Mengqi Wang: Advanced molecular tools for diagnostic analyses of RNA and antibodies in situ and in solution

Abstract

Advanced molecular diagnostics uses in vitro biological assays to detect nucleic acids or proteins even in low concentrations across samples, allowing for the identification of biomarkers, monitoring the course of the disease over time, and selection of appropriate therapy. In this thesis, I focus on development and early applications of several molecular tools of expected value in research, and eventually also clinically. 

In papers I and II, proximity extension assay (PEA) was for the first time modified to measure specific antibody responses, rather than protein levels as in the standard PEA. We call the method AbPEA and the technique was used to sensitively measure antibody responses to the spike protein or the nucleocapsid of SARS-CoV-2. We demonstrated that AbPEA has high specificity, sensitivity, and broad dynamic range, along with multiplexing potential, offering performance similar to that of other methods for antibody measurements. We demonstrated utilization of blood and saliva samples in paper I and paper II, respectively, which further establish that our approach has great potential for large-scale screening and biobanking. 

In paper III, we aimed to investigate how the protein composition of extracellular vesicles (EVs) differed among blood samples collected from healthy individual or ones with either mild or severe COVID-19. Proximity barcoding assay was applied to obtain a comprehensive overview of the protein composition of large numbers of individual EVs, demonstrating interesting differences. 

In paper IV, we enhanced padlock-RCA-based RNA genotyping in situ by using another newly developed technology for highly selective detection of DNA or RNA sequence variants, referred to as super RCA (sRCA). Our analysis showed that this approach can improve the selectivity for sequence variants during in situ detection of mutant or wild-type transcripts, and the signals representing superRCA reaction products are prominent and easily distinguished from any background.