Biology subjects

Zhang, T.-h.

Publications and source records attributed to Zhang, T.-h..

5 recordsLinked to original sources

bioRxiv2026

PQBP1 couples HIV-1 capsid recognition to cGAS recruitment through conformational remodeling

Pattern recognition receptors (PRRs) must selectively engage pathogen-derived signals to potentiate inflammation and antimicrobial responses. Polyglutamine-binding protein 1 (PQBP1) acts upstream of cyclic GMP-AMP synthase (cGAS) during HIV-1 infection through the recognition of viral capsid. However, the mechanism by which capsid binding enables cGAS recruitment remains unclear. As an intrinsically disordered protein, PQBP1 samples an ensemble of conformational states whose distribution depends on ligand engagement. Here we show that capsid engagement shifts this population toward a conformation competent for cGAS binding. Capsid binding at the N-terminus of PQBP1 redistributes conformational sampling within the WW domain and distal polar-rich domain (PRD). Alanine substitutions within these capsid-responsive regions retain capsid binding yet disrupt infection-dependent cGAS recruitment, indicating that capsid binding and cGAS recruitment depend on distinct regions of PQBP1. Together, these findings define a mechanism by which HIV-1 capsid engagement remodels PQBP1 into a cGAS-competent state, coupling capsid recognition to innate immune activation. IMPORTANCEPolyglutamine-binding protein 1 (PQBP1) initiates innate immune detection of HIV-1 by recognizing the incoming viral capsid. We show that capsid engagement reshapes PQBP1 conformational dynamics, and we identify distal regions required for infection-dependent cGAS association. These findings provide a mechanistic framework for how pathogen recognition is coupled to downstream innate immune activation.

molecular biology↗

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2025

Extreme high-diversity barcoded HIV library enables single cell multi-omics analysis of viral expression and fate determination

HIV-1 persists as a global health challenge due to its ability to establish latent reservoirs that evade eradication by antiretroviral therapy (ART). This study introduces a high-diversity barcoded HIV-1 library combined with a novel peptide barcode system to enable single-cell multi-dimensional analysis of viral integration, transcription, splicing, and translation of distinct viral mRNA isoform. Our method revealed over 80 distinct HIV-1 splicing isoforms and uncovered significant temporal variation in mRNA diversity, driven by integration site and chromatin context. By linking HIV-1 5UTR with peptide barcoding, we quantified the translation efficiency of alternative 5' UTRs and demonstrated correlations with abundance of each viral mRNA isoform. Additionally, we showed that latency reversal agents, such as SAHA and Bryostatin, selectively reactivate proviruses depending on their genomic and chromatin context and leads to distinct viral RNA splicing program. This platform revealed the diversity of HIV-infected cells at levels of transcripts as well as at proteins, and subsequently the fate determination. The detailed understanding of the stochastic diversity and dynamic nature of HIV-1 latency, inform the development of targeted therapies to eliminate latent reservoirs.

microbiology↗

bioRxiv2019

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.

evolutionary biology↗

bioRxiv2017

High-throughput fitness profiling of Zika virus E protein reveals different roles for N-linked glycosylation during infection of mammalian and mosquito cells

Zika virus (ZIKV) infection causes Guillain-Barre syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and therefore considered one of the major determinants in ZIKV pathogenesis. Here, we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting N-linked glycosylation at N154 position display the most divergence. Through characterizing individual mutants, we show that, while ablation of N-linked glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, it either had little impact on ZIKV infection on certain human cells or decreased infection through entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells.\n\nHighlightsO_LIGene-wide mapping of functional residues of E protein in human and mosquito cells.\nC_LIO_LIMutations affecting N-linked glycosylation display the most dramatic difference.\nC_LIO_LIN-linked glycosylation decreases ZIKV entry into mosquito cells.\nC_LIO_LIN-linked glycosylation is important for DC-SIGN mediated infection of human cells.\nC_LI

microbiology↗