Biology subjects

Bonissone, S. R.

Publications and source records attributed to Bonissone, S. R..

3 recordsLinked to original sources

bioRxiv2024

Serum proteomics reveals high-affinity and convergent antibodies by tracking SARS-CoV2 hybrid immunity to emerging variants of concern

The rapid spread of SARS-CoV2 and continuing impact on human health has prompted the need for effective and rapid development of monoclonal antibody therapeutics. In this study, we interrogate polyclonal antibodies in serum and B cells from whole blood of three donors with SARS-CoV2 immunity to find high-affinity anti-SARS-CoV2 antibodies to escape variants. Serum IgG antibodies were selected by affinity to the receptor-binding domain (RBD) and non-RBD sites on the spike protein of Omicron subvariant B.1.1.529 from each donor. Antibodies were analyzed by bottom-up mass spectrometry, and matched to single- and bulk-cell sequenced repertoires for each donor. Antibodies observed in serum were recombinantly expressed, and characterized to assess domain binding, cross-reactivity between different variants, and capacity to inhibit RBD binding to host protein. Donors infected with early Omicron subvariants had serum antibodies with subnanomolar affinity to RBD that show binding activity to a newer Omicron subvariant BQ.1.1. The donors also showed a convergent immune response. Serum antibodies and other single- and bulk-cell sequences were similar to publicly reported anti-SARS-CoV-2 antibodies, and characterized serum antibodies had the same variant-binding and neutralization profiles as their reported public sequence. The serum antibodies analyzed were a subset of anti-SARS-CoV2 antibodies in the B cell repertoire, which demonstrates significant dynamics between the B cells and circulating antibodies in peripheral blood.

immunology↗

bioRxiv2019

Serum proteomics expands on identifying more high-affinity antibodies in immunized rabbits than deep B-cell repertoire sequencing alone

AO_SCPLOWBSTRACTC_SCPLOWRabbits are a model for immunology studies, and monoclonal antibodies developed from rabbits have been sought after to empower immunoassays in a variety of applications. High-throughput characterization of circulating serum antibodies in response to specific antigens is highly impactful for both humoral immunology studies and antibody development. A combination of high throughput sequencing of antibody transcripts from B cells and proteomic analysis of serum antibodies, an approach referred to as immunoproteogenomics, is applied to profile the immune response of rabbits to {beta}-galactosidase (Beta-gal) in both recombinant antigen and peptide antigen immunization formats. The use of intact protein antigen resulted in observing 56.3% more heavy chains CDR3s in serum than immunization with peptide antigens. Additionally, sampling peripheral blood mononuclear cells (PBMCs) for B-cell repertoire sequencing at different time points throughout the immunization was found to capture 47.8%-72.8% of total proteomically observed heavy chain CDR3s, and would serve well in replacing sequencing the B cell rich, but more difficult to access spleen or bone marrow compartments. Despite B-cell repertoire sequencing to depths of 2M to 10M reads, we found proteomic evidence supporting at least 10% of serum antibodies are still missed. Further improvements to proteomic analysis techniques would enable more precise characterization of antibodies circulating in serum and determine antibody protein sequences missed by repertoire sequencing.

immunology↗

bioRxiv2019

Immunoglobulin gene conversion identification and analysis

Immunoglobulins are highly diverse, diverging from their originating germline genes driven primarily by somatic recombination and hypermutation. However, somatic gene conversion is a strong driver of immunoglobulin diversity in some species, including rabbits and chickens. It is considerably harder to detect by sequence analysis than point mutations, and currently no dedicated tools exist for identifying these events. We present GECCO, the first dedicated gene conversion identification tool for immunoglobulins based on modified, simultaneous, pairwise alignments to host and donor references. We benchmark our approach on simulated repertoires and find GECCO has high recall, low false positive rate, and is insensitive to somatic mutations. We apply this new approach to characterize gene conversion events at the repertoire level in hyper-immunized rabbits, to show patterns of donor V gene preferences and donor tract length distributions. The dedicated gene conversion identification method we present allows for the characterization of a new feature of antibody repertoires that has not been possible thus far. GECCO will benefit future studies to explore the prevalence of immunoglobulin gene conversion in additional species.

immunology↗