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Results for “cell signaling”

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At least 19 recordsLinked to original sources
PubMed2026

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

MOTIVATION: Algorithms for ligand-receptor network inference have emerged as commonly used tools to estimate cell-cell communication from reference single-cell data. Many studies employ these algorithms to compare signaling between conditions and lack methods to statistically identify signals that are significantly different. We previously developed the cell communication inference algorithm Domino, which considers ligand and receptor gene expression in association with downstream transcription factor activity scoring. We developed the dominoSignal software to innovate upon Domino and extend its functionality to test statistically differential cellular signaling. RESULTS: This new functionality includes the compilation of active signals as linkages from multiple subjects in a single-cell data set and testing condition-dependent signaling linkage. The software is applicable for analysis of single-cell data sets with multiple subjects as biological replicates as well as with bootstrapped replicates from data sets with few or pooled subjects. We use simulation studies to benchmark the number of subjects in compared groups and cells within an annotated cell type sufficient to accurately identify differential linkages. We demonstrate the application of the Differential Cell Signaling Test (DCST) in the dominoSignal software to investigate consequences of cancer cell phenotypes and immunotherapy on cell-cell communication in tumor microenvironments. These applications in cancer studies demonstrate the ability of differential cell signaling analysis to infer changes to cell communication networks from therapeutic or experimental perturbations, which is broadly applicable across biological systems. AVAILABILITY: dominoSignal is available through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/dominoSignal.html.

Cell Communication↗
PubMed1976

Differentiation for aggregation in the cellular slime moulds: the emergence of autonomously signalling cells in Dictyostelium discoideum.

The results of experiments on small populations of Dictyostelium discoideum, directed towards the measurement of the development in time of the competence of the cells to signal autonomously, are reported. This competence is quantified by X3, the intrinsic probability that a given cell may turn autonomous. The data show an early exponential growth in time of X3, followed by saturation. The saturation value depends on the population size suggesting that the differentiation is a co-operative phenomenon. The differentiation of autonomous cells starts roughly 7 h after the removal of food and saturates within 21 h.

Cell Aggregation↗
PubMed1978

PH oscillations in cell suspensions of Dictyostelium discoideum: their relation to cyclic-amp signals.

Cells of Dictyostelium discoideum known to release cyclic AMP (cAMP) rhythmically in the form of pulses, change with the same period of about 8 min the pH of their medium. The pH is used here as an indicator to investigate the effect of externally added cAMP pulses on the oscillations. Both a temporary increase in amplitude and a permanent phase shift can be induced. The phase-response curve indicates that the period can be increased and decreased by rhythmic stimulation with cAMP pulses.

Cyclic AMP↗
PubMed2001

Regulation of thyroid cell proliferation by TSH and other factors: a critical evaluation of in vitro models.

TSH via cAMP, and various growth factors, in cooperation with insulin or IGF-I stimulate cell cycle progression and proliferation in various thyrocyte culture systems, including rat thyroid cell lines (FRTL-5, WRT, PC Cl3) and primary cultures of rat, dog, sheep and human thyroid. The available data on cell signaling cascades, cell cycle kinetics, and cell cycle-regulatory proteins are thoroughly and critically reviewed in these experimental systems. In most FRTL-5 cells, TSH (cAMP) merely acts as a priming/competence factor amplifying PI3K and MAPK pathway activation and DNA synthesis elicited by insulin/IGF-I. In WRT cells, TSH and insulin/IGF-I can independently activate Ras and PI3K pathways and DNA synthesis. In dog thyroid primary cultures, TSH (cAMP) does not activate Ras and PI3K, and cAMP must be continuously elevated by TSH to directly control the progression through G(1) phase. This effect is exerted, at least in part, via the cAMP-dependent activation of the required cyclin D3, itself synthesized in response to insulin/IGF-I. This and other discrepancies show that the mechanistic logics of cell cycle stimulation by cAMP profoundly diverge in these different in vitro models of the same cell. Therefore, although these different thyrocyte systems constitute interesting models of the wide diversity of possible mechanisms of cAMP-dependent proliferation in various cell types, extrapolation of in vitro mechanistic data to TSH-dependent goitrogenesis in man can only be accepted in the cases where independent validation is provided.

Animals↗
PubMed1979

IgG recruiting component (GRC): B cell-derived signal for IgG antibody synthesis.

