Students, Postdoctoral Fellows, and Faculty Team Up to Advance Immunology Research on COVID-19

Members of the Sinai Immunology Review Project. From left to right: Matthew Spindler; Louise Malle; Berengere Salome, PharmD, PhD ; Miriam Merad, MD, PhD ; Luisanna Paulino; Verena van der Heide, PhD; and Nicolas Vabret, PhD. Via Zoom, left to right, top row to bottom: Alvaro Moreira, MD; Robert Samstein, MD, PhD; Rachel Levantovsky; Matthew Park, Conor Gruber; and Emma Risson.

The unprecedented generation of non-peer-reviewed scientific information about COVID-19 in just a few months helped galvanize more than 50 members of the Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai into forming a group to parse through the data.

The effort, called the Sinai Immunology Review Project, is composed of faculty, postdoctoral fellows, and graduate students. By sharing their knowledge and expertise, project members evaluate the quality of the research being posted to the bioRxiv and medRxiv preprint servers and help advance the most significant findings that are related to their field. Peer review is quality control provided by a panel of experts who evaluate whether a study has used proper research methods and is scientifically valid.

“Reviewing the preprinted studies benefits the authors and the scientific community, provides the public with access to what is being discussed, and helps reinforce scientific credibility,” says one of the project leaders, Nicolas Vabret, PhD, Assistant Professor of Medicine (Hematology and Medical Oncology) and a member of the Precision Immunology Institute at the Icahn School of Medicine. “To help pick the best treatments for COVID-19 you need to have a strong understanding of the pathology of the disease and we are able to help with this.” Many of the researchers who are working from home during this pandemic welcome the collaborative opportunity to contribute to the field.

Since mid-March, the project’s participants have ranked more than 2,000 studies according to their immunological relevance and written 130 reviews that are then posted alongside the corresponding study on the preprint servers. To ensure that the best science is elevated, each summary is written by a fellow or student specializing in a specific area of the immune system and then reviewed by a faculty member. A website built by Nicolas Fernandez, PhD, a computational scientist at Mount Sinai’s Human Immune Monitoring Center, hosts all of the reviews.

Recognition of this work recently led the editors of Nature Reviews Immunology to reach out to Miriam Merad, MD, PhD, Mount Sinai Professor of Immunology and Director of the Precision Immunology Institute, to form a unique collaboration. Mount Sinai is now publishing three short commentaries in the publication each week on the most promising immunological findings on COVID-19.  Within a few days of launching the collaboration with Nature Reviews Immunology, Mount Sinai’s work was viewed more than 10,000 times.

Project co-leader Robert Samstein, MD, PhD, Assistant Professor of Radiation Oncology, and a member of the Precision Immunology Institute, says, “This has been a massive effort. It’s been a great opportunity for Mount Sinai’s trainees to integrate all of their knowledge and provide a summary for the scientific community,” so quickly and efficiently. “The huge flurry of output on COVID-19 by the scientific community is unprecedented and this effort is responding to that.”

While speed and the open sharing of information are vital to enhancing further understanding of the COVID-19 health emergency, the peer-review process is an essential part of scientific advancement and the preprint servers that are now publishing all of this new information were never meant as a replacement. In the absence of the peer-review process, members of the Immunology Project are stepping in to provide their expertise in the best way they can, says Dr. Samstein.

“By doing this we can really help make it easier for policy makers, physicians, and scientists to see what the best information is as it evolves and have a direct impact on treatments,” adds Dr. Vabret.

As time goes on, the medical and scientific community is learning more about the disease and calling into question some of its earliest hypotheses about possible treatments. This makes the need to highlight quality science to inform decision-making a continued priority, according to Dr. Vabret.

Mount Sinai’s Antibody Test for COVID-19 Receives Emergency Use Authorization from FDA

A renowned team of virologists, pathologists, and clinicians at the Mount Sinai Health System developed, validated, and launched a blood test for COVID-19 antibodies that received the U.S. Food and Drug Administration’s (FDA) emergency use authorization late Wednesday.

The blood test determines whether individuals have antibodies to the SARS-CoV-2 virus that causes COVID-19. It is used for the qualitative detection of human IgG antibodies in serum and plasma that is collected from individuals suspected of having been infected with SARS-CoV-2.

Early development of the assay, led by Florian Krammer, PhD, Professor of Microbiology at the Icahn School of Medicine at Mount Sinai, enabled Mount Sinai to become the first health system in the nation to undertake a convalescent plasma program that transfers the antibody-rich plasma from recovered COVID-19 patients into those who are critically ill.

