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At least 37 records · Page 2Linked to original sources
PubMed2025

Core passive and facultative mTOR-mediated mechanisms coordinate mammalian protein synthesis and decay.

The maintenance of cellular homeostasis requires tight regulation of proteome concentration and composition. To achieve this, protein production and elimination must be robustly coordinated. However, the mechanistic basis of this coordination remains unclear. Here, we address this question using quantitative live-cell imaging, computational modeling, transcriptomics, and proteomics approaches. We found that protein decay rates systematically adapt to global alterations of protein synthesis rates. This adaptation is driven by a core passive mechanism supplemented by facultative changes in mechanistic/mammalian target of rapamycin (mTOR) signaling. Passive adaptation hinges on changes in the production rate of the machinery governing protein decay and allows for partial maintenance of the cellular proteome. Sustained changes in mTOR signaling provide an additional layer of adaptation unique to naive pluripotent stem cells, allowing for near-perfect maintenance of proteome composition. Our work unravels the mechanisms protecting the integrity of mammalian proteomes upon variations in protein synthesis rates. A record of this paper's transparent peer review process is included in the supplemental information.

TOR Serine-Threonine Kinases↗
PubMed2026

Imaging-Guided Omics Technologies for Resolving Rare Cancer States and Advancing Nanomedicine.

The ability to resolve rare and transient cellular states is critical for understanding metastasis, immune evasion, and therapy resistance in cancer, yet these dynamic processes often escape detection by conventional sequencing and imaging approaches. Recent advances at the interface of nanotechnology, high-resolution live-cell imaging, and single-cell/spatial multiomics methods have enabled functional profiling of cells with unprecedented precision within their native microenvironment. In this Mini-Review, we highlight emerging nanoscale platforms that couple real-time phenotypic imaging with molecular readouts, such as FUNseq and CIN-seq, to directly link functional heterogeneity to transcriptomic, proteomic, and epigenomic information. By integrating nanoscale optical imaging, microengineered perturbation tools, and AI-driven computational analysis, these technologies open up new avenues for dissecting rare metastatic, therapy-resistant, or immune-evasive subpopulations. We further discuss how these next-generation imaging-guided single-cell and spatial omics platforms not only advance fundamental cancer biology but also create opportunities to accelerate the development of nanomedicine applications.

Humans↗
PubMed2026

Trimeric autotransporter adhesins driving chain-like adhesion diversify surface colonization strategies in Shiga toxin-producing Escherichia coli.

Bacteria frequently colonize host and environmental surfaces under fluid flow. Chain-like adherence pattern (CLAP) is an EibG-mediated surface colonization phenotype of certain Shiga toxin-producing Escherichia coli (STEC) that lack the locus of enterocyte effacement (LEE). EibG, an immunoglobulin-binding trimeric autotransporter adhesin, drives CLAP, but the temporal dynamics and genetic diversity underlying chain formation remain unclear. Here, we use live-cell time-lapse imaging to show that chains arise from single cells that elongate and divide without separation. Under flow, chains resist detachment and undergo shear-dependent fragmentation at cell-cell junctions, releasing viable clonal units that disperse downstream. Comparative genomics reveals diversity among EibG-related adhesins and identifies distinct lineages, including chain-like adhesins (Cla) that mediate CLAP while lacking IgG binding. Screening of 1,354 genomes from England shows that claB is present in 95.6% of strains from major LEE-negative STEC serotypes, highlighting its epidemiological prevalence. Targeted mutagenesis demonstrates that chain formation and IgG binding are mediated by distinct structural domains, revealing the modular functional architecture of these adhesins. Furthermore, we show that EibG, ClaA, and ClaB confer robust resistance to complement-mediated killing. Collectively, these findings establish CLAP as a dynamic, surface-associated strategy of LEE-negative STEC and reveal diversification among adhesins that drive this behavior.

Bacterial Adhesion↗
PubMed2022

The evolutionary dynamics of extrachromosomal DNA in human cancers.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

Biological Evolution↗
PubMed2026

The TUBG meshwork is associated with centromere dynamics and micronuclear organization.

