Life Science Alliance

Protein S-acylation by ZDHHC5 promotes membrane recruitment of the innate immune receptors NOD1 and NOD2. ZDHHC5 contains an extended cytosolic tail implicated in substrate recruitment, accessory-protein interactions, and enzyme trafficking, but its contribution to NOD1 and NOD2 modification remains unclear. Here, we used mutagenesis and complementation of ZDHHC5 knockout cells to define the regions required for NOD association, S-acylation, and plasma membrane localization. Substitution of three S-acylated cysteines in the tail preserved ZDHHC5 localization and its ability to restore NOD2 membrane recruitment. Progressive truncation revealed that most of the cytosolic tail was dispensable, with a construct comprising residues 1-230 retaining activity towards both NOD1 and NOD2. Further truncation to amino acids 1-218 impaired NOD S-acylation and membrane recruitment without eliminating NOD2 association. Thus, substrate association and productive modification have distinct requirements. C-terminal tail removal also differentially affected accessory-protein association: full-length ZDHHC5 co-immunoprecipitated with both GOLGA7A and GOLGA7B, whereas only GOLGA7B was detectably associated with the 1-230 construct. Together, these findings define a minimal functional ZDHHC5 that supports NOD S-acylation and distinguish the requirements for substrate association, catalytic activity, and accessory-protein interactions. They establish that the extended tail is dispensable for NOD modification under the conditions examined, while identifying differential requirements for GOLGA7A and GOLGA7B association with ZDHHC5.

Cytos Multimodal Pooled Screening (CytosMPS) measures CRISPR guide identity, morphology, native 3' transcriptome, and protein abundance and localization in the same fixed cells. Following IL-1{beta} stimulation, cells with higher nuclear NF-{kappa}B show lower phospho-p38/HSP27 and higher NFKBIA/DUSP1 in the same cell, a measurement neither imaging nor transcriptomics alone provides. TGFBR2 and CTNNB1 perturbations produce distinct multimodal phenotypes. Guide representation and perturbation transcriptional responses agree with an orthogonal single-cell transcriptomic platform.

High throughput sequencing necessitates robust computational tools to contextualize complex transcriptomic data. In this study, we analyzed RNA Seq data from peripheral blood of bacterial pneumonia patients and healthy controls (GEO GSE161731) to investigate systemic molecular responses to infection. Differential gene expression analysis identified significantly upregulated genes in pneumonia. We used GANGO for Gene Ontology (GO) term enrichment and BioFunctional for hierarchical exploration, providing an initial overview of affected biological processes. To deepen interpretation, we leveraged CURIE (www.curieai.tech ), an AI plat-form that cross-references GO terms with scientific literature. CURIE generates narrative explanations, link-ing molecular mechanisms, experimental evidence, and publications to each biological process, moving be-yond simple enrichment. Our combined analysis revealed a coordinated upregulation of pathways involved in DNA repair and replication, transcriptional activation, RNA processing, translation, ribosome biogenesis, mitochondrial respiration, and cofactor binding. By integrating these findings within a broad, literature-supported framework, we highlighted how multiple cellular compartments and processes collaborate to mount an effective response to infection-induced stress. This study underscores the potential of combining classical statistical enrichment with AI based interpretation for a holistic understanding of host-pathogen in-teractions at the transcriptomic level.

Spatiotemporal allocation and dynamic redistribution of centrosomal proteins are critical for coordinating the structural and molecular events that ensure successful cell division. While depletion of the multifunctional protein Optineurin (OPTN) impairs cell-cycle progression, our previous report of the presence of OPTN at key cell-division assemblies raised the question of how its trafficking is coordinated during cell division. In this study, using cell-cycle synchronisation coupled with flow cytometric analysis and confocal microscopy, we report that OPTN progressively dissociates from centrosomes during mitosis, redistributes to cytokinetic structures, accumulates at the spindle midzone, and then concentrates at the midbody during cytokinesis. Moreover, following this transition, OPTN progressively re-emerges at centrosomes during G1 of the subsequent cell cycle. Further, microtubule perturbation and regrowth assays provide evidence that OPTN recruitment and retention at the pericentriolar matrix (PCM) can occur independently of microtubules, whereas its exit is microtubule-dependent. Collectively, this study depicts, for the first time, a detailed movement trail of OPTN, highlighting its centrosome-linked redistribution and microtubule dependency. This context-dependent localisation and trafficking of OPTN across the centrosome-midbody axis establish a definitive spatiotemporal roadmap that can be strategically utilised to study its functional role in cell division.

