Smeal, S. W. | bioRxiv Science

bioRxiv2026

Cell Cycle Regulation of Merkel Cell Polyomavirus Replication and Genome Inheritance in Single Cells

Merkel cell polyomavirus (MCV) establishes a near-ubiquitous, asymptomatic infection in humans but on rare occasions drives Merkel cell carcinoma, an aggressive skin cancer. How MCV replication is coordinated with host cell-cycle progression, and how this coordination shapes infected-cell fate, has remained unresolved. Here we combine reporter virus live-cell imaging, pharmacologic cell-cycle perturbation, flow cytometry, and single-cell transcriptomics to examine MCV replication dynamics. VP1 late gene expression occurs almost exclusively during late S or G2, is associated with prolonged G2 arrest, and frequently culminates in cell death. Strikingly, cells that divide before virus replication give rise to daughter cells that synchronously initiate viral replication and VP1 expression, revealing mitotic inheritance of silent viral genomes, a pattern seen for viruses with a known latency lifecycle. Single-cell RNA sequencing further identifies a transient antiviral and inflammatory response that is subsequently suppressed in surviving, cell cycle arrested cells. These findings define the cell-cycle logic, inheritance, and host consequences of MCV replication at single-cell resolution.

cell biology↗

bioRxiv2024

Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics

Temporal properties of molecules within signaling networks, such as sub-cellular changes in protein abundance, encode information that mediate cellular responses to stimuli. How dynamic signals relay and process information is a critical gap in understanding cellular behaviors. In this work, we investigate transmission of information about changing extracellular cytokine concentrations from receptor-level supramolecular assemblies of I{kappa}B kinases (IKK) downstream to the nuclear factor {kappa}B (NF-{kappa}B) transcription factor (TF). In a custom robot-controlled microfluidic cell culture, we simultaneously measure input-output (I/O) encoding of IKK-NF-{kappa}B in dual fluorescent-reporter cells. When compared with single cytokine pulses, dose-conserving pulse trains prolong IKK assemblies and lead to disproportionately enhanced retention of nuclear NF-{kappa}B. Using particle swarm optimization, we demonstrate that a mechanistic model does not recapitulate this emergent property. By contrast, invoking mechanisms for NF-{kappa}B-dependent chromatin remodeling to the model recapitulates experiments, showing how temporal dosing that prolongs IKK assemblies facilitates switching to permissive chromatin that sequesters nuclear NF-{kappa}B. Remarkably, using simulations to resolve single-cell receptor data accurately predicts same-cell NF-{kappa}B time courses for more than 80% of our single cell trajectories. Our data and simulations therefore suggest that cell-to-cell heterogeneity in cytokine responses are predominantly due to mechanisms at the level receptor-associated protein complexes.

systems biology↗