Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Harnessing cell-encapsulated hydrogels to study astrocyte mechanoresponse in 4D

In glaucoma, the optic nerve head (ONH) is exposed to increased biomechanical strain, impacting the resident astrocytes that maintain neural homeostasis. During disease progression astrocytes exhibit morphologic and metabolic shifts; however, the specific impact of glaucoma-related biomechanical strains on astrocyte behavior remains poorly understood. To address this, we used our previously established 3D cell-encapsulated extracellular matrix (ECM) hydrogel to investigate ONH astrocyte cellular and transcriptomic responses to varying biomechanical strain levels over time. Murine ONH astrocyte were encapsulated within an ECM hydrogel made from photocrosslinkable collagen type I and hyaluronic acid, and subjected to 0, 3, or 10% cyclic compression for 4h and 24h. We found significant restructuring of cytoskeletal morphology, metabolic dysregulation, and astrocyte-mediated ECM modulation that were strain-, duration- and hydrogel subregion-dependent. These phenotypic alterations were associated with diverse transcriptional changes in genes related to cell cycle and morphology, inflammation, metabolism and matrix remodeling that were driven by compressive strain intensity and duration. Our work reveals the direct role of compressive strain in eliciting a complex astrocyte response, supports targeting mechanosensation to prevent these pathologic astrocyte responses, and establishes ECM-based hydrogels as a platform to test mechanisms driving astrocyte mechanodysfunction. Altogether, our study offers new insights into astrocyte responses to biomechanical insult and demonstrates the use of a tunable 3D ECM hydrogel for future mechanistic studies of neurodegeneration. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/660800v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@f355fborg.highwire.dtl.DTLVardef@191e096org.highwire.dtl.DTLVardef@2fae32org.highwire.dtl.DTLVardef@55913c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Intelectin-2 is a broad-spectrum antimicrobial lectin

Mammals regulate the localization, composition, and activity of their native microbiota at colonization sites. Lectins residing at these sites influence microbial populations, but their individual functions are often unclear. Intelectins are found in chordates at mucosal barriers, but their functions are not well characterized. We found that mouse intelectin-2 (mItln2) and human intelectin-2 (hItln2) engage and crosslink mucins via carbohydrate recognition. Moreover, both lectins recognize microbes within native microbial communities, including gram-positive and gram-negative isolates from the respiratory and gastrointestinal tracts. This ability to engage mammalian and microbial glycans arises from calcium-coordinated binding of carbohydrate residues within mucus and microbial surfaces. Microbes, but not human cells, bound by mItln2 or hItln2, suffer a loss of viability. These findings underscore the crucial antimicrobial role of mammalian intelectin-2 in mucosal defense, where it plays offensive (microbial killing) and defensive (mucus crosslinking) roles in regulating microbial colonization.

microbiology↗

bioRxiv2025

The Regulation of COX-2, ABCA1 and ABCG1 by the lncRNA PACERR links the inflammatory response and cholesterol homeostasis

