Biology subjects

Lin, A. Z.

Publications and source records attributed to Lin, A. Z..

4 recordsLinked to original sources

bioRxiv2024

HIV broadly neutralizing antibody escapability drives the therapeutic efficacy of vectored immunotherapy

Broadly neutralizing antibodies (bNAbs) have shown promise for prevention and treatment of HIV. Potency and breadth measured in vitro are often used as predictors of clinical potential; however, human studies demonstrate that clinical efficacy of bNAbs can be undermined by both pre-existing and de novo resistance. Here we find that HIV-infected humanized mice receiving bNAbs delivered via AAV as Vectored ImmunoTherapy (VIT) can be used to identify antibody escape paths, which are largely conserved for each bNAb. Path selection, and consequent therapeutic success, is driven by the fitness cost and resistance benefit of emerging mutations. Applying this framework, we independently modulated bNAb resistance or the fitness cost of escape mutants, resulting in enhanced efficacy of VIT. This escape path analysis successfully explains the therapeutic efficacy of bNAbs, and enables a tractable means of quantifying and comparing the potential for viral escape from therapeutics in vivo. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/603156v4_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@180c86borg.highwire.dtl.DTLVardef@1e6108dorg.highwire.dtl.DTLVardef@148bac7org.highwire.dtl.DTLVardef@1de93ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

QuickFit: A high-throughput RT-qPCR-based assay to quantify viral growth and fitness in vitro

The quantification of viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method that enables the quantification of viral fitness termed QuickFit, which employs large numbers of parallel viral cultures to accurately measure growth rates. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches but with significantly higher throughput and lower error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.

microbiology↗

bioRxiv2023

Dynamical control enables the formation of demixed biomolecular condensates

Macromolecular phase separation underlies the regulated formation and dissolution of biomolecular condensates. What is unclear is how condensates of distinct and shared macromolecular compositions form and coexist within cellular milieus. Here, we use theory and computation to establish thermodynamic criteria that must be satisfied to achieve compositionally distinct condensates. We applied these criteria to an archetypal ribonucleoprotein condensate and discovered that demixing into distinct protein-RNA condensates cannot be the result of purely thermodynamic considerations. Instead, demixed, compositionally distinct condensates arise due to asynchronies in timescales that emerge from differences in long-lived protein-RNA and RNA-RNA crosslinks. This type of dynamical control is also found to be active in live cells whereby asynchronous production of molecules is required for realizing demixed protein-RNA condensates. We find that interactions that exert dynamical control provide a versatile and generalizable way to influence the compositions of coexisting condensates in live cells.

biophysics↗

bioRxiv2022

Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers

The nucleolus is a multilayered structure. Each layer is thought to be a compositionally distinct phase, although how these phases form and interface with one another remains unclear. Using computational, proteomics, in vitro, and in vivo studies, we uncover distinct molecular grammars within intrinsically disordered regions (IDRs) of nucleolar proteins that localize to fibrillar centers (FCs) and dense fibrillar components (DFCs). FC and DFC proteins feature two distinct types of IDRs namely those with long tracts of acidic residues and those with blocks of lysines interspersed by acid-rich-regions. We find that phase separation driven by complex coacervation in mixtures of nucleolar proteins, with their distinctive IDRs, and ribosomal DNA and RNA molecules is sufficient to drive the formation of structural facsimiles of FCs and DFCs. One-Sentence SummaryFacsimiles of core nucleolar substructures were reconstituted via phase separation of key protein and nucleic acid mixtures.

biophysics↗