The B cell-derived soluble factor that has been described as an IgG-recruiting component (GRC) was investigated to: a) ascertain whether it is governed by genetic constraints, b) determine what triggers its synthesis, and c) identify its cellular target. GRC has been shown to be unrestricted by histocompatibility barriers since it enhanced IgG antibody production in mice of diverse genetic backgrounds. Further, we report that eliminating IgG-bearing cells from B cells to be immunized in vitro allows T cells-replacing factor (TRF) to increase the number of IgM but not IgG PFC. Thus, TRF appears to act on IgM-bearing cells by expanding the IgM PFC number. Adding GRC 48 hr after the addition of TRF to such IgG-depleted cells caused expression of IgG PFC. Hence, B cells lacking IgG but possessing IgM surface immunoglobulins appear to be those that are acted upon by GRC. These data indicate that in whole splenic cell populations, GRC is derived from IgG-bearing B cells that are stimulated by antigen and a component in TRF.

Animals↗
PubMed2026

A wild soybean MADS-box gene GsAGL62 improves seed weight by enhancing cytokinin signaling and cell proliferation.

Soybean seed weight is a key yield determinant, but the transcriptional mechanisms connecting hormone signaling to seed growth are poorly understood. Here, we identify GsAGL62, a wild soybean MADS-box transcription factor located within a previously mapped hundred-seed weight (HSW) locus and a domestication-associated selective sweep. Functional analyses show that overexpression of GsAGL62 in cultivated soybean significantly increases HSW, whereas ethyl methanesulfonate (EMS)-induced gmagl62 mutants reduce it. Integrated transcriptomic and metabolomic analyses reveal that GsAGL62 enhances cytokinin accumulation and signaling cytokinin-associated responses, accompanied by increased expression of genes involved in cell proliferation. Mechanistically, GsAGL62 directly binds to the promoter of the conserved growth inhibitor GmATPK2 and represses its transcription. Consistently, independent EMS-induced gmatpk2 mutants exhibit increased seed weight, supporting GmATPK2 as a downstream negative regulator of seed growth. Population genetic analyses further reveal strong differentiation of GsAGL62 promoter haplotypes during soybean domestication and improvement. These haplotypes show differential promoter activities and are associated with distinct agronomic performance, suggesting that cis-regulatory variation at GsAGL62 contributes to its selection during soybean improvement. Collectively, our findings establish a regulatory module linking GsAGL62 to cytokinin-associated responses, cell proliferation, and seed growth, and highlight GsAGL62 as a potential target for soybean yield improvement.

Cell proliferation↗
PubMed1976

Automation in cervical cancer screening. Part 1: fixed cell scanning systems.

Cytology automation is highly desirable if a mass cancer screening system is to be effective, and has been the subject of widespread research and development effort. Several experimental systems have been developed based on fixed cell scanning or flow techniques, but clinical trials have produced disappointing results. The major problem with these early systems has been that of false positive "abnormal cell" signals caused by cell overlaps and artifacts. Most current research is devoted to the development of better techniques for cell presentation, to the improvement of pattern recognition techniques, and to the exploitation of novel cell parameters in flow systems.

Automation↗
PubMed2025

Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators.

Cell signaling plays a critical role in regulating cellular state, yet uncovering regulators of signaling pathways and understanding their molecular consequences remains challenging. Here, we present an iterative experimental and computational framework to identify and characterize regulators of signaling proteins, using the mTOR marker phosphorylated RPS6 (pRPS6) as a case study. We present a customized workflow that uses the 10x Flex assay to jointly profile intracellular protein levels, transcriptomes, and CRISPR perturbations in single cells. We use this to generate a "glossary" dataset of paired protein-RNA measurements across targeted perturbations, which we leverage to train a predictive model of pRPS6 levels based solely on transcriptomic data. Applying this model to a genome-wide Perturb-seq dataset enables in silico screening for pRPS6 and nominates novel regulators of mTOR signaling. Experimental validation confirms these predictions and reveals mechanistic diversity among hits, including changes in signaling output driven by anabolic activity, cellular proliferation and multiple stress pathways. Our work demonstrates how integrated experimental and computational approaches provide a scalable framework for multimodal phenotyping and discovery.

Journal Article↗
PubMed2026

Altered ECM deposition and cell adhesion signaling in a human cortical organoid model of fragile X syndrome.

