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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 19 recordsLinked to original sources

bioRxiv2026

Functional characterization of Rho GTPase activating proteins SYDE1 and SYDE2

The human genome encodes more than 60 proteins containing Rho GTPase activating protein (RhoGAP) domains, many of which remain understudied with respect to their target specificity and biological roles. SYDE1 and SYDE2 are two such orphan RhoGAPs, for which there are few studies characterizing their biochemical and cellular functions and conflicting reports identifying their cognate GTPases. We previously identified SYDE1 and SYDE2 in a screen for substrates of the c-Jun N-terminal kinases. Here, we show that SYDE1 and SYDE2 are preferentially phosphorylated by JNK1 relative to other mitogen-activated protein kinases (MAPKs) at sites proximal to a kinase docking region. Purified SYDE1 and SYDE2 are shown to have significant catalytic GAP activity toward RhoA, Rac1, and Cdc42. However, neither up- nor down-regulation of SYDE1/2 expression leads to detectable changes in bulk GTP loading of any of these GTPases. Nevertheless, we demonstrate that SYDE1 and SYDE2, in a partially GAP-dependent manner, increase cell spreading and number of focal adhesions, and promote more directionally persistent migration in HEK293 cells. Together, these findings establish SYDE1 and SYDE2 as robust JNK substrates with catalytic activity toward a set of Rho GTPases and reveal basic functions of SYDE1 and SYDE2 in regulating cell morphology, adhesion, and migration.

cell biology↗

bioRxiv2026

The filopodial scaffold polyphosphate dictates cell adhesion-versus-invasion decisions

Inorganic polyphosphate (polyP) is an ancient polymer conserved across all life, serving cell type and location specific functions in every major compartment. Yet its role at the plasma membrane, where it accumulates to peak levels in many primary cells, is largely unknown. Here we identify polyP as a stabilizing component of filopodia, actin based membrane protrusions that govern cell adhesion, contact inhibition, and chemotaxis. Elevating cellular polyP increases filopodial stability and enhances cell adhesion, whereas reducing polyP accelerates filopodial disassembly and promotes cell migration. Mechanistically, we find that polyP acts as a structural filopodial scaffold, recruiting and organizing IRSp53, a membrane curvature inducing protein. We show that metastatic fibroblasts and breast cancer organoids carry markedly reduced and intracellularly reorganized polyP levels relative to their non transformed counterparts. Restoring endogenous polyP via lipid nanoparticle delivery suppresses their invasive phenotypes and reverses prometastatic gene expression signatures, implicating polyP as a primordial tumor suppressor.

cell biology↗

bioRxiv2026

Mitochondrial transfer mediates metabolic communication between beta cells and islet macrophages

Pancreatic islet macrophages support islet homeostasis and adapt their metabolic program in response to environmental cues, including beta cell released factors. Intercellular mitochondrial transfer is a biological process that modulates cellular responses. To test whether beta cells, which are strongly secretory, transfer mitochondria to islet macrophages, we generated mice with beta cell-specific expression of mitochondrial GFP (PhAMfloxIns1Cre). We demonstrate that beta cells transfer mitochondria to islet macrophages in vivo and in vitro. Diabetogenic stressors did not alter the frequency of mitochondrial transfer and macrophages containing beta cell-derived GFP exhibit increased protein synthesis rates. RNA-seq identified upregulation of activity-regulated cytoskeleton associated protein (Arc) in macrophages receiving beta cell-derived mitochondria, while disruption of actin cytoskeleton dynamics prevented mitochondrial transfer. Together, these findings identify mitochondrial transfer as a previously unrecognized mechanism of beta cell-macrophage communication that may contribute to islet homeostasis and immune regulation.

cell biology↗

bioRxiv2026

Tendon-derived injectable bio-instructive gel augments tenogenic differentiation of iMSC-SCX cells and extracellular matrix remodeling

