Deans' stroke musings: Severe COVID-19 is associated with molecular signatures of aging in the human brain

Changing stroke rehab and research worldwide now.Time is Brain! trillions and trillions of neurons that DIE each day because there are NO effective hyperacute therapies besides tPA(only 12% effective). I have 523 posts on hyperacute therapy, enough for researchers to spend decades proving them out. These are my personal ideas and blog on stroke rehabilitation and stroke research. Do not attempt any of these without checking with your medical provider. Unless you join me in agitating, when you need these therapies they won't be there.

What this blog is for:

My blog is not to help survivors recover, it is to have the 10 million yearly stroke survivors light fires underneath their doctors, stroke hospitals and stroke researchers to get stroke solved. 100% recovery. The stroke medical world is completely failing at that goal, they don't even have it as a goal. Shortly after getting out of the hospital and getting NO information on the process or protocols of stroke rehabilitation and recovery I started searching on the internet and found that no other survivor received useful information. This is an attempt to cover all stroke rehabilitation information that should be readily available to survivors so they can talk with informed knowledge to their medical staff. It lays out what needs to be done to get stroke survivors closer to 100% recovery. It's quite disgusting that this information is not available from every stroke association and doctors group.

Tuesday, December 6, 2022

Severe COVID-19 is associated with molecular signatures of aging in the human brain

Hopefully all the vaccines I got will prevent severe COVID-19. I did get COVID-19 this summer during a trip to Mexico but it must have been the Omicron variety since I barely got sick at all.

Severe COVID-19 is associated with molecular signatures of aging in the human brain

Nature Aging (2022)Cite this article

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Abstract

As coronavirus disease 2019 (COVID-19) and aging are both accompanied by cognitive decline, we hypothesized that COVID-19 might lead to molecular signatures similar to aging. We performed whole-transcriptome analysis of the frontal cortex, a critical area for cognitive function, in individuals with COVID-19, age-matched and sex-matched uninfected controls, and uninfected individuals with intensive care unit/ventilator treatment. Our findings indicate that COVID-19 is associated with molecular signatures of brain aging and emphasize the value of neurological follow-up in recovered individuals.

Main

COVID-19 is an acute respiratory disease often accompanied by neurological sequelae¹. Individuals with previous severe COVID-19 exhibit a 10-year average drop in their global cognitive performance², mimicking accelerated aging. Complementary studies combining neuroimaging and cognitive screening implicate COVID-19-induced impairment of the frontal cortex^3,4, a critical area for cognitive function, but molecular evidence of aging-like effects in the brain is lacking.

To address this, we performed RNA-sequencing (RNA-seq) analysis of 54 postmortem frontal cortex samples, including samples from 21 individuals with severe COVID-19 (previous neurological history was limited to Alzheimer’s disease in one person and epilepsy in another) and 1 asymptomatic individual aged between 23 and 84 years old, 22 age-matched (±2 years) and sex-matched uninfected controls with no history of neurological or psychiatric disorders, an age-matched and sex-matched uninfected individual with Alzheimer’s disease, and an additional independent control group of 9 uninfected individuals with history of intensive care unit (ICU) or ventilator treatment (22–85 years old; ICU/VENT; Fig. 1a and Supplementary Fig. 1a; see Supplementary Table 1 for clinical information; COVID-19 cohort). All COVID-19-cases were determined by positive pre-mortem or peri-mortem testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection via nasopharyngeal swab qPCR and history of hospitalization, whereas uninfected control samples were collected before the COVID-19 pandemic (with three exceptions in the ICU/VENT group that had negative SARS-CoV-2 qPCR tests at the time of death, and no COVID-19 history and/or negative serological test).

