Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors (preprint)

Severe coronavirus disease 2019 (COVID-19) is characterized by systemic inflammation and can result in protracted symptoms. Robust systemic inflammation may trigger persistent changes in hematopoietic cells and innate immune memory through epigenetic mechanisms. We reveal that rare circulating hematopoietic stem and progenitor cells (HSPC), enriched from human blood, match the diversity of HSPC in bone marrow, enabling investigation of hematopoiesis and HSPC epigenomics. Following COVID-19, HSPC retain epigenomic alterations that are conveyed, through differentiation, to progeny innate immune cells. Epigenomic changes vary with disease severity, persist for months to a year, and are associated with increased myeloid cell differentiation and inflammatory or antiviral programs. Epigenetic reprogramming of HSPC may underly altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.

Immunogenicity of COVID-19 mRNA Vaccines in Patients with Acute Myeloid Leukemia and Myelodysplastic Syndrome (preprint)

Immunocompromised patients are particularly susceptible to serious complications from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Two mRNA vaccines, BNT162b2 and mRNA-1273, have been shown to have excellent clinical efficacy in immunocompetent adults, but diminished activity in immunocompromised patients. In this study, we measured anti-spike SARS-CoV-2 antibody response, avidity, and surrogate neutralizing antibody activity in Coronavirus Disease 2019 (COVID-19) vaccinated patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Anti-spike SARS-CoV-2 antibody was present in 89% of AML and 88% of MDS patients, but median antibody levels for were lower than in healthy controls (p=0.001 and p=0.04, respectively). SARS-CoV-2 antibody avidity and neutralizing antibody activity from AML patients were significantly lower than controls (p=0.028 and p=0.002, respectively). There was a trend toward higher anti-spike SARS-CoV-2 antibody levels after mRNA-1273 vaccination. Antibody avidity was greater in patients after mRNA-1273 versus BNT162b2 (p=0.01) and there was a trend toward greater neutralizing antibody activity after mRNA-1273 versus BNT162b2 vaccination.

Integrative Metabolomic and Proteomic Signatures Define Clinical Outcomes in Severe COVID-19 (preprint)

The novel coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has ravaged global healthcare with previously unseen levels of morbidity and mortality. To date, methods to predict the clinical course, which ranges from the asymptomatic carrier to the critically ill patient in devastating multi-system organ failure, have yet to be identified. In this study, we performed large-scale integrative multi-omics analyses of serum obtained from COVID-19 patients with the goal of uncovering novel pathogenic complexities of this disease and identifying molecular signatures that predict clinical outcomes. We assembled a novel network of protein-metabolite interactions in COVID-19 patients through targeted metabolomic and proteomic profiling of serum samples in 330 COVID-19 patients compared to 97 non-COVID, hospitalized controls. Our network identified distinct protein-metabolite cross talk related to immune modulation, energy and nucleotide metabolism, vascular homeostasis, and collagen catabolism. Additionally, our data linked multiple proteins and metabolites to clinical indices associated with long-term mortality and morbidity, such as acute kidney injury. Finally, we developed a novel composite outcome measure for COVID-19 disease severity and created a clinical prediction model based on the metabolomics data. The model predicts severe disease with a concordance index of around 0.69, and furthermore shows high predictive power of 0.83-0.93 in two previously published, independent datasets.

COVID-19 Serology in New York State Using a Multiplex Microsphere Immunoassay (preprint)

The emergence of SARS-CoV-2, leading to COVID-19, necessitated the development of new molecular and serological tests. Here, we describe a multiplexed serological assay developed as the global pandemic moved into New York State in the spring of 2020. The original microsphere immunoassay used a target antigen from the SARS-CoV-1 virus responsible for the 2003 SARS outbreak, but evolved to incorporate multiple SARS-CoV-2 protein antigens (nucleocapsid, spike and spike domains, spike and nucleocapsid proteins from seasonal human coronaviruses). Besides being highly versatile due to multiplex capabilities, the assay was highly specific and sensitive and adaptable to measuring both total antibodies and antibody isotypes. While determining the assay performance characteristics, we were able to identify antibody production patterns (e.g., kinetics of isotypes, individual variations) for total antibodies and individual antibody classes. Overall, the results provide insights into the laboratory response to new serology needs, and how the evolution and fine-tuning of a serology assay helped contribute to a better understanding of the antibody response to SARS-CoV-2.