The Cytokine Storm & COVID-19

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The Cytokine Storm & COVID-19

Post by trader32176 »

AI used to define the cytokine storm implicated in fatal COVID-19

9/24/20 ... ID-19.aspx

A new study published on the preprint server bioRxiv* in September 2020 reports the use of artificial intelligence (AI) to identify an invariant or universal host immune response found in all viral pandemics so far. The association of this response with severe COVID-19 phenotypes indicates a new understanding of the human immune response in viral pandemics.

The use of machine learning helped surmount obstacles posed by the variable immune response in different individuals and identify the underlying gene expression profiles amid all the other noise. They used patient cohorts across many viral pandemics for this purpose, exploiting the resulting pattern of gene expression to study the immune response in COVID-19.

ACE2-centric Study Design

In order to find a validated signature for the current pandemic from over 45,000 datasets of gene expression data in humans, mice, and rats, in multiple pandemics, the researchers used the angiotensin-converting enzyme 2 (ACE2) as ‘seed’ gene in the computational approach.

This was for three reasons. Firstly, it is the viral receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and its expression reflects innate immune gene expression and tissue susceptibility to the virus. Secondly, it effectively inhibits the renin-angiotensin-aldosterone system (RAAS), a potent pro-inflammatory system. Thirdly, it is disrupted by infections, and this leads to unregulated inflammatory activity.

Informatics Approach

The researchers used a machine learning tool called Boolean Equivalent Correlated Clusters (BECC) in order to find the underlying invariant gene expression relationships in respiratory viral pandemics. They identify the immense advantages of this approach thus:” The BECC algorithm focuses exclusively on “Boolean Equivalent” relationships to identify potentially functionally related gene sets. Once identified, these invariant relationships have been shown to spur new fundamental discoveries with translational potential, and most importantly, offer insights that aid the navigation of uncharted territories where nothing may be known.”

ViP Signature Characteristic of Viral ‘Cytokine Storm’

The researchers found that 166 genes were consistently related to ACE2, with a decline in expression during convalescence. This pattern occurred uniformly across all viral pandemics (not necessarily respiratory virus pandemics), for which reason it was named the ‘Viral Pandemic’ (ViP) Signature.

The majority of the 166 genes were involved in immune responses, including interferon and cytokine signaling within the innate immune system, as well as the adaptive immune system. Thus, they indicated the host immune response to a viral infection per se, as expected, since the cytokine storm in any viral pandemic is known to be due to an exuberant host immune response.

Surprisingly, however, this pattern was detected despite the ACE2-centric approach, though ACE2 is not the viral entry receptor for influenza. It continued unchanged despite filtering through unrelated datasets in vitro and in vivo. Again, the cytokine-receptor pair IL15/IL15RA was found to be invariably associated with ACE2 expression regardless of the dataset.

This agrees with previous findings that IL15 is central in lung injury and determines its severity, while its deletion protects mice from lethal influenza.

The signature was also associated with ACE2-expressing lung epithelium and myeloid cells, indicating a close link between ACE2-mediated viral entry and ACE2-associated host gene activation.

20-Gene Subset Detects Disease Severity

Ranking of the 166 genes for their ability to distinguish severe or critical influenza led to the emergence of a subset of 20 genes that could accurately classify healthy and infected patients as well as mild and severe disease. This subset marks DNA damage, stress-induced senescence, and cell cycle alterations as well as neutrophil degranulation, thus indicating disease severity and death.

The 166-gene ViP signature classified healthy vs. infected patients in all five peripheral blood cells, but the subset was most accurate in neutrophils. The researchers say this indicates that “the cells of the innate immune system are the primary contributors of disease severity.”

COVID-19 Induces ViP Signatures in Lung Epithelium and Immune Cells

Both 166-gene and 20-gene signatures perfectly classified healthy and SARS-CoV-2-infected samples in vitro in all tissues and all lung cell types. The former also distinguished these sets in alveolar epithelium, macrophages, CD4 cells, and NK cells. It was also able to distinguish mild and severe COVID-19 in the first and last cell types.

The 20-gene subset recapitulated these findings best with the same two cell types. This indicates, the authors say, that the signature of disease severity and fatality was prominently expressed in lung epithelium, which is a source of virus-induced IL15, and NK cells, which are the primary IL15 target.

NK cells exposed to virally infected epithelial cells showed both these signatures, thus explaining the findings in COVID-19 patients, and indicating that these could be attributed solely to the effects of IL15.

IL15 Storm Mediates COVID-19 Severity

The obvious association of the two ViP signatures with IL15/IL15RA in the same organ, namely, the lung, suggests the one causes the other. As predicted by these findings, severe COVID-19 is defined most often by exaggerated IL15-dominated cytokine release beginning in the lung, as shown by examining samples from a group of symptomatic COVID-19 patients with varying clinical severity (including autopsy specimens from those who died).

Immunopathogenetic Model of COVID-19

The study shows that the immune system plays a significant role in the pathogenesis of COVID-19. The disease begins with the activation of 166 genes in airway epithelial cells as well as myeloid lineage cells, and other immune cells, leading to IL-15 secretion.

This is supported by earlier studies in which the bronchial cells were shown to express IL15 and IL15RA/B genes constitutively. The synthesis and secretion of IL15 are induced by IFNγ as well. These studies indicate that prolonged and over-intense exposure of NK cells to cytokines leads to their exhaustion and death.

This agrees with recent findings that NK cells are seen to be exhausted and reduced in number in severe COVID-19, as early as 3-6 days from symptom onset.

The authors say, “Fatal COVID-19 is characterized by a paradoxical immune response, i.e., suppression of epithelial and NK cell functions (immunosuppression) in the setting of a cytokine storm (overzealous immune response).”