This study investigates how γ-tubulin and the centrosome contribute to interphase centromere dynamics and nuclear organization. Although classically associated with mitotic microtubule nucleation, here we show that γ-tubulin associates with chromatin and is enriched within centromere-defined volumes. Using live-cell imaging, immunofluorescence, and chromatin immunoprecipitation sequencing, we detect γ-tubulin-associated signal at satellite-rich, centromere-proximal chromatin. Reduced γ-tubulin levels are associated with increased centromere fluorescence intensity and reduced mobility, linking the γ-tubulin network to centromere organization. Under acute cisplatin-induced stress, centromere mobility increases, whereas centromere clustering is observed in separate fixed-cell analyses. Ser131 phosphorylation is associated with γ-tubulin self-assembly and centromere-related dynamics. Additionally, γ-tubulin accumulates in micronuclei, coinciding with increased replication-associated signal and DNA fluorescence. In primary clear cell renal cell carcinoma cells, stress is associated with higher γ-tubulin fluorescence intensity within centromere-defined volumes. Together, these findings support an association between the γ-tubulin meshwork and centromere organization, chromatin compartmentalization, and responses to genomic stress.

Centromere↗
PubMed2024

Transient Zn2+ deficiency induces replication stress and compromises daughter cell proliferation.

Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S phase for timely completion of S phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is chelated during the mother cell's S phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.

Zinc↗
PubMed1979

Crawling movements of lymphocytes on and beneath fibroblasts in culture.

Some lymphocytes become highly motile upon immunological stimulation in vivo or in vitro. When introduced into a culture of 3T3 or L cells and followed by live-cell microscopy, some of these lymphocytes were observed to crawl on top of, along the edges of, and preferentially beneath the attached fibroblasts. The crawling could be as rapid as 20 mum/min, easily detectable without a time-lapse device. The striking ability of crawling lymphocytes to penetrate beneath attached 3T3 cells provided a quantitative means to compare the crawling activity of different lymphocyte populations under various conditions. Crawling was diminished by inhibitors of energy metabolism, by agents that disrupt the cytoskeleton, and by absence of Mg(2+) and Ca(2+), but not of Ca(2+) alone. Crawling lymphocytes were virtually absent in normal thymus and spleen cells. They increased greatly in 5-day mixed lymphocyte cultures and in peritoneal exudate lymphocytes taken after mice had been immunized with allogeneic tumor cells. T cells accounted for most of the crawlers. Of two T-cell leukemias tested, R1(+) cells were crawlers whereas EL-4 cells were not. The H-2 haplotype of the 3T3 fibroblasts (i.e., whether syngeneic or allogeneic) had no apparent effect on lymphocyte crawling activity. The crawling may relate to the exploration of cell surface antigens by lymphocytes (immune surveillance), to the mode of action of cytotoxic T cells, to the migration of lymphocytes across blood vessel walls, or to the penetration of lymphocytes into "solid" masses of normal tissue or tumor cells.

Animals↗
PubMed2026

DENND3-p.R534S disrupts dyadic microdomain architecture to drive potentially pro-arrhythmic calcium and electrophysiologic instability.

