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Kumari, S.

Publications and source records attributed to Kumari, S..

At least 19 recordsLinked to original sources

Plasticity degeneracy underlies flexible formation and reconfiguration of spatial representations in hippocampal granule cells

Learning and memory require neural representations that are simultaneously robust and adaptable. How do neural systems reconcile these opposing demands of stability and flexibility? Here, we use hippocampal granule cells, which transform spatially diffuse entorhinal inputs into sparse sharply-tuned spatial representations, to address this fundamental question using emergence, stabilization, remapping, and suppression of place-fields as ideal systems to study stability-flexibility balance. Employing an unbiased population-based approach involving different strengths of plasticity in several components, we show that sharply tuned place-cell firing does not arise from a unique plasticity mechanism. We employed a population of heterogeneous, experimentally constrained biophysical models of dentate gyrus granule cells receiving cortical grid-field and contextual inputs to demonstrate that spatially restricted synaptic potentiation is insufficient to selectively route spatial information. Instead, each of the four distinct target transitions, namely reliable emergence, stabilization, remapping, and suppression of place-fields, were achievable by coordinated plasticity spanning excitatory synapses and several intrinsic ion channels. Across each of these four transitions, we identify numerous mechanistically distinct plasticity combinations that generate equivalent functional outcomes. These solutions are non-random and highly diverse, exhibiting weak dependence among individual plasticity components despite converging onto constrained functional states, through a combination of targeted amplification and global suppression of spatial firing. Our findings reveal extensive plasticity degeneracy in hippocampal spatial coding and suggest that flexible neural representations emerge not from unique plasticity rules involving one single component, but from a repertoire of alternative plasticity routes that are capable of implementing the same computation.

neuroscience↗

GLOBAL ANALYSIS OF PROTRUSION-TRANCSRIPTOMES IDENTIFIES DISTINCT CATEGORIES OF LOCALIZED RNAS IN NON-NEURONAL CELLS

RNA localization to protrusions in non-neuronal cells is an emerging molecular process, distinct from the canonical mechanism characterized in neurons. Here, we describe a fractionation workflow optimized for non-neuronal cells that increases sensitivity and reproducibility of transcriptome-wide quantification of protrusion-localized RNAs. Using the optimized method, we identify six categories of protrusion-localized RNAs in non-neuronal cells from mice, including long non-coding RNAs and pseudogenes, and observe spatially distinct subsets of mitochondrially-localized RNAs. Taken together, our results reveal previously unappreciated spatial regulation of diverse transcripts and point toward broadly acting unifying principles that extend across cell types and species.

molecular biology↗

Standardising Cellulose Production From Acetobacter diazotrophicus

Bacterial cellulose (BC) is a biopolymer that comes from natural sources. It has high purity, crystallinity, mechanical strength, and biocompatibility, which makes it suitable for various biomedical and industrial uses. Unlike plant cellulose, BC does not contain lignin or hemicellulose. This results in better material quality and simpler processing. However, producing BC on a large scale is limited by high production costs, expensive culture media, and dependence on a few bacterial strains. It is essential to find cost-effective production methods and alternative microbial sources to expand its commercial use. This study looked at the cellulose-producing ability of Acetobacter diazotrophicus, a safe and relatively unexplored bacterium, under different growth conditions. We compared bacterial growth and cellulose production using Hestrin-Schramm (HS) medium, the standard for BC production, and LB supplemented with glucose (LB+Glucose), which we explored as a more affordable option. We analyzed growth rates, inoculum age, and pH levels to find the best conditions for cellulose production. We observed faster bacterial growth in HS medium, with a doubling time of 3.906 hours, compared to 6.241 hours in LB+Glucose medium. Cellulose production was greatly affected by inoculum age, with successful synthesis from cultures that were agitated for 36 to 40 hours. The highest cellulose yield was at pH 6.0 in HS medium (4.6 mg/mL) and at pH 5.5 in LB+Glucose medium (3.6 mg/mL). FTIR analysis confirmed the presence of characteristic functional groups of bacterial cellulose. These results suggest that Acetobacter diazotrophicus is a promising and cost-effective option for producing bacterial cellulose and highlight the importance of medium composition, inoculum age, and pH for optimizing production.