ViP Profiles Shape Therapy and Indicate Efficacy of Treatment

These researchers had earlier shown that the 166-gene ViP signatures were attenuated during the convalescence period of several respiratory virus pandemics. This finding was demonstrated by the current researchers, who went on to explore their role as an indicator that treatment was causally associated with this response.

To answer this question, they examined earlier interventional studies for HCV, HIV, Zika, and Ebola, involving the use of effective anti-virals. In all these cases, this signature accurately categorized treated vs. non-treated samples, with the former showing attenuation of the ViP signature.

For instance, liver biopsies taken from HCV patients were classified using this signature into those treated with directly acting anti-viral agents (DAAs) and those not treated. Similar results were found with HIV patient samples, treated or not with antiretroviral drugs.

The scientists say, “These findings suggest ‘causality’ between treatment (anti-viral therapies) and response (attenuation of the ViP signature), and imply that attenuation of the 166-gene ViP signature is a desirable therapeutic goal.”

SARS-CoV-2 Virus Is Responsible for The Host Response

The next question was to relate the host immune response to the SARS-CoV-2 virus. They used hamsters treated with anti-SARS-CoV-2 antibody to completely block viral binding to the ACE2 receptor and then challenged with the virus, comparing them with another group pretreated with a control antibody.

They found that firstly, the test group showed neither the 166-gene or the 20-gene ViP signatures so characteristic of the infected lungs. Secondly, the absence of these signatures accompanied the absence of excessive immune cell infiltration or the obliteration of alveolar space. Finally, IL15 and IL15 receptor expression were markedly lower in these tissues.

The researchers feel that this bears out the ACE2-centric approach, showing that when an antibody prevents ACE2-virus binding, the ViP signature and IL 15 cytokine storm are suppressed, while effective treatment reverses both.

Shared Host Response Signature

The researchers point out a “major and unexpected finding,” which is that all viral pandemics have the same host immune response, though the severity, clinical features, etiological virus, and lethality may be entirely different. This may indicate the fundamental importance of ACE2 expression for the host immune response in most viral infections.

Not only does the ViP signature characterize the host immune response to a viral pandemic, but also offers a way to monitor the occurrence and extent of such a response.

The study also showed that the cytokine storm in all pandemics was mediated by uncontrolled IL15 and IL15RA activation. The higher the level of IL15, the more severe the disease was. IL15 levels were significantly higher in men of advanced age, who are known to be a high-risk group for severe COVID-19 worldwide. The lung epithelium and myeloid cells are the chief contributors to the ViP signature and IL15/IL15RA.

Finally, they detected a subset of 20 genes, a signature suggesting severe disease in all viral pandemics.

In their words, “The ViP signatures begin to paint a picture of ‘paradoxical immunosuppression’ at the heart of fatal COVID-19, in which, the observed NK cell exhaustion/depletion in severe COVID-19 could be a consequence of an overzealous IL15 storm, leading to their senescence and apoptosis.”

Thus, this study provides a valuable framework for understanding how the disease develops. The findings “not only pinpointed the precise nature of the cytokine storm, the culprit cell types and the organs, but also revealed disease pathophysiology, and helped formulate specific therapeutic goals for reducing disease severity.”

Further refining of the ViP signature through repeated filtering using newer and larger COVID-19 datasets may make it more precise and reliable. Even now, however, it can be used to inform therapeutic tools and to lay out a screening plan for potential therapeutic agents, not only in COVID-19 but also other viral pandemics.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
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The Cytokine Storm & COVID-19

Post by trader32176 »

SARS-CoV-2 viroporin triggers NLRP3 inflammasome causing a severe inflammatory response

10/30/20 ... ponse.aspx

Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes the coronavirus disease (COVID-19), may develop mild to severe symptoms. In some patients, the infection causes a cytokine storm resulting from a heightened inflammatory response.

Now, a team of researchers at the University of Florida report that the SARS-CoV-2 viroporin triggers the NLR Family Pyrin Domain Containing 3 (NLRP3) inflammasome, which is responsible for the inflammatory pathology in severely ill COVID-19 patients.

What is a cytokine storm?

A cytokine storm syndrome occurs when several medical conditions emerge, and the immune system produces too many inflammatory signals. This syndrome can lead to organ failure and death.

Cytokines are small glycoproteins produced by many types of cells in the body. When these molecules are released, they can trigger body functions, including the control of cell proliferation, endocrine activity, and regulating immune and inflammatory responses.

When there is an infection, various inflammatory cytokines are produced at a much higher rate. These molecules also recruit other immune cells to the site of injury, potentially causing organ damage.

Recently, the cytokine storm has received more attention due to the COVID-19 pandemic. Though health experts and clinicians are learning more each day, cytokine storm seems to be a part of the reason why people develop life-threatening symptoms from COVID-19.

The study

In the study, published on the preprint server bioRxiv*, the researchers said that the heightened inflammatory response results from the assembly and activation of a cell-intrinsic defense platform known as the inflammasome.

The researchers assessed the influence of the SARS-CoV-2 ORF3a, which is thought to be a protein with ion channel activity (viroporin) that activates the NLRP3 inflammasome. ORF3a also plays a role in virus replication and the development of the disease.

Viroporins are a group of proteins that participate in many viral functions, such as promoting the release of viral particles from cells. These proteins also affect cellular functions, including membrane permeability, glycoprotein trafficking, and the cell vesicle system. Though not essential for virus replication, some of these small proteins can generate pores that facilitate ion transport across cell membranes. As a result, they ensure virus release that can activate inflammasomes.

Inflammasomes gather and respond to invading organisms as a component of the innate immune system. Hence, they form the first line of defense against invading pathogens and infection.

With the inflammatory response a contributor to severe illness in COVID-19 patients, it is important to develop therapies that can help block infection and halt virus replication. The team investigated the influence of ORF3a on the inflammatory machinery. They also defined key amino acid residues on ORF3a required to activate the inflammatory response.

