Microfluidic immuno-serolomic assay reveals systems level association with COVID-19 pathology and vaccine protection
How to develop highly informative serology assays to evaluate the quality of immune protection against COVID-19 has been a global pursuit over the past years including the NCI SeroNet initiative. Despite the wide-spread adoption of vaccination that has demonstrated exceptional efficacy, patients with altered immunity such as hematologic malignancies and autoimmune disease remain at risk, requiring rapid serological as well as immunological evaluation at the full range to manage these patients. Here, we develop a microfluidic high-plex immuno-serolomic assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrates the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It is applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis reveals distinct immune mediator protein modules that exhibit a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identifies that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and is further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level. Overall design: By combining single-cell RNA sequencing (scRNA-seq) and co-measurement of B cell receptor (BCR) repertoires, we characterized the heterogeneity of circulating B cells from the one COVID infected patient with chronic lymphocytic leukemia and one COVID patient with non-hematologic cancer.