Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts, 2023, Guarnieri et al.

SNT Gatchaman · Aug 10, 2023

Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts
Joseph W. Guarnieri; Joseph M. Dybas; Hossein Fazelinia; Man S. Kim; Justin Frere; Yuanchao Zhang; Yentli Soto Albrecht; Deborah G. Murdock; Alessia Angelin; Larry N. Singh; Scott L. Weiss; Sonja M. Best; Marie T. Lott; Shiping Zhang; Henry Cope; Victoria Zaksas; Amanda Saravia-Butler; Cem Meydan; Jonathan Foox; Christopher Mozsary; Yaron Bram; Yared Kidane; Waldemar Priebe; Mark R. Emmett; Robert Meller; Sam Demharter; Valdemar Stentoft-Hansen; Marco Salvatore; Diego Galeano; Francisco J. Enguita; Peter Grabham; Nidia S. Trovao; Urminder Singh; Jeffrey Haltom; Mark T. Heise; Nathaniel J. Moorman; Victoria K. Baxter; Emily A. Madden; Sharon A. Taft-Benz; Elizabeth J. Anderson; Wes A. Sanders; Rebekah J. Dickmander; Stephen B. Baylin; Eve Syrkin Wurtele; Pedro M. Moraes-Vieira; Deanne Taylor; Christopher E. Mason; Jonathan C. Schisler; Robert E. Schwartz; Afshin Beheshti; Douglas C. Wallace

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis.

We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)–encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated.

During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs.

These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.

Link | PDF (Science Translational Medicine, paywalled)

Hoopoe · Aug 10, 2023

Next thing they're going to say that the dysregulation persists in long covid because of something in the blood that just doesn't go away.

John Mac · Aug 10, 2023

Stat article on the study:
Study mapping how SARS-CoV-2 disrupts mitochondria suggests a cause for long Covid

https://www.statnews.com/2023/08/09/long-covid-mitochondria-sars-cov-2/

SNT Gatchaman · Aug 10, 2023

Hoopoe said: ↑

Next thing they're going to say that the dysregulation persists in long covid because of something in the blood that just doesn't go away.
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It is unclear why the removal of the virus did not reverse the OXPHOS inhibition in the viscera, but the continued inhibition of mitochondrial gene expression in the hearts, kidneys, and livers likely contributed to lethality in these COVID-19 cases. For individuals in whom visceral nDNA mitochondrial gene transcription was partially reactivated and who survived severe COVID-19, the sustained partial inhibition of OXPHOS potentially could be a contributor to long COVID, with chronic inhibition of mitochondrial bioenergetics contributing to the chronic malaise associated with COVID-19.
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The irreversible inhibition of visceral mitochondrial transcription could also contribute to the multisystem symptoms of long COVID.
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In the murine part of their study —

Unexpectedly, however, mitochondrial gene expression was down-regulated in the cerebella and strongly induced in the striata of the hamster brains. The absence of viral effects on lung mitochondrial gene expression where viral RNA was high compared with robust changes in mitochondrial gene expression in the brain where viral RNA was absent raised the possibility that modulation of energy metabolism in distant tissues might be because of ISR activation producing diffusible factors such as GDF15, which could potentially modulate mitochondrial function in tissues far from the initial site of infection.
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We have a tag for GDF15.

SNT Gatchaman · Aug 12, 2023

This paper is not open-access but here are some of the available references from the introduction —

A comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular overdrive for SARS-CoV-2 infection (2022, Nature European Journal of Human Genetics, open access)

SARS-CoV-2 infection enhances mitochondrial PTP complex activity to perturb cardiac energetics (2021, iScience, open access)

Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring toward glycolysis (2021, iScience, open access)

Role of miR-2392 in driving SARS-CoV-2 infection (2021, Cell Reports, open access, thread)

Mitochondria and microbiota dysfunction in COVID-19 pathogenesis (2020, Mitochondrion, open access)

Circulating levels of GDF-15 and calprotectin for prediction of in-hospital mortality in COVID-19 patients: A case series (2020, Journal of Infection, open access)

Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis (2020, American Journal of Physiology-Cell Physiology, open access)

ER and Nutrient Stress Promote Assembly of Respiratory Chain Supercomplexes through the PERK-eIF2α Axis (2019, Molecular Cell, open access)

eIF2B activator prevents neurological defects caused by a chronic integrated stress response (2019, eLife, open access)

New mitochondrial DNA synthesis enables NLRP3 inflammasome activation (2018, Nature, Cached)

The small molecule ISRIB rescues the stability and activity of Vanishing White Matter Disease eIF2B mutant complexes (2018, eLife, open access)

Mitochondrial DNA in innate immune responses and inflammatory pathology (2017, Nature Reviews Immunology, Cached)

Mitonuclear protein imbalance as a conserved longevity mechanism (2013, Nature, Cached)

Kalliope · Aug 12, 2023

The study is briefly discussed in today's TWiV Clinical update with Dr. Daniel Griffin and Prof. Vincent Racaniello wonders if this finding may be relevant for other viruses too.

