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At least 109 records · Page 6Linked to original sources
PubMed1996

Clinical application of flow cytometry to urological malignancies.

Flow cytometric DNA analysis provides rapid, quantitative objective information regarding the biological behavior of urological malignancies. Moreover, clinical applications of the many recent advances made the flow cytometry are expected to materialize soon. For instance, flow cytometric DNA ploidy analysis for human bladder cancers may provide a significant diagnostic and prognostic potential. Also, flow cytometric DNA analysis of irrigation specimens produces a higher sensitivity than conventional cytology for detecting bladder cancer. However, there are obvious pitfalls with this approach since diploid or near-diploid tumors cannot always be recognized by DNA analysis alone. One of the most significant advantages possible with flow cytometry is its capability of analyzing simultaneously multiple parameter on single cells. The integration of the DNA content with proliferative activity should yield important information significant to the biological behavior of individual tumors. Flow cytometric DNA/bromodeoxyuridine bivariate analysis can be used as an effective adjunct to histological examination for prognostication and decision-making in treatment of bladder cancer patients. Therefore, multiparameteric flow cytometric analysis can be used to isolate specific tumor cells from mixed cell populations, and should receive even increased attention as a valuable diagnostic technique and prognostic factor. In the present review, the efficacy of flow cytometric DNA ploidy analysis integrated with cell proliferation markers is discussed.

Cell Division↗
PubMed1989

Columnar specificity of intrinsic horizontal and corticocortical connections in cat visual cortex.

A prominent and stereotypical feature of cortical circuitry in the striate cortex is a plexus of long-range horizontal connections, running for 6-8 mm parallel to the cortical surface, which has a clustered distribution. This is seen for both intrinsic cortical connections within a particular cortical area and the convergent and divergent connections running between area 17 and other cortical areas. To determine if these connections are related to the columnar functional architecture of cortex, we combined labeling of the horizontal connections by retrograde transport of rhodamine-filled latex microspheres (beads) and labeling of the orientation columns by 2-deoxyglucose autoradiography. We first mapped the distribution of orientation columns in a small region of area 17 or 18, then made a small injection of beads into the center of an orientation column of defined specificity, and after allowing for retrograde transport, labeled vertical orientation columns with the 2-deoxyglucose technique. The retrogradely labeled cells were confined to regions of orientation specificity similar to that of the injection site, indicating that the horizontal connections run between columns of similar orientation specificity. This relationship was demonstrated for both the intrinsic horizontal and corticocortical connections. The extent of the horizontal connections, which allows single cells to integrate information over larger parts of the visual field than that covered by their receptive fields, and the functional specificity of the connections, suggests possible roles for these connections in visual processing.

Animals↗
PubMed1997

Efficiency of single-cell polymerase chain reaction from stained histologic slides and integrity of DNA in archival tissue.

Molecular analysis of isolated single cells is a powerful tool for studying heterogeneity within a population of cells and for clarifying issues of cell origin and clonality. Here, we investigate the applicability of molecular techniques at a single-cell level by using routinely processed archival tissue. An ultraviolet laser in conjunction with a computer-controlled micromanipulator and a microscope were used for the contamination-free isolation of single tumor cells from stained sections of diffuse-type gastric cancer. A total of 1,328 single cells and 654 clusters of 10-30 cells each, taken from specimens of 14 patients, were analyzed for parts of the E-cadherin gene by the polymerase chain reaction (PCR). With increasing length in base pairs (bp) of the amplified fragments, the efficiency of single-cell PCR as measured by the rate of detectable amplification products declined from approximately 25% (156, 213, and 228 bp) to 14% (246 bp) and 11% (264 and 296 bp). For groups of 10-30 cells, a similar effect was seen at a higher level at 33% (246 bp), 31% (264 bp), and 26% (296 bp), respectively. To our knowledge, this is the first report that has studied the outcome of single-cell PCR on a large systematic scale. The average degree of DNA disintegration in paraffin-embedded, stained tissues was estimated to be approximately 100 bp when the aforementioned data were used in a mathematical model. This study provides evidence that in order to obtain reasonable sensitivity with single-cell PCR, short fragments, preferably < 200 bp long, should be used. Furthermore, whenever applicable, pooling of cells of interest may be another favorable option.

DNA↗
PubMed2025

scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data.