What the study found

The team found that the SARS-CoV-2 ORF3a protein primes and activates the inflammasome through the efflux of potassium ions and the kinase NEK7. They also found that though the coronavirus ORF3a protein has separated from its homologs in other coronaviruses, some of the newly divergent residues are crucial for the activation of the NLRP3 inflammasome. Further, they are conserved in virus isolates across continents.

Overall, the team noted that an essential viroporin needed for the release of SARS-CoV-2 from infected cells could also activate the NLRP3 inflammasome.

“ORF3a’s indispensability to the virus’s life cycle makes it an important therapeutic candidate. Moreover, while different from its homologs in other coronaviruses, the high conservation of the newly divergent SARS-CoV-2 ORF3a across isolates from several continents combined with our observation that multiple single point mutations reduce its ability to activate the inflammasome, argues against rapid emergence of resistance phenotypes,” the team explained.

The team also explained that targeting ORF3a may help block virus spread and inflammation. Hence, the study can help in formulating new therapies that can reduce the severe and fatal outcomes of COVID-19 in people who are high risk. These include those who have underlying medical conditions.

“These findings reveal ORF3a and NLRP3 to be attractive targets for therapy,” the team added.

Finding a way to reduce mortality tied to COVID-19 is essential. The number of people infected so far is nearing 45 million, with over 1.18 million lives lost.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.


Cytokine storm: ... Storm.aspx
COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) - ... 7b48e9ecf6

Journal reference:

Xu, H., Chitre, S., Akinyemi, I., Loeb, J. et al. (2020). SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway. bioRxiv ... 7.357731v1
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The Cytokine Storm & COVID-19

Post by trader32176 »

SARS-CoV-2 causes a unique cytokine storm, study finds

11/18/20 ... finds.aspx

After many months of studying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the pathogen responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic – much is still unknown. However, evidence points to the occurrence of a cytokine storm in severe and critical cases of COVID-19. This is not unique to COVID-19 and has occurred in the majority of severe coronavirus and influenza epidemics.

However, there are some striking differences in the cytokine release syndrome (CRS) in these conditions and that which occurs in COVID-19. A new study published on the preprint server medRxiv* in November 2020 reports some of the unique elements of COVID-19-induced CRS and how understanding these distinctive characteristics of the disease could help in formulating specific interventions and therapies.

Cytokine storm

A cytokine storm, or CRS, refers to a hyper-inflammatory response involving the dysregulated activation of a large number of immune and inflammatory cells; these cells pour out a flood of pro-inflammatory cytokines. This sets up a positive feedback loop or a vicious cycle of inflammation. Cytokine storms are associated with higher rates of mortality in severe and critical COVID-19 cases.

Earlier studies have described the process as beginning with cytokine-induced widespread tissue damage, followed by multi-organ dysfunction and death in the absence of rapid intervention.

CRS resolution is a typical sequel, and is characterized by high levels of anti-inflammatory cytokines, such as the type I interferon (IFN) signaling cascades mediated by IFN-α and IFN-β. These, in turn, activate IL-12 and IFN-γ, which is a type II IFN. Type I IFN pathways are inhibited by IL-10, and certain viral proteins, which can delay or modulate this response, as observed in severe COVID-19.

Looking for differences in CRS in five viral infections

The fact remains that the immune response in different viral infections, including SARS-CoV and MERS-CoV – two betacoronaviruses in the same family as SARS-CoV-2 – as well as and influenza A, is not specifically understood, especially in their early stages. Such knowledge could help prevent a disease’s progression to its severe stage and the development of CRS.

The current study focuses on the differences in the cytokines released by these viruses. The researchers used available prepublished and published literature for information on 98 cytokines, including interferons, interleukins, tumor growth factors and chemokines associated with CRS.

They examined especially changes in these molecules in patients infected by five important CRS-causing viruses: the two influenza A virus subtypes H5N1 and 91 H7N9, SARS-CoV, MERS-CoV and SARS-CoV-2. They ended up with 38 significant cytokines that had been measured in actual patients.

While 16 cytokines were raised in a specific viral infection in at least one study, only five were raised in all five viral infections. This does not consider the magnitude of change, however.

Disruption of immune response in betacoronaviruses (beta-CoVs)

They observed that all measured cytokines were elevated in influenza A infections, but with the betacoronaviruses (beta-CoVs), the pattern was more nuanced, with some cytokines at baseline levels. The cytokine response in COVID-19 is midway between that of the other beta-CoVs and the influenza A viruses. They concluded that this indicated the ability of beta-CoVs to evade the immune response.

There were eight cytokines clusters based on the direction of change in their secretion following infection by each of these viruses. The first cluster, I, contains TNF-α with IL-2 and IL-10. The first is pro-inflammatory and the others anti-inflammatory. A rise was seen only in influenza.

Similarly, clusters III and VI, containing pro-inflammatory cytokines like IL-6, type I and II IFNs, and several chemokines, generally recorded a rise. Cluster IV includes cytokines like IL-4 and IL-5, mostly unchanged in CoV infections but raised in influenza. IL-4 plays a role in Th2 differentiation, and the latter cells can secrete IL-5 to modulate the recruitment of eosinophils.

With cluster VII and VIII, IL-15 and CCL5 are unchanged in COVID-19, but the former is involved in NK cell differentiation as part of the innate immune antiviral response. CCL5 is responsible for eosinophil infiltration, a key process in post-COVID-19 recovery. Cluster II includes cytokines that were measured only in H7N9, and cluster V only in COVID-19.

CRS in beta-CoV infections

COVID-19 is associated with a beta-CoV-like response in terms of pro-inflammatory cytokines, but preserves some, like IL-2 and IL-10, that would be expected to be raised in a viral infection. Thus, SARS-CoV-2 induces a markedly weaker type I IFN response than the other beta-CoVs or the influenza A viruses.