In the US, 33 million musculoskeletal injuries have been reported per year, with 50% involving tendons and ligaments in both athletic and aging populations. Tendon repair often results in the formation of biomechanically inferior scar tissue rather than functional regeneration. Local cell therapy is garnering significant interest in tendon repair because it provides a targeted means to repopulate defects with potent therapeutic cells. Here, we developed a porcine tendon-derived thermoresponsive extracellular matrix hydrogel (TG) as an injectable, bio-instructive carrier for scleraxis-overexpressing induced mesenchymal stem cell derived tenocytes (iTenocytes), with the goal of improving cell retention and overall transplantation success. TG was compositionally distinct from purified collagen (PC, from rat tail type 1 collagen) and exhibited favorable material properties for a minimally invasive percutaneous strategy, including thermoresponsive gelation, shear-thinning injectability, retention at the injection site, and controlled biodegradation. In vitro, TG supported three-dimensional cell residence, promoted cell interconnectivity and redistribution at the matrix interface, and increased collagen type I release from iTenocytes compared to those embedded in PC. Transcriptomic and proteomic analyses further showed that TG enhanced programs associated with tenogenic maturation, extracellular matrix assembly, focal adhesion, mechano-transduction, and remodeling. In a rat Achilles tendon partial defect model, both optical imaging and histological analyses demonstrated retention of iTenocytes at the injection site. Additionally, confocal imaging demonstrated retention of iTenocytes within the defect site for up to 10 days. Together, these findings identify TG as a biofunctional injectable carrier that supports the tenogenic characteristics of iTenocytes and enhances their local persistence after transplantation.

cell biology↗

bioRxiv2026

Modelling human haematopoietic stem cell commitment ex vivo identifies IL-33 as a regulator of megakaryopoiesis

Commitment events to specific blood lineages arise from single hematopoietic stem cells (HSCs) and are influenced by stress, inflammation and disease. However, the understanding of how such events are regulated in human haematopoiesis is limited by the lack of tractable in vitro models. In this study, we introduce a novel Early Progenitor Differentiation (EPD) assay to study the initial lineage commitment of human 49+ HSCs, in a system faithfully recapitulating cell states observed in vivo. Combining single cell -omics approaches and single cell functional assays, we show that IL-33 acts directly on human 49f+ HSCs activating the MAPK pathway to enhance their commitment towards Megakaryocytic-Erythroid-Mast cell Progenitors and subsequently megakaryopoiesis. This occurs without affecting HSC self-renewal via accelerated establishment of chromatin programmes associated with Erythroid and Megakaryocyte and mast cells lineages. Our findings demonstrate the utility of the EPD model to identify molecular regulators of human HSC differentiation and uncover a new role of IL-33 in haematopoiesis.

cell biology↗

bioRxiv2026

Ribosomal proteins are major substrates of starvation-induced endosomal microautophagy in Drosophila.

Maintenance of cellular homeostasis requires tight coordination between protein synthesis and degradation, particularly at old age and under conditions of stress including starvation. Autophagy contributes to sustain this balance by degrading cytoplasmic proteins and organelles. It thus is essential to prevent the accumulation of damaged proteins and organelles and to recycle nutrients. Of the three forms of autophagy, macroautophagy, chaperone mediated autophagy, and (endosomal) microautophagy (e-MI), the latter remains the least well understood. During e-MI, cytosolic substrate proteins are captured into late endosomes via ESCRT-dependent multivesicular body formation and then degraded in late endosomes or lysosomes. e-MI is thought to contribute to protein quality control under basal conditions and under stress. Importantly, very little is known about the endogenous substrates of e-MI in flies and thus about its physiological role. Performing integrative multi-omic analyses in Drosophila larval fat body that has functions similar to mammalian liver and adipose tissue, we identified 153 high-confidence endogenous e-MI substrates with the degradation of ribosomal proteins by e-MI being the most strongly affected functional category. Generally, we found that starvation caused the depletion of proteins involved in translation, aminoacyl-tRNA synthesis, and ribosomal biogenesis, without affecting their level of transcripts. Importantly, we observe a striking specificity between e-MI and macroautophagy, as the two pathways largely target distinct protein sets including different subsets of ribosomal proteins. Our metabolomic analysis further shows that genetic inhibition of e-MI reverses the reduced levels of amino acid caused by starvation. Together, our findings reveal ribosome turnover as a central physiological function of Drosophila e-MI and establish e-MI as a pathway driving metabolic adaptation during starvation.

cell biology↗

bioRxiv2026

Adeno-Associated Virus Mediated Expression of Bcl-xL Attenuates Apoptosis in Fuchs Endothelial Corneal Dystrophy