The discussion of the paper begins at 25:49

https://www.youtube.com/watch?v=ZEsP6j3B6Iw

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Kalliope · Aug 13, 2023

Simon Décary on Twitter:
If I understand this paper right, this may be one of the most important piece of data to date to demonstrate how SARS-CoV-2 inhibits mitochondrial homeostasis, which could explain the pathophysiology of post-exertional malaise.

https://twitter.com/user/status/1690812430580846592

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Kalliope · Aug 13, 2023

Eric Topol Long Covid: Mitochondria, the Big Miss, and Hope

quote:

This week there was news on Long Covid in two very different directions—emergence of strong data to support mitochondrial dysfunction as the basis for the condition in some people—and learning how the $1.15 billion allocation to the NIH RECOVER initiative has largely been wasted. In this edition of Ground Truths, I’ll review this news and offer a plan to get clinical trials testing treatments into high gear.

Sick Mitochondria as a Root Cause

When we published our review of Long Covid earlier this year, we highlighted the key established underpinnings as shown in the Figure below. As you’ll note, mitochondria was not one of them. There was a body of data emerging to support the role of mitochondria, as we asserted: ”Long COVID research has found mitochondrial dysfunction including loss of mitochondrial membrane potential and possible dysfunctional mitochondrial metabolism, altered fatty acid metabolism…” and that this had also been seen in myalgic encephalomyelitis(ME/CFS).

A new paper In Science Translational Medicine by leaders in mitochondria biology has advanced the case for direct interactions between SARS-CoV-2 and critical mitochondrial proteins for the potential basis of Long Covid—at least in some people.

SNT Gatchaman · Aug 13, 2023

Selected quotes from Introduction —

Whereas COVID-19 is primarily considered an inflammatory disease, recent evidence suggests that SARS-CoV-2 inhibits mitochondrial function, consistent with a central role for mitochondria in cellular metabolism and innate immune regulation. SARS-CoV-2 infection markedly alters mitochondrial morphology, with matrix condensation and swollen cristae. This is associated with decreased oxidative phosphorylation (OXPHOS) polypeptides, decreased mitochondrial inner membrane protein import systems, and increased production of mitochondrial reactive oxygen species (mROS).
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The mitochondrion generates energy by OXPHOS, which encompasses about 160 polypeptides, most dispersed across the chromosomes, but with 13 critical polypeptides encoded by the maternally inherited mitochondrial DNA (mtDNA). These mtDNA polypeptides are translated on mitochondrial ribosomes using mtDNA-encoded ribosomal RNAs (rRNAs) and the tRNAs that punctuate the polypeptide genes. Nuclear DNA (nDNA) encodes more than one thousand mitochondrial genes whose proteins are synthesized on cytosolic ribosomes and imported into the mitochondrion through the translocase of the outer mitochondrial membrane (TOMM) and inner mitochondrial membrane (TIMM) import complexes.
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OXPHOS encompasses four electron transport chain enzyme complexes (I, II, III, and IV) plus the ATP synthase (complex V). Complexes I, III, IV, and V are assembled from both nDNA- and mtDNA-encoded proteins, and all of the multi-subunit OXPHOS complexes are assembled via intermediate-stage subassembly modules
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SARS-CoV-2 viral polypeptides bind to multiple host polypeptides, up to 16% of which are mitochondrial proteins
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For example, the SARS-CoV-2 M protein interacts with the mitochondrial leucyl-tRNA (TARS2) and asparaginyl-tRNA (NARS2) synthases and the coenzyme Q (CoQ) synthesis protein COQ8B.
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In human blood cells, SARS-CoV-2 infection is associated with down-regulation of mtDNA transcripts, mitochondrial function, and increased glycolysis
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treatment with the ROS scavengers N-acetyl cysteine (NAC) and MitoQ reduced HIF-1α, glycolytic proteins, pro-inflammatory cytokine mRNAs, and viral load. The mammalian target of rapamycin complex 1 (mTORC1) stimulated nutrient uptake favoring glycolytic metabolism by activating c-Myc, stabilizing HIF-1α, and impairing mitochondrial biogenesis
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Impairment of mitochondrial protein synthesis can result in an imbalance in the ratio of nDNA- and mtDNA-coded mitochondrial proteins, which can activate the mitochondrial (UPR-MT) and the cytosolic (UPR-CT) unfolded protein responses, which will, in turn, trigger the integrated stress response (ISR).
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Activation of ATP4/5 induces GADD34, CHOP, and the mitokines fibroblast growth factor 21 (FGF21) and growth and differentiation factor 15 (GDF15), as well as inducing OXPHOS supercomplex assembly factor SCAF1. SARS-CoV2 infection activates the ISR and is associated with elevated FGF21 and GDF15.
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SNT Gatchaman · Aug 13, 2023