AIMS: Inherited ventricular arrhythmias (VAs) frequently occur in the absence of pathogenic variants in canonical ion channel genes, suggesting alternative mechanisms of electrical instability. DENND3 is a guanine nucleotide exchange factor that regulates Rab GTPase-mediated trafficking, but its role in cardiac excitation-contraction coupling and membrane microdomain organization remains undefined. METHODS AND RESULTS: We studied induced pluripotent stem cell-derived cardiomyocytes generated from a CRISPR/CAS9-engineered ultra-rare DENND3-p.R534S variant-inserted line (previously identified in an idiopathic ventricular fibrillation pedigree) and matched isogenic controls. Multielectrode array recordings, live-cell calcium imaging, super-resolution imaging using expansion microscopy, and biochemical analyses were used to assess electrical activity, calcium handling, membrane architecture, and calcium release unit organization. Potentially therapeutic studies were performed using genetic and pharmacologic inhibition of Rab11b. DENND3-p.R534S induced pluripotent stem cell-derived cardiomyocytes exhibited multicellular electrical instability characterized by increased beat-to-beat variability, arrhythmic activity, conduction slowing, and prolonged excitation-contraction delay. These abnormalities were accompanied by heterogeneous and dyssynchronous calcium cycling despite preserved expression of major calcium-handling proteins. Super-resolution imaging revealed disruption of BIN1-dependent membrane architecture and nanoscale uncoupling of Cav1.2 and RyR2. Inhibition of Rab11b restored BIN1 organization, re-established dyadic coupling, normalized calcium cycling, and improved electrical stability. CONCLUSION: These findings support a model in which altered trafficking balance contributes to disruption of membrane microdomain organization, leading to dyadic uncoupling, calcium instability, and electrical dysfunction. Modulation of the Rab11b-mediated trafficking pathway restored structural and functional abnormalities, supporting the trafficking-associated pathway as a potential therapeutic target in DENND3-associated ventricular arrhythmia.

Myocytes, Cardiac↗
PubMed2023

Transient Zn2+ deficiency induces replication stress and compromises daughter cell proliferation.

Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S-phase for timely completion of S-phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is removed during the mother cell's S-phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S-phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.

Biological sciences↗
PubMed2025

Polyamines buffer labile iron to suppress ferroptosis.

Polyamines are essential and evolutionarily conserved metabolites present at millimolar concentrations in mammalian cells. Cells tightly regulate polyamine homeostasis through complex feedback mechanisms, yet the precise role necessitating this regulation remains unclear. Here, we show that polyamines function as endogenous buffers of redox-active iron, providing a molecular link between polyamine metabolism and ferroptosis. Using genome-wide CRISPR screens, we identified a synthetic lethal dependency between polyamine depletion and the key ferroptosis suppressor, GPX4. Mechanistically, we show that polyamine deficiency triggers a redistribution of cellular iron, increasing the labile iron pool and upregulating ferritin. To directly visualize this iron buffering in living cells, we developed a genetically encoded fluorescent reporter for redox-active iron. Live-cell analysis revealed a striking inverse correlation between intracellular polyamine levels and redox-active iron at single-cell resolution. These findings reposition polyamines as key regulators of iron homeostasis, with implications for ferroptosis-linked disease states and cellular redox balance.

Journal Article↗
PubMed2026

Mechanistic trade-offs between local and long-range signaling activity in natural and synthetic morphogens.

Hedgehog family morphogens present an interesting paradox: Despite being hydrophobic because of dual-lipid modifications, they form spatial concentration gradients that are highly conserved and essential for many aspects of metazoan development. Using live-cell single-molecule tracking and engineered synthetic signaling ligands, we isolated the distinct contribution of each lipid modification to Hedgehog diffusion and signaling potency. We found that although both lipid modifications enhance signaling potency, they do so through different mechanisms. Palmitate directly promotes receptor engagement, whereas cholesterol topologically confines secreted morphogens on the cell surface, effectively using the lipid membrane as a nonsignaling co-receptor that enriches ligands locally at the cost of restricting long-range diffusion. Our results on the function of cholesterol point to an intrinsic trade-off between signaling potency and gradient formation, with implications for the evolution and mechanism of nonsignaling co-receptors.

Signal Transduction↗
PubMed1977

Adoptive transfer of immunity from mice immunized with ribosomes or live yeast cells of Histoplasma capsulatum.