Cyclooxygenase-2 (COX-2) has an established role in inflammation and its inhibition by non-steroidal anti-inflammatory drugs (NSAIDs) is clinically efficacious1,2. However, placebo-controlled trials of COX-2 inhibitors have revealed a cardiovascular hazard. This has been attributed to suppression of COX-2 dependent cardioprotective prostaglandins (PGs), especially prostacyclin, produced by endothelial (EC) and vascular smooth muscle cells (vSMC) 1-3. Upstream of these effects, we have found that the COX-2 antisense long non-coding RNA (lncRNA) PACERR interacts with discrete RNA binding proteins to mediate the cell specific COX-2 response to both anti-[high-density lipoprotein (HDL)] and pro-inflammatory [lipopolysaccharide (LPS)] stimuli. PACERR exerts its action both in cis and in trans, controlling the expression of COX-2 and the cholesterol transport genes, ABCA1 and ABCG1. When cells are exposed to HDL, PACERR is transcribed, leading to the release of bound histone acetyltransferase p300 and its relocation to the promoter of COX-2 which is then transcribed leading to PG formation. In concert, PACERR also releases heterogeneous nuclear ribonucleoprotein L (hnRNPL) which relocates to the ABCA1 and ABCG1 gene loci, controlling mRNA alternative splicing and subsequent cholesterol efflux to HDL. Silencing PACERR, with an antisense oligonucleotide (ASO), augments the COX-2 and cholesterol efflux in response to HDL. In response to HDL, PACERR associates with its neighboring gene, cytosolic phospholipase A2 (cPLA2/PLA2G4A) both interacting with an enhancer element affecting cPLA2 transcriptional activation and escorting the cPLA2 protein to the nuclear membrane. There, it releases arachidonic acid, further activating COX-2 but limiting ABCA1 and ABCG1 by suppressing the formation of the LXR/RXR heterodimers required for their transcription when cholesterol efflux is no longer required4. In response to LPS, PACERR controls the action of the NF{kappa}B repressive protein, I{kappa}B{zeta}. When PACERR is silenced in a humanized mouse model with the ASO, I{kappa}B{zeta} is free to bind to the NF{kappa}B site in the COX-2 promoter, suppressing transcription, PG formation and systemic inflammation. In summary, these studies reveal dual and complementary mechanisms by which PACERR modulates PG production by COX-2. In response to HDL, it enhances production of prostacyclin whereas it dampens production of the PG response to LPS.

cell biology↗

bioRxiv2025

Commensal to pathogen switch in Streptococcus pneumoniae is governed by a thermosensing master regulator

Opportunistic pathogens switch from a commensal to pathogenic state by sensing and responding to a variety of environmental cues, including temperature fluctuations. Minor temperature oscillations can alert the pathogen to a changing niche ecosystem, necessitating efficient sensing and rapid integration to trigger behavioral change. This is typically achieved through master regulators, which act as umbrella systems dictating pleiotropic phenotypes. Here, we uncover a pivotal role of minor temperature shifts in transition of Streptococcus pneumoniae (SPN) from commensal to virulent lifestyles, mediated via an RNA thermosensing (RNAT) element within the untranslated region of the global regulator CiaR. By positively regulating the expression of the surface adhesin, Phosphorylcholine (PCho), in response to elevated temperature, CiaR potentiates pneumococcal infection. Engineering the RNAT structure to create translation restrictive or permissive versions allowed us to demonstrate how modulation in expression of CiaR could alter pneumococcal invasion capability, influencing infection outcomes. Moreover, intranasal administration of PCho mitigated SPN-induced bacteraemic pneumonia. Since a majority of opportunistic respiratory bacterial pathogens decorate their surface with PCho, this signaling arm could be exploited for anti-infective interventions. Significance statementOur nasopharyngeal area is dominated by opportunistic pathogens, such as Streptococcus pneumoniae (SPN), which typically reside as harmless bystanders. However, in individuals with heightened nasopharyngeal inflammation, resulting from allergy, viral infection or an immature or senescent immune system, these seemingly innocuous microbes, including SPN, switch to virulent lifestyles. We reveal an elegant mechanism for rewiring of SPN virulence genes upon sensing temperature oscillations in the nasopharynx by the master regulator CiaR. Elevated nasopharyngeal temperatures due to pathologic conditions is sensed by thermosensing ciaR mRNA. This primarily promotes SPN surface decoration by PCho which facilitates improved invasion, triggering virulence phenotypes. Our findings point towards adoption of a common mechanism for switch to virulent lifestyles by variety of microbes sharing the specific respiratory niche.

microbiology↗

bioRxiv2025

Cardiac Adaptations in the Cave Nectar Bat Eonycteris spelaea: Insights into Metabolic Resilience and Stress Response