Shortening of the poly(A) tail initiates mRNA decay, and the human CCR4-NOT is the principal cytoplasmic deadenylase. Although its subunits have been defined, their functions have not been comprehensively evaluated in cells. We depleted each CCR4-NOT subunit and measured transcriptome-wide effects. CCR4-NOT regulated transcripts from thousands of genes, many of which associated with the complex in cells. Distinct groups of transcripts responded according to the modular organization of the complex, while subsets exhibited unique responses to specific subunits. Poly(A) tail analysis revealed that the CNOT7 and CNOT8 deadenylases are the predominant regulators of poly(A) tail length in these cells. CCR4-NOT targets were enriched in regulatory pathways including cell proliferation, apoptosis, stress responses, and cancer-related processes. Bioinformatic analysis identified sequence determinants and candidate recruitment factors associated with CCR4-NOT regulation. The results define the breadth and specificity of CCR4-NOT-mediated mRNA decay and provide a resource for dissecting regulatory mechanisms and biological roles.

Aberrant signaling of receptor tyrosine kinases (RTKs), including the hepatocyte growth factor receptor MET, contributes to colorectal cancer (CRC) progression and is tightly regulated by endocytic trafficking. We previously showed that combined deletion of the endosomal sorting proteins SNX1 and SNX2 disrupts MET trafficking and enhances downstream signaling in HCT116 CRC cells. However, their individual contributions remained unresolved. Using CRISPR/Cas9-engineered SNX1- and SNX2-KO HCT116 cells, we examined their roles in MET trafficking and signaling. Loss of SNX2, but not SNX1, markedly reduced SNX5 and SNX6 protein levels without affecting transcript abundance. SNX2 deficiency also increased total MET under serum-containing conditions without altering MET transcript or cell-surface receptor levels. Following HGF stimulation, loss of SNX2, but not SNX1, transiently delayed MET trafficking to EEA1+ early and RAB7+ late endosomes, while recycling and lysosomal trafficking remained largely unaffected. This was accompanied by enhanced and sustained HGF-induced AKT activation. Together, these findings identify SNX2 as a predominant regulator of early MET endosomal trafficking in HCT116 cells and reveal functional asymmetry between SNX1 and SNX2. They support a role for SNX2 in spatial regulation of MET signaling through receptor trafficking, consistent with the association of low SNX2 expression with poorer survival in CRC patients.

Cell-type marker genes are definitional characteristics of a cell type, and in single-cell RNA sequencing atlases they are commonly nominated through differential expression (DE) testing. The Wilcoxon rank-sum test is the default method for marker gene discovery in Seurat and a recommended method in Scanpy, two widely used computational software packages for scRNA-seq analysis. Structurally, Wilcoxon's standardized statistic grows with sample size at a fixed underlying effect, meaning computed rankings across clusters of unequal size are incomparable. We quantified this effect across three atlas datasets - lung, kidney, and brain. Mean Wilcoxon score scaled with log cluster size at Pearson correlation r = 0.90-0.95 in each organ. In contrast, a classification-based comparator, NS-Forest, showed low correlation with cluster size (r = 0.10-0.28). This DE-cluster size relationship remained essentially unchanged after controlling for classification performance through partial correlation, decayed monotonically under cluster size downsampling, and was reproduced in simulation with marker quality fixed. The Wilcoxon rank-sum test can be transformed into a rank-based effect size by normalizing by the target-background pair count, removing the positive size dependence. However, this effect size nominates an identical set of candidate genes as the original statistic, indicating the cluster size dependence and poor specificity of DE nominated genes are separate problems. Genes nominated under default settings were substantially less specific to their target clusters, with median on-target fractions of 0.204 (lung), 0.166 (kidney), and 0.083 (brain), compared to NS-Forest's marker genes (0.580, 0.687, 0.364), revealing the relatively poor specificity that highly scoring DE genes exhibit.