Fuchs Endothelial Corneal Dystrophy (FECD) is characterized by progressive corneal endothelial cell loss and the formation of corneal guttae. Currently, there is a global shortage of donor corneas and new strategies are needed to reduce the need for corneal transplantation. While adeno-associated viruses (AAVs) have the capacity to deliver anti-apoptotic genes to human corneal endothelial cells (CECs), this has not been fully explored as a therapeutic strategy for FECD. In this study, we evaluated the transduction efficiency of self-complementary (sc-) and single-stranded (ss-) AAV2 serotypes in human CECs and ex vivo tissues and assessed whether AAV-mediated expression of Bcl-xL could attenuate apoptosis in FECD. Seventeen scAAV2 serotypes were screened for transduction efficiency in normal human CECs via green fluorescent protein (GFP) expression. The top 4 AAV2 serotypes were further evaluated in FECD cell lines, healthy cadaveric donor specimens, and FECD patient specimens. FECD cell lines were transduced with anti-apoptotic ssAAV2/5-Bcl-xL (AAV2/5-CAG-eGFP-P2A-BCLXL) and treated with etoposide to induce apoptosis. We found that scAAV2/5 demonstrated high transduction efficiency across all normal and FECD cell lines and tissues. We observed that ssAAV2/5-mediated expression of Bcl-xL provided significant protection against etoposide-induced apoptosis in FECD CECs (71.68%{+/-}0.69 vs 23.96%{+/-}8.88%, p=0.018). Our findings show that AAVs have the potential for therapeutic gene delivery to the human corneal endothelium, and that targeting the Bcl-xL mediated apoptotic pathway can be further explored as a therapeutic for FECD.

cell biology↗

bioRxiv2026

Combined Image-Based Profiling and Biochemical Analysis of GCaMP Overexpression Effects on Mammalian Cells

Protein-based fluorescent sensors are a powerful addition to the biology toolbox for their ability to be stably expressed within living organisms, tissues, cells, and subcellular compartments, with the capacity to report on the presence of specific target molecules or other analytes. At the same time, sensor components will unavoidably present opportunities for unintended interaction with endogenous cellular machinery, potentially confounding both sensor function and cell health. Interactions with host components may not be readily predictable during the sensor design process, especially when simultaneously optimizing many other sensor parameters such as fluorescence response, dynamic range, and kinetics. Characterizing effects of sensor expression on cells is currently a laborious ad hoc process; new methods to characterize the cell expression effects of sensors and their variants could dramatically improve sensor design pipelines, laying the groundwork to recognize potentially problematic expression side effects earlier in the iterative design and testing workflow. Here, we take a dual high-content imaging-based and biochemical approach to examine sensor interactions with native cell biology, focusing on the widely used GCaMP calcium sensor. We identify a morphology-based signature of the cellular effects of high sensor expression in a neuroblastoma cell line. Subsequently, we identify biochemical interactions between GCaMP and a component of the mammalian cytoskeleton and track morphological features in sensor-expressing cells that lack these structural components. Our findings present an entry point for engineering new minimally cross-reactive sensor versions given a contextual biological understanding of sensor overexpression. We anticipate that as this and related workflows are incorporated into sensor engineering pipelines, bioorthogonality can be more systematically assessed and prioritized in diverse sensor scaffolds.

cell biology↗

bioRxiv2026

Hormetic heat shock activates HLH-30/TFEB independently of canonical nutrient-sensing pathways

In Caenorhabditis elegans, a brief, sublethal heat shock (HS) induces a hormetic response that increases resistance to subsequent stress and extends lifespan. These benefits require hlh-30, the ortholog of mammalian transcription factor EB (TFEB). Although HS induces robust HLH-30 nuclear translocation, how this response is regulated remains poorly understood. Nutrient- and energy-sensing pathways, including mTORC1 and AMPK, regulate HLH-30/TFEB subcellular localization under other physiological conditions, but whether they mediate its nuclear translocation during HS is unknown. Here, we show that, although HS inhibited mTORC1 and dephosphorylated its conserved HLH-30 S201 target site, HLH-30 S201 phosphorylation was dispensable for HS-induced HLH-30 nuclear localization and hormetic protection. Moreover, HS remained protective in hlh-30 mutants when mTORC1 activity was reduced, revealing an HLH-30-independent component of the hormetic response. HS also activated AMPK and aak-2 was required for hormetic protection but dispensable for HS-induced HLH-30 nuclear localization and autophagosome formation. Together, these findings demonstrate that although HS engages canonical mTORC1 and AMPK signaling, these pathways do not account for HS-induced HLH-30 nuclear localization and instead make distinct contributions to hormetic protection. Our findings reveal stress-specific regulation of HLH-30/TFEB and point to additional mechanisms that drive its activation during heat stress.