AimsBats are unique mammals with remarkable adaptations, including powered flight, which demands significant energy expenditure. While previous studies have documented basic structural characteristics of bat hearts, a comprehensive understanding of their response to physiological stress remains unexplored. This study investigates the cardiac adaptations of the cave nectar bat Eonycteris spelaea to elucidate the mechanisms underlying their unique physiological capabilities. Methods and ResultsWe performed RNA sequencing to analyse the cardiac gene expression profile of E. spelaea and 6 other bat species in comparison to mouse and human hearts, revealing enriched transcriptomic signatures related to oxidative phosphorylation and fatty acid metabolism across multiple bat species. Metabolomic profiling compared acylcarnitine metabolites and tricarboxylic acid (TCA) cycle intermediates between bat and mouse hearts, indicating a distinct acylcarnitine profile and increased levels of TCA cycle intermediates in bats, suggesting enhanced metabolic capacity. Structural adaptations were assessed through anatomical and histological analyses on cardiac tissues, showing thicker left ventricular walls and increased vascular density in bats without pathological hypertrophy. Functional characteristics were evaluated using dobutamine stress echocardiography, demonstrating superior cardiac reserve in bats with significant increases in ejection fraction, stroke volume, and cardiac output under stress conditions. Additionally, isolated cardiomyocytes were treated with Angiotensin II (Ang II) to assess stress responses. Bat cardiomyocytes displayed resistance to Ang II-induced hypertrophy and mitochondrial dysfunction compared to mice, further highlighting their resilience to stress-induced damage. ConclusionThe unique adaptations observed in bat hearts, including enhanced metabolic pathways, structural remodelling, and cellular resilience contribute to their ability to meet the high energy demands of powered flight while maintain cardiac function under stress. These insights into bat cardiac physiology provide valuable information on cardioprotective mechanisms that could be applicable to other species. Translational PerspectiveBats exhibit remarkable cardiac adaptations that sustain the high energy demands of powered flight while resisting stress-induced damage. These insights into evolutionarily conserved cardioprotective mechanisms highlight potential therapeutic pathways for preventing heart failure, including resistance to hypertrophy and mitochondrial dysfunction under stress. Studying non-model organisms like bats may offer innovative approaches to enhance metabolic and stress resilience in human hearts, paving the way for translational research in cardiovascular disease management and treatment.

systems biology↗

bioRxiv2025

Expression of Arabidopsis Extracellular Vesicle Protein Markers in Nicotiana benthamiana Reveals Distinct Vesicle Subpopulations

Mammalian extracellular vesicles (EVs) are heterogeneous in nature based on their protein content, RNA content, density, size, and functions. In contrast, our understanding of plant EV diversity is quite limited. Multiple plant EV protein markers have been identified. Two of these, TETRASPANIN 8 (TET8) and PENETRATION 1 (PEN1), appear to mark distinct subpopulations of plant EVs. To further assess the diversity of plant EV subpopulations, we purified EVs from N. benthamiana transiently expressing multiple EV marker proteins and then assessed colocalization of these markers using high resolution Total Internal Reflection Fluorescence Microscopy (TIRF-M). We confirmed that TET8 and PEN1 indeed mark distinct EV populations, as they colocalized only 4.7% of the time. This value was nearly identical to that found for EVs purified from transgenic Arabidopsis co-expressing these two markers, demonstrating that transient expression of Arabidopsis EV proteins in N. benthamiana can be used to assess EV subpopulations, bypassing the requirement of generating transgenic plants for every marker combination of interest. We then used the N. benthamiana system to assess colocalization of PEN1 and TET8 with the EV markers PATELLIN1 (PATL1), ANNEXIN2 (ANN2), and RPM1-INTERACTING PROTEIN4 (RIN4). PATL1 and ANN2 colocalized with PEN1 56.6% and 46.6% of the time, respectively, whereas they colocalized with TET8 only 28.4% and 30.8% of the time, respectively. In contrast to PATL1 and ANN2, the RIN4 protein colocalized with TET8 more frequently than with PEN1 (30% versus 13%). Together, these results indicate that plant EVs are heterogeneous in their protein cargos and that TET8 marks a distinct subpopulation of EVs. PEN1, PATL1, and ANN2 commonly mark the same EV population that is distinct from TET8-labeled EVs, while RIN4 more often associates with TET8-labeled EVs. These findings suggest that plants possess at least two different pathways for EV biogenesis and secretion.