With SARS, both type I IFN and the downstream IL-12 are activated due to the involvement of mature dendritic cells, with IL-12 indirectly activating IFN-γ, but not IL-10. This could perpetuate the positive feedback loop CRS causes.

In MERS, type I IFN is induced in only some individuals, but not IL-12, IL-10 or IFN-γ. Strangely, IL-10, which was formerly thought to be anti-inflammatory, is now being shown to have pro-inflammatory activity.

Both these beta-CoV infections induce impaired innate immune responses allowing alveolar macrophages or neutrophils to be infected, causing increasingly severe lung injury. The persistent pro-inflammatory cytokine state causes acute respiratory distress syndrome (ARDS) and severe lung damage, leading to higher mortality rates. In fact, SARS was associated with death in around 10% of patients, and MERS in around 34%, compared with 2.3% in COVID-19.

Again, in severe SARS, IL-10 levels are very low but high in MERS. Despite this, in MERS, low IL-4 and IL-2 levels release IFN-γ from inhibition, and high IFN-γ titers induce type II IFN levels.

CRS in influenza A

In influenza A, however, the antiviral response is rapid, with an intact negative feedback loop inhibiting excessive inflammation. IFN-I is modulated by viral proteins, but remains intact and can be hyperactivated to cause mortality in severe influenza. Similarly, failure to trigger TGF-β can increase the severity of illness.

A curious finding is that while the cytokines that regulate inflammatory cascades are enabled in influenza A, CRS can still occur. This may be the result of TGF-β deficit, with, additionally, a characteristic impairment of CD4 and CD8 T cells, despite their abundant number, in CRS. Again, the typical anti-inflammatory phenotype of monocytes that is expected to occur at high antigen presentation, as in progressive infection, fails to manifest. The monocytes thus remain in a chronic pro-inflammatory activation state, which prevents the host response from subsiding.

Further study would help understand how CRS occurs in severe influenza, by outlining the population expansion and activation profile of both innate and adaptive immune cells.

What are the implications?

The primary difference between the beta-CoVs and influenza viruses seems to be that while resolution of CRS is poor in the former, the immune system in the latter infection remains capable of resolving the cytokine storm.

The unique feature of SARS-CoV-2 is the disruption of downstream signaling after type I IFN activation. This upsets the equilibrium of inflammatory and anti-inflammatory cytokines. In about 80% of cases, however, the inflammation does resolve. Here again, SARS-CoV-2 stands out from the other beta-CoVs in the high degree of CRS resolution.

In short, the researchers say, “SARS-CoV-2-mediated infections are characterized by a clear dysregulation of type-I IFN response, and consequently the downstream cytokine signature such as IL-4, IL-12, IL-2, IL-10 and the downstream type II IFN response.”

By helping to map these responses, it may be possible to develop therapeutics that reduce the severity of CRS these infections, or even prevent its development.
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The Cytokine Storm & COVID-19

Post by trader32176 »

Scientists discover potential strategy to prevent inflammation in COVID-19 patients

11/19/20 ... ients.aspx

The COVID-19 pandemic continues to cause significant illness and death while treatment options remain limited. St. Jude Children's Research Hospital scientists have discovered a potential strategy to prevent life-threatening inflammation, lung damage, and organ failure in patients with COVID-19. The research appeared online in the journal Cell.

The scientists identified the drugs after discovering that the hyperinflammatory immune response associated with COVID-19 leads to tissue damage and multi-organ failure in mice by triggering inflammatory cell death pathways. The researchers detailed how the inflammatory cell death signaling pathway worked, which led to potential therapies to disrupt the process.

"Understanding the pathways and mechanism driving this inflammation is critical to develop effective treatment strategies," said corresponding author Thirumala-Devi Kanneganti, Ph.D., vice chair of the St. Jude Department of Immunology. "This research provides that understanding. We also identified the specific cytokines that activate inflammatory cell death pathways and have considerable potential for treatment of COVID-19 and other highly fatal diseases, including sepsis."

COVID-19, cytokines, and inflammatory cell death

COVID-19 is caused by the SARS-CoV-2 virus. The infection has killed more than 1.2 million people in less than one year and sickened millions more.

The infection is marked by increased blood levels of multiple cytokines. These small proteins are secreted primarily by immune cells to ensure a rapid response to restrict the virus. Some cytokines also trigger inflammation.

The phrase cytokine storm has been used to describe the dramatically elevated cytokine levels in the blood and other immune changes that have also been observed in COVID-19, sepsis and inflammatory disorders such as hemophagocytic lymphohistiocytosis (HLH).

But the specific pathways that initiate the cytokine storm and the subsequent inflammation, lung damage and organ failure in COVID-19 and the other disorders was unclear. The cellular and molecular mechanisms that comprehensively define cytokine storm was also lacking.

Kanneganti's team focused on a select set of the most elevated cytokines in COVID-19 patients. The scientists showed that no single cytokine induced cell death in innate immune cells.

The St. Jude investigators then tried 28 cytokine combinations and found just one duo that, working together, induced a form of inflammatory cell death previously described by Kanneganti as PANoptosis. The cytokines are tumor necrosis factor (TNF)-alpha and interferon (IFN)-gamma.

PANoptosis is a unique type of cell death that features coordination of three different cell death pathways-;pyroptosis, apoptosis and necroptosis. PANoptosis fuels inflammation through cell death, resulting in the release of more cytokines and inflammatory molecules.

The investigators showed that blocking individual cell death pathways was ineffective in stopping cell death caused by TNF-alpha and IFN-gamma. A closer look at proteins that make up the pathways identified several, including caspase-8 and STAT1, that were essential for PANoptosis in response to these cytokines. Deleting those proteins blocked PANoptosis in innate immune cells called macrophages.