microbiology↗

Increased expression of Cd74 and MHC II genes by aortic macrophages links atherosclerosis with aging in mice

Atherosclerosis is a chronic inflammatory condition of the arteries leading to myocardial infarction, ischemic stroke and peripheral arterial diseases. Atherosclerotic plaques, which obstruct blood flow contain functionally diverse macrophage populations including pro-atherogenic and atheroprotective subsets. Aging is a major risk factor of atherosclerosis, but the mechanism underlying aging associated risk of atherosclerosis is unclear. Here, using integrated single-cell RNA sequencing data analysis, we demonstrate that specific monocyte and macrophage subsets are enriched in atherosclerotic plaques and the aging aorta of mice. We also show that Cd74 and MHCII genes such as H2-Aa, H2-Ab1, H2-Eb1, and H2-DMb1 are consistently upregulated in the monocytes and macrophages from atherosclerotic plaques, the aging aorta, and the aging bone marrow of mice. Our experimental data also show increased expression of CD74 surface protein by aortic macrophages and bone marrow monocytes from aged mice. In addition, we show increased CD74 expression by RAW264.7 mouse macrophages and THP1 human monocytes following ox-LDL stimulation in vitro. Finally, we demonstrate that monocytes from aged mice adhere more to aortic endothelial cells in co-cultures. Thus, increased monocyte adhesion to endothelial cells may explain the enhanced proportion of specific monocyte and macrophage subsets in the aging aorta, inducing a pre-atherosclerotic condition.

immunology↗

Abbapolin inhibitors of the PLK1 PBD as Prostate Cancer Therapeutics, in vivo activity and synergy with androgen therapy

Polo-like kinase 1 (PLK1) is an established therapeutic target in cancer; however, ATP-competitive kinase inhibitors have shown limited clinical success because of toxicity, acquired resistance, and incomplete inhibition of non-catalytic PLK1 functions. Targeting the Polo-box domain (PBD), which regulates PLK1 localization and substrate recognition, represents an alternative therapeutic strategy but has been hindered by the lack of selective, cell-active small molecules. Here, the optimization and biological characterization of abbapolins, a series of non-peptidic PLK1 PBD inhibitors developed using the REPLACE strategy are described. Structure-guided optimization and screening across the NCI-60 cancer cell panel identified compounds with preferential activity against prostate cancer cells. Proteomic analyses demonstrated that cellular sensitivity correlated with PLK1 protein abundance, supporting an on-target mechanism of action. Abbapolins directly engaged PLK1 in cells, induced selective degradation of endogenous PLK1, and suppressed long-term clonogenic growth. Lead compounds demonstrated favorable pharmacokinetic properties and significantly inhibited prostate tumor growth in xenograft models without detectable systemic toxicity. PLK1 abundance was significantly reduced in treated tumors and correlated with tumor response, identifying PLK1 degradation as a potential pharmacodynamic biomarker. Abbapolins also synergized with enzalutamide in castration- resistant prostate cancer cells, supporting their potential as combination therapies for advanced disease. Collectively, these studies establish selective inhibition of the PLK1 Polo-box domain as a viable therapeutic strategy, provide in vivo proof-of-concept for the REPLACE approach, and identify abbapolins as promising leads for advanced prostate cancer.

cancer biology↗

An optopharmacological tool for on-demand perturbation of branched actin polymerization

Regulated actin cytoskeletal organization and dynamics are essential for life-sustaining processes in eukaryotic cells. The spatiotemporal regulation of filamentous actin can generate a staggering variety of higher-order architectures to meet diverse cellular needs. However, connecting a specific actin substructure to the selective cellular function remains challenging because tools to specifically inhibit F-actin in a spatiotemporally controlled manner are currently limited. To address this crucial technical gap, we have synthesized and characterized a photocrosslinkable small molecule inhibitor of a major and evolutionarily conserved actin nucleation factor, Arp2/3 complex. The new inhibitor "AZ" combines the specificity of a preexisting inhibitor CK666 with photosensitive crosslinking by an Azido group, such that a light-induced, instantaneous, on-demand, irreversible inhibition of Arp2/3 complex-dependent actin nucleation is achieved in a spatiotemporally defined manner at a subcellular, supracellular, and organismal scale. Whole cell treatment with AZ, followed by subcellular photoirradiation, revealed a divergent actin nucleation homeostasis in the cortex of different cells. Thus, AZ could be a powerful tool to infer actin polymerization homeostasis and network properties in live cells-processes which otherwise remain obscure.

