Circulating mitochondrial DNA is an early indicator of severe illness and mortality from COVID-19

Authors: Davide Scozzi,1Marlene Cano,2Lina Ma,2Dequan Zhou,1Ji Hong Zhu,1Jane A. O’Halloran,3Charles Goss,4Adriana M. Rauseo,3Zhiyi Liu,1Sanjaya K. Sahu,2Valentina Peritore,5Monica Rocco,6Alberto Ricci,7Rachele Amodeo,8Laura Aimati,8Mohsen Ibrahim,1,5Ramsey Hachem,2Daniel Kreisel,1Philip A. Mudd,9Hrishikesh S. Kulkarni,2,10 and Andrew E. Gelman1,11

Abstract

Background

Mitochondrial DNA (MT-DNA) are intrinsically inflammatory nucleic acids released by damaged solid organs. Whether circulating cell-free MT-DNA quantitation could be used to predict the risk of poor COVID-19 outcomes remains undetermined.

Methods

We measured circulating MT-DNA levels in prospectively collected, cell-free plasma samples from 97 subjects with COVID-19 at hospital presentation. Our primary outcome was mortality. Intensive care unit (ICU) admission, intubation, vasopressor, and renal replacement therapy requirements were secondary outcomes. Multivariate regression analysis determined whether MT-DNA levels were independent of other reported COVID-19 risk factors. Receiver operating characteristic and area under the curve assessments were used to compare MT-DNA levels with established and emerging inflammatory markers of COVID-19.

Results

Circulating MT-DNA levels were highly elevated in patients who eventually died or required ICU admission, intubation, vasopressor use, or renal replacement therapy. Multivariate regression revealed that high circulating MT-DNA was an independent risk factor for these outcomes after adjusting for age, sex, and comorbidities. We also found that circulating MT-DNA levels had a similar or superior area under the curve when compared against clinically established measures of inflammation and emerging markers currently of interest as investigational targets for COVID-19 therapy.

Conclusion

These results show that high circulating MT-DNA levels are a potential early indicator for poor COVID-19 outcomes.

For More Information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934921/

UniProtKB – P59636 (ORF9B_SARS)

Protein: ORF9b protein database

Gene: 9b

Organism Severe acute respiratory syndrome coronavirus (SARS-CoV) Status Reviewed-Annotation score:-Experimental evidence at protein leveli

Functioni

Plays a role in the inhibition of host innate immune response by targeting the mitochondrial-associated adapter MAVS. Mechanistically, usurps the E3 ligase ITCH to trigger the degradation of MAVS, TRAF3, and TRAF6. In addition, causes mitochondrial elongation by triggering ubiquitination and proteasomal degradation of dynamin-like protein 1/DNM1L.1 Publication

Miscellaneous

The gene encoding this protein is included within the N gene (alternative ORF).

GO – Molecular functioni

GO – Biological processi

Keywordsi

Biological processHost-virus interactionInhibition of host innate immune response by virusInhibition of host MAVS by virusInhibition of host RLR pathway by virusViral immunoevasion

For In-depth Information of ORF-9b Protein: https://www.uniprot.org/uniprot/P59636

SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the AVS/TRAF3/TRAF6 signalosome

.J Immunol 2014 Sep 15;193(6):3080-9. doi: 10.4049/jimmunol.1303196. Epub 2014 Aug 18.

Chong-Shan Shi 1Hai-Yan Qi 2Cedric Boularan 1Ning-Na Huang 1Mones Abu-Asab 3James H Shelhamer 2John H Kehrl 4

Abstract

Coronaviruses (CoV) have recently emerged as potentially serious pathogens that can cause significant human morbidity and death. The severe acute respiratory syndrome (SARS)-CoV was identified as the etiologic agent of the 2002-2003 international SARS outbreak. Yet, how SARS evades innate immune responses to cause human disease remains poorly understood. In this study, we show that a protein encoded by SARS-CoV designated as open reading frame-9b (ORF-9b) localizes to mitochondria and causes mitochondrial elongation by triggering ubiquitination and proteasomal degradation of dynamin-like protein 1, a host protein involved in mitochondrial fission. Also, acting on mitochondria, ORF-9b targets the mitochondrial-associated adaptor molecule MAVS signalosome by usurping PCBP2 and the HECT domain E3 ligase AIP4 to trigger the degradation of MAVS, TRAF3, and TRAF 6. This severely limits host cell IFN responses. Reducing either PCBP2 or AIP4 expression substantially reversed the ORF-9b-mediated reduction of MAVS and the suppression of antiviral transcriptional responses. Finally, transient ORF-9b expression led to a strong induction of autophagy in cells. The induction of autophagy depended upon ATG5, a critical autophagy regulator, but the inhibition of MAVS signaling did not. These results indicate that SARS-CoV ORF-9b manipulates host cell mitochondria and mitochondrial function to help evade host innate immunity. This study has uncovered an important clue to the pathogenesis of SARS-CoV infection and illustrates the havoc that a small ORF can cause in cells.