plant biology↗

bioRxiv2025

The Role of c-Jun Signaling in Cytidine Analog-Induced Cell Death in Melanoma

Melanoma stands as an increasingly pressing health concern. Enhanced mitochondrial metabolism has been reported in melanoma cells that survived treatment with traditional therapeutics, including cytidine analogs like gemcitabine (GEM). These findings suggest that chemotherapeutic drugs may play dual roles in promoting both cell survival and cell death, although the underlying mechanisms require further investigation. Herein, we conducted proteomics analysis on GEM-treated melanoma cells and found a drug-induced activation of DNA damage response and apoptosis, along with cell cycle arrest. Additionally, GEM treatment significantly altered protein networks related to mitochondrial ribosomal activity, the electron transport chain, and translation. Furthermore, we reported an upregulation of the JNK/c-Jun network in connection with the apoptotic proteins. Co-treatment with a Jun N-terminal Kinase (JNK) inhibitor, JNK-IN-8 (JNKi), significantly increased cell survival, suggesting the involvement of c-Jun signaling in GEM-induced cell death. Additionally, proteomics analysis revealed that JNKi downregulated apoptosis in co-treated cells, highlighting the potential role of the JNK/c-Jun network inhibition in chemotherapeutic tolerance. Collectively, our findings bridge gaps in understanding how melanoma cells respond to cytidine analogs by demonstrating the multifaceted effects of these agents in 1) inducing JNK-mediated apoptotic cell death, and 2) promoting a state of cell cycle inhibition.

cancer biology↗

bioRxiv2025

Expression and In-silico Structural analysis of N-acetylglucosamine transporter, Ngt1 in model fungal pathogen, Candida albicans

IntroductionThe commensal yeast, Candida albicans, has the enormous metabolic flexibility to utilize alternative carbon sources such as N-acetylglucosamine (GlcNAc) at the infection sites, thereby facilitating its adaptive strategies to colonize and thrive within diverse host niches. In Candia, GlcNAc specific transporter (Ngt1) imports GlcNAc at cell surface to induce signaling through the master regulator Ngs1 at the chromatin level. Thus, GlcNAc signaling is responsible for changing its habitat from commensal to pathogenic life style. ObjectiveThe current study aims at understanding the expression, structural and functional intricacies of Ngt1 that determines to GlcNAc sensitivity, specificity and its transport which is a prerogatory step in the GlcNAc signaling process in Candida. MethodThe 3-D structure of Ngt1 was predicted using AlphaFold. We have carried out docking studies using AutoDoc suite for native and Site directed mutant versions of Ngt1 with GlcNAc to determine role of critical amino acids and further, tunnel analysis to reveal the transport mechanism. These findings lead to the designing structure-based Ngt1blockers via virtual screening of natural compound libraries. ResultsOur docking studies on Ngt1 with GlcNAc revealed the useful insights in to mechanism and the role of critical amino acids (Ala 324, Ile 325, Tyr 329, and Asp 332) responsible for interaction. In our analysis, Asn 195, located within transmembrane helix and part of the UNC-93-like transmembrane regulatory protein domain, was identified as critical residue for GlcNAc interaction compared with other mutated residues. Interestingly, the tunnel analysis of Ngt1 transporter revealed presence potential pathways in Ngt1 protein for effective GlcNAc transport. ConclusionThis study provides basic insights in to the structural aspects of Ngt1 and its interaction with GlcNAc that can be further explored for the development effective therapeutic agents for control of infection caused by the Candida. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/648653v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1dbd0eforg.highwire.dtl.DTLVardef@721896org.highwire.dtl.DTLVardef@ac2742org.highwire.dtl.DTLVardef@4591b0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Structural and functional analysis of Ngt1 protein. Flow chart depicting Ngt1 3D modeling (AlphaFold2), docking studies Ngt1-wild type and SDM proteins with GlcNAc ligand, tunnel analysis reflecting transport of GlcNAc, and virtual screening to identify potential inhibitors (Brucine). C_FIG

