Biology subjects

Saadat, S.

Publications and source records attributed to Saadat, S..

3 recordsLinked to original sources

bioRxiv2026

Basic-peptide depletion and precursor masking in bottom-up proteomics

Biomarker proteomics studies report protein identities at the canonical precursor level, yet the underlying mass-spectrometry evidence consists of peptides whose physicochemical properties may diverge from the annotated protein. We reanalyzed peptide-level evidence from public datasets with a proteoform-aware pipeline that maps detected peptides to canonical sequences under a five-level confidence taxonomy, computes sequence-derived physicochemical features for precursors, peptides, and detected regions, and tests class-composition bias against digestion-matched backgrounds. Across ten public studies spanning five result-file formats and 70,020 peptide-evidence rows, detected peptides are depleted in the basic isoelectric-point class relative to their own proteins' theoretical tryptic peptides (fixed-effect odds ratio 0.45, 95% CI 0.44-0.46; leave-one-study-out envelope 0.44-0.49). The depletion is absent among fully tryptic peptides (OR 1.06) and concentrates in missed-cleavage peptides (OR 0.62-0.57), is invariant to detected-abundance stratification, and retains its direction under three independent pI-calculator models. Case studies reveal both directions of precursor-centric masking. Two orthogonal validations ground the framework: a digestion-free synthetic-peptide analysis (basic-class odds ratio 0.73, 95% CI 0.71-0.76 under standard DDA) and a paired top-down benchmark, in which detected regions recover top-down sequence space (90% of spans overlapped) but do not delimit proteoform boundaries (8% containment). Pipeline, data, and code are public.

bioinformatics↗

bioRxiv2024

A Comprehensive Engineering Strategy Improves Potency and Manufacturability of a Near Pan-neutralizing Antibody Against HIV

Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.

bioengineering↗

bioRxiv2021

Mucosal and systemic responses to SARS-CoV-2 vaccination in infection naive and experienced individuals

With much of the world infected with or vaccinated against SARS-CoV-2, understanding the immune responses to the SARS-CoV-2 spike (S) protein in different situations is crucial to controlling the pandemic. We studied the clinical, systemic, mucosal, and cellular responses to two doses of SARS-CoV-2 mRNA vaccines in 62 individuals with and without prior SARS-CoV-2 exposure that were divided into three groups based on serostatus and/or degree of symptoms: Antibody negative, Asymptomatic, and Symptomatic. In the previously SARS-CoV-2-infected (SARS2-infected) Asymptomatic and Symptomatic groups, symptoms related to a recall response were elicited after the first vaccination. Anti-S trimer IgA and IgG levels peaked after 1st vaccination in the SARS2-infected groups, and were higher that the in the SARS2-naive group in the plasma and nasal samples at all time points. Neutralizing antibodies titers were also higher against the WA-1 and B.1.617.2 (Delta) variants of SARS-CoV-2 in the SARS2-infected compared to SARS2-naive vaccinees. After the first vaccination, differences in cellular immunity were not evident between groups, but the AIM+ CD4+ cell response correlated with durability of humoral immunity against the SARS-CoV-2 S protein. In those SARS2-infected, the number of vaccinations needed for protection, the durability, and need for boosters are unknown. However, the lingering differences between the SARS2-infected and SARS2-naive up to 10 months post-vaccination could explain the decreased reinfection rates in the SARS2-infected vaccinees recently reported and suggests that additional strategies (such as boosting of the SARS2-naive vaccinees) are needed to narrow the differences observed between these groups.

immunology↗