This investigation was designed to compare the role of lymphoid cells and immune serum in protective immunity induced by immunization with ribosomes or live yeast cells of Histoplasma capsulatum. Spleen cells, peritoneal cells, and serum from C3H mice immunized with Histoplasma ribosomes or live cells were transferred intravenously to separate groups of syngeneic recipients. All recipients along with a set of immunized and control mice were challenged intravenously with 4 x 10(6) yeast cells of H. capsulatum, and protection was assessed. Immunization with ribosomes or live cells provided 90 to 100% protection. Mice receiving filtered spleen cells or peritoneal cells from donors immunnized with live cells showed 90 to 100% protection; 80 to 90% protection was observed for mice receiving cells from ribosome-immunized donors. In contrast, no evidence of protection was seen in mice receiving serum from either live-cell- or ribosome-immunized mice. Peritoneal cells were far more efficient than spleen cells in adoptive transfer of immunity. The adoptive immunity in recipients persisted for at least 3 weeks after transfer, the longest period tested in the present study. These results indicate that the immunity elicited by immunization with Histoplasma ribosomes or live cells is mediated by a cellular mechanism.

Animals↗
PubMed1979

Protection against experimental cholera by oral or parenteral immunization.

Comparisons were made between the antigenic potency and protective capacity of several cholera toxin derivatives. Rabbits were immunized parenterally with 50 microgram of cholera toxin, A subunit, B subunit, procholeragenoid, or Wyeth glutaraldehyde toxoid 20101. Examination of the antibody response curves revealed that cholera toxin elicited serum antitoxin responses that rose more quickly than in the subunit-immunized animals; however, antitoxin levels were of the same magnitude after 10 weeks. Parenteral immunization with procholeragenoid evoked antibody titers that were similar to the toxin, whereas Wyeth toxoid yielded only one-tenth the level of antitoxin. Oral immunization with procholeragenoid as well as Wyeth toxoid resulted in lower serum antitoxin titers than that achieved with parenteral immunization, despite the oral administration of 10 times the parenteral dose. Analysis of protection against live-cell challenge revealed that parenteral administration of procholeragenoid provided the best protection against fluid accumulation. Oral immunization with procholeragenoid also was very effective, whereas oral immunization with B subunit or Wyeth toxoid resulted in minimal protection. Also, the A subunit provided surprisingly more protection than did cholera toxin.

Administration, Oral↗
PubMed1990

Characterization of Tritrichomonas foetus antigens by use of monoclonal antibodies.

The specificity for and function of monoclonal antibodies against Tritrichomonas foetus were characterized. Four monoclonal antibodies generated by immunization of mice with live T. foetus were selected on the basis of enzyme-linked immunosorbent assay reactions. The approximate molecular masses of the predominant proteins were determined by Western blotting (immunoblotting). Monoclonal antibody TF3.8 recognized a predominant band at approximately 155 kilodaltons, whereas TF3.2 reacted with several bands. Monoclonal antibodies TF1.17 and TF1.15 recognized broad bands between 45 and 75 kilodaltons. The first two antibodies (TF3.8 and TF3.2) did not react with the surface of T. foetus, as determined by live-cell immunofluorescence, agglutination, and immobilization, whereas two other monoclonal antibodies (TF1.17 and TF1.15) did react with surface epitopes, as determined by these criteria. The latter two monoclonal antibodies also mediated complement-dependent killing of T. foetus and prevented of adherence of organisms to bovine vaginal epithelial cells. One antibody, TF1.15, also killed in the absence of complement. Since these functions are in vitro correlates of protection, the antigens recognized by these monoclonal antibodies may induce protective immunity.

Animals↗
PubMed1989

p53-plus-ras-transformed rat embryo fibroblasts express tumor-specific transplantation antigen activity which is shared by independently transformed cells.

p53-plus-ras-transformed rat cell lines express a tumor-specific transplantation antigen that is common to a number (85%) of independently derived p53-plus-ras-transformed cell lines. This has been shown by immunizing rats with irradiated p53-plus-ras-transformed cells and demonstrating protection of these animals by subsequent live-cell tumor challenge. Several c-myc-plus-ras-transformed cell lines (54% of the lines tested) and one adenovirus E1a-plus-ras-transformed cell line (9% of those tested) were shown to share a common tumor-specific transplantation antigen by their ability to immunize a rat against a p53-plus-ras cell line challenge. Several experimental approaches have been used to fractionate and identify the antigen common to these cell lines. The experimental results reported here make it clear that the p53 protein common to most of these transformed cell lines is not likely to be the tumor-specific transplantation antigen.

