental - THP-1 macrophage-like cells not expressing any viral proteins. Values are log2FC of cytokines that were found to be significantly upregulated in this cell line during TLR7/8 stimulation.
- Wuhan - THP-1 macrophage-like cells expressing the Wuhan-Hu-1 N protein. Values are log2FC of cytokines that were found to be significantly upregulated in the parental cell line during TLR7/8 stimulation.
- Delta - THP-1 macrophage-like cells expressing the Delta variant N protein. Values are log2FC of cytokines that were found to be significantly upregulated in the parental cell line during TLR7/8 stimulation.
- Omicron BA.1 - THP-1 macrophage-like cells expressing the Omicron BA.1 variant N protein. Values are log2FC of cytokines that were found to be significantly upregulated in the parental cell line during TLR7/8 stimulation.
Fig6_C_cytokines_Nexpression_log2FCdampened.csv
Description: Log2 fold changes of cytokines in TLR7/8 stimulated compared to unstimulated cells across parental and N-expressing cell lines (specifically, cytokines that are significantly dampened in parental cells).
Columns:
- Parental - THP-1 macrophage-like cells not expressing any viral proteins. Values are log2FC of cytokines that were found to be significantly downregulated in this cell line during TLR7/8 stimulation.
- Wuhan - THP-1 macrophage-like cells expressing the Wuhan-Hu-1 N protein. Values are log2FC of cytokines that were found to be significantly downregulated in the parental cell line during TLR7/8 stimulation.
- Delta - THP-1 macrophage-like cells expressing the Delta variant N protein. Values are log2FC of cytokines that were found to be significantly downregulated in the parental cell line during TLR7/8 stimulation.
- Omicron BA.1 - THP-1 macrophage-like cells expressing the Omicron BA.1 variant N protein. Values are log2FC of cytokines that were found to be significantly downregulated in the parental cell line during TLR7/8 stimulation.
Fig6_E_TEER_HCAEC_FC.csv
Description: These are values were calculated by first taking TEER measurements of human cardiac aortic endothelial cells (HCAECs) that were treated with conditioned medias at hour 0 and hour 24. Those values were divided by each other to obtain the initial fold change (iFC). Then the iFC was compared between relative conditions, such as HCAECs treated with unstimulated macrophage media compared to HCAECs treated with stimulated macrophage media, which gave rise to the final fold change (FC).
Columns:
- TNFa Treated - These values are the FCs of the iFCs of TNFa treated HCAECs relative to completely untreated HCAECs.
- Parental - These values are the FCs of the iFCs of HCAECs treated with medias from unstimulated and TLR7/8 stimulated parental THP-1 macrophage-like cells.
- Wuhan - These values are the FCs of the iFCs of HCAECs treated with medias from unstimulated and TLR7/8 stimulated THP-1 macrophage-like cells expressing the Wuhan-Hu-1 N protein.
- Delta - These values are the FCs of the iFCs of HCAECs treated with medias from unstimulated and TLR7/8 stimulated THP-1 macrophage-like cells expressing the Delta variant N protein.
Fig6_F_TEER_BMEC_FC.csv
Description: These are values were calculated by first taking TEER measurements of human pluripotent stem cell-derived brain microvascular endothelial cells (BMECs) that were treated with conditioned medias at hour 0 and hour 24. Those values were divided by each other to obtain the initial fold change (iFC). Then the iFC was compared between relative conditions, such as BMECs treated with unstimulated macrophage media compared to BMECs treated with stimulated macrophage media, which gave rise to the final fold change (FC).
Columns:
- TNFa Treated - These values are the FCs of the iFCs of TNFa treated BMECs relative to completely untreated BMECs.
- Parental - These values are the FCs of the iFCs of BMECs treated with medias from unstimulated and TLR7/8 stimulated parental THP-1 macrophage-like cells.
- Wuhan - These values are the FCs of the iFCs of BMECs treated with medias from unstimulated and TLR7/8 stimulated THP-1 macrophage-like cells expressing the Wuhan-Hu-1 N protein.
- Delta - These values are the FCs of the iFCs of BMECs treated with medias from unstimulated and TLR7/8 stimulated THP-1 macrophage-like cells expressing the Delta variant N protein.