cell biology↗

bioRxiv2026

Cardiomyocyte prohibitin ablation reprograms cardiac metabolism revealing a pathogenic role for mTORC1 in dilated cardiomyopathy

Maintaining cardiac structure and function throughout the lifespan requires a delicate balance in carbon allocation between energetic and biosynthetic processes. At the nexus of this balance are prohibitins-1 and -2 (PHB1, 2) which form a ring-like complex in mitochondrial and plasma membranes responsible for coordinating cellular growth, metabolism and autophagy. Here we describe how ablation of the PHB complex in cardiomyocytes of adult mice (cPHB1KO) causes unrestrained mechanistic target of rapamycin complex 1 (mTORC1) activity and a Warburg-like reprogramming of glucose metabolism in heart toward enhanced de novo amino acid biosynthesis. These changes are accompanied by disruptions in mitochondrial Ca2+ handling and impaired autophagy, leading to severe dilated cardiomyopathy and mortality within 12 weeks. Using pharmacological and nutritional approaches, we further show that mTORC1 inhibition attenuates pathologic cardiac remodeling only in female cPHB1KO mice. Our findings illustrate novel mechanisms linking the PHB complex with altered carbon flux and pathogenesis of cardiomyopathy.

cell biology↗

bioRxiv2026

TheCellVision.org repository: expansion with high-content cell imaging projects on eukaryotic intracellular organization and DUB biology

High-content cell imaging approaches enable the systematic characterization of cellular function through the acquisition of multimodal information from large cohorts of live single cells. Yet, due to their scale and complexity, data acquired via such approaches are often challenging to meaningfully share across laboratories and effectively use for independent studies. Since its inception, the main purpose of TheCellVision.org repository has been to fill this gap, providing the research community with access to large-scale, multimodal single-cell datasets, in a structured, intuitive, and user-friendly way. Here, we report on the third major update of TheCellVision.org, which involves the expansion of the repository with the addition of data from two single-cell phenomics projects; the Intracellular Organization Dynamics project, which quantitatively maps changes in the morphology of 21 major subcellular structures in live yeast cells elicited by the systematic inhibition of essential genes, and the DUB Biology project, which describes changes in the concentration and localization of the budding yeast proteome in mutants of key deubiquitination enzymes (DUBs). With these additions, the repository now hosts six complementary high-content imaging projects which collectively explore the dynamics of intracellular organization and the proteome during changes in cell state and in response to environmental and genetic perturbations.

cell biology↗

bioRxiv2026

A direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts

Mitochondrial iron homeostasis is fundamental to respiration and redox balance, and its dysregulation is implicated in neurodegeneration, cardiomyopathy, and metabolic diseases. Although lysosomes harbor the major cellular iron reservoir, the prevailing model holds that mitochondria acquire Fe(II) directly from the cytosolic labile iron pool (LIP) via MFRN transporters. Here, we challenge the canonical view by identifying a direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts (MLCs). This VPS39/TOMM22/SFXN1-coordinated pathway enables lysosome-to-mitochondria Fe(II) flux bypassing the cytosolic LIP. Using live-cell structured illumination microscopy (SIM), we visualize direct Fe(II) transfer specifically occurring at MLCs. Multiple lines of evidence confirm that VPS39 and TOMM22 stabilize MLCs, while SFXN1 serves as the core effector protein for this MLC-dependent Fe(II) transport. Notably, SFXN1 knockdown markedly reduces mitochondrial Fe(II) levels independent of its established serine transport function. This pathway reveals a major route for mitochondrial Fe(II) acquisition to support redox homeostasis.

cell biology↗

bioRxiv2026

Functional Contribution of Multienzyme Glucosome Condensates to Cellular Redox Homeostasis in Cancer Cells