To date, Mount Sinai has identified more than 1,900 donors who are eligible to provide their antibodies. A total of 141 patients have received the protocol, and the results are being evaluated clinically.

Under the leadership of Peter Palese, PhD, Horace W. Goldsmith Professor and Chair of the Department of Microbiology, Mount Sinai has built one of the world’s leading academic institutions for the study of viruses and emerging pathogens. “The COVID-19 antibody test is not only helpful in identifying individuals who could be donors for the convalescent plasma program but also identifies persons who can safely go back to work now that they are immune to the virus,” Dr. Palese says. This important step would allow the nation to return to economic productivity.

“We are grateful to the FDA for granting this expanded authorization so that we can deploy this vital test to the community at large,” says Carlos Cordon-Cardo, MD, PhD, Irene Heinz Given and John LaPorte Given Professor and Chair of Pathology, Molecular and Cell-Based Medicine. Dr. Cordon-Cardo oversaw the validation of the test that is produced by the Mount Sinai Laboratory, Center for Clinical Laboratories. The Mount Sinai Hospital’s Clinical Laboratories are certified by the Clinical Laboratory Improvement Amendments and accredited by the College of American Pathologists.

According to Dr. Krammer, the antibody test can, in some cases, pick up the body’s response to infection as early as three days post-symptom onset and is highly specific and sensitive. “We have shared the toolkit needed to set up the test with more than 200 research laboratories worldwide to help mitigate this global crisis,” Dr. Krammer says.

David L. Reich, MD, President of The Mount Sinai Hospital, and Judith A. Aberg, MD, Chief of the Division of Infectious Diseases and Immunology in the Department of Medicine, have led Mount Sinai’s convalescent plasma program. “The exchange of ideas between clinicians and scientists and our intense drive to innovate is the catalyst that led to this achievement,” says Dr. Reich. “Mount Sinai will continue to advance the science and medicine in the fight against COVID-19.”

Preliminary Case Series Leads to New Questions About the Disease Progression of COVID-19 in Patients with Blood Clots in the Lung

Hooman D. Poor, MD, Assistant Professor of Medicine (Pulmonology, Critical Care and Sleep Medicine, and Cardiology)

A small, preliminary case series led by physicians at the Icahn School of Medicine at Mount Sinai found that five severely ill patients with the SARS-CoV-2 virus responded to the blood-clot-busting drug tPA when it was introduced as a life-saving measure. This response, and the large number of critically ill COVID-19 patients who have blood clots in their lungs, have raised new questions concerning the course of the disease and may present new possibilities for treating it.

“This case series pushes us to consider avenues of clinical investigation that are different from what they are now,” says the paper’s first author, Hooman D. Poor, MD, Assistant Professor of Medicine (Pulmonology, Critical Care and Sleep Medicine, and Cardiology). “Perhaps we should be looking at the disease from the standpoint of clots that form in the blood vessels and travel to the lungs.”

Dr. Poor says that more testing will be needed to determine whether the clots are the “inciting events in a subset of patients,” and not a complication that develops after these patients develop acute respiratory distress syndrome (ARDS). “ARDS looks the same, but it’s not,” he says. It requires “dramatically different treatments.”

According to the paper, the critically ill COVID-19 patients had relatively well-preserved lung mechanics, and did not develop stiffness of the lungs, despite severe gas exchange abnormalities. This feature is more consistent with pulmonary vascular disease and not with classic ARDS. The COVID-19 patients also demonstrated markedly abnormal coagulation with elevated D-dimers—small protein fragments present in the blood after a blood clot—and higher rates of venous thromboembolism, a condition where blood clots that form in the deep veins of the legs or groin travel and become lodged in the lungs.

Click here to read the paper titled “COVID-19 Critical Illness Pathophysiology Driven by Diffuse Pulmonary Thrombi and Pulmonary Endothelial Dysfunction Responsive to Thrombolysis.”

Mount Sinai’s paper cited autopsy studies from the SARS outbreak in the early 2000s, which revealed that patients had “pulmonary thrombi, pulmonary infarcts, and microthrombi in other organs.” SARS-CoV-1, the virus that caused SARS, and SARS-CoV-2, which causes COVID-19, belong to the same family of coronaviruses.

With mounting evidence that a consistent pattern of COVID-19 patients are presenting with blood clots, front-line clinicians at the Mount Sinai Health System and throughout the United States are reassessing and modifying existing guidelines that incorporate anticoagulation therapies.