Selected quotes from Results —

Changes in OXPHOS gene transcription in COVID-19 human nasopharyngeal samples

To determine the mechanism by which SARS-CoV-2 inhibited each of the OXPHOS complexes, we examined the mRNAs of individual mitochondrial and bioenergetic polypeptide genes. This revealed that SARS-CoV-2 infection suppressed the expression of groups of human genes associated with specific OXPHOS subassembly modules. This contrasted with the up-regulation of host mitochondrial genes not inhibited by the virus that frequently included either structural or assembly genes of subassembly modules not blocked by infection
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This suggested that groups of subassembly module structural and assembly gene mRNAs may be coordinately regulated and that these coordinately regulated genes could be modulated by SARS-CoV-2
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Changes in OXPHOS gene transcription in COVID-19 human autopsy samples

OXPHOS mRNAs were down-regulated in the COVID-19 autopsy samples of the heart, liver, kidney, and lymph nodes, with the heart exhibiting the most coordinated down-regulation of OXPHOS gene expression.
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confirmed that virtually all OXPHOS mRNAs of the heart were shut down. This was not simply the product of terminal destruction of heart cells because mtDNA transcripts and the COX assembly gene mRNAs, COX16, COX19, and COX20, were up-regulated and PET100 and SCO2 were normally expressed
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This shared transcriptional profile suggests the possibility that transcriptional regulatory elements coordinately regulate groups of OXPHOS genes.
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Thus, nDNA-coded OXPHOS gene transcripts were down-regulated in autopsy tissues with heart > > kidney = liver > lymph node, but, in autopsy lung samples, OXPHOS genes were strongly induced. In the nasopharyngeal samples, the high-titer virus samples experienced strong OXPHOS gene inhibition, but this inhibition was lifted in the lung autopsy tissue as the virus was cleared. In contrast, in the human autopsy heart, kidney, liver, and lymph nodes, OXPHOS gene suppression continued even though the virus had been eliminated
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SNT Gatchaman · Aug 13, 2023

Selected quotes from Results (cont'd) —

SARS-CoV-2 modulation of mitochondrial and glycolytic pathways in human nasopharyngeal and autopsy samples

We next focused on transcriptional changes in processes that complement mitochondrial OXPHOS, including mitochondrial ATP/ADP-Pi exchange, tricarboxylic acid (TCA) cycle, CoQ biosynthesis, mitochondrial fatty acid synthesis (mtFASII), fatty acid oxidation, and the cytosolic protein import system
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At the individual gene level, key mitochondrial inner membrane solute carrier genes were down-regulated in the heart, including the phosphate carrier (SLC25A3), the adenine nucleotide translocases (SLC25A4 and SLC25A6), the citrate carrier (SLC25A1), and the Ca++ -binding aspartate-glutamate carrier (SLC25A12), which are critical for mitochondrial energy production and ATP export.
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In contrast, the ATP-Mg++/Pi transporters (SLC25A24 and SLC25A25), which import ATP into the mitochondria without energetic benefit, were up-regulated in human heart autopsy samples
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Thus, as the virus inhibited mitochondrial energetics, host cells attempted to compensate by importing ATP.
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Expression analysis of genes associated with cytosolic bioenergetic pathways revealed that glycolysis and fatty acid synthesis transcripts were significantly down-regulated in hearts and kidneys, and fatty acid synthesis was down-regulated in livers.
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Among cardiac glycolytic genes in the human heart autopsy tissue, there was a normal expression of lactate dehydrogenase A (LDHA), which converts pyruvate to lactate and favors glycolysis, but a downregulation of lactate dehydrogenase B (LDHB), which converts lactate to pyruvate and favors OXPHOS, a pattern also reported in peripheral blood.
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SARS-CoV-2 modulation of HIF-1α, mTOR, and ISR pathways in human nasopharyngeal and autopsy samples

HIF-1α target genes, glycolysis genes, mTOR signaling genes, and genes of the ISR were up-regulated.
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Activation of HIF-1α not only up-regulates glycolysis but also optimizes complex IV for low oxygen tension conditions by down-regulating COX4i1
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SARS-CoV-2 infection created an imbalance between cytosolic and mitochondrial ribosomal gene expression, which could lead to the activation of the mitochondrial (UPR-MT) and cytosolic (UPR-CT) unfolded protein responses. This activation would inhibit OXPHOS and increase mROS production
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SNT Gatchaman · Aug 13, 2023