Measuring single-cell genomic profiles at different timepoints enables our understanding of cell development. This understanding is more comprehensive when we perform an integrative analysis of multiple measurements (or modalities) across various developmental stages. However, obtaining such measurements from the same set of single cells is resource-intensive, restricting our ability to study them jointly. We introduce scMultiNODE, an unsupervised integration model that combines gene expression and chromatin accessibility measurements in developing single cells, while preserving cell type variations and cellular dynamics. First, scMultiNODE uses a scalable, Quantized Gromov-Wasserstein optimal transport to align a large number of cells across different measurements. Next, it utilizes neural ordinary differential equations to explicitly model cell development with a regularization term to learn a dynamic latent space. Experiments on six real-world developmental single-cell datasets demonstrate that scMultiNODE can integrate temporally profiled multi-modal single-cell measurements more effectively than existing methods that focus on cell type variations and often overlook cellular dynamics. We also demonstrate that scMultiNODE's joint latent space facilitates several insightful downstream analyses of single-cell development, including the investigation of complex cell trajectories and the enabling of cross-modal label transfer. The data and code are publicly available at https://github.com/rsinghlab/scMultiNODE.

autoencoders↗
PubMed2006

Micro hole-based cell chip with impedance spectroscopy.

Electric fields can be used for the characterisation and manipulation of single biological cells. One approach to avoid the effect of electrode polarisation is to position cells on micro holes and to apply the electrical fields via the micro holes. For a correct characterisation and optimal manipulation, the electrical properties of the micro hole/cell interface must be understood. In this article, the electrical characteristics of a micro hole-based cell chip were investigated. By FEM simulation, it was estimated that the impedance measurement with micro hole-based chip is most dependent on the cell adhesion/spread rather than the intra-cellular space (contribution of intra-cellular space to the total impedance: 0.07% at 1 kHz, 0.3% at 1 MHz). The effective frequency range in which the impedance related with cell state on the hole considerably influences total measured impedance was below several kiloHertz. From the experiments, it was shown that the impedance of cell cultured on the hole at the low frequency range is increased during the increase of cultivation period, but is sensitively decreased after applying only several nanolitres of culture medium including 5% dimethlysulfoxide. This micro hole-based chip has a potential for monitoring the cell growth and the membrane integrity of even single cell without any labelling.

Biosensing Techniques↗
PubMed2026

Integrative multi-omics and single-cell analysis identifies EGFR pathway activation and metabolic reprogramming as potential synthetic lethal vulnerabilities in resistance to the FGFR inhibitor AZD4547.

BACKGROUND: Although fibroblast growth factor receptor (FGFR) inhibitors (FGFRi) have demonstrated clinical promise, the inevitable emergence of acquired resistance remains a critical bottleneck, severely compromising their long-term clinical efficacy. The pan-cancer molecular landscape and heterogeneous mechanisms driving this resistance, ranging from genetic alterations to dynamic network rewiring, remain poorly understood. METHODS: We integrated large-scale pharmacogenomic profiling of the FGFR inhibitor AZD4547 from the GDSC2 and PRISM databases with single-cell RNA sequencing to dissect the multi-omics landscape of FGFRi resistance across 312 cell lines from 8 cancer types. This multi-omics framework was further extended by machine learning modeling and systematic synthetic lethality screening to uncover actionable therapeutic targets. In vitro viability assays and western blot analysis were subsequently conducted to experimentally evaluate the predicted FGFR-EGFR synthetic lethality. RESULTS: Our dual-database analysis unveiled a multi-dimensional atlas of FGFRi resistance. We identified cancer-specific genomic drivers, such as ELF4 amplification in glioblastoma, alongside key transcriptomic markers including UCP2 and FSCN1, highlighting a shift towards metabolic reprogramming and epithelial-mesenchymal transition (EMT). Single-cell analysis unveiled that resistance is linked to the heterogeneous enrichment of baseline subpopulations characterized by distinct metaprograms, including cell-cycle dysregulation. Furthermore, a random forest model built on a LASSO-derived transcriptomic signature was constructed, demonstrating promising predictive capability for AZD4547 sensitivity (mean test-set AUC&#x2009;=&#x2009;0.73, 95% CI [0.63, 0.80]); the signature generalized well to erdafitinib but showed limited transferability to some other FGFR inhibitors (e.g. pemigatinib, BGJ398). Most notably, our synthetic lethal screening revealed a convergent reliance on compensatory RTK signaling (specifically EGFR pathway enrichment) and downstream MAPK/PI3K cascades in resistant phenotypes, providing converging computational evidence for EGFR pathway activation as an adaptive bypass mechanism. This predicted synthetic lethality was experimentally supported in two FGFR-dependent cell line models (RT112 and CCLP1), in which combined FGFR-EGFR inhibition produced marked synergistic antiproliferative effects. CONCLUSIONS: This study establishes a comprehensive multi-omics atlas of resistance to the FGFR inhibitor AZD4547, delineating convergent mechanisms of metabolic reprogramming and EGFR-mediated bypass signaling. Our findings characterize the resistance as a dynamic network rewiring and nominate rational combination strategies to overcome this therapeutic bottleneck. While FGFR-EGFR co-inhibition is experimentally supported, metabolic co-targeting remains a computationally derived, hypothesis-generating strategy.