Animals↗
PubMed2026

Anoxia tolerant DNA replication is supported by ATR kinase in the annual killifish Austrofundulus limnaeus.

Hypoxia and anoxia suppress cell proliferation due to an increase in replication stress and activation of DNA damage checkpoints. Embryos of the annual killifish Austrofundulus limnaeus tolerate prolonged anoxia, indicating improved genomic stability under oxygen starvation. We investigated the cell cycle regulation of the anoxia tolerant killifish embryonic cell line PSU-AL-WS40NE during anoxia. Live-cell imaging confirms continued proliferation of WS40NE cells for the first 24 h of anoxia with minimal cell death. Fluorescence imaging shows that cells accumulate in G1 after the first day in anoxia with a rapid entry into S phase upon reoxygenation. Pharmacological inhibition shows a reliance on ataxia telangiectasia and Rad3 related (ATR) signaling, suggesting that increased γH2AX levels are driven by replication stress instead of DNA damage. This conclusion is supported by a lack of induction of a G2 checkpoint, suggesting minimal DNA damage during anoxic exposure. Maintaining cellular proliferation during anoxia and accumulating cells in the G1 phase for extended anoxic exposure is likely one way that embryos of the killifish can survive prolonged anoxia, which provides insight into mechanisms that enable cells to proliferate under metabolic stress.

Animals↗
PubMed2026

Evaluation of 3D Spheroids for AAV Transduction Studies.

Adeno-associated viruses (AAVs) are potent vectors used for gene delivery in gene therapy products. Their development requires in vitro systems that can reliably detect differences in vector design, serotype performance, regulatory element strength, and expression kinetics. These systems must also support applications such as potency assessment and vector optimization. Here, we describe a streamlined three-dimensional spheroid platform optimized for evaluating AAV potency, transgene expression kinetics, and serotype-specific transduction efficacy across diverse cell lines. Uniform spheroids are generated using ultra-low attachment plates and maintained under conditions that support stable architecture and long-term imaging. Following AAV transduction, fluorescent or luminescent readouts are monitored in real time using live-cell imaging systems. This enables quantitative assessment of reporter signal, dose responsiveness, regulatory element activity, and onset time through continuous kinetic imaging. The platform effectively discriminates between potent and weak vector genome designs and among multiple AAV serotypes. This method demonstrates robust performance across both slowly and rapidly dividing cell lines. These results establish its utility as a scalable and physiologically relevant system for preclinical gene therapy evaluation and development.

Dependovirus↗
PubMed2026

Characterizing Riboglow Probes In Vitro as the Basis for Fluorescence Lifetime Imaging In Live Mammalian Cells and Three-Dimensional Cellular Models.

Nearly 80% of the human genome is transcribed into RNA, while less than 2% encode for proteins, indicating that the majority of mammalian transcripts are noncoding and participate in diverse regulatory processes. Therefore, sensing and visualizing RNA molecules in live mammalian cell systems quantitatively are critical to understanding RNA dynamics and interactions, yet remains technically challenging, especially in complex cellular environments. Riboglow is a genetically encoded RNA biosensor in which a short RNA aptamer binds a small-molecule probe, producing a quantifiable fluorescence lifetime turn-on detectable by fluorescence lifetime imaging microscopy (FLIM). Here, we present a detailed workflow for Riboglow-FLIM, including sample preparation, image acquisition, and quantitative analysis of FLIM datasets. The goal of this protocol is to enable quantitative fluorescence lifetime-based RNA detection using Riboglow in controlled and live-cell environments. The protocol is demonstrated in vitro, where RNA dependent lifetime changes are measured, and in live mammalian cells, where FLIM acquisition, region of interest selection, and subcellular analysis are established. Successful implementation requires careful control of experimental and acquisition parameters. Key considerations for reproducible implementation are highlighted. Together, this protocol serves as a practical reference for implementing Riboglow-FLIM and quantitatively assessing RNA visualization in live cells.

Humans↗