cell biology↗

A multitask single-cell analysis framework with knowledge graph as a prior

Single-cell RNA sequencing has reshaped cancer biology by revealing the cellular and molecular diversity of the tumor microenvironment, yet most analysis pipelines still treat clustering, annotation, pathway scoring, metabolic inference, and cell-cell communication as separate tasks. Here, we present scKNIFE (Knowledge graph-based NMF for Inference of Functional Entities), a unified graph-regularized non-negative matrix factorization framework that jointly reconstructs single-cell expression profiles and infers activities of diverse biological entities, including pathways, cell-type markers, metabolic reactions and tasks, ligand-receptor interactions, and cell-state programs. By embedding a heterogeneous knowledge graph directly into the factorization objective, scKNIFE propagates information between biologically related entities through Laplacian regularization while sparsity constraints preserve interpretability. The integrated prior graph spans 47,274 nodes and 506,620 edges, assembled from complementary resources including Gene Ontology, Reactome, Hallmark gene sets, Human-GEM, CellChat, PanglaoDB, Cytopus, and Tabula Muris-derived annotations. Across multiple cancer-focused single-cell datasets, scKNIFE yields competitive to leading performance for clustering and cell-type annotation, while also recovering biologically coherent metabolic programs that agree with dedicated metabolism-focused methods and capture therapy-response-associated states. In addition, the framework supports downstream inference of cell-type-specific biological activities from a single latent representation. Together, these results establish scKNIFE as a modular and extensible framework for end-to-end biological interpretation of single-cell cancer transcriptomics

cancer biology↗

LINE-1 Retrotransposon Activation and 5-Gene Dysregulation as a Common Pathological Signature in Post-Traumatic and Status Epilepticus Models of Epilepsy.

The transition from an initial brain insult to chronic epilepsy remains a critical challenge in clinical neuroscience, often involving complex molecular shifts that are difficult to capture through single-gene analysis. This study investigated the existence of a convergent pathway of genomic instability across two distinct etiological models: iron-induced (FeCl3) post-traumatic epilepsy (PTE) and lithium-pilocarpine-induced (LiCl-Pilo) status epilepticus (SE). By integrating Electrophysiology (EEG), {gamma}-oscillation spectral analysis, multi-unit activity (MUA) recordings with behavioural assessments Morris Water Maze (MWM) and Open Field Test (OFT) we validated and established the chronic hyperexcitability and associated cognitive- emotional co-morbidities of these two models. Which further served as a functional backdrop for investigating a targeted 8-gene panel consisting of GABRA2, KCNN2, KCNAB1, GRIK1, BCL11A, BRD7, STX1B, and PNPO. RT-PCR analysis demonstrated a systemic dysregulation of 5 genes out of these 8 genes, mirroring the simultaneous collapse of inhibitory signalling, membrane stability, and neurotransmitter metabolism seen in human phenotypes. While the clinical roles of these genes are well documented, our study demonstrates that these rat models provide a high-fidelity platform for complex multigene studies and gene-level therapeutic exploration. Furthermore, in-silico docking identified Fisetin as a high-affinity ligand for the dysregulated proteins, offering a promising multi-target strategy for stabilizing the epileptic genome.

neuroscience↗

High Consumption of Coffee Disrupts Nonhomologous End Joining Implications for Genomic Stability