Glucosomes are liquid-liquid phase-separated condensates observed in human cells, formed by phosphofructokinase and other rate-determining enzymes in glycolysis and gluconeogenesis. While glucosomes are spatially formed into small-, medium-, and large-sized assemblies in cancer cells, medium-sized glucosomes are functionally characterized to shunt glucose flux to the pentose phosphate pathway (PPP). As the PPP is the primary pathway responsible for maintaining cytosolic NADPH levels during oxidative stress, we hypothesize that medium-sized glucosomes regulate cellular redox homeostasis through the promotion of the PPP. In this work, we started treating Hs578T cells with hydrogen peroxide (H2O2) to evaluate how glucosomes respond to redox perturbation. High-content imaging demonstrated that H2O2 significantly promotes medium-sized glucosomes at both single-cell and population levels. The extracellular acidification rate by Seahorse extracellular flux analysis then corroborated that H2O2 effectively diverts glycolytic flux to the PPP through the upregulation of medium-sized glucosomes. We then investigated the glutathione redox cycle as a potential mechanistic link between medium-sized glucosomes and H2O2 detoxification. Treatment with oxidized glutathione (GSSG), but not reduced glutathione (GSH), markedly increased the population of cells showing medium-sized glucosomes. Moreover, shRNA-mediated knockdown of glutathione reductase, which converts GSSG to GSH at the expense of NADPH, attenuated H2O2-induced glucosome formation in Hs578T cells. Collectively, we demonstrate that glucosome-mediated metabolic reprogramming couples glucose metabolism to the glutathione redox cycle to facilitate H2O2 detoxification, thereby establishing the functional role of glucosomes in cellular redox homeostasis.

cell biology↗

bioRxiv2026

Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction

Extravasation, the exit of circulating cancer cells from blood vessels, is a critical yet poorly understood step in metastatic dissemination. Here we show that pancreatic ductal adenocarcinoma (PDAC) cells can breach endothelial barriers through two mechanistically distinct modes of extravasation. MIA PaCa-2 cells breach endothelial junctions via filopodia-like protrusions, enabling access to and spread across the basal extracellular matrix (ECM). By contrast, AsPC-1 cells remain rounded atop the endothelium and cross the barrier by triggering rapid retraction of neighbouring endothelial cells. These distinct extravasation modes were also observed in zebrafish larvae. In the mouse lung, AsPC-1 cells arrest, survive, induce endothelial detachment from the basal lamina, and extravasate through this retraction mechanism before metastatic outgrowth. Mechanistically, AsPC-1-secreted factors are sufficient to destabilise endothelial monolayers, and AsPC-1 cells also induce endothelial apoptosis; however, blocking apoptosis does not prevent barrier disruption. By contrast, treatment with saracatinib, a Src-family kinase inhibitor, protects endothelial barriers, limits early vascular disruption in the lung, and delays metastatic outgrowth. Together, these findings reveal that PDAC cells can extravasate via mechanistically distinct routes, suggesting that effective anti-metastatic strategies may need to target multiple modes of endothelial barrier breach rather than a single pathway.

cell biology↗

bioRxiv2026

Glutaminase contributes to MYC-induced cell-autonomous autophagy and to RasV12-dependent non-autonomous autophagy in the Drosophila wing disc epithelium

MYC-driven metabolic reprogramming supports rapid cell growth but also creates metabolic demands that require adaptive mechanisms to maintain cellular homeostasis. Here, combining clonal analysis in Drosophila wing imaginal discs with studies in Schneider S2 cells, we identify glutamine metabolism as a component of Myc-induced autophagy. Myc increased the expression of genes involved in glutamine utilization, including glutaminase (GLS), and enhanced ammonia production, a metabolic by-product of glutaminolysis. Genetic depletion of GLS in clones suppressed the accumulation of Myc-induced Atg8a-positive structures and reduced autophagic flux, demonstrating that glutaminase contributes to the autophagic response elicited by Myc. Exogenous NHCl was sufficient to induce Atg8a-positive structures and partially restored their accumulation following GLS depletion, supporting ammonia as a downstream contributor to this response. Mechanistically, Myc-induced autophagy in clones required the core autophagy factor Atg5 but was not suppressed by depletion of Rheb or Atg1, consistent with an autophagic program that can operate independently of canonical TOR-Atg1 signaling. We further found that Myc activity is required for RasV12-driven epithelial overgrowth and that RasV12 cells induce a pronounced non-cell-autonomous accumulation of Atg8a-positive structures in wild-type cells surrounding RasV12 clones. Depletion of either Myc or GLS in RasV12 cells strongly reduced this neighboring autophagic response, linking Myc-dependent glutamine metabolism in transformed cells to autophagy in the surrounding tissue. Together, our findings identify GLS-dependent glutamine metabolism as a previously unrecognized component of Myc-induced autophagy and extend this relationship to Ras-transformed epithelia, where Myc and Gls contribute to non-cell-autonomous autophagic responses in neighboring cells.

