Biology subjects

Cheng, K. W.

Publications and source records attributed to Cheng, K. W..

3 recordsLinked to original sources

bioRxiv2026

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Modeling cellular behavior requires measurements that capture how cells evolve across time, environments, and interventions. Microscopy is uniquely suited to this goal: it is non-destructive and can be applied to living cells in their native context. Yet its phenotypic resolving power remains incompletely characterized relative to molecular assays. Here, we present a multimodal perturbation atlas of 1,000 pooled CRISPR knockouts in A549 cells, profiled by fluorescence microscopy (42 live, 13 fixed markers), label-free quantitative phase imaging of the same live cells (at single timepoints), and single-cell RNA sequencing (scRNA-seq). We develop deep learning frameworks to interpret the rich cell-biological signatures in these ~65M single-cell profiles. At matched reagent cost, phase imaging exceeds the phenotypic resolution of both fluorescence imaging and scRNA-seq, and more reliably recovers higher-order pathway organization. These results establish intrinsic morphology as a high-precision readout of cellular state, and lay a foundation for live-cell profiling of phenotypic trajectories.

systems biology↗

bioRxiv2025

Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication

Pooled CRISPR knockout (KO) screens using live viruses are a proven and valuable approach for identifying essential host factors acting across viral life cycles. Here we describe the development of a pooled genome-wide CRISPR KO screening approach using stable viral replicon cell lines to specifically identify host factors essential for viral replication. Virus replicons are non-infectious, therefore enabling the study of highly virulent viruses under standard biosafety level 2 containment. We developed a stable fluorescent dengue virus type 2 (DENV-2) replicon cell line to perform a pooled genome-wide FACS-based CRISPR KO screen. This benchmark DENV-2 replicon screen successfully identified host genes previously known to be required for viral DENV-2 replication (e.g., endoplasmic reticulum membrane complex and oligosaccharyltransferase complex components) and confirmed two additional genes (DOHH and ZFP36L2) involved in replication that have not been recovered in prior live virus screens. We applied this replicon screening approach to two highly divergent viruses: chikungunya virus (CHIKV), a positive-sense RNA virus that replicates at the plasma membrane, and Ebola virus (EBOV), a negative-sense RNA virus that replicates in cytoplasmic inclusion bodies. The CHIKV replicon screen identified two genes known to be required for replication (G3BP1 and G3BP2) and several additional, novel genes (CLEC4G, CSDE1, GOLGA7, HNF1A, and PCBD1). We verified two of them (CSDE1 and GOLGA7) in live CHIKV replication assays. A distinct set of genes (EHMT1, EHMT2, and USP7) were recovered in the EBOV replicon screen and were further confirmed using independent transient transfection assays. Thus, viral replicon-based screens provide a useful approach that can be extended to viruses of diverse taxa to identify host pathways essential for viral replication and to uncover potential novel targets for host-directed medical countermeasures.

genomics↗

bioRxiv2020

Leading-edge VASP clusters assemble at sites containing lamellipodin and exhibit size-dependent instability

The shape of many eukaryotic cells depends on the actin cytoskeleton; and localized changes in actin assembly dynamics underlie many changes in cell shape. Polymerases of the Ena/VASP family modulate cell shape by locally accelerating actin filament assembly and slowing filament capping. When concentrated into discrete foci at the leading edge, VASP promotes formation of filopodia, but the mechanisms that drive VASP clustering are poorly understood. Here we show that, in migrating B16F1 cells, VASP molecules assemble on pre-existing foci of the adaptor protein, lamellipodin, and that dimerization of lamellipodin is essential for cluster formation. VASP/lamellipodin clusters grow by accumulating monomers and by fusing, but their growth is limited by a previously undescribed, size-dependent instability. Our results demonstrate that assembly and disassembly dynamics of filopodia tip complexes are determined, in part, by a network of multivalent interactions between VASP, lamellipodin, and actin.

cell biology↗