**Fig. 1: Severe COVID-19 is associated with transcriptomic signatures of aging in the human brain.**

By clustering analyses, COVID-19 transcriptomic cases broadly segregated away from controls, with two of the outliers being from the 23-year-old asymptomatic individual and the 62-year-old individual with comorbid epilepsy; the age-matched/sex-matched controls proximal to COVID-19 cases were from older adults (Fig. 1b and Supplementary Figs. 1 and 2). Uninfected older adults in the ICU/VENT group generally clustered closer to COVID-19-infected individuals, whereas younger ICU/VENT individuals clustered relatively close to controls; two cases cluster separately from all other samples (Supplementary Fig. 1b). Comparison of COVID-19 cases and their corresponding age-matched and sex-matched controls revealed 6,993 differentially expressed genes (DEGs), 3,330 of which were upregulated and 3,663 downregulated (Fig. 1c and Supplementary Table 2). For example, the S100A8 and S100A9 genes, which encode calprotectin and blood circulating levels of which distinguish severe from mild COVID-19 disease⁵, were upregulated among individuals with COVID-19. Pathway enrichment analysis identified numerous significant GO terms associated with aging in the human brain enriched upon severe COVID-19, including positive enrichment of immune-related pathways and negative enrichment of synaptic activity, cognition and memory pathways (Fig. 1d and Supplementary Fig. 3). We also observed significant associations of cellular response to DNA damage, mitochondrial function, regulation of response to stress and oxidative stress, vesicular transport, calcium homeostasis⁶, and insulin signaling/secretion⁷ pathways previously associated with aging processes and brain aging^6,8. Altogether, our analyses suggest that many biological pathways that change with natural aging in the brain also change in severe COVID-19.

As natural brain aging is associated with cognitive decline, we further assessed associations of transcriptomic changes in COVID-19 and cognitive function. We collated frontal cortex transcriptomic data from 633 individuals who underwent the Mini-Mental State Examination (MMSE) while alive and donated their brains at the time of death as part of the ROSMAP study^9,10. We split individuals and their corresponding transcriptomic data based on the median MMSE score: ≥25 as high cognitive performance versus MMSE < 25 as low cognitive performance. From gene-set enrichment analysis (GSEA), we found strong associations between low cognitive performance and COVID-19 (Fig. 1e).

Given the strong associations between aging-regulated pathways and severe COVID-19, we sought to directly test whether COVID-19 is associated with similar gene expression patterns as natural aging in the human brain. We performed RNA-seq analysis of postmortem frontal cortex samples of 10 young (≤38 years old) and 10 older (≥71 years old) uninfected individuals (Supplementary Table 1; aging cohort and Supplementary Fig. 4a) and compared these findings to COVID-19 DEGs. We found striking similarities between individuals with COVID-19 and aged individuals: genes upregulated in aging were upregulated in severe COVID-19; likewise, genes downregulated in aging were also downregulated in severe COVID-19 (see Fig. 1f for age-matched/sex-matched controls versus COVID-19). As further validation, we collated transcriptome-wide datasets from five independent aging cohorts and confirmed this association (Supplementary Fig. 5 and Supplementary Table 4). Intriguingly, we continued to observe a significant association between aging-associated genes and DEGs from individuals with COVID-19 versus uninfected individuals treated with ICU/VENT (Fig. 1g).

To delineate the effects of severe COVID-19 on brain aging directly, we leveraged our aging cohort to derive an aging index (Supplementary Fig. 4), comprising our aging DEGs and condensed by the first principal component across these transcriptomic data. As validation, we applied our predicted aging index to uninfected controls (COVID-19 cohort) and found similarly strong Pearson correlations between the training and test sets (Fig. 2a,b). Applying this model to individuals with COVID-19, we observed a significant increase in the predicted aging index compared to corresponding uninfected age-matched/sex-matched control and uninfected ICU/VENT control groups (Fig. 2c). Additional analysis revealed that the predicted aging index in individuals with COVID-19 was not significantly affected by the presence or absence of cerebrovascular disease (P > 0.05). Thus, severe COVID-19 appears to shift the molecular age of brains relative to both uninfected age-matched and sex-matched controls as well as uninfected ICU/VENT controls. Lastly, using qPCR analysis, we validated several of the top shared DEGs between our COVID-19 cohort and aging datasets (n = 22 per group; Supplementary Fig. 6).

