The study team 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.
Surprisingly the study findings showed that 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.
Importantly, 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.
Alarmingly the study findings 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.
The study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2021.11.24.21266779v1
Although COVID-19 is primarily a respiratory disease, neurological symptoms are also reported in a subpopulation of infected COVID-19 individuals [1], with substantially higher rates (up to 84%) in severe COVID-19 cases [2].
Complementary studies combining neuroimaging and cognitive screening implicate COVID-19-induced impairment of the frontal cortex [4, 5], a critical area for cognitive function [6, 7]. Furthermore, the effects of COVID-19 on the nervous system, including cognitive impairment, are expected to be long-term [3, 8-10].
In healthy populations, the natural process of aging leads to a reduction in frontal cortex activity [11] and cognitive decline [12]. At the molecular level, aging induces distinct molecular signatures in the human brain, including increased activation of immune signaling and decreased synaptic activity [13-15].
Based on the deteriorating effects of COVID-19 on the frontal cortex and on cognitive function, paralleling the effects of aging, we hypothesized that COVID-19 induces molecular signatures of aging in the frontal cortex.
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 -log10 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.
Discussion
Several studies have been published assessing the transcriptomic changes induced by severe COVID-19 in the human brain [16, 17, 30]. In agreement with our findings, single cell RNA-seq studies of COVID-19 frontal cortex have identified increased immune activities [16, 17] and decreased expression of genes involved in synaptic signaling [16], together with the absence of detectable SARS-CoV-2 expression at the time of death [16, 17].
However, no study has yet demonstrated the striking and profound similarities of transcriptomic profiles between COVID-19 disease and aging in the human brain. We believe this is for two reasons: (1) our patient cohort was rigorously age- and sex-matched, and (2) the effects of COVID-19 on the brain are most substantial among patients younger than 65 years of age, multiple of who are represented in our cohort.
Indeed, a recent RNA-seq study of the frontal cortex of COVID-19 individuals all above 67 years of age identified minimal transcriptomic changes (11 differentially expressed genes) [30]. Of the differentially expressed genes reported, we also observed HBA1, HBA2, and HBB genes upregulated in our older patient cohort subset (>65 years of age). Further mechanistic assessment of the brain aging-like profile observed among COVID-19 patients should thus be focused on younger patient cohorts to capture these substantial transcriptomic effects.
We recognize limitations in our study design: the variability in illness duration, the imperfect quality of several samples (as previously reported in similar studies [16]), the modest number of subjects (12 cases and 12 controls), the lack of young COVID-19 subjects, and the specificity of our findings due to COVID-19.
Despite these constraints, we were sufficiently powered to identify substantial transcriptome-wide changes between COVID-19 cases and controls, including among younger patients in our patient cohort. Furthermore, in addition to being age-matched, our experimental sample size is larger than previously reported COVID-19 brain transcriptome studies [16, 17, 30], enabling the identification of aging-associated gene expression signatures in our samples.
Although our study does not examine the specificity of COVID-19-induced transcriptomic changes in the brain, the implications of our findings may readily extend to related pathologies. For instance, prior clinical trials have shown that cognitive impairment is observed in 55% of survivors of severe acute respiratory syndrome (SARS) 12 months after discharge [31].
Such behavioral observations suggest that similar molecular effects in the brain may be observed not only in severe COVID-19 but also in other conditions characterized by increased peripheral and central inflammation, severe hypoxic insults, and microvascular brain pathologies [1, 32].
Aging is a major risk factor for the development of cognitive deficits and neurodegenerative diseases [12, 33, 34]. Although the molecular changes in the brain upon COVID-19 cannot be readily assessed in recovered individuals, our data herein suggest that severe COVID-19 induces premature aging in the human brain, particularly among younger individuals.
Together with previously reported residual cognitive deficits observed in recovered COVID-19 individuals [3], our results imply that increased long-term rates of cognitive decline and neurodegenerative disorders may be observed among COVID-19 patients as a consequence of long COVID.
In light of this possibility, we advocate for neurological follow-up of recovered COVID-19 patients and suggest potential clinical value in modifying risk factors to reduce the risk or delay the development of aging-related neurological pathologies such as dementia [35].