Caffeine, the most widely consumed stimulant worldwide and primarily sourced from coffee, is well known for its central nervous system effects. Emerging evidence indicates that caffeine also modulates key cellular processes, including DNA repair. It inhibits the kinase activity of ATM and ATR-essential DNA damage response proteins, and impairs homologous recombination (HR)-mediated repair through multiple mechanisms. However, its effects on nonhomologous end joining (NHEJ), a major double-strand break (DSB) repair pathway, have been underexplored. In a recent study, we reported that caffeine inhibits NHEJ primarily by interfering with Ligase IV/XRCC4 complex, using in vitro and ex vivo model systems. Given coffees role as a primary dietary caffeine source, this study investigates the impact of Coffea arabica decoction on NHEJ-mediated DSB repair. High-performance liquid chromatography (HPLC) quantified caffeine levels in the decoction, followed by in vitro and ex vivo assays to evaluate NHEJ efficiency. Results demonstrate that coffee decoction inhibits end joining of both compatible and noncompatible DNA ends in cell-free systems derived from normal and cancer cells. Extrachromosomal repair assays confirmed impaired intracellular NHEJ, leading to accumulation of unrepaired DSBs in human cells. Kinetic analysis of {gamma}-H2AX foci formation and resolution revealed persistent DNA breaks and reduced repair kinetics. Reconstitution experiments verified that the decoction specifically targets the Ligase IV/XRCC4 complex. These findings, building on our previous work, establish coffee decoction as a potent NHEJ inhibitor, mirroring purified caffeines effects. This underscores caffeines interference with endogenous DNA repair, with profound implications for cancer therapy by sensitizing tumors to genotoxic treatments.

biochemistry↗

Heterogeneous pro-inflammatory response to BRAFV600E-induced thyroid tumor development

BackgroundThe tumor immune microenvironment likely plays a central role in progression of thyroid cancer. As for most other solid tumors, it is unknown if immune dysregulation contributes to earlier, subclinical stages of thyroid tumor development, or whether thyroid tumor heterogeneity might involve differential expression of pro-inflammatory mediators. MethodsThe time course of tumor-associated inflammation was studied in Tg-CreERT2;Braf CA/+ mice representing a model of BRAFV600E-driven papillary thyroid carcinoma (PTC). Tumor growth was estimated by histological examination and magnetic resonance imaging. Cytokine expression was monitored by quantitative RT-PCR, RNAScope and Western blot analyses. ResultsBased on spontaneous BrafCA activation due to leaky Cre activity in a minority of targeted cells tumors developed within a preserved thyroid tissue architecture to multifocal papillary thyroid carcinoma (PTC) over a period of 12 months. Tumorigenesis was accompanied by a gradually increased mRNA and protein expression of interleukin-1beta (IL-1{beta}), interleukin-6 and tumor necrosis factor-alpha (TNF-) starting already before Braf mutant cells commenced neoplastic growth. RNAScope revealed that both follicular cells and stromal cells expressed Il1b whereas Il6 and Tnfa transcripts were mostly confined to neoplastic epithelia. Early cytokine expression was associated with oncogene-induced senescence, whereas during tumor development (3-6 months) and in advanced tumor stages (at 12 months) the cytokine expression pattern differed among glands and tumor foci of the same gland accompanied by a highly variable locoregional lymphocytic infiltration. Oral treatment of mutant mice for 1 month with PLX4720, a vemurafenib prodrug, partially reduced cytokine expression along with inhibited tumor growth and redifferentiation of thyroid function. The magnitude of reduced cytokine expression differed much between glands and among mice of both sexes. ConclusionsThese findings indicate that oncogenic BRAFV600E targeted to the thyroid both stimulates endogenous production of IL-1{beta}, IL-6 and TNF- and recruits inflammatory cells to foci of early tumor development. PTCs of different clonal origin are distinguished by differential expression of pro-inflammatory cytokines. The anti-inflammatory effect of mutant Braf kinase inhibition varies presumably related to heterogeneous tumor development, which evolves from stochastic BrafCA activation suggesting there are clonally different probabilities of acquiring drug resistance among Braf mutant thyroid follicular cells.