Fragile X Syndrome (FXS) is the most common inherited intellectual disability, and the most common monogenic cause of autism spectrum disorder (ASD). It is caused by epigenetic silencing of the FMR1 gene leading to the loss of FMRP, an RNA-binding protein that regulates local mRNA translation in neuronal dendrites, crucial for synapse development. Three-dimensional (3D) brain organoid models derived through in vitro differentiation of pluripotent stem cells offer a powerful tool to dissect the underlying mechanisms of neurodevelopmental disorders. Here, we generated human FXS and control organoids using isogenic human embryonic stem cell clones with and without the FXS mutation. Our results show that mature FXS cortical brain organoids can be derived by inhibiting the TGFβ and Wnt pathways. Moreover, expression analyses including immunofluorescence, qRT-PCR, proteomics and western blotting reveal altered levels of neuronal markers and ECM deposition along with modulated downstream signaling molecules. Interestingly, in silico analysis of proteomics revealed several altered pathways, such as cell adhesion, regulation of neurogenesis and cell cycle that are implicated in FXS. Collectively, our unique FXS-organoids derived from isogenic hESC lines may serve as a model for studying the pathology of FXS disorder and for developing therapeutical intervention.

Humans↗
PubMed1975

Chemotactic signals induce cell differentiation in Dictyostelium discoideum.

Experiments carried out with the aid of cellophane membranes demonstrate that the morphogenetic block of certain nonaggregating, "aggregateless," mutants may be overcome by diffusible factors excreted by aggregating wild-type cells. The same differentiation process into aggregation-competent cell is observed if mutant amoebae are subjected to external 3':5'-cAMP pulses imposed at 5 min intervals. Wild-type amoebae also respond to cAMP pulses, since the onset of differentiation is more precocious in pulsed than in unpulsed populations. These data suggest that chemotactic signals act as an inducer of cell differentiation.

Adenosine Monophosphate↗
PubMed2026

Multi-Ancestry Genome-Wide Association with Fine-Mapping Identifies Novel Loci for Pigment Dispersion Syndrome and Pigmentary Glaucoma.

PURPOSE: Pigment dispersion syndrome and pigmentary glaucoma are important causes of ocular hypertension and glaucomatous optic neuropathy, yet their genetic determinants remain incompletely defined, particularly across diverse ancestries. This study aimed to use a large multi-ancestry cohort from the All of Us Research Program to investigate the genetic basis of pigment dispersion syndrome and pigmentary glaucoma. DESIGN: Case-control study. PARTICIPANTS: In total, 572 cases and 37 808 controls with array genotyping and 537 cases and 35 493 controls with whole-genome sequencing. METHODS: Using electronic health record phenotyping in the All of Us Research Program, we performed multi-ancestry genome-wide association analyses using both array-based data and whole-genome sequencing-based data, comparing patients with pigment dispersion syndrome or pigmentary glaucoma to those without either condition. We also performed Firth penalized regression and Fisher analyses, and we performed principal component analyses to assess effect sizes across genetic ancestries. We applied statistical fine-mapping, examined for cross-trait overlap, and assessed expression quantitative trait locus associations for lead variants. MAIN OUTCOME MEASURES: P values and odds ratios of lead loci from genome-wide association analyses; size of credible sets determined from fine-mapping; allele frequency of lead variants in cases, controls, and the general population; expression quantitative trait loci effect size and P values linking lead variants to gene expression. RESULTS: We identified 4 loci reaching genome-wide significance across analyses, including signals near EPHA7 (which mediates cell-cell signaling), within TYR (involved in melanin synthesis and replicated from prior studies), within LINC01138, and near OTX2. Statistical fine-mapping refined 3 of these loci to single-variant 95% credible sets and narrowed the TYR locus to small credible sets, prioritizing possible causal variants. Effect estimates were broadly consistent across genetic ancestry clusters. Lead variants showed regulatory evidence in expression quantitative trait locus, including reduced EPHA7 expression. CONCLUSIONS: These findings implicate both melanogenesis and cell-cell adhesion and signaling pathways in pigment dispersion syndrome and pigmentary glaucoma. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Genome-wide association study↗
PubMed1979

Lymphokine production in primary mixed lymphocyte culture (MLC). III. Alloantigen signals cell-cell interactions involved in migration inhibition factor and immune interferon release.

The alloantigen differences stimulation migration inhibition factor (MIF) and immune interferon (i-IF) release in primary one-way murine mixed lymphocyte cultures are reported. Differences at H-2 and Mls coded alloantigens induce both MIF and i-IF release, while the differences at multiple minor histocompatibility antigens induce MIF release only. Both MIF and i-IF release are T-lymphocytes dependent events. However, while T-lymphocytes are sufficient for MIF release, the presence of macrophages is required for i-IF release.

Animals↗
PubMed1978

Intermediary role of macrophages in the passage of suppressor signals between T-cell subsets.