bioinformatics↗

bioRxiv2025

AdapToR: Adaptive Topological Regression for quantitative structure-activity relationship modeling

Quantitative structure-activity relationship (QSAR) modeling has become a critical tool in drug design. Recently proposed Topological Regression (TR), a computationally efficient and highly interpretable QSAR model that maps distances in the chemical domain to distances in the activity domain, has shown predictive performance comparable to state-of-the-art deep learning-based models. However, TRs dependence on simple random sampling-based anchor selection and utilization of radial basis function for response reconstruction constrain its interpretability and predictive capacity. To address these limitations, we propose Adaptive Topological Regression (AdapToR) with adaptive anchor selection and optimization-based reconstruction. We evaluated AdapToR on the NCI60 GI50 dataset, which consists of over 50,000 drug responses across 60 human cancer cell lines, and compared its performance to Transformer CNN, Graph Transformer, TR, and other baseline models. The results demonstrate that AdapToR outperforms competing QSAR models for drug response prediction with significantly lower computational cost and greater interpretability as compared to deep learning-based models.

bioinformatics↗

bioRxiv2025

Elucidating tissue and sub-cellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote

SUMOylation is essential in plant and animal cells, but it remains unknown how SUMO components act in concert to modify specific targets in response to environmental stresses. In this study we characterise every SUMO component in the Arabidopsis root to create the first complete SUMO Cell Atlas in eukaryotes. This unique resource reveals wide spatial variation, where SUMO proteins and proteases have sub-functionalized in both their expression and subcellular localisation. During stress SUMO conjugation is mainly driven by tissue specific regulation of the SUMO E2 ligase. Stress-specific modulation of the SUMO pathway reveals unique combinations of Proteases being targeted for regulation in distinct root tissues by salt, osmotic and biotic signals. Our SUMO Cell Atlas resources reveal how this PTM influences cellular and tissue scale adaptations during root development and stress responses. We provide the first comprehensive study elucidating how multiple stress inputs can regulate an entire PTM system.

plant biology↗

bioRxiv2025

Neuronal modulation of the superior colliculus associated with visual spatial attention represents perceptual sensitivity, independent of perceptual decision and motor biases

Neurons in the superior colliculus (SC), like those in the cerebral cortex, are strongly modulated in response to shifts in attention, but make a contribution that is distinct from attention-related modulations in visual cortex. It has been a point of contention whether attention-related enhancement of neuronal activity in SC is associated with selective increase in behavioral sensitivity (d) in neurons response fields or with animals decision bias, which is closely linked with motor planning. By independently controlling monkeys perceptual decision and motor criterion, we show that SC activity is strongly correlated with perceptual sensitivity at the neurons response field. Responses of the same SC neurons were unchanged in the face of correspondingly large changes in the perceptual decision criterion. Furthermore, the SC activity did not convey information about perceptual detection on individual trials. These results suggest that the SC contributes to the component of attentional states related to heightened perceptual sensitivity.