Potential for repurposing TNF-alpha and IFN-gamma blockers to treat COVID-19

Because TNF-alpha and IFN-gamma are produced during COVID-19 and cause inflammatory cell death, the investigators questioned whether these cytokines were responsible for the clinical manifestations and deadly effects of the disease. They found that the TNF-alpha and IFN-gamma combination triggered tissue damage and inflammation that mirror the symptoms of COVID-19 along with rapid death.

Neutralizing antibodies against TNF-alpha and IFN-gamma are currently used to treat inflammatory diseases in the clinic. The investigators found that treatment with these antibodies protected mice from death associated with SARS-CoV-2 infection, sepsis, HLH and cytokine shock.

" The findings link inflammatory cell death induced by TNF-alpha and IFN-gamma to COVID-19," Kanneganti said. "The results also suggest that therapies that target this cytokine combination are candidates for rapid clinical trials for treatment of not only COVID-19, but several other often fatal disorders associated with cytokine storm."

- Thirumala-Devi Kanneganti, PhD, Study Corresponding Author, Vice Chair of the St. Jude Department of Immunology

Added co-first author Rajendra Karki, Ph.D., a scientist in the Kanneganti laboratory: "We were excited to connect these dots to understand how TNF-alpha and IFN-gamma trigger PANoptosis." Co-first author Bhesh Raj Sharma, Ph.D., a scientist in the Kanneganti laboratory, added: "Indeed, understanding how PANoptosis contributes to disease and mortality is critical for identifying therapies."

Redefining cytokine storm

Based on this fundamental research, Kanneganti and her colleagues have proposed a definition of a cytokine storm that puts the cytokine-mediated inflammatory cell death via PANoptosis at the center of the process. The researchers noted that PANoptosis results in the release of more cytokines and inflammatory molecules, which intensifies systemic inflammation.

"We have solved a major piece of the cytokine storm mystery by characterizing critical factors responsible for initiating this process, and thereby identifying a unique combination therapy using existing drugs that can be applied in the clinic to save lives," Kanneganti said.
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

PTC299 inhibits SARS-CoV-2 replication and suppresses production of inflammatory cytokines

12/1/20 ... kines.aspx

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a severe global public health crisis. As of today, the virus has infected 63.75 million people and claimed the lives of over 1.47 million worldwide, showing that there is an urgent need for effective therapeutic treatments to fight this disease.

Study: The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines

SARS-CoV-2 is a single-stranded-RNA virus of the Coronaviridae family that is 79.5% similar to SARS-CoV-1 in terms of genetic sequence.

In the early phases of COVID-19, the virus multiplies rapidly and causes mild to severe symptoms. In severe cases, it triggers a cytokine storm characterized by excessive production of inflammatory cytokines
. This uncontrolled inflammation can lead to hyperpermeability of the vasculature, acute respiratory distress syndrome, multi-organ failure, and death.

Acute respiratory distress syndrome is one of the most common causes of COVID-19-related mortality. In addition, increased levels of interleukin (IL)-6 and IL-17 are said to be linked to severe pulmonary complications and death.

A bioavailable potent inhibitor of dihydroorotate dehydrogenase

PTC299 is an orally bioavailable inhibitor of dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme of the de novo pyrimidine biosynthesis pathway.

Studies have shown that cultured cells treated with PTC299 can inhibit DHODH activity, leading to increased DHO (DHODH enzyme-substrate) levels. In other studies, cancer patients treated with PTC299 had increased blood DHO levels, indicating successful DHODH inhibition in these patients.

PTC299 has been generally well tolerated and manifested a favorable pharmacokinetic profile in oncology patients in extensive studies, supporting the investigation of PTC299 for use in the treatment of COVID-19.

Evaluating the antiviral activity of PTC299 against SARS-CoV-2

In an article published in the journal Virus Research, a team of researchers from various US institutions discussed their study that evaluated the antiviral activity of PTC299 against a group of RNA viruses in vitro.

The specific focus of the study was SARS-CoV-2, and they also assessed the ability of PTC299 to reduce the uncontrolled production of inflammatory cytokines in severe COVID-19 patients.

The researchers described the anti-COVID-19 potential of PTC299 in tissue culture, where it manifests dose- and DHODH-dependent inhibition of SARS-CoV-2 replication with a selectivity index greater than 3,800. PTC299 also inhibited replication of other RNA viruses such as the Ebola virus and also blocked the production of IL-6, IL-17A, IL-17 F, and vascular endothelial growth factor (VEGF) in tissue culture models. The combination of favorable pharmacokinetic and human safety profiles, cytokine inhibitory activity, and anti-SARS-CoV-2 activity renders PTC299 a promising treatment option for COVID-19.

“PTC299 is a highly potent inhibitor of SARS-CoV-2 replication that also suppresses production of a subset of pro-inflammatory cytokines, suggesting it has the potential to act through this dual mechanism to treat the viral and immune components of COVID-19.”

PTC299 inhibits SARS-CoV-2 replication and also suppresses cytokine production

Based on these findings, the authors concluded that PTC299 is a potent inhibitor of SARS-CoV-2 replication that also suppresses the production of pro-inflammatory cytokines, suggesting a dual mechanism of action that can help treat the viral and immune components of COVID-19. Owing to its ability to inhibit both viral replication and cytokine production, the authors think that PTC299 may be an effective option for treating both early and later stages of COVID-19.

The dual action of PTC299 is in contrast with direct-acting antivirals that are mostly effective in the early phase of the disease and with anti-inflammatory drugs that are effective only in the later phase of COVID-19.

“The novel dual mechanism of action of PTC299 distinguishes it from most other therapeutics being investigated in the clinic for the treatment of COVID-19, as many of these target either viral-specific processes or the immune response, but not both.”

Studies have shown that it is vital to combine antiviral therapy with immune suppressants because using molecules that control only the cytokine storms may make viral clearance difficult.