As the main microtubule network organisers of animal cells, centrosomes orchestrate diverse cellular processes. Centrosomes have been linked to cancer when numerically or structurally aberrant, yet their precise roles at different cancer stages remains to be defined. Here, we study centrosome function in the epithelial-to-mesenchymal transition (EMT), a key driver of cancer initiation, progression and metastasis. We first depleted centrosomes in a breast cancer mesenchymal-like model, resulting in insignificant cellular or nuclear rearrangements. We then investigated non-carcinogenic breast cells undergoing the EMT via TGF{beta} signalling, and removed the centrosomes before triggering this transition. Stimulated epithelial cells acquired a mesenchymal phenotype and rearranged their cytoskeleton. By contrast, stimulated cells lacking centrosomes retained epithelial morphology, showed little cytoskeletal remodelling, yet still altered nuclear shape and upregulated key EMT markers. Transcriptome analysis revealed reduced expression of important genes involved in extracellular matrix organisation and a downregulation of cell junction components when lacking centrosomes; further analysis revealed paxillin showing reduced colocalisation with actin focal adhesions. Centrosomes thus prove essential for cytoskeletal remodelling in the EMT of breast cancer cells.

Centriolar satellites are membrane-less organelles that store, modify and traffic proteins, in particular those of the centrosome and the primary cilium, and their deregulation is linked to ciliopathies, neurodevelopmental and neurodegenerative disorders. Satellite number, size, intensity and spatial distribution vary with cell type and cell state, yet satellites are usually quantified by a single readout, the pericentrosomal fluorescence intensity in maximum-projected images, which cannot distinguish changes in satellite number, size and position. Here we present SatelliteQ, an open-source Fiji and Python workflow for object-based quantification of satellites in 2D, 3D and time-lapse images. SatelliteQ segments satellites, detects centrosomes or primary cilia in the same cells, and reports satellite number, size, intensity, distance to the centrosome, shape and spatial distribution per satellite and per cell, with interactive graph and spatial viewers. Its measurements correlate closely with Imaris-based quantification; absolute values depend on segmentation settings and analysis mode, whereas the biological differences tested here were preserved across matched settings. Using SatelliteQ, we resolved distinct spatial signatures of satellite dispersal induced by microtubule depolymerization and by disruption of weak hydrophobic interactions, quantified differences between cell types and the scaling of satellite number with cell size, captured PCM1 granule dynamics in living cells, and compared satellite organization between ciliated and unciliated cells. Depletion of the ciliopathy-associated satellite protein CEP290 altered satellite abundance and pericentrosomal organization, while patient-derived cells carrying CEP290 mutations displayed divergent satellite phenotypes that were not explained by ciliation alone. SatelliteQ thus establishes satellite properties as a multidimensional cellular phenotype and provides an accessible framework for exploring satellites as an organelle-level readout in disease.

Samp1 is an inner nuclear membrane protein required for myogenic differentiation and involved in chromatin organization at the nuclear periphery. Here, we investigated whether these functions are connected by studying the effects of Samp1 depletion during C2C12 myogenic differentiation using immunofluorescence microscopy, RNA sequencing, FRIC, and chromosome-positioning analysis. Samp1-depleted cells showed strongly reduced MyHC expression and virtually abrogated multinucleated fiber formation. Although cell-cycle withdrawal was not prevented, the transcriptional program driving differentiation was drastically perturbed, with reduced muscle-associated transcripts and incomplete repression of genes normally downregulated during myogenesis. Samp1 depletion also disrupted peripheral chromatin organization and prevented the accumulation of peripheral heterochromatin typically seen during differentiation. In addition, radial chromosome distribution was disrupted, evidenced by the failure of chromosome 8 to reposition to the nuclear periphery during differentiation. Together, these findings link the requirement for Samp1 in myogenic differentiation to its role in genome organization at the nuclear periphery.

