Thread by @patientled

Good morning! The @polybioRF 2024 Fall Symposium is kicking off shortly, and we will be live tweeting the entire event! Follow along on this 🧵 1/

https://twitter.com/polybioRF/status/1854546173199110511

Some details on new interventional trial on larazotide for pediatric Long COVID, the only pharmacological trial currently ongoing for children. Study is being expanded to include adults, check out the QR code for more info. /70

Next up is Dr. Marcelo Freire from UCSD talking about Mucosal-System molecular signatures in Long COVID. His lab asks, how does oral tissue harbor pathogens? How do mucosal membranes influence viral persistence? /71

Constructing the human salivary proteome to better understand how saliva can inform our understanding of health and disease. Datasets are publicly available! /72

Proteomic analysis from people recovered from COVID-19 had signatures of immune and vascular dysfunction. Not Long COVID per se, but demonstrates lasting impacting of infection (measured up to 90 days post-infection). /73

Novel analytical pipelines for salivary protein biomarker identification using machine learning /74

Total Long COVID cases had decreased IgA in plasma, but increased IgG in saliva. This suggests continual IgA production in the oral mucosa, which could indicate viral persistence /75

Correction - above tweet should say "increased IgA", not IgG /76

More features from neutrophils - developing a method of quantify netosis with immunofluorescence. Spike protein appears to enhance NETosis /77

Now we have Dr. Yingleong (Rigel) Chan from UMass Chan Medical School, presenting on the influence of SCoV2 infection in Alzheimer's and neurodegenerative diseases. A very important area of study! /78

Dr. Chan highlights the fact that long-term adverse outcomes of SCoV2 infection are still unknown. We know viruses can lead to things like cancer, autoimmune disease, and dementia a very long time after clearing the acute infection. /79

Alzheimer's Disease (AD) is now thought to be initiated by neurotropic viral infection, which causes an accumulation of pathological processes over many decades. /80

Dr. Chan's lab uses cerebral organoids to model a functional brain in vitro. We can use these organoids to study the way infections impact the brain. In this example, they found HSV-1 infection increased expression of AD-related genes /81

Viral proteins were not detected in infected organoids but RNA was detectable, suggesting SCoV2 may be entering some kind of latent/non-replicative state. Most of these changes subside by 24 hrs, but astrocyte marker GFAP increased /82

Hypothesis: SCoV2 infects astrocytes, eventually resulting in cell death and release of GFAP and viral RNA. Future research will focus on characterizing astrocyte responses, interaction with herpesvirus infections that can trigger AD. /83

Next up is Dr. Zian Tseng who will discuss the COVID POST SCD (POstmortem Systematic invesTigation of Sudden Cardiac Death) Study /84

Sudden Cardiac Death (SCD) is a very common postmortem diagnosis but is poorly defined, often diagnosed without any kind of autopsy or physical exam. Goal is to work with San Francisco medical examiner to investigate causes of natural SCD. /85

Very ambitious study design, performing autopsy on 97% of individuals who died suddenly outside of a hospital setting. Only half of these individuals died from something cardiac related! /86

This type of study design can be leveraged to study tissues in Long COVID patients who die suddenly, providing a crucial resource to study viral persistence in people who are NOT hospitalized /87

Can compare results from surveillance study from before vs after onset of COVID-19 pandemic. Have already discovered EBV transcripts in the gut of pre-2020 tissues. Over 1200 unique biospecimens! /88

Next up we have Dr. Gene Tan who will discuss antibody responses in a Long COVID case control study at UCSD /89

Found a decrease in generation of neutralizing antibodies in people with Long COVID versus convalescent controls (CC), which was driven by a greater effect size in females /90

What is driving this disparity? Generated chimeric proteins in a SCoV1 backbone, which allows us to determine which specific domain of the molecule is impact neutralization. Both groups had antibodies against RBD, but disparity appeared when NTD was included /91

Note that these are preliminary results and need to be further validated, but suggests females have greater difference in NTD reactivity /92

Differences in immunogenicity against alphacoronavirus and betacoronavirus, suggests there may be conserved regions among betacoronaviruses that influence response in LC patients /93

In another set of experiments, they replicated data showing that female Long COVID participants had higher IgG responses to EBV, would like to follow people with high or low IgG to see if it impacts prevalence of LC. Interestingly, no differences with VZV /94

