Cell systems最新文献

Physiological adaptation to environmental stress involves distinct molecular responses leading to either stress resistance, which maintains proliferation by degrading the stressor's effects, or tolerance, which prioritizes survival over proliferation. While these strategies are complementary, their coordination remains unclear. Using microfluidics and live-cell imaging, we investigated the genetic basis of their interplay during the response to hydrogen peroxide (H₂O₂) in budding yeast. We found that deleting zwf1Δ, which controls NADPH synthesis via the pentose phosphate pathway (PPP), reduced resistance but unexpectedly enhanced tolerance to H₂O₂. This trade-off was further characterized through genetic and environmental interventions and found to be conserved in bacteria. Our results support a model in which redox signaling shifts cells to a nutrient-dependent tolerant state via protein kinase A inhibition when the H₂O₂ homeostatic response is overwhelmed. This framework could inform synergistic therapies targeting resistance and tolerance to prevent drug escape and disease relapse. A record of this paper's transparent peer review process is included in the supplemental information.

Responses of endothelial cells to elevated levels of vascular endothelial growth factor (VEGF), frequently accompanying local decrease in oxygen supply, include loosening of cell contacts, rearrangement of cells in vessel remodeling, and ultimately, angiogenic growth. How these complex processes, occurring on diverse time scales, are coordinated and how they are guided by a single key signaling input is still incompletely understood. Here, we show that the various phenotypic responses associated with VEGF signaling are controlled at different steps of a pathway involving sequential activation of Src, tumor endothelial marker 4 (TEM4), YAP, and components of pro-angiogenic Notch signaling. Notably, due to feedback regulation at different pathway levels, the functional outcomes are controlled by oscillations of the pathway components occurring on distinct time scales. Deeper pathway layers integrate faster upstream responses and control progressively slower phenotypic outcomes. This signal-decoding pathway organization can ensure a high degree of complexity in a vital physiological process. A record of this paper's transparent peer review process is included in the supplemental information.

Metal ions have crucial roles in cells, but the impact of their availability on biological networks is underexplored. We systematically quantified yeast cell growth and the corresponding metallomic, proteomic, and genetic responses to perturbations in metal availability along concentration gradients of all growth-essential metal ions. We report a remarkable metal concentration dependency of cellular networks, with around half of the proteome, and most signaling pathways such as target of rapamycin (TOR), being metal responsive. Although the biological response to each metal is distinct, our data reveal common properties of metal responsiveness, such as concentration interdependencies and metal homeostasis. Furthermore, our resource indicates that many understudied proteins have functions related to metal biology and reveals that metalloenzymes occupy central nodes in metabolic networks. This work provides a framework for understanding the critical role of metal ions in cellular function, with broader implications for manipulating metal homeostasis in biotechnology and medicine.

After birth, tissues grow until they reach adult size, with each organ exhibiting unique cellular dynamics, growth patterns, and stem or non-stem cell sources. Using multiscale experimental and computational approaches, we found that aortic enlargement follows distinct growth principles, scaling with the vertebral column. Expansion proceeds via two temporally coordinated, spatially stochastic waves of proliferation aligned with blood flow, each with unique cell-cycle kinetics, with the first wave featuring cycles as short as 6 h. Single-cell RNA sequencing revealed increased fatty acid metabolism accompanying cell enlargement. Mathematical modeling and experiments showed that endothelial cell extrusion is essential for maintaining homeostatic aortic size as it adjusts for proliferation excess. Using a genetic model of achondroplasia, we mechanistically demonstrated that the aorta preserves proper scaling by increasing cell extrusion while keeping proliferation rates intact. These findings provide a blueprint of the principles orchestrating aortic growth, which relies entirely on the proliferation of resident differentiated cells. A record of this paper's transparent peer review process is included in the supplemental information.