Mount Sinai has provided treatment guidelines for its eight hospitals that address the significant role microthrombi—tiny clots composed of platelets—may play in patients with severe cases of COVID-19. The new guidelines help to inform clinical decision-making on administering anti-coagulation therapy for critically ill patients throughout the Health System. They call for patients who require hospitalization to be assessed for blood clots in their lungs by measuring their oxygen levels, testing for markers of clotting in their blood, and assessing their difficulty breathing or shortness of breath. Patients in intensive care units may also be eligible for a clinical trial at Mount Sinai that will examine the use of thrombolysis in respiratory failure due to COVID-19.

The recommendation was made by a panel of expert clinicians within Mount Sinai, and was based on published and rapidly emerging data, international and local experience, and autopsy reports.

Recently, the International Society on Thrombosis and Haemostatis recommended that all hospitalized COVID-19 patients, even those not in intensive care units, should receive prophylactic-dose low molecular weight heparin—a blood thinner—unless they have contraindications, such as active bleeding.

“If patients with COVID-19 show a small problem with their lungs, perhaps we should start them on blood thinners to prevent the clots from reaching the point where we have to administer tPA,” says Dr. Poor. “However, this treatment paradigm with early anticoagulation will need to be evaluated with well-designed clinical trials.”

Mount Sinai Turns Hundreds of Machines for Sleep Apnea into Hospital Ventilators, Shares Instructions Worldwide

Members of the Mount Sinai team that created the ventilator prototype seen here, included, from left, Drew Copeland, RPSGT; Thomas Tolbert, MD; Brian Mayrsohn, MD; and Hooman Poor, MD.

A team of pulmonologists, anesthesiologists, sleep and critical care specialists, and medical students at the Mount Sinai Health System are reconfiguring hundreds of donated machines that are typically used at home for sleep apnea and deploying them as ventilators to be used for severely ill patients who are hospitalized with COVID-19. Mount Sinai has shared the protocols and instructions with the Greater New York Hospital Association and the American Thoracic Society, as well as with other hospitals that are dealing with a national shortage of invasive ventilators during this pandemic. COVID-19 affects the respiratory system and has greatly increased the number of patients who are entering intensive care units and require assisted breathing.

When Mount Sinai received a shipment of 200 ResMed VPAP ST machines as a donation from Elon Musk, Chief Executive Officer of Tesla, Inc., in late March, a Health System task force was immediately organized to repurpose them. Within several days, the team put together a prototype that was tested in the Simulation HELPS Center at Mount Sinai, a unique laboratory run by the Department of Anesthesia that enables clinicians to simulate human responses to innovative technologies and procedures.

Three important modifications were made by the Mount Sinai team. First, a connection to an endotracheal tube replaced the typical mask that can present a risk of COVID-19 aerosolization; second, alarms that can alert clinicians if there is a problem with air flow were included; and third, the team enabled doctors and respiratory therapists to view and control the machine’s settings from outside the patient’s room, so they do not need to enter the room to make minor adjustments.

These VPAP machines will be used as an option under the current circumstances at Mount Sinai to prevent a shortage of invasive ventilators needed to serve the ongoing surge of patients. They are preferable to splitting invasive ventilators that serve two patients at the same time, a move that many hospitals are concerned they may have to pursue as a last resort.

Among the clinicians leading the effort at Mount Sinai is Charles A. Powell, MD, Janice and Coleman Rabin Professor of Medicine, Chief of the Division of Pulmonary, Critical Care, and Sleep Medicine, and Chief Executive Officer of the Mount Sinai – National Jewish Health Respiratory Institute. Dr. Powell says the machines can be used “in patients who do not require all the power of a regular ventilator, freeing up those conventional devices for the acutely ill.” He adds, “Our objective is to share our protocols widely with our colleagues around the globe facing this crisis. This project is a demonstration of the success of the team science collaborative research infrastructure at Mount Sinai that allowed us to make these innovations quickly.”

Any type of high-performing sleep device that delivers a comparable level of pressure to the ResMed VPAP ST model can work as a repurposed ventilator, according to Drew Copeland, Director of Operations for the Sleep Program at the Mount Sinai Health System. He says, “For many patients, this can save their life. We are not yet at a critical mass for ventilators but we may be getting there. This is a moving target. Hopefully, we can keep pace.”

After the first prototype was developed, Mr. Copeland enlisted a team of medical students from the Icahn School of Medicine at Mount Sinai to write the instructional user manual. They completed it in one day.

The students are now assembling the machines to be used throughout the Health System’s eight hospitals in the event of a shortage of invasive ventilators. Two floors of the medical school’s library have been set up as a staging area for the makeshift assembly line. The goal is to have all of the machines ready to be deployed by the end of this week.

