Project description:We present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. This approach enabled the identification of three multiple myeloma cell surface antigens, and cognate monoclonal antibody probes.
Project description:Epstein-Barr virus (EBV) is a ubiquitous human gammaherpesvirus causally linked to several malignancies, including several lymphomas and solid tumors. Despite its high global prevalence, a comprehensive profile of humoral responses to EBV is yet to be described. Moreover, how HIV-1 co-infection influences this response can reveal new insights into how cancer risk increases in people with HIV-1 (PWH). Here, we employed phage immunoprecipitation and sequencing (PhIP-Seq) using the VirScan phage-display library to map antibody responses against the EBV proteome in 115 adults from sub-Saharan Africa, with and without HIV-1 co-infection (43 HIV-positive, 72 HIV-negative) at peptide-level resolution. We identified EBNA1, EBNA2, EBNA3B, and the viral capsid antigen protein BFRF3 as the most immunodominant EBV proteins. Differential antibody reactivities between EBV Type 1 and Type 2 were observed against EBNA2, with increased antibody recognition near the C-terminal transactivation domain (C-TAD) observed for Type 1. A specific region of EBNA1 containing the nuclear localization sequence (NLS) was the most frequently targeted epitope of the EBV proteome. Our comprehensive and high-resolution analysis identified several immunodominant EBV proteins that are targeted by most individuals regardless of HIV-1 status. HIV-1 co-infected individuals (PWH) had increased antibody recognition against most EBV proteins compared to HIV-uninfected individuals, but the magnitudes against those responses varied across the proteome. Overall, our findings suggest that HIV-1 co-infection alters both the breadth and magnitude of anti-EBV responses, potentially reflecting increased viral reactivation and HIV-driven mechanisms of immunosuppression that may impact the magnitude of Ab responses in EBV.
Project description:In recent years, high throughput discovery of human recombinant monoclonal antibodies (mAbs) has been applied, to greatly advance our understanding of the specificity, and functional activity of antibodies, against HIV. Thousands of antibodies have been generated and screened in functional neutralization assays, and antibodies, associated with cross-strain neutralization and passive protection in primates, have been identified. To facilitate this type of discovery, a high throughput-screening tool is needed, to accurately classify mAbs, and their antigen targets. In this study, we analyzed and evaluated a prototype microarray chip, comprised of HIV-1 recombinant proteins gp140, gp120, gp41, and several membrane proximal external region peptides. The protein microarray analysis of 11 HIV-1 envelope-specific mAbs revealed diverse binding affinities and specificities across clades. Half maximal effective concentrations, generated by our chip analysis, correlated significantly (P<0.0001) with concentrations from ELISA binding measurements. Polyclonal immune responses in plasma samples, from HIV-1 infected subjects, exhibited different binding patterns and reactivity against printed proteins. Examining the totality of the specificity of the humoral response in this way reveals the exquisite diversity, and specificity of the humoral response to HIV.
2015-03-10 | GSE66659 | GEO
Project description:Phage display library for antibody screening
Project description:An effective broadly reactive antibody response is crucial to prevent viral infections. A small number of people living with HIV (PLWH) develop broadly neutralizing antibodies (bNAbs) targeting multiple HIV strains. We performed combined cell-free DNA (cfDNA) and cell-free RNA (cfRNA) sequencing in 42 plasma samples from a longitudinal cohort of 14 PLWH, of whom 7 developed bNAbs and 7 matched controls. cfRNA profiling revealed early immune activation signatures and distinct microbial associations linked to bNAb development.
Project description:A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. We report the design of mRNA-delivered membrane-bound form of a stabilized native-like Env trimer (BG505 MD39.3) and comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates.
Project description:Genome wide DNA methylation profiling of CD4 T cells from uninfected and HIV-infected individuals (viremic, ART-suppressed and elite controllers [EC]) The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,577 CpGs in DNA from peripheral CD4 T cells samples. Samples included: 22 from HIV-uninfected individuals (uninfected group), 42 from HIV-infected individuals (21 from HIV-infected viremic (viremic group) and 21 from the same participants after viral suppression (viral load< 50 copies HIV-1 RNA/plasma) by antiretroviral therapy administrarion (ART group), and 21 from elite controllers (EC group)
2023-01-16 | GSE143942 | GEO
Project description:Pan-coronavirus phage display profiling of COVID-19 patient samples
| PRJNA724692 | ENA
Project description:Phage display for antibody PD1 1.1 and PD1 2.1