cancer biology↗

Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals

The thyroid has a remarkable evolution, first appearing in invertebrate chordates as an integral exocrine constituent of the pharyngeal endostyle that is transformed into an endocrine gland during metamorphosis in basal vertebrates. In mammals, the thyroid acquires a second endocrine cell type, calcitonin-producing C-cells, which for long were inferred a neural crest origin, shuttled to the embryonic thyroid by the ultimobranchial bodies. However, recent lineage tracing experiments firmly establish these neuroendocrine cells also derive from foregut endoderm. Key questions remaining unanswered are how thyroid primordia independently develop and, unlike in all non-mammalian vertebrates, merge into a dual endocrine organ. Here, by leveraging a single-cell transcriptome atlas derived from mouse pharyngeal endoderm and its subsequent cell fates, we characterize the global gene expression profile of thyroid- and ultimobranchial-derived progenitor cells and identify comprehensive gene regulatory networks of lineage-specific transcription factors and novel target genes predicted to differentially regulate cell proliferation, plasticity and differentiation during development. Spatiotemporal analyses reveal C-cell precursors are triggered to undergo epithelial-mesenchymal transition (EMT) and cell-autonomously down-regulate collagen IV and degrade laminin that delineates the ultimobranchial body epithelium. However, the EMT program is not fully deployed until both cell lineages are mixed and propagate conjointly thus forming the typical thyroid histoarchitecture of follicles and parafollicular C-cells, every follicle/C-cell unit being enveloped by a renewed basement membrane. Mixed-type thyroid carcinoma recapitulates a synchronous lineage growth pattern but only the neuroendocrine tumor cells are able to escape the compound follicle boundaries and become invasive adopting a C-cell precursor-like migratory phenotype.

developmental biology↗

Intrinsic excitability of rat hippocampal granule cells increases along the dorsal-to-ventral axis

The dentate gyrus (DG) of the hippocampus exhibits striking anatomical and functional heterogeneity along its dorsoventral axis, yet the intrinsic electrophysiological diversity of its principal excitatory neurons, the granule cells, across the dorsoventral axis remains unexplored. Here, we systematically examined the electrophysiological properties of DG granule cells across the dorsal, intermediate, and ventral regions of the rat hippocampus. We found a progressive increase in input resistance, impedance amplitude, and firing rate of granule cells, accompanied by a gradual slowdown in repolarization kinetics of their action potentials along the dorsal-to-ventral axis. Our analyses demonstrated that granule cells acted as class I integrators that lacked strong resonance properties across the dorsoventral axis. We performed pairwise correlation and dimensionality reduction analyses to reveal weak dependencies across physiological measurements and the absence of distinct clusters for dorsal, intermediate, or ventral granule cells. Importantly, blade-specific analyses of granule cell physiology revealed that all measurements manifested pronounced heterogeneities even within a given dorsoventral section and a specific blade. Strikingly, ventral granule cells in the infrapyramidal blade manifested higher firing rates compared to their counterparts in the suprapyramidal blade. These blade-specific differences were limited to the ventral granule cells, with negligible distinctions between granule cells in the two blades of either dorsal or intermediate hippocampus. Together, our findings unveil a progressive increase in excitability of DG granule cells along the dorsal-to-ventral axis and a blade-specific granularity of firing properties, adding new dimensions to the several known anatomical, molecular, and behavioral differences across the hippocampal dorsoventral axis.

neuroscience↗

Muscular dystrophy-associated lamin variants disrupt cellular organization through a nucleolar-ribosomal axis controlling cytoplasmic macromolecular crowding

Emery-Dreifuss muscular dystrophy (EDMD) arises from mutations in nuclear lamins or emerin. Current pathological models emphasize defects in nuclear mechanics and transcription regulation. Yet these models do not fully explain the complexity of EDMD or other laminopathies. Here, we uncover an emerging pathway linking nuclear lamina defects to the reorganization of cytoplasmic biophysics, revealing how nuclear dysfunction cascades throughout the cell. Using Caenorhabditis elegans EDMD models, we demonstrate that lamin mutations dramatically alter cytoplasmic organization, reducing macromolecular crowding and increasing diffusivity of 40 nm Genetically Encoded Multimeric (GEM) nanoparticles. These striking biophysical changes coincide with nuclear positioning defects and collapsed endoplasmic reticulum architecture, mirroring phenotypes associated with ribosome depletion. We propose a mechanism where mutations in the C. elegans lamin lmn-1 disrupt nucleolar density and ribosome biogenesis, creating a nucleolar-ribosomal axis that propagates defects from the nucleus to the cytoplasm. Genetic interactions between lmn-1 and ribosomes support this regulatory relationship. While individual depletion of other nuclear envelope proteins produces minimal effects, combined loss of the functionally redundant emerin ortholog emr-1 and LEM-domain protein lem-2 phenocopied lmn-1 mutants, demonstrating that cytoplasmic biophysical disruption lies at EDMDs pathogenic core. Our findings establish a paradigm where nuclear lamina defects fundamentally rewire cellular biophysics through nucleolar-ribosomal dysfunction, opening transformative therapeutic avenues for treating laminopathies.