Post-translational modifications (PTMs) and splicing are both important regulatory processes controlling protein function; therefore, we developed PTM-POSE (PTM projection onto splice events) to explore the interplay between them. PTM-POSE identifies potential PTM sites associated with alternative isoforms or splice events, enabling comprehensive analysis of how PTMs affect isoform function, protein interactions, and enzymatic regulation. Through systematic analysis of Ensembl transcripts with PTM-POSE, we highlighted two key mechanisms by which splicing diversifies PTMs across isoforms-exclusion of a PTM site (32%) or alteration of the flanking sequences surrounding the PTM (2%). In experiment-specific analysis of PTM-associated splicing events, we identified the potential rewiring of protein-interaction and kinase-substrate networks, suggesting coordinated connections between PTM signaling. We provide our tool and associated data publicly to enable further exploration of splicing-PTM relationships. A record of this paper's transparent peer review process is included in the supplemental information.

No life is possible without metal ions. The selection and functions of metals in living systems are complex and affected by the chemical environment. A systemic study by integrative metallomics offers new information on the interplay between the metallome, metabolome, genome, and proteome.

Pathological events often impact tissue regions in a spatially variable manner, making it challenging to identify therapeutic targets. Spatial transcriptomics (ST) is a powerful technology to map spatially variable molecular mechanisms, yet suitable analytical methods have been lacking. We introduce spatially resolved pathology score (SPaSE), an optimal transport-based algorithm to compare ST data from diseased and control tissues. SPaSE computes a "pathology score" for each spot in the diseased sample, quantifying the pathological impact at that spot. In post-myocardial infarction (post-MI) mouse hearts, these scores delineated zones that matched independent expert annotations. Modeling pathology scores from gene expression revealed signatures predictive of varying pathological severity. The scoring model learned from mouse data showed accurate predictions on human post-MI data. We also demonstrated SPaSE's efficacy on additional simulated and real ST data from traumatic brain injury and Duchenne muscular dystrophy mouse models. SPaSE is a useful addition to the existing ST algorithms. A record of this paper's transparent peer review process is included in the supplemental information.

Cell and gene therapies often express nonhuman proteins, which carry a risk of anti-therapy immunogenicity. An emerging consensus is to instead use modified human protein domains, but these domains include nonhuman peptides around mutated residues and at interdomain junctions, which may also be immunogenic. We present a modular workflow to optimize protein function and minimize immunogenicity by using existing machine learning models that predict protein function and peptide-major histocompatibility complex (MHC) presentation. We first applied this workflow to existing transcriptional activation and RNA-binding domains by removing potentially immunogenic MHC II epitopes. We then generated small-molecule-controllable transcription factors with human-derived DNA-binding domains targeting non-genomic DNA sequences. Finally, we established a workflow for creating deimmunized zinc-finger arrays to target arbitrary DNA sequences and upregulated two therapeutically relevant genes, utrophin (UTRN) and sodium voltage-gated channel alpha subunit 1 (SCN1A), using it. Our modular workflow offers a way to potentially make cell and gene therapies safer and more efficacious using state-of-the-art algorithms.

Does an ecological community allow stable species coexistence? Identifying the general effects of competitive, mutualistic, and predator-prey interactions on stability remains a central problem of systems ecology because established approaches cannot account for the full network arrangement of these interactions. Here, we therefore analyze all interaction networks of N≤5 species with Lotka-Volterra dynamics by combining exact results and numerical exploration. We find that a very small subset of these networks is "impossible ecologies," in which stable coexistence is non-trivially impossible. We prove that the possibility of stable coexistence is determined by similarly rare "irreducible ecologies." Statistical sampling shows that this probability varies over orders of magnitude even in ecologies that differ only in the network arrangement of identical interactions. Thus, our approach reveals that the full network structure of interactions can influence stability of coexistence more than the established effect of interaction-type proportions. A record of this paper's transparent peer review process is included in the supplemental information.

Gene replacement therapies can generate unnaturally high levels of transgene expression, potentially compromising their safety or efficacy. Variable gene delivery compounds this problem, leading to heterogeneous expression. To address this limitation, ComMAND, a microRNA-based biomolecular circuit assisted by computational models, reduces cell-to-cell variation in gene expression.