neuroscience↗

bioRxiv2025

Sirtuin 2 controls global protein synthesis by regulating Rheb-GTPase

Upregulated global protein synthesis is associated with the development and progression of several diseases and disorders. Strategies like calorie restriction and pharmacological inhibition of protein synthesis, have exhibited health-promoting effects. However, the complex molecular events that regulate global protein synthesis are not completely understood. Here, we report that SIRT2, a histone deacylase, negatively regulates global protein synthesis by inhibiting the mTORC1 pathway via deacetylating Rheb and promoting Rheb degradation. Our in vitro results suggest that SIRT2 deficiency increases protein synthesis, whereas SIRT2 overexpression suppresses protein synthesis. SIRT2-deficient mice exhibit age-associated and neurohormone-induced cardiac hypertrophy. Here, we report increased global protein synthesis in the hearts of young SIRT2-deficient mice, which may contribute to the development of cardiac hypertrophy. Conversely, cardiac-specific overexpression of SIRT2 reduces global protein synthesis in mice hearts. Mechanistically, SIRT2 binds to and deacetylates Rheb at K151 residue to enhance ubiquitin-proteosome-mediated degradation of Rheb. Depletion of Rheb rescues the increased protein synthesis in SIRT2-inhibited conditions. Our findings suggest that SIRT2 activation can be a potential therapeutic for treating diseases associated with increased protein synthesis.

cell biology↗

bioRxiv2025

MCMC-CE: A Novel and Efficient Algorithm for Estimating Small Right-Tail Probabilities of Quadratic Forms with Applications in Genomics

Quadratic forms of multivariate normal variables play a critical role in statistical applications, particularly in genomics and bioinformatics. However, accurately computing small right-tail probabilities (p-values) for large-scale quadratic forms is computationally challenging due to the intractability of their probability distributions, as well as significant numerical constraints and computational burdens. To address these problems, we propose MCMC-CE, an innovative algorithm that integrates Markov Chain Monte Carlo (MCMC) sampling with the cross-entropy (CE) method, coupled with leading-eigenvalue extraction and Satterthwaite-type approximation techniques. Our approach efficiently estimates small p-values for quadratic forms with their ranks exceeding 10,000. Through extensive simulation studies and real-world applications in genomics, including genome-wide association studies and pathway enrichment analyses, our method demonstrates advantageous numerical accuracy and computational reliability compared to existing approaches such as Davies, Imhofs, Farebrothers, Liu-Tang-Zhangs and saddlepoint approximation methods. MCMC-CE provides a robust and scalable solution for accurately computing small p-values for quadratic forms, facilitating more precise statistical inference in large-scale genomic studies.

bioinformatics↗

bioRxiv2025

Perturbed cyclic strain results in a mechanically-induced, premature senescent phenotype in cardiac fibroblasts

The cardiovascular system operates under continuous cyclic mechanical stretch, and changes in mechanics and biochemical responses observed in cardiovascular disorders activate the cardiac fibroblasts (CFs) and increase cellular senescence in the tissue. However, it is unclear if cellular senescence is initiated from biomechanical stimulus alone. Here, we subjected murine CFs to uniaxial stretch and perturbed the mechanical stimulation to examine the impact on induction of a senescent phenotype. Loss of stretch magnitude and increase in frequency, mimicking an injurious hypertrophic or fibrotic response, led to a senescence-like phenotype, including cell cycle, lamin B expression, and DNA damage. Mechanical induction of CF senescence relied on p53/p21, whereas CF senescence induction triggered by reactive oxygen species or involving a mutation in lamin A/C gene occurred through p16. Moreover, mechanical induction of premature senescence was associated with decreases in the nuclear envelope protein emerin. These results demonstrate perturbed mechanical stimulation can initiate a senescent state and altered nuclear integrity may initiate this phenotype. TeaserPerturbed mechanics initiates a premature senescent-like phenotype in cardiac fibroblasts.

biophysics↗

bioRxiv2025

Protein dynamics affect O2-stability of Group B -hydrogenase from Thermosediminibacter oceani