cell biology↗

Utility of recombinant envelope domain III as a diagnostic antigen for the specific detection of Kyasanur Forest Disease

Kyasanur Forest Disease (KFD), commonly known as "monkey fever," is a highly neglected tropical disease caused by the Kyasanur Forest Disease Virus (KFDV). KFD is endemic to Western Ghats of Karnataka, India, with seasonal outbreaks during December to June every year. As there is no standard treatment regime, KFD can be fatal with a mortality rate of 2-10%. Currently, KFD is detected through a non-specific IgM-ELISA followed by RT-PCR, which often delays diagnosis, leading to increased disease severity and even death. To address this, we focused on developing a specific antigen-based KFD detection. The KFDV Envelope Domain III (EDIII) and Non-Structural 1 (NS1) proteins were chosen as detection markers, cloned, and expressed using pET28a(+) vector in BL-21 (Rosetta) E. coli and purified. These proteins were used to raise polyclonal antibodies in rabbits and the antibody titre was found to be 1:256,000 and 1:512,000 against rEDIII and rNS1 proteins, respectively. Importantly, these polyclonal antibodies showed no cross-reactivity against corresponding dengue virus EDIII and NS1 proteins. Using polyclonal antibodies against rEDIII, we developed sandwich ELISA for the specific detection of KFD, which has demonstrated high specificity and sensitivity. Further, anti-rEDIII polyclonal antibodies also detected full-length KFDV-E protein expressed in mammalian cells, confirming the antibody specificity for the native viral antigen.

microbiology↗

Mechanism-aware inference of response to targeted cancer therapies

Targeted therapies like small-molecule inhibitors often work by blocking proteins that cancer cells rely on for survival. Omics based modeling of drug sensitivity alone lack mechanistic grounding. We propose FORGE (Factorization Of Response and Gene Essentiality) a simple yet powerful joint matrix factorization framework that co-models drug response and target gene essentiality, enabling the stratification of promising treatment groups for targeted therapy consideration. FORGE also provides Benefit Score -- a predictive score that estimates treatment efficacy from basal gene expression profiles. We validated the predictive performance of FORGE across multiple targeted therapies, including Erlotinib (EGFR inhibitor) and Daporinad (NAMPT inhibitor). Our meta-analysis of large scale in-vitro studies underscores FORGEs ability to identify common determinants of drug vulnerabilities and target gene essentiality. Such convergences were not observed when treatment vulnerabilities and gene essentialities were modeled independently. We also demonstrated the universality of Erlotinib Benefit Scores by transferring transformations learned from high-throughput drug response studies across other published datasets, including the TAHOE-100M single-cell perturbation atlas and patient-derived xenograft studies. FORGE successfully identified key regulators within the molecular pathways targeted by these therapies, reinforcing its potential for mechanistically grounded treatment stratification.

cancer biology↗

Using targeted therapy to promote a pro-inflammatory tumour microenvironment and anti-tumour immune response in high grade serous ovarian cancer