Benzamides↗
PubMed1995

Efficiency of various dissociation methods for the preparation of thyroid single cell suspensions.

For comparison of the physiological potential of single thyroid cells versus cells integrated into follicles it would be ideal to work with suspensions consisting exclusively of single cells instead of a mixture of single cells and follicle fragments. In this study, various techniques for the isolation of single cells have been tested for their effect on cell viability, the ultrastructure of the isolated cells, the percentage of single cells and the ability of these cells to form follicles in culture. In addition, the cells were characterized for the preservation of their morphology and the ability to respond to TSH by comparing their immunocytochemical staining pattern with anti-vimentin and anti-ras p21 antibody to that of the intact thyroid tissue. Dispase treatment of thyroid tissues alone produced suspensions with a relatively small proportion of single cells. These cells stained with anti-vimentin and anti-ras p21 antibody to a similar percentage as thyroid cells in the intact gland. A combination of dispase treatment with either filtration or trypsin treatment severely compromised the viability of the cells. A high proportion of single cells with a good viability could be obtained either by centrifugation of dispase treated tissues or by culturing of dispase treated tissues as monolayers and subsequent detachment from the culture vessels with trypsin. Whereas the immunological staining with anti-vimentin and anti-ras oncogene antibody in the centrifuged cells resembled that of intact tissue, cells cultured as monolayers reacted differently. The differences in the immunological staining were still observed when the cells which had been grown as monolayers were stimulated with TSH. Differential centrifugation appeared to be the ideal method for the isolation of unaltered and viable single cells but is a rather laborious method to obtain larger amounts of single thyroid cells.

Animals↗
PubMed2026

Decoding regional keratinization in human oral mucosa through high-resolution spatial transcriptomics.

Oral mucosa exhibits region-specific keratinization, essential for periodontal health, yet the spatial and molecular mechanisms driving these differences remain poorly understood. This study aimed to generate a high-resolution spatial transcriptomic atlas of the human oral mucosa around the mucogingival junction, to reveal stromal-epithelial interactions, that distinguish keratinized from non-keratinized programs. Formalin-fixed paraffin-embedded specimens from the mucogingival junction area of two healthy donors were analyzed with the 10&#x2009;&#xd7;&#x2009;Genomics Visium HD platform, yielding two keratinized and two non-keratinized regions. Spatial clustering, pseudotime trajectory inference, cell-type integration with a single-cell reference, and ligand-receptor network analysis were applied to delineate epithelial and stromal compartments. Sixteen reproducible clusters, recapitulating tissue architecture, were identified and revealed distinct transcriptional signatures, distinguishing gingiva from lining mucosa. Pseudotime analysis revealed bifurcating epithelial lineages, originating from a shared basal progenitor layer into keratinized and non-keratinized programs. Gingival keratinization was driven by stromal collagen ligands (COL1A1, COL1A2, COL6A1, COL6A2) engaging epithelial receptors (CD44, SDC1), further reinforced within the epithelium by desmosomal adhesion via DSG1-DSC2/3. Gingival keratinization emerges from integrated stromal collagen signaling and epithelial adhesion. This spatially resolved framework advances understanding of oral mucosal specialization and provides a foundation for biologically guided regenerative therapies.

Humans↗
PubMed2025

Sparse deconvolution of cell type medleys in spatial transcriptomics.

Mapping cell distributions across spatial locations with whole-genome coverage is essential for understanding cellular responses and signaling However, current deconvolution models aim to estimate the proportions of distinct cell types in each spatial transcriptomics spot by integrating reference single-cell data. These models often assume strong overlap between the reference and spatial datasets, neglecting biology-grounded constraints such as sparsity and cell-type variations, as well as technical sparsity. As a result, these methods rely on over-permissive algorithms that ignore given constraints leading to inaccurate predictions, particularly in heterogeneous or unmatched datasets. We introduce Weight-Induced Sparse Regression (WISpR), a machine learning algorithm that integrates spot-specific hyperparameters and sparsity-driven modeling. Unlike conventional approaches that neglect biology-grounded constraints, WISpR accurately predicts cell-type distributions while preserving biological coherence, i.e., spatially and functionally consistent cell-type localization, even in unmatched datasets. Benchmarking against five alternative methods across ten datasets, WISpR consistently outperformed competitors and predicted cellular landscapes in both normal and cancerous tissues. By leveraging sparse cell-type arrangements, WISpR provides biologically informed, high-resolution cellular maps. Its ability to decode tissue organization in both healthy and diseased states highlights WISpR's practical utility for spatial transcriptomics, particularly in challenging settings involving noise, sparsity, or reference mismatches.

