Analysis workflow of publicly available RNA-sequencing datasets

Sanchis, Pablo; Lavignolle, Rosario; Abbate, Mercedes; Lage-Vickers, Sofía; Vázquez, Elba S.; Cotignola, Javier; Bizzotto, Juan; Gueron, Geraldine

doi:10.1016/j.xpro.2021.100478

Cited by 10 publications

(12 citation statements)

References 11 publications

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“…During our analyses we included two more recently published COVID-19 datasets, two transcriptome studies from inflammatory diseases and one dataset with cohorts of other respiratory infectious diseases to compare with specific transcriptome signatures resulting from our first analysis. After evaluating the study design, number of samples, and other relevant information (e.g., COVID-19 severity), we obtained raw count files (non-normalized) after trimming and alignment to the reference genome and followed guidelines to perform a meta-analysis report [ 38 ], which recommended that we include at least three or four studies to reach a minimum of 1000 participants [ 39 ] in order to increase the statistical power of our analysis by increasing the signal-to-noise ratio. This resulted in a cohort of 1596 individuals derived from 11 datasets with transcriptome data generated from different platforms ( Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

Schimke

Marques

Baiocchi

et al. 2022

Cells

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Severe COVID-19 patients present a clinical and laboratory overlap with other hyperinflammatory conditions such as hemophagocytic lymphohistiocytosis (HLH). However, the underlying mechanisms of these conditions remain to be explored. Here, we investigated the transcriptome of 1596 individuals, including patients with COVID-19 in comparison to healthy controls, other acute inflammatory states (HLH, multisystem inflammatory syndrome in children [MIS-C], Kawasaki disease [KD]), and different respiratory infections (seasonal coronavirus, influenza, bacterial pneumonia). We observed that COVID-19 and HLH share immunological pathways (cytokine/chemokine signaling and neutrophil-mediated immune responses), including gene signatures that stratify COVID-19 patients admitted to the intensive care unit (ICU) and COVID-19_nonICU patients. Of note, among the common differentially expressed genes (DEG), there is a cluster of neutrophil-associated genes that reflects a generalized hyperinflammatory state since it is also dysregulated in patients with KD and bacterial pneumonia. These genes are dysregulated at the protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins that point to neutrophil hyperactivation in COVID-19 patients admitted to the intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.

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Section: Methodsmentioning

confidence: 99%

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

Schimke

Marques

Baiocchi

et al. 2022

Cells

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“…Normalization, batch effect correction, and differential expression were performed with R package DEseq2 v1.28.1 [13]. Age was categorized according to the WHO guidelines [14]: <30 years old, every 10 years between 30 and 70 years old, and ≥70 years old as described [15]. To stratify COVID-19 positive patients based on viral load at the time of diagnosis, we used the PCR cycle threshold (Ct) of the N1 viral gene amplification as a surrogate variable for viral load (Ct > 24 = low; Ct = 24-19 = medium; Ct < 19 = high).…”

Section: Analysis Of Publicly Available Rna-seq Datasetsmentioning

confidence: 99%

Effect of Ivermectin and Atorvastatin on Nuclear Localization of Importin Alpha and Drug Target Expression Profiling in Host Cells from Nasopharyngeal Swabs of SARS-CoV-2- Positive Patients

Segatori

Garona

Caligiuri

et al. 2021

Viruses

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Nuclear transport and vesicle trafficking are key cellular functions involved in the pathogenesis of RNA viruses. Among other pleiotropic effects on virus-infected host cells, ivermectin (IVM) inhibits nuclear transport mechanisms mediated by importins and atorvastatin (ATV) affects actin cytoskeleton-dependent trafficking controlled by Rho GTPases signaling. In this work, we first analyzed the response to infection in nasopharyngeal swabs from SARS-CoV-2-positive and -negative patients by assessing the gene expression of the respective host cell drug targets importins and Rho GTPases. COVID-19 patients showed alterations in KPNA3, KPNA5, KPNA7, KPNB1, RHOA, and CDC42 expression compared with non-COVID-19 patients. An in vitro model of infection with Poly(I:C), a synthetic analog of viral double-stranded RNA, triggered NF-κB activation, an effect that was halted by IVM and ATV treatment. Importin and Rho GTPases gene expression was also impaired by these drugs. Furthermore, through confocal microscopy, we analyzed the effects of IVM and ATV on nuclear to cytoplasmic importin α distribution, alone or in combination. Results showed a significant inhibition of importin α nuclear accumulation under IVM and ATV treatments. These findings confirm transcriptional alterations in importins and Rho GTPases upon SARS-CoV-2 infection and point to IVM and ATV as valid drugs to impair nuclear localization of importin α when used at clinically-relevant concentrations.

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“…During our analysis we included two more recently published COVID-19 datasets, two transcriptome studies from inflammatory diseases and one dataset with cohorts of other respiratory infectious diseases to compare with specific transcriptome signatures resulting from our first analysis. After evaluating study design, number of samples, and other relevant information (e.g., COVID-19 severity), we obtained raw count files (non-normalized) after trimming and alignment to the reference genome and followed guidelines to perform a meta-analysis report [38], which recomended to include at least three or four studies to reach a minimum of 1000 participants [39] in order to increase the statistical power of our analysis by increasing the signal-to-noise ratio. This resulted in a cohort of 1596 individuals derived from 11 datasets with transcriptome data generated from different platforms ( Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

Severe COVID-19 shares a common neutrophil activation signature with other acute inflammatory states

Schimke

Marques

Baiocchi

et al. 2021

Preprint

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Clinical and hyperinflammatory overlap between COVID-19 and hemophagocytic lymphohistiocytosis (HLH) has been reported. However, the underlying mechanisms are unclear. Here we show that COVID-19 and HLH have an overlap of signaling pathways and gene signatures commonly dysregulated, which were defined by investigating the transcriptomes of 1253 subjects (controls, COVID-19, and HLH patients) using microarray, bulk RNA-sequencing (RNAseq), and single-cell RNAseq (scRNAseq). COVID-19 and HLH share pathways involved in cytokine and chemokine signaling as well as neutrophil-mediated immune responses that associate with COVID-19 severity. These genes are dysregulated at protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins which converge to neutrophil hyperactivation in COVID-19 patients admitted to intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.

show abstract

Analysis workflow of publicly available RNA-sequencing datasets

Cited by 10 publications

References 11 publications

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

Effect of Ivermectin and Atorvastatin on Nuclear Localization of Importin Alpha and Drug Target Expression Profiling in Host Cells from Nasopharyngeal Swabs of SARS-CoV-2- Positive Patients

Severe COVID-19 shares a common neutrophil activation signature with other acute inflammatory states

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