For More Information: https://pubmed.ncbi.nlm.nih.gov/25135833/

Inflammasome activation at the crux of severe COVID-19

Authors: Setu M. Vora,1,2Judy Lieberman,2,3 and Hao Wu1,2

Abstract

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), results in life-threatening disease in a minority of patients, especially elderly people and those with co-morbidities such as obesity and diabetes. Severe disease is characterized by dysregulated cytokine release, pneumonia and acute lung injury, which can rapidly progress to acute respiratory distress syndrome, disseminated intravascular coagulation, multisystem failure and death. However, a mechanistic understanding of COVID-19 progression remains unclear. Here we review evidence that SARS-CoV-2 directly or indirectly activates inflammasomes, which are large multiprotein assemblies that are broadly responsive to pathogen-associated and stress-associated cellular insults, leading to secretion of the pleiotropic IL-1 family cytokines (IL-1β and IL-18), and pyroptosis, an inflammatory form of cell death. We further discuss potential mechanisms of inflammasome activation and clinical efforts currently under way to suppress inflammation to prevent or ameliorate severe COVID-19.

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has so far infected more than 190 million people and caused death of more than 4.1 million people worldwide. The virus primarily infects the respiratory tract, causing fever, sore throat, anosmia and dyspnoea, but its tissue tropism still remains to be fully understood. As many as 10–15% of patients develop severe pneumonia, with some cases progressing to hypoxia and acute respiratory distress syndrome (ARDS), which requires mechanical ventilation in a critical care setting and has high mortality. Patients can also develop multi-organ failure, acute kidney injury and disseminated intravascular coagulation, among a host of other disorders111. Aside from supportive care, only a few treatments have been approved for COVID-19, and their reduction of mortality has been limited1214. Although several vaccines against SARS-CoV-2 have been approved and are being administered internationally, there will still be a significant number of infections owing to people who are not vaccinated in regions with inadequate access or acceptance of vaccination. In addition, while global vaccination efforts strive to meet the challenge of ending the pandemic, the appearance of immune-evasive viral variants and the unlikelihood of reaching immediate herd immunity underscore the continued need for additional treatments mitigating disease progression1519.

Most researchers agree that an inappropriate hyperinflammatory response lies at the root of many severe cases of COVID-19, driven by overexuberant inflammatory cytokine release. Consistently, co-morbidities, such as obesity, diabetes, heart disease, hypertension and ageing, which are prognostic of poor outcome, are associated with high basal inflammation7,11,20,21. It has been proposed since the beginning of the pandemic that these co-morbidities and the ensuing hyperinflammatory response may be aetiologically linked through overactive inflammasome signaling, which may account for the association of these co-morbidities with severe COVID-19 in the context of chronic inflammation as well as for COVID-19 progression in the context of a robust acute inflammatory response to infection2229. However, many of the studies that seek to understand the immune response to SARS-CoV-2 are based on RNA sequencing, often of thawed cells, and infected, activated or dying cells do not survive freeze–thaw well, which could skew results. Moreover, inflammasome activation does not directly induce transcriptional responses, and its detection is less straightforward than that of most other signaling pathways. Nonetheless, several studies are now accumulating that support direct (infection-induced) and indirect inflammasome activation and the critical role of inflammasomes in severe COVID-19. Here we discuss the available evidence, potential mechanisms and the implications for therapy.

Key to inflammation and innate immunity, are large, micrometer-scale multiprotein cytosolic complexes that assemble in response to pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs) and trigger proinflammatory cytokine release as well as pyroptosis, a proinflammatory lytic cell death30,31 (Fig. 1). Upon activation by PAMPs or DAMPs, canonical inflammasome sensors — mainly in monocytes, macrophages and barrier epithelial cells — oligomerize and recruit the adaptor apoptosis-associated speck-like protein containing a CARD (ASC) to form inflammasome specks, within which the inflammatory caspase 1 is recruited and activated. Inflammasome sensors are activated in response to different triggers and differ in their overall specificities to PAMPs or DAMPs. NLRP3, the most broadly activated inflammasome sensor and a member of the nucleotide-binding domain- and leucine-rich repeat-containing protein (NLR) family, responds to an array of insults to the cell that cause cytosolic K+ efflux, Ca2+ cytosolic influx or release of mitochondrial reactive oxygen species (ROS)31,32. These insults include extracellular ATP, membrane permeabilization by pore-forming toxins and large extracellular aggregates such as uric acid crystals, cholesterol crystals and amyloids30. Other sensors, such as AIM2 and NLRC4, are tuned to recognize specific PAMPs and DAMPs, such as cytosolic double-stranded DNA and bacterial proteins, respectively31. In a parallel pathway, the mouse inflammatory caspase 11 and human caspase 4 and caspase 5 sense PAMPs and DAMPs such as bacterial lipopolysaccharide (LPS) that gain cytosolic access and endogenous oxidized phospholipids, leading directly to membrane damage or pyroptosis, and secondary K+ efflux followed by noncanonical NLRP3 inflammasome activation3336.