Dr. Tan's conclusions: /95

Next is Chiara Giannarelli from NYU on cardiovascular complications of SARS-CoV-2. Early in the pandemic, they noticed that one particular cardiovascular complication during acute disease – myocardial infarction, specifically from the accumulation of lipids in arteries. /96

Discussing investigations of coronary autopsy specimens showing that the virus was more more in the vascuature compared to perivascular fat. And they also found infected macrophages. /97

Continued investigations showed delayed clearance in foam cells after infections. They then went on to see that the infected tissues had a significant inflammatory response. /98

Suppressing NRP1+ in macrophages supressed SARS-CoV-2 infection. Takeaway is that SARS-CoV-2 infects macrophages and increases plaque inflammation. This could help explain why heart attack is more common after infection. Is there a vascular reservoir? /99

Collecting samples now to try to identify the relationship between this particular reservoir and symptoms. Also planning to correlate with other immune responses. /100

Next: Christopher Dupont from the J Craig Venter Institute talking about tissue data and analysis pipelines.
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Very clear as of ~15 years ago that the microbes in our body are very diverse. Every epithelial layer of the body has a different microbiome, so it's important to build data pipelines that are able to manage the scale and diversity of the microbiome./102

Very impressive slides show the level of detail the team is able to manage – gathering entire viral and bacterial genomes from different samples, like oral plaque and ligament from samples taken during CCI surgery /103

Partnering with industry to develop and test methods to allow for more accessible access to some of these techniques. Also looked at lung microbiome with data from Price lab (discussed many times today!) Challenges with samples, but new techniques were developed! /104

Also looking at endometriosis samples. /105

Next: Benjamin Readhead from Arizona State on validation of CMV-based biomarkers for Alzheimer's clinical trials. Or: There and Back Again, A Herpes Tale (love the LOTR reference!) /106

Talking about how Alzheimer's associated CD83+ microglia subtype is associated with IgG4 production in colon – a type of IgG that is considered to be anti-inflammatory. /107

Hypothesis is that persistent CMV infection in gut might be related to Alzheimers! /108

Almost everyone with the CD83+ microglia had a gut CMV infection. /109

Wondered if vagus nerve could be the connection between infection in gut and brain - samples again showed a correlation in people with CD83+ microglia /110

Considering clinical trials of of antivirals against CMV in CD83+ Alzheimer's but even without treatments, a blood-based biomarker for CD83+ microglia would be valuable. /111

Next is Matthew Frank from University of Colorado Boulder talking about a “multiple hit” model of LC. /112

Neuroinflammation is present in LC and can drive symptoms. SARS-CoV-2 antigens are neuroinflammatory. Looking at a "two hit" model involving priming and then a second hit that produces a neuroinflammatory response. /113

Experimenting in a mouse model. S1 is injected into CNS, then a week later a bacteria injection is done to see what types of responses occur. /114

Findings are that the first hit changes the effects after the second hit. What drives this priming phenomenon? Could lower corisol be modulating the immune system /115

Found that S1 produces a chronic reduction in brain glucocorticoids – which might be reducing production, which would have profound effects throughout the body. /116

Lower glucocorticoids might disinhibit immune cells, making the brain more vulnerable to later immune challenges like infections. /117

Next is Max Qian from J Craig Venter Institute talking about using machine learning to identify Long Covid endotypes. /118

Unsupervised cluster analysis is not effective in grouping pwLC – so they use an approach called Deep Poisson Factor Modeling. /119

Symptom surveys often have dozens or hundreds of data points, so they had to identify the right number of "topics" to use in analysis. They were able to group specific symptoms into groups that are often correlated. /120

After testing a variety of clustering approaches, they identified 16 patient clusters based on symptom signature. /121

Some symptoms were in multiple clusters, so they worked on slimming things down into a smaller number of groups. /122

An example is a cluster of pulmonary, neurological, and cardiovascular symptoms. Another example is one with sensory, hormonal, and GI symptoms. /123

Now they are ready to apply this to assay (not just questionnaire) data and continue to identify new patterns. /124

Up next! "Potential SARS-CoV-2 persistence & T cell activity in the female reproductive tract" —— Nadia Roan, PhD @UCSF /125

@UCSF @UCSF has found viral persistence in GI tract, which is immune tolerant. This led to interest in another immune tolerant site, female reproductive tact /126