**Fig. 2: Severe COVID-19 and cytokine treatment of neurons are associated with increases in predicted age.**

Finally, we sought to determine pathophysiologic mechanisms that may explain the association of COVID-19 with aging. We considered that this could be due to multiple factors, including SARS-CoV-2 viral infection in the frontal cortex or COVID-19-induced systemic inflammation. In agreement with previous studies^11,12, SARS-CoV-2 viral RNA was not detected in samples from individuals with COVID-19 (at the time of death; Supplementary Fig. 7), suggesting that the observed gene expression changes are unlikely due to direct effects of the viral RNA in the frontal cortex. On the other hand, our transcriptomic pathway analyses identified upregulation of tumor necrosis factor (TNF) and type I/II interferon response pathways in the frontal cortex of individuals with COVID-19 (Fig. 2d). Indeed, interferons and TNF have been implicated in brain aging and aging-induced cognitive decline^6,13,14,15. Among individuals with COVID-19 with available peripheral cytokine data, we indeed observed increased TNF levels (3.5–24.2 pg ml⁻¹ at 0–2 d before death in three individuals; values > 2.8 pg ml⁻¹ are considered elevated; data were not available for the rest of the individuals). In line with our findings, a mouse model of SARS-CoV-2 infection exhibited elevation of pro-inflammatory cytokines in cerebrospinal fluid, including interferon gamma (IFN-γ) and TNF, in the absence of viral neuroinvasion¹⁶. To test whether TNF and type I/II interferons can modulate the expression of aging-regulated genes, we performed a transcriptomic analysis (RNA-seq) on human primary neurons treated with different doses of TNF, interferon beta (IFN-β) or IFN-γ. Interestingly, TNF and to a lesser extent IFN-γ and IFN-β increased the predicted aging index of cytokine-treated neurons, suggestive of the induction of an aging-like effect (Fig. 2e,f). We also found that cytokines upregulated the expression of aging-regulated genes that were upregulated in individuals with COVID-19 such as TRIM22, CHI3L1, C1S and IFITM1 and downregulated the expression of aging-regulated genes that were downregulated in individuals with COVID-19 such as CCND2, ACTR3B and EPHA5 (Supplementary Fig. 8). Taken together, our data suggest that COVID-19-induced TNF and type I/II interferons may lead to significant deteriorating effects in the brain in the absence of SARS-CoV-2 neuroinvasion.

Aging is a major risk factor for the development of cognitive deficits. Our results, together with previously reported residual cognitive deficits reported in recovered cases², imply that aging-associated and cognitive decline-associated gene expression changes observed in individuals with COVID-19 may lead to increased rates of cognitive decline. Furthermore, we provide evidence that these aging-regulated gene expression changes may be mediated in part by circulating TNF and type I/II interferons, suggesting that acute management of severe COVID-19-induced inflammation may be neuroprotective. We recognize limitations in our study including: the variability in illness duration, the imperfect quality of several samples and the specificity of our findings due to COVID-19. Despite these constraints, our study was sufficiently powered to identify substantial transcriptome-wide changes in individuals with COVID-19. In addition to being larger than previously reported COVID-19 brain transcriptome studies^11,12,17, our COVID-19 cases were matched by age and sex to uninfected controls, enabling the identification of aging-associated gene expression signatures in our samples. Furthermore, we included ICU/VENT uninfected samples as an additional independent control group to distinguish COVID-19 from other comorbidities requiring ICU monitoring and/or ventilation. The generalizability of our results to individuals who had mild COVID-19 or who recovered from COVID-19 remains to be determined. Given our findings, we advocate for neurological follow-up of individuals who recovered from COVID-19 and suggest potential clinical value in modifying risk factors to reduce the risk or delay the development of aging-related neurological pathologies and cognitive decline¹⁸.