Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2

Abstract

The coronavirus SARS-CoV-2 is the causative agent for the disease COVID-19. To capture the IgA, IgG, and IgM antibody response of patients infected with SARS-CoV-2 at individual epitope resolution, we constructed planar microarrays of 648 overlapping peptides that cover the four major structural proteins S(pike), N(ucleocapsid), M(embrane), and E(nvelope). The arrays were incubated with sera of 67 SARS-CoV-2 positive and 22 negative control samples. Specific responses to SARS-CoV-2 were detectable, and nine peptides were associated with a more severe course of the disease. A random forest model disclosed that antibody binding to 21 peptides, mostly localized in the S protein, was associated with higher neutralization values in cellular anti-SARS-CoV-2 assays. For antibodies addressing the N-terminus of M, or peptides close to the fusion region of S, protective effects were proven by antibody depletion and neutralization assays. The study pinpoints unusual viral binding epitopes that might be suited as vaccine candidates .

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein

“…Microarray assays were carried out according to the method described by SK-Hotop et al [39]. Briefly, 15-mer peptides of the four structural SARS-CoV-2 proteins (Ref.…”

Structure of SARS-CoV-2 M protein in lipid nanodiscs

“…1, S2). The N-terminus (amino acids [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] and C-terminus (amino acids [205][206][207][208][209][210][211][212][213][214][215][216][217][218][219][220][221][222] are not resolved in the map and were not modeled. Loops connecting transmembrane helices (amino acids 36-42 and 71-78) are the least well resolved regions of the structure.…”

“…Despite this, the M protein sequence has remained virtually unchanged–a testament to the critical role that M plays in viral replication and assembly 35 . Furthermore, while only 20 amino acids in length, the N-terminus of M has been found to be highly immunogenic in COVID-19 patients 8–11 . M has also been shown to modulate innate immune response and could contribute to lung injury often seen in severe cases 25,26 .…”

“…M organizes the assembly and structure of new virions and is essential for virus formation [2][3][4][5] . M is the most abundant membrane protein in the viral envelope and anti-M antibodies are found in plasma of patients infected with SARS-CoV-2 and other coronaviruses [6][7][8][9][10][11] . Based on its functional importance and immunogenicity, M has been proposed as a target for coronavirus vaccines or therapeutics.…”

Advances in antibody discovery from human BCR repertoires

“…Antibody binding epitope Mapping (AbMap), a combination of phage-displayed peptide libraries with next-generation sequencing, was developed to determine 200 antibody-specific epitopes in a single run ( Qi et al, 2021 ). Additionally, microarrays consisting of 648 overlapping peptides that cover the four major structural proteins of the SARS-CoV-2 virus have been constructed: Spike, Nucleocapsid, Membrane, and Envelope ( Hotop et al, 2022 ). This microarray fingerprint of positive serum samples was learned by a machine learning model and the epitopes were used to diagnose COVID-19 positive and negative donors ( Hotop et al, 2022 ).…”