Telomeres, the ends of linear chromosomes, form a cap composed of specific telomeric DNA associated with specialized proteins that ensures efficient protection against chromosome degradation and, consequently, overall genome instability. Three main complexes have been implicated in chromosome end protection, namely telomerase, shelterin, and the CST complex (CTC1/Cdc13-STN1-TEN1). In a recent study, we uncovered mutants of the S. cerevisiae CST in which damage was sensed both by the two major spindle checkpoints and the major DNA damage checkpoint. In the best-studied of these mutants, stn1-sz2, the stability and organization of the mitotic tubulin spindle was profoundly affected, as were the organization of the centrosomes and the kinetochores. Here, we find that the stn1-sz2 mutant is hypersensitive to deletion mutants of two members of the kinetochores, Ctf19 and Mcm21, which correlated with mis-localization of their associated subunit in the COMA complex, Okp1, during anaphase. Defects in interactions between the kinetochores and the tubulin spindle are entirely sensed by the SAC (spindle assembly checkpoint). Here, we find that some of the stn1-sz2 damage is recognized by the Mad2 checkpoint protein independently from the SAC. The data presented here contribute to a better understanding of the damage in stn1-sz2, the prototype of novel mutants of telomeric CST characterized by mitotic-spindle-damage in addition to the classical telomeric-DNA-damage.

Myelin is an essential and highly specialized membrane in the central and peripheral nervous systems that enwraps axons to accelerate electrical transmission and support neuronal health. The generation of this multilamellar structure requires a tightly coordinated synthesis of specific proteins and lipids. Among these are sphingolipids (SLs), which are major components of myelin. SL production is initiated by the serine palmitoyltransferase (SPT) enzyme complex, the rate-limiting enzyme in the de novo SL biosynthesis pathway. ORMDL proteins (ORMDL1-3) are the regulatory subunits of SPT, which, by sensing ceramide levels, tune SL flux. Although ORMDL3 has been linked to asthma and peripheral myelination, its role in CNS myelination and the CNS myelin-making oligodendrocytes (OLGs) remains unclear. We therefore assessed the function of ORMDL3 in OLs by generating a Cnp-Cre-driven, oligodendrocyte-specific Ormdl3 conditional knockout (cKO) mouse model. Loss of Ormdl3 selectively increased myelin SLs, particularly long-chain sulfatides, without altering ceramide or galactosylceramide abundance. These changes are most prominent around postnatal day 35, a developmental period of active myelin turnover. Ultrastructural analysis of optic nerves shows a thicker myelin sheath and increased axon caliber in cKO mice. Unexpectedly, deletion of Ormdl3 also increases levels of major myelin proteins (MBP, MOG, and PLP) and is accompanied by dynamic, region- and sex-dependent regulation of enzymes involved in sulfatide biosynthesis, without altering OLGs number or maturation. Together, for the first time, these findings identify Ormdl3 as a key regulator of SL homeostasis during developmental myelination and suggest that it helps synchronize lipid synthesis with myelin protein expression.

The MRTFs (myocardin-related transcription factors) are essential for effective cytoskeletal function during differentiation and development. To investigate the role played by the MRTFs in T cell development and function we inactivated Mrtfb in Mrtfa-null mice at the DN2 stage (MrtfabKOT animals). Positive selection, and development of MrtfabKOT regulatory (Treg), {gamma}{delta}, and NK T cells proceeded normally. Thymic egress was impaired, however, with mature T cells accumulating at the cortico-medullary junction, and in vitro MrtfabKOT thymocytes exhibited impaired cytoskeletal responses to S1P and migratory cytokines. MrtfabKOT mice were lymphopenic, with defective homeostatic proliferation and T cell homing to peripheral lymphoid organs. Although thymocyte negative selection was unaffected, MrtfabKOT animals develop autoimmune phenotypes in lacrimal gland and intestinal mucosa. Using the experimental colitis model, we show that these phenotypes reflect functional deficits in MrtfabKOT Treg cells. Our findings show that MRTF-SRF signalling plays an unanticipated role in thymocyte egress and immune tolerance, and reveal a role of the MRTFs in Treg function.

Pleckstrin homology (PH) domains are typically assumed to be phosphoinositide-binding modules, although most lack strong lipid specificity and their broader ligand repertoire remains poorly defined. We find that many yeast PH domains bind Nsr1p, the ortholog of nucleolin, also identified as a PH domain ligand, suggesting widespread recognition of negatively charged protein regions. The phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding PLC{delta}1 PH domain also binds a highly phosphorylated region of IRBIT through the same site that recognizes PtdIns(4,5)P2. Using high-throughput integrated phosphopeptide (Hi-P) screening, we surveyed 38,624 mammalian sequences containing three documented phosphoserines. PLC{delta}1-PH bound numerous phosphorylated and unphosphorylated acidic peptides, and phosphorylation generally strengthened pre-existing interactions rather than conferring strict specificity, without requiring a fixed phosphoserine spacing. Instead, favored phosphopeptides combined a key phosphoserine with upstream acidic residues. Structural modeling suggests that this phosphoserine occupies the canonical inositol phosphate binding pocket, while adjacent acidic residues make delocalized electrostatic contacts. Thus, PH domains can recognize various patterns of protein negative charge, expanding their potential regulatory roles beyond membrane targeting.

