Biology subjects

Bonny, A. R.

Publications and source records attributed to Bonny, A. R..

9 recordsLinked to original sources

bioRxiv2026

E-cadherin-mediated neighborhood surveillance dictates pre-malignant outcomes

Stratified epithelia accumulate oncogenic mutations throughout life, yet overgrowths are rare. How epithelia detect and eliminate aberrant clones remains poorly understood. Using a mouse model of oncogenic clonal mosaicism in the skin, we find that pre-malignant epidermal cells redistribute E-cadherin to interfaces shared with wild-type neighbors, generating local tension heterogeneity that triggers elimination by cell competition. We show that gain or loss of E-cadherin can each drive competitive elimination, and although mechanical routes differ, both establish tension heterogeneity between neighbors, rather than any absolute adhesion state, as the critical determinant of epidermal fitness. This mechanism carries the seeds of its own failure: these tension differentials precipitate clonal sorting, depleting the wild-type contacts that surveillance requires. Pre-malignant cells then become supercompetitors, eliminating wild-type neighbors and expanding hyperplastically. Mechanical heterogeneity therefore endows tissues with an active, yet inherently fragile error-correction system whose collapse initiates a switch in competitive status, increasing tumorigenesis susceptibility.

cell biology↗

bioRxiv2026

Immune cells adapt to distinct stem cell niches to govern tissue homeostasis

Summary ParagraphIn adult tissues, epithelial stem cells exist within distinct residences, each endowing them with exclusive instructions for regenerative fitness under homeostasis and stress. Key components of these niches are immune cells, which classically protect the host against external and internal threats. Whether and how stem cell:immune cell crosstalk contributes to normal tissue biology remains less clear. Here, we discover functional adaptation of resident lymphocytes within two distinct skin stem cell niches and show that through this communication, each niche adjusts to meet diverse tissue demands. In the upper hair follicle, where microbial load is high, T cells express lymphotoxin-{beta} and stimulate adjacent receptor-positive epithelial stem cells to form an immune-competent niche that controls microbial expansion. By contrast, in the epidermis, these T cells produce amphiregulin to maintain continuous stem cell reconstitution of the skins barrier. Concomitantly, they express the immune checkpoint protein LAG-3, which autorestricts lymphocyte numbers, and hence amphiregulin levels, thereby preventing over-proliferative responses. Finally, when epidermal T cells are absent, dermal lymphocytes restore the imbalance by colonizing and adapting to their new niche. Our findings unveil functional specialization and homeostatic resilience of immune-stem cell niches, each tailored to suit the demands of distinct tissue microenvironments.

immunology↗

bioRxiv2026

A commensally regulated immune rheostat fine-tunes skin barrier fitness

At the skins surface, the epidermis must balance stem cell renewal with barrier maintenance to withstand environmental stress and shield against pathogens. Here, we identify a microbial-immune-epithelial feedback mechanism that integrates environmental information into stem cell regulation. Specifically, we show that Langerhans cells--an intra-epithelial macrophage population-- orchestrate this circuit by producing prostaglandin E2, which restrains stem cell proliferation, promotes epidermal differentiation and maintains barrier integrity during homeostasis. Upon pathway disruption, stem cells become overactivated, impairing differentiation and compromising barrier function. Upstream, Langerhans cell activity is tuned by the local microbial environment in a rheostat-like fashion, coupling commensal sensing to stem cell control. Our findings provide a general framework for how barrier tissues achieve adaptive homeostasis amid continual external challenge.

immunology↗

bioRxiv2023

Stem cells tightly regulate dead cell clearance to maintain tissue fitness

Summary ParagraphMacrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial number of these dying cells are cleared by non-professional phagocytes, local epithelial cells that are critical to organismal fitness. How non-professional phagocytes sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying their multifunctionality. Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires both local lipids produced by apoptotic corpses to activate RXR, and tissue-specific retinoids for RAR{gamma} activation. This dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an effective mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.

cell biology↗

bioRxiv2022

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

Many transcription factors (TFs) translocate to the nucleus with varied dynamic patterns in response to different inputs. A notable example of such behavior is RelA, a subunit of NF-{kappa}B, which translocates to the nucleus with either pulsed or sustained dynamics, depending on the stimulus. Our understanding of how these dynamics are interpreted by downstream genes has remained incomplete, partly because ubiquitously used environmental inputs activate other transcriptional regulators in addition to RelA. Here, we use an optogenetic tool, CLASP (controllable light-activated shuttling and plasma membrane sequestration), to control RelA spatiotemporal dynamics in mouse fibroblasts and quantify their effect on downstream genes using RNA-seq. Using RelA-CLASP, we show for the first time that nuclear translocation of RelA, without post-translational modifications or activation of other transcriptional regulators, is sufficient to activate downstream genes. Furthermore, we find that TNF, a common endogenous input, regulates many genes independently of RelA, and that this gene regulation is different from that induced by RelA-CLASP. Genes responsive to RelA-CLASP show a wide range of dynamics in response to a constant RelA input. We use a simple promoter model to recapitulate these diverse dynamic responses, as well as data collected in response to a pulsed RelA-CLASP input, and extract features of many RelA-responsive promoters. We also pinpoint many genes for which more complex models, involving feedback or multi-step promoters, may be needed to explain their response to constant and pulsed TF inputs. This study introduces a new robust tool for studying mammalian transcriptional regulation and demonstrates the power of optogenetic tools in dissecting the quantitative features of important cellular pathways.