To summarize, PTC299 is orally bioavailable, has been widely studied in humans, has well established pharmacokinetic and safety profiles and is tolerated well, all of which and prior clinical experience with the compound endorse further development of this molecule for use in COVID-19 treatment.

“These findings and prior clinical experience with PTC299 support the further development of this novel molecule for the treatment of COVID-19.”

Journal reference:

Jeremy Luban, Rachel Sattler, Elke Mühlberger, Jason D. Graci, Liangxian Cao, Marla Weetall, Christopher Trotta, Joseph M. Colacino, Sina Bavari, Caterina Strambio-De-Castillia, Ellen L. Suder, Yetao Wang, Veronica Soloveva, Katherine Cintron-Lue, Nikolai A. Naryshkin, Mark Pykett, Ellen M. Welch, Kylie O’Keefe, Ronald Kong, Elizabeth Goodwin, Allan Jacobson, Slobodan Paessler, Stuart Peltz, The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines, Virus Research, 2020,, ... 0220311539
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

FASLG gene may drive cytokine-linked adverse COVID-19 outcomes with age

12/8/20 ... h-age.aspx

Early on in the COVID-19 pandemic, it became clear that the elderly population over 60 years of age was at greater risk from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Some scientists have attributed this to the increased prevalence of chronic underlying disease in this age group, which poses an independent risk factor for adverse outcomes in COVID-19. A new study published on the preprint server bioRxiv* in December 2020 reveals the role played by certain genetic factors in this group, in particular the FASLG gene belonging to the tumor necrosis factor (TNF) family.

Coagulation Abnormality in SARS-CoV-2 Infections

The SARS-CoV-2 virus causes an asymptomatic or mild infection in most cases. In those patients with more severe illness, it affects the lung parenchyma, primarily resulting in edema of the lung alveoli, the deposition of fibrin, and hemorrhage. Vascular changes are characteristic of this condition, manifesting in some as thrombosis of the microvasculature, leading to intravascular coagulation, and, in the critically ill, multi-organ failure.

The fact that many severe COVID-19 patients display signs of disrupted coagulation, including heart attacks, pulmonary embolism, and thrombosis, causing increased death rates following the infection, is concerning. These changes are associated with inflammatory dysregulation, leading to a cytokine storm. The hyper-intense levels of pro-inflammatory mediators activate immune cells and platelets and causes hyperactivation of the coagulation cascade.

They examined the blood transcriptomics data during aging from 670 males and females in the Genotype-Tissue Expression (GTEx) database. They aimed to identify the differentially expressed genes (DEGs) in whole blood in COVID-19 patients aged 20-79 years, with particular reference to the genes that translated into proteins that interact with viral proteins.

They then explored the DEG-related SARS-CoV protein-protein interactions (PPI) because of the close similarity between this virus and SARS-CoV-2. This was followed by gene ontology studies to gain insights into the function of the DEGs and PPIs, to better understand the association between these PPIs and the pathogenesis and potential druggability of the disease.

The samples were stratified by age group, in the following subsets: 30-39, 40-49, 50-59; 60-69 and 70-79. Each of these groups was compared with the age group 20-29 years. To be considered a DEG, a log2 magnitude or more significant change was required, with a false discovery rate (FDR) < 0.05.

They found a unique gene expression pattern in the youngest age group. There were 22 relevant DEGs in blood samples from older patients. The number of DEGs and PPIs was found to increase with age seen from the age of 50 onwards, with 62, 251, and ~900 DEGs in the age groups of 50-59, 60-69, and 70-79, respectively.

In the 50-79 pooled age group, five genes, namely, FASLG, CTSW, CTSE, VCAM1, and BAG3, were overexpressed.

Functional Relevance

FASLG is overexpressed in both sexes after the age of 50, but the cathepsin genes, CTSW and CTSE are high after 60, along with the adhesion molecule VCAM1 and the chaperone regulator molecule (BAG3). The PPI network of these enriched targets showed FASLG, SRC, VCAM1, BAG3, and HSPA5 to be primarily involved in interactions between the virus and immune components, inflammation, platelet activation and aggregation. Interestingly, all these were linked to the plasma membrane in some way.

A gene ontology (GO) analysis was then carried out in samples from aged individuals to understand how these changes affected host function. They found the closest functional relevance was with immune function, subcellular organization, adhesion of cells, signaling and stimulus-response, biological regulation, and development.

The CTSW and CTSE proteins were related to viral endosomal exit, but the other three were found to interact with ORF8, and perhaps with the spike protein.

FASLG and CTSW gene expression was linked to NK cells, CD8+ T cells, and memory T cells. CTSE expression was higher in males above 50 compared to females. CTSE is expressed on immune cells that bear MHC-II antigens and might be a potential therapeutic target in COVID-19.

VCAM1 and BAG3 showed age-dependent expression, the latter mainly on CD4+ T cells, naive T cells, and CD14+ monocytes. These genes are related to virus-host cell interactions via the spike protein, allowing viral entry into the bloodstream. The resulting increase in SRC and HSPA5 in those aged 79-79 causes platelet aggregation and activation, and this, in turn, may trigger the coagulation cascade.

VCAM1 was unique in showing increased transcription levels in individuals aged 60-69 relative to those aged 20-29, in both sexes. This being an endothelial adhesion marker, it may correlate with the presence of diffuse endothelial inflammation and infection of endothelial cells, with thromboembolism, all directly correlated with the severity of disease and coagulopathy.

BAG3 expression was predominant for CD4+ memory T cells, naïve T cells and CD14+ monocytes. These blood cells did not significantly express VCAM1 and CTSE genes.

Age-Related DEGs and Cytokine Storm

In other viral illnesses, including SARS and MERS, and influenza, cytokine monitoring can reduce the mortality rate. However, in severe COVID-19, interferon levels drop, these being antiviral factors, while interleukins rise to high levels, along with other pro-inflammatory molecules – TNF, IL-6, IL-1β and some chemokines such as CCL-2 and -3.