SARS-CoV2: How a Low-Powered Virus Turns Deadly 

File photo of the team from the tenOever Laboratory, from left to right: Kohei Oishi, PhD, Tristan Jordan, PhD, Daniel Blanco-Melo, PhD, Skyler Uhl, PhD candidate, Ben tenOever, PhD, Rasmus Moeller, PhD candidate, Maryline Panis, Lab Manager, Ben Nilsson-Payan, PhD, and Daisy Hoagland, PhD candidate

Early laboratory tests show the SARS-CoV2 virus, which leads to COVID-19, behaves very differently from the flu or common respiratory syncytial virus (RSV) in that it travels under the radar and enters human and animal cells quietly, eliciting a low-powered immune response that tends to fester, according to preliminary research led by Benjamin tenOever, PhD, the Fishberg Professor of Medicine, and Director of the Virus Engineering Center for Therapeutics and Research, at the Icahn School of Medicine at Mount Sinai. The observations, which provide a snapshot of how cells and organisms respond to the SARS-CoV2 virus, were based on studying RNA from live animal models and human cell lines. RSV often occurs in young children with symptoms that mimic the common cold.

“The take-home message of what we found so far is that the immune response to the virus is actually very muted,” says Dr. tenOever. In a typical reaction to the flu or RSV, the body secretes a whole family of proteins or interferons that assemble to take on a variety of functions to prepare for an imminent attack. Some of the interferons directly inhibit the virus. But with the SARS-CoV2 virus, Dr. tenOever says, “We see little to no evidence that the virus-infected cells are secreting these proteins. So a program that should be induced is not launching.” At most, the defense appears to be only 40 percent to 50 percent as strong as it would be for the flu or RSV.

The new virus behaves differently in another way, as well. Whereas the flu is particularly wily in dismantling the innate immune response in several places, SARS-CoV2 does not appear to do so, according to postdoctoral fellow Daniel Blanco Melo, PhD, who was a lead author of the study in Dr. tenOever’s lab. “We may find that the immune response is being blocked by this new virus too, but it won’t be in the same way as the flu,” he says.

According to the scientists, the preliminary findings show that the very stealth nature of SARS-CoV2 may actually account for its lethalness, a hypothesis that complements the virus’s long clinical progression, with many severely ill patients being hospitalized for more than 10 days. The hypothesis also supports the clinical evidence that patients need a strong immune system to fight COVID-19, the disease produced by the SARS-CoV2 virus. Under the leadership of Miriam Merad, MD, PhD, the Mount Sinai Professor in Cancer Immunology and Director of the Precision Immunology Institute, Mount Sinai is working to improve outcomes in critically ill patients who experience an excessive inflammatory response.

“It would almost appear that if you are a healthy individual under the age of 50 and you get this virus your immune system would have no problem tackling it, inhibiting it, and getting rid of it,” says Dr. tenOever. “But in older individuals and those who have comorbidities—those whose immune system is waning—our early data would suggest that their reduced immune system means they’re not aggressively neutralizing this virus, which leaves it to fester in the lungs and keep replicating.” This low-grade inflammation in the body allows the virus to remain under the radar for days as the patient’s lungs become increasingly damaged.

“Maybe what we’re seeing is a slow burn in some people that eventually takes its toll over 10 to 20 days,” says Dr. tenOever. “In the end, the immune system is reacting both to the virus and to the accumulating damage being done to the lungs. So the body goes into this mode of overly trying to repair itself from lungs that are leaking fluid and becoming hypoxic.  By the time these patients come to the hospital it is more about controlling the inflammation to the damage induced by the virus than inhibiting the virus itself.”

Mone Zaidi, MD, PhD, Receives a Lifetime Honor

Mone Zaidi, MD, PhD, left, accepting the honor in February from Steven Chu, PhD, President of the American Association for the Advancement of Science and Nobel laureate in Physics.

Mone Zaidi, MD, PhD, Director of the Mount Sinai Bone Program, and Professor of Medicine (Endocrinology, Diabetes and Bone Disease) at the Icahn School of Medicine at Mount Sinai, has been named a Fellow of the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society. Dr. Zaidi, who accepted the award on Saturday, February 15, at the AAAS conference in Seattle, Washington, was selected for his seminal contributions to endocrinology and skeletal biology, particularly the discovery of pituitary-metabolic circuits that regulate body fat, bone mass, and metabolism.

The lifetime honor was awarded to 443 scientists, of whom 35, including Dr. Zaidi, are in medical sciences. He says, “I am grateful that the research conducted by my laboratory colleagues is appreciated as having an impact on the scientific community.”