Severe COVID-19 induces molecular signatures of aging in the human brain

Abstract

Coronavirus disease 2019 (COVID-19) is predominantly an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and remains a significant threat to public health. COVID-19 is accompanied by neurological symptoms and cognitive decline, but the molecular mechanisms underlying this effect remain unclear. As aging induces distinct molecular signatures in the brain associated with cognitive decline in healthy populations, we hypothesized that COVID-19 may induce molecular signatures of aging. Here, we performed whole transcriptomic analysis of human frontal cortex, a critical area for cognitive function, in 12 COVID-19 cases and age- and sex-matched uninfected controls. COVID-19 induces profound changes in gene expression, despite the absence of detectable virus in brain tissue. Pathway analysis shows downregulation of genes involved in synaptic function and cognition and upregulation of genes involved in immune processes. Comparison with five independent transcriptomic datasets of aging human frontal cortex reveals striking similarities between aged individuals and severe COVID-19 patients. Critically, individuals below 65 years of age exhibit profound transcriptomic changes not observed among older individuals in our patient cohort. Our data indicate that severe COVID-19 induces molecular signatures of aging in the human brain and emphasize the value of neurological follow-up in recovered individuals.

Fig 1.. Severe COVID-19 induces global transcriptomic changes in the frontal cortex of the brain.

a. Left, age and sex of each individual in COVID-19 or control groups (n=12/group) analyzed in this cohort. Each COVID-19 case was matched with an uninfected control case by sex and age (±2 years). Right, schematic of study approach. Schematic was generated with BioRender. b. t-distributed stochastic neighbor embedding (TSNE) analysis of frontal cortex transcriptomes from COVID-19 cases and uninfected controls. c. qPCR assessment of SARS-CoV-2 viral RNA in the frontal cortex using the nCOV_N1 primer set. PS1 and PS2 correspond to the 2019-nCoV_N_Positive Control RUO Plasmid (IDT) at concentrations of 1,000 and 2,000 copies/μl, respectively (a technical duplicate/concentration was used to estimate the corresponding mean; for control and COVID-19 samples n=13/group). d. Volcano plot representing the differentially expressed genes (DEGs) of the frontal cortex of COVID-19 cases versus matched controls. Red points, significantly upregulated genes among COVID-19 cases (false discovery rate < 0.05). Blue points, significantly downregulated genes among COVID-19 cases. Black points, highlighted significant genes with corresponding gene symbols. e. Gene ontology (GO) biological pathway enrichment analysis of COVID-19 versus control brain DEGs. Gene ranks were determined by signed −log 10 false discovery rates of DEGs. FDR, gene set enrichment analysis false discovery rate. f. Heatmap of relative gene expression levels of significant DEGs associated with the “cognition” (GO: 0050890) GO term across COVID-19 and control samples. Color legend, scaled gene expression levels across subjects, normalized via variance-stabilized transformation.

Fig 2.. Severe COVID-19 induces transcriptomic signatures of aging in the human brain.

a. COVID-19-associated DEGs were assessed for enrichment of brain aging DEGs curated from each of five independent patient cohort studies (Lu et al., 2004, n=21 [14]; Loerch et al., 2008, n=28 [21]; Gibbs cohort, n=37 [38, 42]; ROSMAP cohort, n=117 [–43]. Common Mind Consortium/CMC cohort, n=155 [39, 42]; n refers to the number of individuals analyzed in each cohort). Schematic was generated with BioRender. b and c. Gene set enrichment analysis of COVID-19 DEGs, using significantly up- (top) or down-regulated genes (bottom) in the Lu et al. (2004) (b) and Loerch et al. (2008) (c) cohorts as gene sets. DEG ranks were assigned by signed −log10 false discovery rates from COVID-19 versus control frontal cortex. NES, normalized enrichment score, p, GSEA p-value. See also Supplementary Fig. 5. d. qPCR assessment of candidate COVID-19 DEGs associated with aging (n=13/group). *p<0.05; **p<0.01; ***p<0.001. Data are expressed as fold change relative to control ± SEM. e and f. Volcano plots representing the DEGs of the frontal cortex of COVID-19 cases versus controls among patients < 65 (e, n=7/group) or > 65 (f, n=5/group) years of age. Red points, significantly upregulated genes among COVID-19 cases (false discovery rate < 0.05). Blue points, significantly downregulated genes among COVID-19 cases. Black points, significant genes with corresponding gene symbols. g and h. Gene set enrichment analysis of COVID-19 DEGs among individuals ≤ 65 years of age, using significantly up- (left) or down-regulated genes (right) in the Lu et al. (2004) (g) and Loerch et al. (2008) (h) cohorts as gene sets. DEG ranks were assigned by signed −log 10 FDR values from COVID-19 versus control brains among individuals ≤ 65 years of age. NES, normalized enrichment score. p, GSEA p-value. See also Supplementary Fig. 7.