cell biology↗

bioRxiv2026

Activation and inactivation pathways of a p53-like transcription factor govern lipid homeostasis in yeast

Membrane fluidity depends on unsaturated acyl chains that are generated in Saccharomyces cerevisiae by the desaturase Ole1, whose expression is primarily under the control of the transcription factor Mga2. Here, we show that the endoplasmic reticulum-anchored Mga2 precursor is ubiquitinated by the E3 ligase Rsp5 and then processively degraded by the proteasome until proteolysis stalls at a defined site, releasing a soluble fragment that enters the nucleus and activates Ole1 transcription. Unexpectedly, Mga2 contains a DNA-binding domain and a trans-activation-like segment structurally and functionally related to those of the human tumor suppressor p53. The mature transcription factor is degraded in the nucleus in a DNA binding-dependent manner; blocking this degradation causes unsaturated acyl chains to accumulate in lipid droplets, a detoxification response required for cell viability. These findings define the pathways that activate and inactivate Mga2, and uncover an evolutionary connection between the yeast lipid homeostasis regulator Mga2 and p53.

cell biology↗

bioRxiv2026

Tau isoforms modulate the axon initial segment controlling axonal trafficking and neuronal excitability

The axon initial segment (AIS) is a specialized neuronal compartment integrating action potential initiation with selective control of axonal trafficking. The microtubule associated protein tau is a central regulator of cytoskeletal organization and transport, yet how distinct tau isoforms contribute to AIS development and function remains unclear. Here, we examined the role of tau isoform relative abundance in regulating AIS establishment, maturation, excitability, and transport selectivity using murine primary neurons and human induced pluripotent stem cell (hiPSC)-derived neurons combined with super resolution imaging, electrophysiology, and live trafficking assays. We found that tau expression levels and isoform content modulate the timing and robustness of AIS maturation. In murine neurons, tau deficiency or predominance of 3 repeat (3R) tau delays Ankyrin G accumulation and AIS stabilization without preventing AIS formation. hiPSC-derived neurons display an intrinsic AIS developmental program accompanied by progressive changes in tau isoform content. Super resolution DNA PAINT reveals that endogenous tau decorates axonal microtubules in discrete nanoclusters with compartment specific distributions. Modulation of the endogenous 3R/4R tau balance in hiPSC-derived neurons shows that isoform composition, independently of tau levels, regulates AIS positioning and Ankyrin G organization. Functionally, shifts towards 3R-tau reduce sodium currents, impair action potential firing, and alter lysosomal transport dynamics within the AIS. Together, these findings identify tau isoform balance as a developmental regulator of AIS maturation, linking cytoskeletal organization to neuronal excitability and transport gating. Because the aberrant alternative tau splicing of exon 10 is a defining feature of primary tauopathies, our results provide mechanistic insight into how imbalanced tau isoforms may contribute to neuronal dysfunction.

cell biology↗

bioRxiv2026

PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy

Organelles form an interconnected network whose morphology, positioning and interactions reflect cellular state. However, reproducibly quantifying these organelle phenotypes across large cell populations and diverse cell types remains a significant challenge. Here we present PRISM (Plasmid-based Reporter for Intracellular Spectral Microscopy), a PiggyBac-integrable construct encoding five unique fluorescent organelle reporters for spectral microscopy, with an accompanying modular analysis pipeline. PRISM stably labels the Golgi, peroxisomes, endoplasmic reticulum, mitochondria and lysosomes in multiple cell types while remaining compatible with additional molecular or functional probes. The workflow extracts over 500 metrics per cell, describing organelle morphology and distribution alongside pairwise and higher-order contacts. We use PRISM to characterise organelle responses to cytoskeletal perturbation, map PI(4)P redistribution during lysosomal damage, and reveal how Zika virus remodels the organelle landscape during infection. PRISM provides a reproducible approach for investigating organelle network remodelling across biological contexts

cell biology↗