@UCSF And sex differences show women are more likely to develop #LongCovid /127

@UCSF Their study is leveraging HIV infrastructure to study to get the multiple biopsies from 5 female patients and 5 controls /128

@UCSF The endometrium has high T cell frequency compared to other sites. /129

Example of HIV study methods they are borrowing to look for SARS CoV2 infect cells /130

More examples of how their HIV infrastructure can look for persistent infected cells/131

Study just started! /132

UP NEXT: "Larazotide in the treatment of SARS-CoV-2 spike protein translocation/ 'leaky gut'” — Alessio Fasano, MD @Harvard /133

@Harvard How long are kids infectious? /134

@Harvard Virus may leak from GI tract and have IG reflecting on going antigen exposure /135

@Harvard Spectrum between MIS-C and #LongCovid /136

@Harvard Larazotide may increase clearance of spike /137

FDA approved clinical trial now under way /138

Demographics of study /139

Bottom line: Larazotide group seem to recover earlier /140

Spike cleared much faster in Larazotide group /141

Spike correlates with GI symptoms and inflammation /142

Larazotide group had faster and sustained recovery, now they're doing trial in #LongCovid /143

UP NEXT: "Long COVID: Defining the viral RNA reservoir in the gastrointestinal tract" — Sara Cherry, PhD University of Pennsylvania

Use more sophisticated models to map infection. Detected virus much longer in GI tract than bronchial cultures. /145

Paxlovid has activity in GI tract but Molonupiravir did not. /146

Genes induced in gut are not in induced in the lung / 147

Different consideration for treating: interferon and JAK inhibitor — do we block or not? /148

Need to find which antivirals and anti inflammatories are active in the gut /149

UP NEXT: "Low-dose rapamycin long COVID clinical trial" — @microbeminded2, @polybioRF

@microbeminded2 @polybioRF Rapamycin was isolated in 1960's expedition in Easter Island - the natives did not contract tetanus while walking barefoot, and they were interested what was in the soil. /150

@microbeminded2 @polybioRF In low doses, it may support immune system and is being used in lifespan extension, including dogs! /151

@microbeminded2 @polybioRF When talking about lifespan, @polybioRF is interested in the impact of infection on lifespan! /152

@microbeminded2 @polybioRF Is something in rapamycin controlling infection, leading to extended lifespan? People have lower infection rate on the drug. /153

@microbeminded2 @polybioRF It also up-regulates interferon signaling! /154

Led to enhanced response to influenza vaccine /155

Rapamycin led to more mild cases of COVID, and NO CASES of #LongCovid /156

RCT pilot trial of 80 #LongCovid patients announced — @VirusesImmunity will measure interferon, t-cell, and viral persistence! Also measure endopat. /157

@VirusesImmunity LAST SPEAKER: "Long COVID, ME/CFS, and Lyme+ clinical trial and clinical care updates" — @PutrinoLab, PhD Icahn School of Medicine at Mount Sinai /158

@VirusesImmunity @PutrinoLab Trial on Humanity Neurotech — brand new, no one has tried this! /159

@VirusesImmunity @PutrinoLab 60% of #LongCovid patients report cognitive dysfunction significant enough to affect daily function even mild cases lead to this. /160

@VirusesImmunity @PutrinoLab Neuroinflamation is clear driver of #LongCovid related cognitive impairment, is demonstrated on imaging /161

@VirusesImmunity @PutrinoLab Therapeutics that target to neuroinflammation, i.e. LDN. Some drugs exist, but efficacy and response are spotty! /162

@VirusesImmunity @PutrinoLab Neuroinflammation has relationship to mitochondria dysfunction, complex-co-dependent cycle. So we can influence mitochondria.. If you stress just enough you can cause significant anti-inflammatory effect on neurons. This is what the device does!/163

@VirusesImmunity @PutrinoLab Placebo controlled trial will be started in Jan 2025! People can use device from home, and use on daily basis. 4 weeks, and reassess baseline. See if any improvement, and if it sustains afterwards. /164

@VirusesImmunity @PutrinoLab Questions:
- Metformin useful ? @PutrinoLab: some really respond with PEM, some don't. GI side effects can be issue - dose sensitivity. /165

@VirusesImmunity @PutrinoLab @polybioRF creating new framework for trials of what drugs prevent #LongCovid /166

@VirusesImmunity @PutrinoLab @polybioRF That's a wrap! Thank you @polybioRF for this incredible symposium!