For More Information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351223/

Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis

Authors: Keshav K. Singh,* Gyaneshwer Chaubey,* Jake Y. Chen, and Prashanth Suravajhala

Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell’s mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19.

For More Information: https://journals.physiology.org/doi/full/10.1152/ajpcell.00224.2020

SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE 2

Authors: Yuyang LeiJiao ZhangCara R. SchiavonMing HeLili ChenHui ShenYichi ZhangQian YinYoshitake ChoLeonardo AndradeGerald S. ShadelMark HepokoskiTing LeiHongliang WangJin ZhangJason X., et. al.

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection relies on the binding of S protein (Sprotein (Spike glycoprotein) to ACE (angiotensin-converting enzyme) 2 in the host cells. Vascular endothelium can be infected by SARS-CoV-2,1 which triggers mitochondrial reactive oxygen species production and glycolytic shift.2 Paradoxically, ACE2 is protective in the cardiovascular system, and SARS-CoV-1 S protein promotes lung injury by decreasing the level of ACE2 in the infected lungs.3 In the current study, we show that S protein alone can damage vascular endothelial cells (ECs) by downregulating ACE2 and consequently inhibiting mitochondrial function.

For More Information: https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.121.318902

COVID-19: A Mitochondrial Perspective

Authors: Pankaj Prasun 1

Coronavirus disease 2019 (COVID-19) is the worst public health crisis of the century. Although we have made tremendous progress in understanding the pathogenesis of this disease, a lot more remains to be learned. Mitochondria appear to be important in COVID-19 pathogenesis because of its role in innate antiviral immunity, as well as inflammation. This article examines pathogenesis of COVID-19 from a mitochondrial perspective and tries to answer some perplexing questions such as why the prognosis is so poor in those with obesity, metabolic syndrome, or type 2 diabetes. Although effective vaccines and antiviral drugs will be the ultimate solution to this crisis, a better understanding of disease mechanisms will open novel avenues for treatment and prevention.

For More Information: https://pubmed.ncbi.nlm.nih.gov/33872068/

Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis

Authors: Keshav K. Singh,* Gyaneshwer Chaubey,* Jake Y. Chen, and Prashanth Suravajhala

Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell’s mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19.

For More Information: https://journals.physiology.org/doi/full/10.1152/ajpcell.00224.2020

The Thorny Problem Of COVID-19 Vaccines And Spike Proteins

Authors: W. Glen Pyle

Almost since the beginning of the COVID-19 pandemic, a piece of the SARS-CoV2 virus called the “spike protein” has drawn interest from researchers and healthcare professionals.

New research by Yuyang Lei and colleagues published in the journal Circulation Research sheds new light on how the spike protein might play a critical role in the widespread damage caused by SARS-CoV2, and offers insight into treating the complications of COVID-19.

Vaccine skeptics have seized on the study to cast doubt on the safety of vaccines. But a review of the study’s findings shows that the concerns raised by vaccine doubters are much ado about nothing.

The Study

The vascular endothelium is an important player in the illness and death associated with COVID-19. The endothelium is a system of cells that line and protect the inside of blood vessels. SARS-CoV2 injures the endothelium leading to blood clots, heart attack, pulmonary embolism, and stroke. Despite the established link between COVID-19 and these cardiovascular complications, the mechanism by which they develop is unknown.

Researchers from Jiaotong University; the University of California, San Diego; and the Salk Institute used a pseudovirus coated with spike protein to investigate the effects of the viral protein on endothelial cells. Pseudoviruses – which were first developed over 50 years ago – contain the outer shell of the virus, but they lack the viral genes needed to reproduce.

Hamsters treated with the spike protein coated pseudovirus showed lung damage similar to that seen in humans infected with SARS-CoV2. When researchers added pseudovirus to cultured endothelial cells they found that the mitochondria inside the cells were injured. Since mitochondria are responsible for providing energy to cells, their dysfunction can cause cell death.

When isolated pulmonary arteries were exposed to the spike protein carrying pseudovirus there was some disruption in the ability of the blood vessels to dilate. The decreased ability to expand blood vessels that serve the lungs could impair the ability of the body to take up oxygen from lungs that are damaged by the virus.

The novelty of this study was the discovery that the spike protein itself causes damage, and that the pathway triggered by the spike protein could explain the widespread cardiovascular complications that develop in COVID-19 patients.

For More Information: https://www.science20.com/w_glen_pyle/the_thorny_problem_of_covid19_vaccines_and_spike_proteins-254373