Naive T cells are poised for activation and contain a pool of translationally repressed ribosomal protein (RP) mRNA prepared to induce ribosome biogenesis to support protein synthesis, cell growth and proliferation. RP mRNA are the prototypical members of a class of transcripts initiating at cytosine followed by a CU rich element called terminal oligo pyrimidine (TOP) RNAs. TOP RNAs are regulated by an RNA binding protein LARP1, which promotes transcript stabilisation and translational repression. We investigated LARP1 function in T cell activation by generating cross-linking immunoprecipitation (CLIP) datasets detailing the LARP1-RNA interactions in naive and activated CD4+ T cells and identifying novel TOP RNAs. TOP RNAs identified by this analysis were functionally diverse. RP mRNAs were typified by high stability, and translational repression in naive T cells followed by MTORC1-dependent translation increases following T cell activation. However, other TOP RNAs varied in these aspects of their regulation. Notably, TOP RNAs with longer 3'UTRs had a relaxed dependency on LARP1 for stability and a reduced dependency on MTORC1 for their translation. Transcription start site heterogeneity also impacted TOP RNA regulation by generating a mixture of transcript isoforms with different TOP motif lengths. Longer terminal oligo pyrimidine stretches were associated with a greater dependency on MTORC1 for translation. Differential regulation of TOP RNAs may allow tuneable translational responses to MTORC1 and indicates potential roles for LARP1 beyond translation regulation and stability.

The targeting function of nuclear localization signals (NLSs) is generally considered independent of a protein's native sequence or fold and is readily transferable to heterologous cargos. Contrary to this paradigm, rapid nuclear translocation of phosphorylated STAT1 (pSTAT1) following cytokine stimulation requires importin {beta}, Ran-GTP, and the importin 5 isoform, which recognizes a non-transferable NLS. Here, we present cryo-EM structures of pSTAT1 bound to importin 5, revealing an asymmetric 2:1 complex that diverges from canonical NLS-mediated cargo recognition. Importin 5 occupies the DNA-binding groove of the pSTAT1 dimer, with a single STAT1 N-terminal domain positioning the C-terminal Armadillo repeats 9-10 (S1B domain) orthogonal to the DNA-binding interface. This interface is also targeted by the Ebola virus protein VP24, an antagonist of interferon signaling. We further show that Ran-GTP alone is insufficient to trigger nuclear release of pSTAT1, which additionally requires the exportin CAS. A cryo-EM reconstruction of the CAS-Ran-GTP-5 complex, supported by in vitro competition assays, demonstrates that CAS and pSTAT1 are mutually exclusive ligands for importin 5. Together, these findings define the molecular choreography of cytokine-induced STAT1 nuclear translocation and release, establishing a general paradigm for STAT family signaling.

The transport of about 70 enzymes to lysosomes depends on mannose 6-phosphate signals formed by GNPTAB. Editing of Gnptab in an intestinal mouse cell line revealed the loss of multiple lysosomal enzymes associated with the accumulation of sphingomyelins, ceramides, and cholesterol, and reduced levels of bis(monoacylglycero)phosphate (BMP) in lysosomal proteomes and lipidomes. By cross-correlation we identified two subsets of lysosomal lipid-modifying enzymes linked with mixed unsaturated or di-monosaturated BMP. Autophagy-related proteins functioning in early stages of autophagosome formation associated with neutral ceramides, whereas proteins involved in autophagosome-lysosome fusion correlated with negatively charged BMPs. Therefore, the high cholesterol and low BMP level of lysosomes might be causal for impaired autophagic flux in GNPTAB deficient cells. We propose a functional axis of three lysosomal proteins as potential target to improve the autophagic flux in cells with dysfunctional lysosomes and in a newly established intestinal organoid model suitable as novel experimental tool.