Humans↗
PubMed2026

Clonotypic characterization defines B-cell drivers of clonal expansion and intratumor heterogeneity in IgM monoclonal gammopathies.

Waldenstr&#xf6;m macroglobulinemia (WM) and IgM monoclonal gammopathy of undetermined significance (MGUS) share the same cell of origin but differ in clonal size. Compared with other B-cell neoplasms, the lymphoplasmacytic clone in WM can be rather small, limiting our understanding of clonal expansion. We applied an integrative approach using single-cell RNA with B-cell receptor (BCR) sequencing, the assay for transposase-accessible chromatin, and whole-genome sequencing to characterize the tumor clone in patients with IgM MGUS, smoldering WM (SWM), and symptomatic WM (WM). IgM MGUS and low- or intermediate-risk SWM harbored multiple B-cell clones compared to WM. CD9, JCHAIN, RASSF6, and DUSP22 were the main markers of the dominant B-cell clone at gene expression and chromatin activity levels, with CD9 preferentially expressed in plasma cell-like tumor cells. POU2F2 had high activity in the tumor clone and was linked to CD9 regulatory regions. MYD88 and IGLL5 mutations, mainly associated with the mutational signature SBS5, were present in minor clones, whereas the MYD88 mutation was also detected in nonexpanded B-cells. The 6q deletion was present in tumor cells from high-risk patients, which harbored fitness advantage over copy-neutral tumor cells. Coding mutations clustered tumor and minor clones from oligoclonal patients and were associated with abnormal transcriptional programs. The B-cell clones also showed enriched predicted interactions with monocytes. Our integrative single-cell approach reveals the importance of clone size in IgM gammopathy and identifies key markers promoting clonal expansion.

Journal Article↗
PubMed1987

Role of membrane glycoproteins in mediating trophic responses.

During growth and differentiation the plasma membrane has a key role not only in the reception and transmission of extracellular signals such as hormones and growth factors, but also in communicating cellular response to the cellular microenvironment. Cellular response to trophic stimuli includes alterations of cell shape and cell surface antigenicity, of cell-cell recognition and cellular adhesion, of cell matrix binding and the adaptation of cell surface receptors. The plasma membrane is therefore regarded as a 'central agency' for the integration of a single cell into the complex system of a tissue or of an organism. The numerous functions of the plasma membrane are mainly mediated by membrane integrated glycoproteins or glycolipids both sharing the common feature of covalently bound oligosaccharide side chains. Specific alterations of oligosaccharide structure and metabolism associated with growth, differentiation and various pathologic conditions suggest a specific role for the oligosaccharide moieties in the regulation of cell surface functions (Table 1). This review intends to focus on the role of plasma membrane glycoproteins describing briefly principles of glycoprotein structure and function, and characteristics of their biosynthesis and degradation.

Animals↗
PubMed2025

ShortCake: an integrated platform for efficient and reproducible single-cell analysis.

SUMMARY: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple "flavors," enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility. AVAILABILITY AND IMPLEMENTATION: The ShortCake image is available on DockerHub (https://hub.docker.com/r/rnakato/shortcake) and Zenodo (DOIs: 10.5281/zenodo.17116765 and 10.5281/zenodo.17118158). The source code is available on GitHub (https://github.com/rnakato/ShortCake).

Single-Cell Analysis↗
PubMed1998

Integration of human herpesvirus 6 in a Burkitt's lymphoma cell line.