BACKGROUNDHigh-grade serous ovarian cancer (HGSOC) is characterized by elevated replication stress and an immunosuppressive microenvironment. A synergistic combination of checkpoint kinase 1 inhibitor (CHK1i) with low-dose hydroxyurea (LDHU) promotes a unique ATR-independent moderate replication stress response with potent anti-tumour effects. The ability of this approach to reprogram the tumour immune microenvironment (TIME) to overcome the immunosuppression and promote an anti-tumour immune response in HGSOC is the focus of this study. METHODSWe investigated the therapeutic potential of CHK1i+LDHU in established HGSOC cell cultures, fresh tumour cell explants from HGSOC patient ascites, and syngeneic mouse models, assessing tumour cell killing, immunogenic cell death, pro-inflammatory cytokine/chemokine expression, and anti-tumour immune responses. RESULTSCHK1i+LDHU effectively killed ovarian cancer cells regardless of chemotherapy resistance, BRCA2 mutation and homologous recombination repair status in vitro. In vivo, treatment significantly reduced tumour burden and ascites accumulation. CHK1i+LDHU enhanced expression of pro-inflammatory cytokines/chemokines and triggered immunogenic cell death in tumour. In syngeneic models, treatment promoted CD8+ cytotoxic T cell-dependent anti-tumour responses and reduced immunosuppressive signalling within the TIME. CONCLUSIONSCHK1i+LDHU is a promising therapy for chemotherapy-resistant HGSOC, combining direct cytotoxic effects with reprogramming the TIME to reduce immunosuppression and activate a CD8+ T cell-dependent anti-tumour response.

cancer biology↗

Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma - the three major skin cancers - collectively comprise over 70% of all cancer cases. Despite their prevalence, much understanding of cellular interactions in the skin cancer microenvironment is needed, both in the outer skin layer where the cancer originates and at the deeper junctional and dermal layers into which it progresses. To address this gap, we integrated 12 complementary spatial and single-cell technologies to generate orthogonally-validated cell signatures, spatial maps, and interactomes for cSCC, BCC, and melanoma. Through comprehensive comparisons and integrating these spatial methods, we provided practical benchmarking guidelines for experimental design and analysis. By identifying keratinocyte cancer cells and melanomas, we found distinct signatures of these cells compared to non-cancer keratinocytes and melanocytes. Spatial integration of transcriptomics, proteomics and glycomics uncovered cancer niches enriched for cancer initiating cells (melanocytes or keratinocytes) and fibroblast and T-cell (MKFT) clusters, with altered tyrosine and pyrimidine metabolism. Ligand-receptor analysis across >700 cell-type combinations and >1.5 million interactions highlighted key roles for CD44, integrins, and collagens, with CD44-FGF2 emerging as a potential therapeutic target. Consistently, melanoma showed strong MFT interactions, validated by Opal Polaris, RNAScope, Proximal Ligation Assay and two additional single-cell spatial platforms (making a total of 14 technologies). For population-scale generalisation, genetic associations from >500,000 individuals were mapped onto spatial skin tissues, identifying SNPs enriched in domains containing melanocytes and T cells and their ligand-receptor pairs, shedding light on functional mechanisms linking genetic heritability to cells within cancer tissue. We built an interactive multiomics resource for exploring spatially-resolved molecular signatures and cellular crosstalk in skin cancer, available at https://skincanceratlas.com.

cancer biology↗

Actin waves guide an outward movement of microclusters in the lymphocyte immunological synapse

The lymphocyte immune response begins with antigen recognition on antigen-presenting cells, leading to the formation of the immunological synapse--a specialized interface for biochemical and biophysical exchange. At the synapse, most antigen-engaged receptor microclusters move inward toward the central supramolecular activation cluster (cSMAC) via retrograde F-actin flow, eventually clearing from the cell surface. This retrograde movement and receptor downregulation maintain antigen receptor homeostasis, critical for adaptive immunity, though its regulation remains unclear. Using live T cells, we identified a significant pool of antigen-engaged microclusters moving anterogradely toward the cell periphery, rather than the cSMAC. This movement was driven by actin waves propagating outward and coupling to microclusters through the Wiskott-Aldrich Syndrome Protein. These findings reveal a previously unrecognized mode of actin dynamics--anterograde actin waves--that co-exist with retrograde flow and direct microclusters away from the downregulation zone. This dual actin behavior underscores the complex cytoskeletal mechanisms T cells employ to regulate receptor distribution and maintain signaling homeostasis during immune activation.

immunology↗