Biology subjects

Venkataraman, T.

Publications and source records attributed to Venkataraman, T..

6 recordsLinked to original sources

bioRxiv2026

A phage display library to dissect antibody responses to human coronavirus spike proteins

Coronaviruses are widespread human pathogens with demonstrated pandemic potential. We developed a phage immunoprecipitation sequencing (PhIP-Seq) library, C-Spike, enabling the profiling of serum antibody responses to coronavirus spike proteins. The C-Spike library includes peptides from 49 Alpha- and Betacoronavirus spike proteins, including pandemic coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS-CoV), seasonal coronaviruses (HKU1, OC43, 229E, NL63), and selected animal coronaviruses of spillover interest. The library includes a series of 46 amino acid-long peptides covering each spike, with adjacent tiles overlapping by 23 amino acids. Additionally, the library contains alanine-scanned versions of each peptide, tiling three alanine residues at every position across the peptide length, allowing for precise identification of motifs important for antibody binding. We validate C-Spike and its associated bioinformatic analysis pipeline using control antibodies and sera with known reactivity. C-Spike complements existing approaches like neutralization assays to enable deep characterization of antibody responses to coronavirus spike proteins, enabling precise determination of sites important for antibody binding.

immunology↗

bioRxiv2023

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn

We investigated a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To enhance this approach, we developed Dolphyn, a novel method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn improves the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals, while also reducing the number of synthesized peptides by 78%. In our study on gut phages, we discovered that the immune system develops antibodies to bacteria-infecting viruses in the human gut, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.

bioengineering↗

bioRxiv2022

Comprehensive profiling of antibody responses to the human anellome using programmable phage display

Viruses belonging to the diverse Anelloviridae family represent a major constituent of the commensal human virome. Aside from their widespread prevalence and persistence in humans and their absence of detectable pathologic associations, little is known about the immunobiology of the human anellome. In this study, we employed the Phage ImmunoPrecipitation Sequencing (PhlP-Seq) assay for comprehensive analyses of antibody binding to 56 amino acid long anellovirus peptides. We designed and constructed a large and diverse "AnelloScan" T7 phage library comprising more than 32,000 non-redundant peptides representing the ORF1, ORF2, ORF3 and TTV-derived apoptosis-inducing protein (TAIP) sequences of more than 800 human anelloviruses (spanning three genera). We used this library to profile the antibody reactivities of serum samples from 156 subjects. The vast majority of anellovirus peptides were not reactive in any of the subjects tested (n=~28,000; ~85% of the library). Antibody reactive peptides were largely restricted to the C-terminal region of the putative capsid protein, ORF1. To characterize antibody responses to newly acquired anellovirus infections, we screened a longitudinal cohort of matched blood-transfusion donors and recipients. Most transmitted anelloviruses did not elicit detectable antibody reactivity in the recipient (29 out of a total of 40 transmitted anelloviruses) and the remainder demonstrated delayed reactivity (~100-150 days after transfusion). This study represents the first large-scale epitope-level serological survey of the antibody response to the human anellome. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/486145v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@132dfforg.highwire.dtl.DTLVardef@130c47dorg.highwire.dtl.DTLVardef@b3fc97org.highwire.dtl.DTLVardef@8c49f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors

Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via programmable Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, costeffective approach for multiplexed detection of exposure and response to thousands of microbial protein products. Here we designed and constructed a library of 95,601 56 amino acid peptide tiles spanning a subset of environmental proteins more likely to be associated with immune responses: those with "toxin" or "virulence factor" keyword annotations. PhIP-Seq was used to profile the circulating antibodies of ~1,000 individuals against this "ToxScan" library of 14,430 toxins and virulence factors from 1,312 genera of organisms. In addition to a detailed analysis of six commonly encountered human commensals and pathogens, we study the age-dependent stability of the ToxScan profile and use a genome-wide association study (GWAS) to find that the MHC-II locus modulates the selection of bacterial epitopes. We detect previously described anti-flagellin antibody responses in a Crohns disease cohort and identify a novel association between anti-flagellin antibodies and juvenile dermatomyositis (JDM). PhIP-Seq with the ToxScan library provides a new window into exposure and immune responses to environmental protein toxins and virulence factors, which can be used to study human health and disease at cohort scale.

immunology↗

bioRxiv2021

Antiviral Antibody Epitope Selection is a Heritable Trait

There is enormous variability in human immune responses to viral infections. However, the genetic factors that underlie this variability are not well characterized. We used VirScan, a high-throughput viral epitope scanning technology, to analyze the antibody binding specificities of twins and SNP-genotyped individuals. These data were used to estimate the heritability and identify genomic loci associated with antibody epitope selection, response breadth, and the control of Epstein-Barr Virus (EBV) viral load. We identified 4 epitopes of EBV that were heritably targeted, and at least two EBNA-2 binding specificities that were associated with variants in the MHC class-II locus. We identified an EBV serosignature that predicted viral load in white blood cells and was associated with genetic variants in the MHC class-I locus. Our study provides a new framework for identifying genes important for pathogen immunity, with specific implications for the genetic architecture of EBV humoral responses and the control of viral load. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

genetics↗

bioRxiv2020

Protease Activity Profiling Via Programmable Phage Display

Endopeptidases catalyze the internal cleavage of proteins, playing pivotal roles in protein turnover, substrate maturation and the activation of signaling cascades. A broad range of biological functions in health and disease are controlled by proteases, yet assays to characterize their activities at proteomic scale do not yet exist. To address this unmet need, we have developed SEPARATE (Sensing EndoPeptidase Activity via Release and recapture using flAnking Tag Epitopes), which uses monovalent phage display of the entire human proteome at 90-aa peptide resolution. We demonstrate that SEPARATE is compatible with several human proteases from distinct catalytic classes, including Caspase-1, ADAM17, and Thrombin. Both well-characterized and newly identified substrates of these enzymes were detected in the assay. SEPARATE was used to discover a non-canonical Caspase-1 substrate, the E3 ubiquitin ligase HUWE1, a key mediator of apoptotic cell death. SEPARATE is a novel methodology to enable efficient, unbiased assessment of endopeptidase activity using a phage-displayed proteome.

molecular biology↗