Selected quotes from Results (cont'd) —

miR-2392 induced by SARS-CoV-2 regulates mitochondrial mRNA function in human nasopharyngeal and autopsy samples

SARS-CoV-2 infection is associated with an increase in miR-2392, with the seed sequence of the induced miRNA matching the host miRNA sequence.
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miR-2392 has been reported to enter the mitochondrion and bind to ACO2, and this complex then binds to the mtDNA tRNA-Gln gene (MT-TQ)
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Analysis of miR-2392 seed sites among the about 1000 known nDNA mitochondrial genes revealed that 362 mitochondrial mRNAs harbored miR-2392 binding sites
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Two nDNA mitochondrial mRNAs harbored four miR-2392 binding sites: the complex I and IV assembly factor genes, COA1, and the fatty acid activation acyl-CoA thioesterase gene, ACOT11.
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Furthermore, genes encoding OXPHOS complexes I to V, mitochondrial biogenesis, mitochondrial fusion, mitophagy, and antioxidant proteins had one or two miR-2392 sites, including the mitochondrial antiviral protein mRNA MAVS. Some of the same OXPHOS transcripts that were up-regulated in response to SARS-CoV-2 infection harbored miR-2392 seed sites.
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Metabolic flux in host cells in response to SARS-CoV-2 infection

we used alterations in host mRNAs to estimate the flux rates of metabolites through bioenergetics pathways in human nasopharyngeal samples and autopsy tissues [...] analysis confirmed that the functions of the mitochondrial bioenergetics pathways and antioxidant defense pathways were suppressed
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SNT Gatchaman · Aug 13, 2023

Selected quotes from Discussion —

Unexpectedly, however, mitochondrial gene expression was down-regulated in the cerebella and strongly induced in the striata of the hamster brains. The absence of viral effects on lung mitochondrial gene expression where viral RNA was high compared with robust changes in mitochondrial gene expression in the brain where viral RNA was absent raised the possibility that modulation of energy metabolism in distant tissues might be because of ISR activation producing diffusible factors such as GDF15, which could potentially modulate mitochondrial function in tissues far from the initial site of infection.
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The host cells compensated for the viral inhibition of host mitochondrial function caused by viral protein binding to mitochondrial proteins, by up-regulating mitochondrial biogenesis. To sustain OXPHOS inhibition and glycolysis stimulation, the virus next inhibited host mitochondrial gene transcription. Thus, in the human nasopharyngeal samples with high and medium viral loads, we observed marked down-regulation of the mitochondrial transcripts of specific clusters of structural or assembly genes required for the biogenesis of individual OXPHOS complex subassembly modules. The virus only needs to block the synthesis of one or more subassembly modules to inactivate the entire OXPHOS complex. The host attempts to compensate by up-regulating mitochondrial gene transcription, but only those structural and assembly genes not specifically blocked by the virus can be induced.
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SARS-CoV-2 maintained OXPHOS inhibition and glycolytic induction by inhibition of mitochondrial protein functions, selective disruption of OXPHOS module transcription, miRNA-mediated inhibition of mtDNA transcription, and miRNA-mediated inhibition of nDNA mitochondria mRNA translation.
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The host innate immune response becomes fully activated upon induction of the ISR and CMPK2-mediated mtDNA activation of the inflammasome. Impaired mitochondrial protein synthesis creates an imbalance in nDNA and mtDNA proteins, activating UPR-MT and UPR-CT , which activate the ISR. The ISR shuts down cytosolic protein synthesis, activates mitochondrial single-carbon metabolism, and elaborates mitokine production including GDF15. SARS-CoV-2 viroporins E and Orf3a permit the influx of Ca ++ into host cells, which is taken up by the mitochondrion to activate the TCA cycle. This generates excess NADH, which overloads the electron transport chain increasing mROS production.
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It is unclear why the removal of the virus did not reverse the OXPHOS inhibition in the viscera, but the continued inhibition of mitochondrial gene expression in the hearts, kidneys, and livers likely contributed to lethality in these COVID-19 cases. For individuals in whom visceral nDNA mitochondrial gene transcription was partially reactivated and who survived severe COVID-19, the sustained partial inhibition of OXPHOS potentially could be a contributor to long COVID, with chronic inhibition of mitochondrial bioenergetics contributing to the chronic malaise associated with COVID-19. ISR activation and Cmpk2-mediated inflammasome activation could contribute to systemic inflammatory symptoms and perhaps cytokine storm. The irreversible inhibition of visceral mitochondrial transcription could also contribute to the multisystem symptoms of long COVID.
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Hoopoe · Aug 14, 2023

@DMissa any comment please?

mariovitali · Oct 11, 2023

I think this part needs to be repeated :

Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
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Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts, 2023, Guarnieri et al.

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