Researchers have discovered new ways in which the COVID-19 virus causes human immune cells to overreact, a deadly part of the disease.

Led by researchers from NYU Grossman School of Medicine and the Perlmutter Cancer Center at NYU Langone Health, the new study found that SARS-CoV-2, the pandemic virus, interacts with specific proteins on immune cells, causing these cells to release abnormally high levels of immune signaling proteins called cytokines (a "cytokine storm"). These cytokines, in turn, cause fluid buildup in the lungs and makes it hard to breathe.

Before the current study, SARS-CoV2 was thought to interact mostly with a protein called angiotensin converting enzyme 2 (ACE2), which is present on the outer surfaces of lung cells. The virus evolved to have a protein spike that snags ACE2 as the first step in invading human lung cells, where the virus multiplies. Accordingly, all approved COVID-19 antiviral drugs and vaccines work by interfering with, or protecting against, this viral spike/ACE2 interaction.

Mounting evidence, however, suggests that the virus also interacts directly with human immune cells, which have little ACE2 on their surfaces. Published online in the journal Immunity, the new study identified six surface proteins on immune cells that attach to the viral spike protein, but in different places than ACE2.

The virus does not appear to replicate in immune cells, as it does when it binds with ACE2 on lung cells, but instead, the newfound interactions cause damaging immune responses, say the study authors. Based on their new understanding, the team generated nanobodies, a type of protein-based therapeutic, to block viral attachment to both ACE2 and the newfound immune cell surface proteins (receptors).

"Our results suggest that we can simultaneously keep SARS-CoV2 from invading lung cells while also blocking the dangerous hyperactivation that the viral spike protein causes in immune cells," says corresponding study author Jun Wang, PhD, assistant professor in the Department of Pathology at NYU Langone Health. "Such dual action, if confirmed in human studies, could more fully address a disease that has taken more than 3.3 million lives globally."

In the study, the authors used a technique called single-cell RNA-sequencing to examine which genes were expressed, and consequently, which proteins were built, in cells present in lung fluid taken from COVID-19 patients, including cells lining the lungs (epithelial cells) and immune cells.

Their high-speed receptor screening approach identified and described the six human immune cell membrane proteins that bound to SARS-CoV-2 spike protein. Five were C-type lectins, carbohydrate-binding protein units with many biological functions, including in immune defenses. The authors also found that SARS-CoV-2 spike attaches to Tweety family member 2, a protein that controls the entry of charged particles (chloride) into cells, and possibly a switch that activates immune cells. Importantly, the team found the virus spike interacts with these activating surface proteins mostly on myeloid cells, a group of vital immune cells that arise in bone marrow and circulate in the blood.

In addition, the study authors generated nanobodies that blocked SARS-CoV-2 Spike/ACE2 and myeloid cell interactions. Nanobodies are smaller derivatives of antibodies, immune proteins that form a surveillance system by recognizing invading microbes. Industry designs synthetic antibodies that specifically glom onto targets of their choice, which can change the action of disease-causing proteins. More recently, researchers began fine-tuning just pieces of antibodies, called nanobodies, which are easier to make.

"Our study will change how the field thinks about mechanisms behind COVID-19, demonstrating that viruses can directly reprogram immune cells with potentially deadly consequences," says co-first study author Qiao Lu, PhD, a post-doctoral scholar in Jun's lab.

As a next step, he says, the research team plans to explore their nanobody's potential in pre-clinical and clinical studies in patients with severe cases of COVID-19, as well as in those with emerging virus mutants that cause more severe symptoms.

Along with Wang, co-corresponding authors for the study were Siyuan Ding in the Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, and Qi Xie of the Institute of Basics Medical Sciences, Westlake Institute for Advanced Study in Hangzhou, China.  Along with Lu, co-first authors were Jia Liu of the Department of Pathology at NYU Langone Health; and Shuai Zhao of Westlake University. Also study authors from the Department of Pathology at NYU Grossman School of Medicine were Triantafyllia Karakousi, Ze Zhang, Xufeng Chen, Marianna Teplova, Tenny Mudianto, Jasper Du, Alberto Herrera, Sergei Koralov, Iannis Aifantis; and Leopoldo Segal in the Department of Medicine; as well as Payal Damani-Yokota, Maria Kaczmarek, Stephen Yeung, Kamal Khanna, and Kenneth Stapleford in the Department of Microbiology. 

Additional study authors were Xiaojuan Ran, Hongzhen Tang, Haijing Deng, Zhilin Long, Shumin Jin, Peng Lin, and Ming Zhou of the Institute of Basics Medical Sciences, Westlake Institute for Advanced Study; Maria Florencia, Gomez Castro, Juhee Son, Ruochen Zang, Broc McCune, Rita Chen, and Michael Diamond of the Washington University School of Medicine, St.  Louis; Maudry Laurent-Rolle, Jack Hsu, Tina Tianjiao Su, and Peter Cresswell of the Department of Immunobiology at Yale University School of Medicine; Jianbo Dong, Betty Huang, Yue Liu of Ab Studio Inc.; Fei Tang, Xianwen Ren, and Zemin Zhang of the Beijing Advanced Innovation Center for Genomics at Peking University; Renhong Yan and Qiang Zhou of the Joint Research Center of Hangzhou First Hospital Group and Westlake University; Jia Cui of Kactus Biosystems in Shanghai; James Zhu and Tao Wang of the Quantitative Biomedical Research Center at University of Texas Southwestern Medical Center; and Jianzhu Ma of the Department of Computer Science at Purdue University.

This work is supported by internal funds provided by the Office of Science & Research at NYU Langone Health, Westlake Education Foundation, Tencent Foundation grant XHTX202001008, Hangzhou Science and Technology Development Foundation grant 20202013A05, a Cancer Research Institute Irvington Postdoctoral Fellowship, and National Institutes of Health grants P30 DK052574, R00 AI135031, R01 AI150796, R01 AI157155, R01 AI143861, AI143861S1, and R01-AI059167. Wang, Lu, and Liu from NYU, Huang, Dong and Yue Liu from Ab Studio Inc., are named as inventors on patent applications that describe the anti-SARS-CoV-2 blocking nanobodies. Wang is also a paid consultant for Lilly Asia Ventures and Rootpath Genomics (work not related to the current study).