We have examined the ability of macrophages (Mphi) to transmit T-cell derived suppressor signals to other T cells. The suppressor signal studied is an antigen-specific factor which suppresses the ability of adoptively transferred, sensitized lymphocytes to express contact hypersensitivity in normal recipients. We have found that this factor binds to peritoneal exudate Mphi via cell surface structures which can be blocked with heat-aggregated gamma globulin. Dead (HK) Mphi bind the factor but fail to present it in a functional way to assay (immune) T cells, whereas live (L) Mphi perform both functions. Further, L Mphi can retrieve the factor in an active form from the surfaces of HK Mphi. Based on these and other findings (1-5), we discuss the possibility that Mphi may play as important a role in presenting T-cell communication signals to the cells of the immune system as they do in presenting antigen.

Animals↗
PubMed2026

Genome-wide CRISPRi screen in human iNeurons identifies novel negative mTOR regulator genes associated with focal cortical dysplasia.

Focal cortical dysplasia (FCD) is a common cause of focal epilepsy that typically results from brain mosaic mutations in the mTOR cell signaling pathway. To identify new potential FCD genes, we developed an in vitro CRISPRi screen in human neurons and used FACS enrichment based on the FCD biomarker, phosphorylated S6 ribosomal protein (pS6). Using whole-genome (110,000 gRNAs) and candidate (129 gRNAs) libraries, we discovered 6 new genes in which loss of function significantly increases pS6 levels: LRRC4, EIF3A, TSN, HIP1, PIK3R3, and URI1. Further analysis of the mTOR pathway showed that only two of the genes, PIK3R3 and HIP1, caused hyperphosphorylation throughout the AKT/mTOR/S6 signaling pathway. Importantly, potential pathogenic variants in these two genes have been reported in resected brain tissue from a single FCD patient each, supporting the predictive validity of our screen. Knocking down each of the 6 genes in iNeurons made mTOR signaling resistant to the loss of neurotrophic factor signaling, specifically GDNF; even without GDNF, pS6 levels remained comparable to GDNF-stimulated controls. Thus, we have identified negative regulators of neuronal mTOR signaling in the context of lost neurotrophic factor support. Our data expand the set of genes that are likely to regulate mTOR pathway signaling in neurons, provide biological confirmation for candidate genes identified in human tissue, and suggest additional targets for investigating somatic gene variants in resected FCD tissues. The identification of novel mTOR regulators using iNeurons also highlights the importance of genetic screening in disease-related cell types.

Brain mosaicism↗
PubMed1978

Activation of B cell subsets by T-dependent and T-independent antigens.

The capacity of the trinitrophenyl haptenic group coupled to a series of chemically dissimilar carriers to cross-stimulate putative T-dependent and T-independent B-cell subpopulations was determined by using an in vitro limiting dilution technique to generate primary IgM responses. TNP-Ficoll and TNP-dextran, two T-independent antigens with little or no polyclonal mitogenicity, stimulate the same population of anti-TNP precursors, which is distinct from the precursor population activated by TNP-LPS, a T-independent polyclonal mitogen, or by TNP-HRBC, a T-dependent antigen. TNP-LPS and TNP-HRBC activate the same precursor population, indicating that LPS can substitute for the T cell signal in T-dependent B-cell responses, whereas nonmitogenic T-independent antigens cannot. However, the cumulative evidence from this and other laboratories suggests that LPS and T-dependent antigens activate B cells by different mechanisms. TNP conjugates of Ficoll and dextran, which are relatively poor inducers of polyclonal B cell activation, induced larger anti-TNP clones than did TNP-LPS, a strong polyclonal mitogen. Macrophages are required for the anti-TNP-Ficoll/anti-TNP-dextran response, whereas, a similar requirement has not been shown for the anti-TNP-LPS response. Thus, macrophages may function as polyclonal B cell activators in T-independent responses. Experiments in which TNP was coupled directly onto the macrophage surface support this hypothesis. B-cell heterogenity in T-dependent responses is suggested by experiments using the C3 receptor as a marker for functional subpopulations of B cells. Murine T cells cooperate with B cells that carry a receptor for C3 and with at least some B cells which lack the C3 receptor in a primary in vitro antibody response. In vitro culture experiments using populations of B cells fractionated on the basis of the C3 receptor showed that CR+ cells were unable to make T-dependent antibody responses in the presence of anti-C3 antibody, whereas the response of CR- B cells was unaffected. Using irradiated, carrier-primed spleen cells from B10.A mice as a source of helper cells for B cells derived from various congenic strains in an in vitro primary IgM response to TNP-KLH, CR+ B cells cooperated across haplotype differences in the I region of the MHC, whereas CR- B cells did not. Preliminary mapping experiments for the genetic restriction of CR- B cells suggest complementation between the I-A and I-C subregions of the MHC. These findings tentatively suggest the existence of alternative cooperative pathways between T cells and B cell subpopulations.

Animals↗