FigS2_B_RNAseq_GOTerms_RLRNupshifted.csv
Description: Biological process gene ontology (GO) terms for the up-shifted DEGs during RLR stimulation.
Columns:
- Category - Gene Ontology (GO) category from which the term is derived (e.g., biological process, molecular function, cellular component)
- Term - GO identifier and descriptive name of the enriched biological term
- Count - Number of genes from the input list associated with the given GO term
- % - Percentage of genes in the input list that are associated with the given GO term
- PValue - Raw p-value indicating the statistical significance of enrichment for the GO term
- Genes - List of input genes that are associated with the given GO term
- List Total - Total number of genes in the input gene list used for enrichment analysis
- Pop Hits - Number of genes in the background population associated with the given GO term
- Pop Total - Total number of genes in the background population
- Fold Enrichment - Degree of enrichment calculated as the ratio of observed gene count to expected gene count for the GO term
- Bonferroni - Bonferroni-corrected p-value for multiple hypothesis testing
- Benjamini - Benjamini-Hochberg adjusted p-value controlling for false discovery rate
- FDR - False discovery rate–adjusted p-value indicating significance after multiple testing correction
FigS3_A_qPCR_VariantsinMDM_Ntranscript.csv
Description: Expression levels of nucleocapsid transcripts in primary human monocyte-derived macrophages (MDMs) infected with SARS-CoV-2 variants.
Columns:
- ...1 - Indicates which donor cells were used for infection
- Omicron BA.1, ...3, ...4 - primary MDMs infected with the SARS-CoV-2 Omicron BA.1 variant.
- WA1, ...6, ...7 - primary MDMs infected with the SARS-CoV-2 USA-WA1/2020 strain.
- Delta, ...9, ...10 - primary MDMs infected with the SARS-CoV-2 Delta variant.
FigS3_B_qPCR_VariantsinMDM_IRT_donor1.csv
Description: Relative expression levels of inflammation-related transcripts (IRT) during infection with SARS-CoV-2 variants in MDMs from donor 1.
Columns:
- ...1 - Gene symbols corresponding to each transcript analyzed
- WA-1, ...3, ...4, - Expression values for WA-1–infected cells across replicates
- Delta, ...6, ...7 - Expression values for Delta-infected cells across replicates
- Omicron BA.1, ...9, ...10 - Expression values for Omicron BA.1–infected cells across replicates
FigS3_C_qPCR_VariantsinMDM_IRT_donor2.csv
Description: Relative expression levels of inflammation-related transcripts (IRT) during infection with SARS-CoV-2 variants in MDMs from donor 2.
Columns:
- ...1 - Gene symbols corresponding to each transcript analyzed
- WA-1, ...3, ...4, - Expression values for WA-1–infected cells across replicates
- Delta, ...6, ...7 - Expression values for Delta-infected cells across replicates
- Omicron BA.1, ...9, ...10 - Expression values for Omicron BA.1–infected cells across replicates
Methods Summary
Brief description of how data were generated and processed:
- RNA-seq reads were quantified using Salmon (v1.10.2)
- Differential expression analysis was performed using edgeR (v4.9.5)
- Transcription factor prediction was performed by submitting select DEGs to Erichr to search for the most relevant regulatory transcription factors in the TRRUST database
- qPCR data were analyzed using the ΔΔCt method
- Cytokine data were log2-transformed and normalized to untreated controls
Software and Dependencies
- R (2024.12.1+563)
- edgeR (v4.9.5)
- Salmon (v1.10.2)
- GraphPad Prism (v10.4.1)
Data Availability
Raw sequencing data have been deposited in:
- GEO: GSE327545
- PRIDE: PXD067631
This Dryad repository contains processed datasets and additional data used to generate figures.
Notes
- File names correspond directly to figure panels in the manuscript
- IRT - Inflammation-related transcripts
- CL097 - this is a molecule used to stimulate TLR7/8
- pIC - shorthand for poly I:C, a molecule to used to stimulate TLR3 or RLRs
- TLR - acronym for toll-like receptor
- RLR - acronym for RIG-I-like receptor
- SARS-CoV-2 - severe acute respiratory syndrome coronavirus 2
- qPCR - quantitative polymerase chain reaction
- GO - gene ontology
- BP - biological process
Contact Information
For questions regarding this dataset, please contact:
Pablo A. Alvarez
paalalva@g.ucla.edu