Hepatic stellate cells (HSCs) are the key cellular drivers of liver fibrosis. During liver injury and chronic inflammation HSCs adopt an activated phenotype and secrete fibrotic extracellular matrix (ECM) components such as collagen 1. Mechanical cues derived from the fibrotic ECM drive and support the activation of HSCs, via mechanisms that involve integrins and the mechano-sensitive transcriptional regulator YAP1. It is not yet well understood how external mechanical cues are translated into a molecular response that alters YAP1 nuclear shuttling. There is evidence that suggests the PDZ and LIM domain protein (PDLIM) 5 can regulate YAP1 shuttling in human epithelial cells. We therefore investigated whether PDLIM5 is expressed in HSCs and contributes to YAP1 associated HSC mechano-activation. PDLIM5 protein was detected in HSCs in fibrotic human and mouse liver. PDLIM5 transcript and protein were expressed by primary human and mouse HSCs and by the immortalised HSC LX-2 cell line. PDLIM5 localised with actin stress fibres suggesting a role in HSC adhesion. Co-immunoprecipitation and proximity ligation in LX-2 cells support an association between PDLIM5 and YAP1. We used pharmacological (paclitaxel) and genetic (siRNA and CRISPRi) approaches to inhibit PDLIM5 in HSCs. Inhibiting PDLIM5 reduced YAP1 nuclear localisation and fibrotic gene (COL1A1, ACTA2) expression in LX-2 cells. Overall, these data support a role for PDLIM5 in regulating YAP1 localisation and fibrogenic gene expression in HSCs.

The biochemical and structural basis of NAIP/NLRC4 inflammasome activation is well understood. Far less well known are the spatiotemporal processes within cells that play a role in the activation of the NAIP/NLRC4 inflammasome. We used super-resolution imaging technology, including MINFLUX nanoscopy, to investigate the human hNAIP/hNLRC4 inflammasome in primary human macrophages following the phagocytosis of a specific Yersinia enterocolitica strain. hNAIP, which senses components of the bacterial type III secretion system (T3SS) and activates NLRC4, was recruited to bacteria-containing phagosomes after they were disrupted by the T3SS. Disruption of a single phagosome within a macrophage was sufficient to cause the accumulation of NLRC4 and NLRP3 (a sensor of another inflammasome), as well as the adapter protein ASC, in a dense condensate known as a speck. This subsequently led to plasma membrane permeation and pyroptosis. It appeared that, with increasing infection time, clusters containing NLRC4 and NLRP3/NLRC4 gradually acquired ASC for speck formation. MINFLUX-nanoscopy was able to visualise hNAIP at disrupted phagosomes with nanometre resolution, and also revealed the number and organisation of NLRC4 inflammasome discs within a speck, as well as their hNAIP content, for the first time. Surprisingly, the number of NLRC4 inflammasome discs varied considerably, ranging from 35 to 249 per speck. Also, only a small fraction of these seemed to contain hNAIP. Our results significantly improve our understanding of the process by which the hNAIP/NLRC4 inflammasome is activated in macrophages that have ingested bacteria containing a T3SS.

Bis(monoacylglycero)phosphate (BMP), a lysosomal phospholipid essential for lipid catabolism and cholesterol clearance, has a noncanonical S,S glycerol configuration found in no other mammalian phospholipid, a feature necessary for its stability in the lysosome. How cells invert glycerol stereochemistry to build S,S-BMP has remained unexplained since this configuration was discovered five decades ago. Here, we show that the endoplasmic reticulum-resident Batten disease protein CLN6 is a Ca2+-dependent epimerase that isomerizes glycerophosphoglycerol (GPG) from R,S-GPG to S,S-GPG. CLN6-deficient cells, mouse tissues, and patient samples predominantly contain R,S-GPG, S,R-lysophosphatidylglycerol (LPG), and R,S-BMP instead of their S,S counterparts, with a net depletion of BMP. Purified CLN6 catalyzes GPG epimerization in vitro, an activity abolished by a pathogenic substitution in its substrate-binding pocket. Consistently, exogenous S,S-GPG restores BMP synthesis and relieves lipid storage in CLN6-null cells. Our work establishes stereochemical commitment upstream of acylation, placing CLN6, CLN8, and CLN5 in sequence in BMP biosynthesis and unifying the lipid defect across these neurodegenerative disorders.