In fact, the gene expression profile in the oldest group is inversely related to that in the youngest group. In individuals over 50 years of age, inflammatory and immune pathways were activated most highly. This finding is significant since severe and critical COVID-19 is thought to be mediated by this surge in cytokines causing systemic inflammation.

Cytokines are carried at high levels throughout the body by the blood, and this may mediate multiple organ dysfunction.

FASLG in NK and CD8+ T Cells Drives Hypercytokinemia

Fas ligand, FasL, is a transmembrane homotrimer, part of the same family as TNF. The Fas/FasL complex formation triggers a signaling pathway that results in the assembly of the death-inducing signaling complex (DISC) within the cell. The outcome is the death by apoptosis of immune cells and of infected cells, along with the apoptosis-independent induction of severe inflammation.

This complex may activate T cells and NK cells that come into contact with SARS-CoV-2 during the stage of viremia. The outcome may be both an intensified immune response and exhaustion of the activated blood cells. By promoting the incorporation of cFLIP to the DISC, FasL results in the activation of the transcription factors NF-kB and ERK/AP-1. This is also promoted by IL-8 within the cells of the bronchiolar epithelium. Macrophages secrete TNF-α when bound to FasL. FasL in turn, causes IL-2 release and T cell proliferation.

FasL was found to be derived chiefly from CD8+ T cells and NK cells in COVID-19 patients, and might be among the array of host proteins with which the viral ORF8 interacts. This viral protein is secreted in large amounts and reduces MHC-I expression on cells. This may be why the virus spreads so rapidly and eludes immune recognition and clearance. Fas/FasL signaling also impacts endothelial function and neutrophil lifespan and apoptosis of infected cells, along with potential viral replication. Thus, this may be a potential therapeutic target.

The ligation of Fas on CD8+ T cells can cause their differentiation and activation, which may explain their low count in these patients. This may also, along with the corresponding overactivation of macrophages and CD4+ T cells, drive the cytokine storm. Both immune and inflammatory cells have been found to infiltrate the patient’s lung tissues in COVID-19, and IL-6 is high in critically but not moderately ill patients.


Some studies indicate that the altered expression of DEGs in older individuals is a reflection of existing dysregulation, which is exacerbated by the virus, and that this accounts for the worse outcomes. The authors conclude, “The increased expression of FASLG in blood during aging may explain why older patients are more prone to severe acute viral infection complications. Because hypercytokinemia is described as the framework for disease severity and high-risk death, we highlight FASL as a prognostic biomarker and a therapeutic proposal to modulate inflammation in elderly patients with COVID-19.”

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.


Journal reference:

Chuffa Sr. L. G. et al. (2020). The aging whole blood transcriptome reveals a potential role of FASLG in COVID-19. bioRxiv preprint. doi: 10,000,000,, ... 4.412494v1
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

Intestinal bacteria may affect severity of COVID-19, researchers find

1/12/21 ... -19-study/

The bacteria lurking in COVID-19 patients’ intestines may play a role in how sick they get from the illness, according to new research.

Although the coronavirus is primarily a respiratory disease, there is increasing evidence that suggests the GI tract is involved, scientists at the Chinese University of Hong Kong said.

The team studied samples from 100 patients treated at two Hong Kong hospitals to see how the so-called microbiome in the digestive system might affect recovery from the deadly bug.

“Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication,” they wrote in the British Medical Journal’s publication Gut.

“Based on several patients surveyed in this study for up to 30 days after clearing SARS-CoV-2, the gut microbiota is likely to remain significantly altered after recovery from COVID-19,” they said.

The researchers said patients with severe illness exhibit high blood plasma levels of inflammatory cytokines
and inflammatory markers — and that there is “substantial involvement” of the GI tract during infection, given “altered gut microbiota composition in SARS-CoV-2 infected subjects.”

Cytokines, which are molecules that allow your cells to talk to each other, play a crucial role for healthy immune function. Too many cytokines, however, can result in what’s known as a “cytokine storm.”

“These results suggest that gut microbiota composition is associated with the magnitude of immune response to COVID-19 and subsequent tissue damage and thus could play a role in regulating disease severity,” they wrote.

The scientists also found that because a small subset of patients showed gut microbiota dysbiosis, or imbalance, even 30 days after recovery, this could be a potential explanation for why some symptoms persist in what is known as long COVID.
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

Scientists Discover 'All-Natural' COVID Treatment That Can Prevent 'Cytokine Storm' In Severe Patients

2/26/21 ... -treatment

A team of scientists from Israel and Iceland has published a new report showing that an extraction of spirulina algae has the potential to reduce the severity of COVID-19 in advanced cases.

The research, first published in a peer-reviewed journal called Marine Biotechnology, found that an extract of photosynthetically manipulated Spirulina is 70% effective in inhibiting the release of the cytokine TNF-a, a small signaling protein used by the immune system.

According to the Jerusalem Post, the research was conducted in a MIGAL laboratory in northern Israel with algae grown and cultivated in Iceland by the Israeli company VAXA. VAXA received funding from the European Union to explore and develop "natural" treatments for coronavirus.

In a small percentage of patients, infection with the coronavirus causes the immune system to release an excessive number of TNF-a cytokines, resulting in what is known as a cytokine storm. The storm causes acute respiratory distress syndrome and damage to other organs, the leading cause of death in COVID-19 patients.

“If you control or are able to mitigate the excessive release of TNF-a, you can eventually reduce mortality,” said Asaf Tzachor, a researcher from the IDC Herzliya School of Sustainability and the lead author of the study.

