COVID-19 patients and Dementia: Frontal cortex transcriptomic data

Abstract

Since the association of SARS-Cov-2 infection with Nervous System (NS) manifestations, we performed RNA-sequencing analysis in Frontal Cortex of COVID-19 positive or negative individuals and affected or not by Dementia individuals. We examined gene expression differences in individuals with COVID-19 and Dementia compared to Dementia only patients by collecting transcript counts in each sample and performing Differential Expression analysis. We found eleven genes satisfying our significance criteria, all of them being protein coding genes. These data are suitable for integration with supplemental samples and for analysis according to different individuals' classification. Also, differential expression evaluation may be implemented with other scientific purposes, such as research of unannotated genes, mRNA splicing and genes isoforms. The analysis of Differential Expressed genes in COVID-19 positive patients compared to non-COVID-19 patients is published in: S. Gagliardi, E.T. Poloni, C. Pandini, M. Garofalo, F. Dragoni, V. Medici, A. Davin, S.D. Visonà, M. Moretti, D. Sproviero, O. Pansarasa, A. Guaita, M. Ceroni, L. Tronconi, C. Cereda, Detection of SARS-CoV-2 genome and whole transcriptome sequencing in frontal cortex of COVID-19 patients., Brain. Behav. Immun. (2021). https://doi.org/10.1016/j.bbi.2021.05.012.

Keywords: Brain; Gene expression; SARS-CoV-2; Transcriptomics.

Fig. 1

Coding and non-coding RNA counts after deep sequencing, demultiplexing and alignment.

Fig. 2

Heatmap of top 11 Differentially Expressed (DE) genes. Samples from COVID-19 positive individuals with Dementia (n = 7) are marked in light blue, while patients with Dementia (n = 6) are marked in pink. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article).

Fig. 3

Volcano plots obtained from DE analysis of patients with Dementia who died with COVID-19 (n = 7) versus patients with Dementia only (n = 6). The most upregulated genes are towards the right, the most downregulated genes are towards the left, and the most statistically significant genes are towards the top. Red dots represent significant up- and down-regulated genes which have |log2(fold change)|≥ 1 and a p-value ≤ 0.1. Blue, green and grey dots represent non-significant DE detected genes, because they do not satisfy both requirements. The top 4 DE genes are labelled (Ensembl ID). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article).

Fig. 4

Quality assessment of FASTQ sequences data for paired end and right reads. Each plot shows the mean quality value across each base position in the read for all the analyzed samples.

Fig. 5

Panel A shows Principal component analysis result on the whole dataset. Panel B shows an estimate of the dispersion parameter for each gene. In Panel C, the heatmap of the sample-to-sample distance is shown. It was obtained with DeSeq2 package on regularized-logarithm transformed counts. Color code is reported above the heatmap.