Human herpesvirus 6 (HHV-6) genome has been found in several human lymphoid malignancies, but configuration of the HHV-6 genome has not been well delineated. We established the HHV-6-positive, Epstein-Barr virus-negative Burkitt's lymphoma cell line Katata. In this study we investigated the status of the HHV-6 genome in Katata cells. Neither linear nor circular HHV-6 DNA was detected by Gardella gel analysis. The fluorescence in situ hybridization technique enabled us to directly visualize the integrated HHV-6 DNA at the single-cell level. Only one integrated site of viral DNA was detected in metaphase chromosomes and it was preferentially located at the long arm of chromosome 22 (22q13). Treatment of the cells with 12-O-tetradecanoyl-phorbol-13-acetate (TPA) or with calcium ionophore A23187 led to induction of the HHV-6 immediate-early gene as well as the late gene. Sodium n-butyrate also gave rise to expression of the HHV-6 genes. The TPA inducibility was synergistically enhanced when combined with A23187 or n-butyrate. Our study provides, for the first time, an in vitro model system of latent HHV-6 infection whose genome is integrated into host DNA of lymphoma cells.

Blotting, Southern↗
PubMed2025

Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data.

Gene regulatory networks (GRNs) provide a global representation of how genetic/genomic information is transferred in living systems and are a key component in understanding genome regulation. Single-cell multiome data provide unprecedented opportunities to reconstruct GRNs at fine-grained resolution. However, the inference of GRNs is hindered by insufficient single omic profiles due to the characteristic high loss rate of single-cell sequencing data. In this study, we developed scMultiomeGRN, a deep learning framework to infer transcription factor (TF) regulatory networks via unique integration of single-cell genomic (single-cell RNA sequencing) and epigenomic (single-cell ATAC sequencing) data. We create scMultiomeGRN to elucidate these networks by conceptualizing TF network graph structures. Specifically, we build modality-specific neighbor aggregators and cross-modal attention modules to learn latent representations of TFs from single-cell multi-omics. We demonstrate that scMultiomeGRN outperforms state-of-the-art models on multiple benchmark datasets involved in diseases and health. Via scMultiomeGRN, we identified Alzheimer's disease-relevant regulatory network of SPI1 and RUNX1 for microglia. In summary, scMultiomeGRN offers a deep learning framework to identify cell type-specific gene regulatory network from single-cell multiome data.

Deep Learning↗
PubMed1994

Regulation of intestinal epithelial barrier function by TGF-beta 1. Evidence for its role in abrogating the effect of a T cell cytokine.

Maintenance of the integrity of the single-cell-thick intestinal epithelium as an in vivo barrier between environmental Ags and mucosal immunocytes is pivotal for health. The T cell cytokine IFN-gamma consistently disrupts this epithelial barrier in vitro, but the substances in mucosa that may be responsible for sustaining or enhancing barrier function have not been clearly identified. Therefore, we characterized the effect on the epithelial barrier of TGF-beta 1 and three prominent neuropeptides (VIP, substance P, somatostatin) by using a model system in which barrier function of a mature polar human colonic epithelial (T84) cell monolayer is reflected in 1) the electrical potential difference across the apical to basolateral surface of each cell, 2) the transmonolayer permeability to macromolecules such as horseradish peroxidase, and 3) lactate dehydrogenase release into the medium indicating epithelial cell cytolysis. Whereas T84 monolayers exposed to TGF-beta 1 alone demonstrated a modest increase in electrical resistance and barrier integrity, TGF-beta 1 showed a striking ability to reduce the capacity of IFN-gamma to disrupt epithelial barrier function. Characterization studies demonstrated that this TGF-beta 1 effect was prolonged (e.g., days) after a single exposure, progressive over the dose range 0.1 to 2.5 ng/ml, reversible with increased concentrations of IFN-gamma, and more pronounced when TGF-beta 1 exposure was to basolateral rather than to apical epithelial membranes. Macromolecular (horseradish peroxidase) penetration of epithelium was not simultaneously altered by TGF-beta 1 and epithelial cellular injury was minimal as gauged by lactate dehydrogenase release. Additional studies using a human pathogen demonstrated that TGF-beta 1 delayed and decreased the barrier disruption caused by exposure to Cryptosporidium parvum. TGF-beta 1 may be the first of a new class of cytokines that maintains and/or enhances barrier function of human enterocytes, in part by countering the effect of a T cell cytokine.

Animals↗
PubMed2006

Simultaneous optical measurements of cytosolic Ca2+ and cAMP in single cells.

Understanding the temporal and spatial integration of the Ca2+ and adenosine 3',5'-monophosphate (cAMP) signaling pathways requires concurrent measurements of both second messengers. Here, we describe an optical technique to simultaneously image cAMP and Ca2+ concentration gradients in MIN6 mouse insulinoma cells using Epac1-camps, a Förster (or fluorescence) resonance energy transfer (FRET)-based cAMP biosensor, and Fura-2, a fluorescent indicator of Ca2+. This real-time imaging method allows investigation of the dynamic organization and integration of multiple levels of signal processing in single living cells.

Animals↗