systems biology↗

bioRxiv2020

TuNR: Orthogonal Control of Mean and Variability of Endogenous Genes in a Human Cell Line

Stochastic fluctuations at the transcriptional level contribute to isogenic cell-to-cell heterogeneity in mammalian cell populations. However, we still have no clear understanding of the repercussions of this heterogeneity, given the lack of tools to independently control mean expression and variability of a gene. Here, we engineered a synthetic circuit to independently modulate mean expression and heterogeneity of transgenes and endogenous human genes. The circuit, a Tunable Noise Rheostat (TuNR), consists of a transcriptional cascade of two inducible transcriptional activators, where the output mean and variance can be modulated by two orthogonal small molecule inputs. In this fashion, different combinations of the inputs can achieve the same mean but with different population variability. With TuNR, we achieve low basal expression, over 1000-fold expression of a transgene product, and up to 7-fold induction of the endogenous gene NGFR. Importantly, for the same mean expression level, we are able to establish varying degrees of heterogeneity in expression within an isogenic population, thereby decoupling gene expression noise from its mean. TuNR is therefore a modular tool that can be used in mammalian cells to enable direct interrogation of the implications of cell-to-cell variability.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2020

Stress-Induced Transient Cell Cycle Arrest Coordinates Metabolic Resource Allocation to Balance Adaptive Tradeoffs

The ability of a cell to mount a robust response to an environmental perturbation is paramount to its survival. While cells deploy a spectrum of specialized counter-measures to deal with stress, a near constant feature of these responses is a down regulation or arrest of the cell cycle. It has been widely assumed that this modulation of the cell cycle is instrumental in facilitating a timely response towards cellular adaptation. Here, we investigate the role of cell cycle arrest in the hyperosmotic shock response of the model organism S. cerevisiae by deleting the osmoshock-stabilized cell cycle inhibitor Sic1, thus enabling concurrent stress response activation and cell cycle progression. Contrary to expectation, we found that removal of stress-induced cell cycle arrest accelerated the adaptive response to osmotic shock instead of delaying it. Using a combination of time-lapse microscopy, genetic perturbations and quantitative mass spectrometry, we discovered that unabated cell cycle progression during stress enables the liquidation of internal glycogen stores, which are then shunted into the osmotic shock response to fuel a faster adaptation. Therefore, osmo-adaptation in wild type cells is delayed because cell cycle arrest diminishes the ability of the cell to tap its glycogen stores. However, acceleration of osmo-adaptation in mutant cells that do not arrest comes at the cost of acute sensitivity to a subsequent osmo-stress. This indicates that despite the ostensible advantage faster adaptation poses, there is a trade-off between the short-term benefit of faster adaptation and the vulnerability it poses to subsequent insults. We suggest that cell cycle arrest acts as a carbon flux valve to regulate the amount of material that is devoted to osmotic shock, balancing short term adaptation with long-term robustness.

systems biology↗

bioRxiv2020

PDE-constrained optimization for estimating population dynamics over cell cycle from static single cell measurements

MotivationUnderstanding how cell cycle responds and adapts dynamically to a broad range of stresses and changes in the cellular environment is crucial for the treatment of various pathologies, including cancer. However, measuring changes in cell cycle progression is experimentally challenging, and model inference computationally expensive. ResultsHere, we introduce a computational framework that allows the inference of changes in cell cycle progression from static single-cell measurements. We modeled population dynamics with partial differential equations (PDE), and derive parameter gradients to estimate time- and cell cycle position-dependent progression changes efficiently. Additionally, we show that computing parameter sensitivities for the optimization problem by solving a system of PDEs is computationally feasible and allows efficient and exact estimation of parameters. We showcase our framework by estimating the changes in cell cycle progression in K562 cells treated with Nocodazole and identify an arrest in M-phase transition that matches the expected behavior of microtubule polymerization inhibition. ConclusionsOur results have two major implications: First, this framework can be scaled to high-throughput compound screens, providing a fast, stable, and efficient protocol to generate new insights into changes in cell cycle progression. Second, knowledge of the cell cycle stage- and time-dependent progression function allows transformation from pseudotime to real-time thereby enabling real-time analysis of molecular rates in response to treatments. AvailabilityMAPiT toolbox (Karsten Kuritz 2020) is available at github: https://github.com/karstenkuritz/MAPiT.

systems biology↗

bioRxiv2018

A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells

The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. Current methods that permit the assembly of DNA circuits in mammalian cells are laborious, slow, expensive and mostly not permissive of rapid prototyping of constructs. Here we present the Mammalian ToolKit (MTK), a Golden Gate-based cloning toolkit for fast, reproducible and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of a curated library of characterized, modular parts that can be easily mixed and matched to combinatorially assemble one transcriptional unit with different characteristics, or a hierarchy of transcriptional units weaved into complex circuits. MTK renders many cell engineering operations facile, as showcased by our ability to use the toolkit to generate single-integration landing pads, to create and deliver libraries of protein variants and sgRNAs, and to iterate through Cas9-based prototype circuits. As a biological proof of concept, we used the MTK to successfully design and rapidly construct in mammalian cells a challenging multicistronic circuit encoding the Ebola virus (EBOV) replication complex. This construct provides a non-infectious biosafety level 2 (BSL2) cellular assay for exploring the transcription and replication steps of the EBOV viral life cycle in its host. Its construction also demonstrates how the MTK can enable important and time sensitive applications such as the rapid testing of pharmacological inhibitors of emerging BSL4 viruses that pose a major threat to human health.

synthetic biology↗