During cultivation, growth conditions were adjusted to control the algae’s metabolomic profile and bioactive molecules, something that Tzachor refers to as “enhanced” algae.
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

NLRP3 inflammasome inhibitors may help treat early COVID-19, says study

2/26/21 ... study.aspx

A new study by researchers in the U.S. further supports the hypothesis that the unregulated release of inflammatory cytokines is responsible for the local and systemic inflammation that is associated with multi-organ damage and death in severe coronavirus disease 2019 (COVID-19). This could lead to the identification of possible drug targets in early disease.

The ongoing COVID-19 pandemic is caused by infection with the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The disease is characterized by severe lung injury and systemic inflammatory damage to multiple organs. The presence of very high levels of inflammatory cytokines in these patients has led to it being termed a cytokine release syndrome (CRS) or cytokine storm.

The study, which was released as a preprint on the bioRxiv* server, reports the value of targeting the NLRP3 inflammasome in early infection with this virus to prevent the CRS and its associated adverse outcomes.

Cytokine storm in COVID-19

In earlier research, the use of the IL-1 Receptor antagonist (IL-1Rα) anakinra in mild to moderate COVID-19 has been reported, indicating a reduction in mortality with this approach. The IL-1β inhibitor, canakinumab, a neutralizing monoclonal antibody, has also been reported to reduce adverse outcomes.

However, IL-1β must be processed within the cell before it is activated. This processing occurs mostly within the inflammasomes. Inflammasomes are macromolecular complexes found within the cytosol.

The NOD-, LRR- and pyrin domain-containing 3 (NLRP3) inflammasome has been found to be activated by several SARS-CoV-2 proteins. These include the open reading frame (ORF) 3a, ORF8b, and viroporin 3a.

In vitro studies confirm that the virus induces the formation of this inflammasome. The presence of aggregates of NLRP3 inflammasomes in the lungs of patients who died of COVID-19 further supports this.

These inflammasomes are also found in the peripheral blood mononuclear cells (PBMCs) of such patients. Overall, these findings indicate that NLRP3 inflammasome activation occurs in moderate to severe COVID-19.

The case for early NLRP3 inhibition

If early treatment of such cases was possible, it might prevent the need for hospitalization and ease the enormous burden currently being placed on healthcare services. The current study aims to explore the potential for early inhibition of NLRP3 inflammasome activation and the resulting IL-1β release in COVID-19.

NLRP3 activation leads to CRS

There is a twofold elevation of IL-1β following SARS-CoV-2 infection, while the IL-6 levels are still higher, relative to their levels in healthy individuals. The levels of the natural IL-1 Receptor antagonist (IL-1Ra) are 2.5-fold higher in infected people.

This is a common finding in autoinflammatory conditions rather than infection, with both IL-6 and IL-1Ra being induced by IL-1β. In addition, tumor necrosis factor-alpha (TNFα), IL-10, and urokinase plasminogen activator receptor (uPAR) are all at significantly higher levels in these patients, even without overt disease symptoms or signs. Such a rise in the latter is associated with adverse outcomes in COVID-19.

Circulating white blood cells in SARS-CoV-2 infected patients with asymptomatic or mild COVID-19 showed a twofold rise in NLRP3 levels, while the expression of IL-1β in these cells was 5.5-fold higher. These show a strong correlation with each other at both gene and protein levels.

There was a fourfold rise in the expression of caspase-1, again, in significant association with NLRP3 levels.

The conclusion drawn from these findings is that SARS-CoV-2 infection triggers a molecular cascade that ends in higher levels of NLRP3 activation and IL-1β release, with the latter being the pivot on which disease severity turns.

The observable worsening of the clinical disease features, and the fatal outcomes, occur later in the course of the infection, when viral RNA is often undetectable in the tissues. At this point, the exaggerated secretion of cytokines is the most obvious feature.

This temporal pattern indicates that CRS is a downstream event of IL-1β secretion, the latter triggering the release of other inflammatory cytokines that end in organ damage.

Current anti-inflammatory therapies

Unlike anakinra and canakinumab, therefore, inhibitors of active IL-1β processing and release might help to prevent this often fatal cascade of reactions. As such, patients infected with the virus could be treated by a specific inhibitor of NLRP3 early in the course of the infection, thus bypassing the entire IL-1β-CRS cycle.

The only oral inhibitor specific against NLRP3 at present is OLT1177 (rINN dapansutrile), which has been found to be of use in two inflammatory conditions, gout exacerbations and heart failure.

Colchicine has been reported to be of use in reducing hospitalizations and/or deaths in COVID-19 patients. This drug also reduces cardiovascular events. The underlying mechanism in both cases is likely to be its ability to inhibit IL-1b-mediated inflammation.

Colchicine is not a direct inhibitor of NLRP3, however, and it does have other effects, on the cytoskeleton components called microtubules and integrins, as well as cell migration.

What are the implications?

The study demonstrates that “early in SARS-CoV-2 infection, NLRP3 activation takes place and initiates the CRS. Thus, NLRP3 is a target to reduce the organ damage of inflammatory cytokines of the CRS.”

A reduction in NLRP3 activation could also reduce Il-18 processing, a significant gain as the latter is involved in the onset of the Macrophage Activation Syndrome (MAS)-like disease in COVID-19. High levels of circulating IL-18 are associated with increased severity of disease and poor prognosis in COVID-19.

The use of a compound that specifically inhibits NLRP3 activation would thus prevent both IL-1βas well as IL-18 release, thus combating COVID-19 by two different pathways.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:

Marchetti, C. et al. (2021). Targeting of the NLRP3 Inflammasome 1 for early COVID-19. bioRxiv preprint. doi:, ... 4.432734v1
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Re: The Cytokine Storm & COVID-19

Post by trader32176 »

This is the first time I've seen NLRP3 mentioned in studies Tim.

Studies that are in the mainstream pandemic news.

I'm still paying attention to the Bio edge. Very few comment on the edge because they don't study enough to know where it is.

( curncman, rrao11, strawpatch, howzitgoing, and RB are watching the edge also - imo)

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