In the pursuit of sustainable green energy generation, [FeFe]-hydrogenases have attracted significant attention due to their ability to catalyze hydrogen production. However, the sensitivity of these enzymes to O2 is a major obstacle for their application as biocatalysts in energy conversion technologies. In the search for an O2-stable [FeFe]-hydrogenase, we identified the hydrogenase ToHydA from Thermosediminibacter oceani that belongs to the rarely characterized Group B (M2a) [FeFe]-hydrogenases. Our findings demonstrate that ToHydA exhibits remarkable O2-stability, even under prolonged O2 exposure. By characterizing site-directed mutagenesis variants, we found that the highly conserved proton-transporting cysteine protects H-cluster from O2-induced degradation by forming Hinact state. The additional cysteine residue in the TSCCCP motif of ToHydA, a feature unique to Group B (M2a) [FeFe]-hydrogenases, enhances the flexibility of that motif and facilitates the formation of the Hinact state. Moreover, ToHydA possesses unique features, including the formation of an unusual Hinact resting state that distinguishes the enzyme from other [FeFe]-hydrogenases. Our atomistic molecular dynamics simulations reveal a previously unrecognized cluster of hydrophobic residues centered around the proton-transporting cysteine-bearing loop. This structural feature appears to be a common molecular characteristic in hydrogenases that form the O2-protected Hinact state. By exploiting these molecular features of ToHydA, future research can aim to rationally design hydrogenases that combine high catalytic activity with enhanced O2 stability, to develop more efficient and durable catalysts. Table of Contents Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/643706v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@96b4aorg.highwire.dtl.DTLVardef@62f367org.highwire.dtl.DTLVardef@59f170org.highwire.dtl.DTLVardef@fa2fd7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Bulk exocytosis of large intracellular apical precursor organelles establishes apical domain identity during de novo lumen formation

The formation of a microvilli-rich lumen is a key event in epithelial polarity development and tissue morphogenesis. During de novo lumenogenesis, epithelial cells establish luminal identity by directing apical cargo to an apical membrane initiation site (AMIS). Although this process has been widely studied, the mechanisms governing AMIS formation and its progression into a luminal precursor remain poorly understood. Here we combined quantitative light and electron microscopy with proximity proteomics to investigate the mechanistic basis of lumen initiation in MDCK-II cells. Contrary to prevailing models, we find that apical cargo is delivered to the AMIS in large intracellular apical precursor organelles, termed vacuolar apical compartments (VACs). VACs possess a preassembled microvilli-rich cortex and undergo exocytic fusion at the AMIS to generate a nascent lumen. Moreover, lumen initiation is tightly coordinated with the assembly and rearrangement of apical cell-cell junctions and requires the Crumbs complex protein PatJ, which controls the architecture of the apical-lateral border and connects the tight junction to the apical cortex. Together, our results identify PatJ as a critical organizer of the apical-lateral interface and indicate that VACs act as specialized transport organelles that deliver a preassembled apical cortex to the AMIS, enabling rapid and efficient lumen initiation.

cell biology↗

bioRxiv2025

The inflammatory skin disease map (ISD map): an interactive computational resource focused on psoriasis and atopic dermatitis molecular mechanisms

BackgroundInflammatory skin diseases (ISD), including atopic dermatitis (AD) and psoriasis (PsO), emerge from a complex network of inter- and intracellular biochemical interactions under the influence of genetic and environmental factors. The complexity of ISD mechanisms hinders translation of research findings into effective treatments and may explain the low remission rates despite the availability of modern targeted therapies. ObjectiveTo model AD- and PsO-associated mechanisms as networks of context-specific molecular interactions, the so-called ISD map, and to check the usefulness of this map as a graphically guided review of AD and PsO mechanisms and as a mechanistic hypothesis-generating platform. MethodsThe ISD map was built by assembling mechanistically resolved causal interactions obtained from relevant biomedical literature via manual curation. ResultsWe demonstrate that the ISD map (https://imi-biomap.elixir-luxembourg.org/) serves as an interactive, graphical review of AD and PsO molecular mechanisms and as a mechanistic hypothesis-generating platform. By analysing the map structure itself or the map integrated with genetics and functional genomics data, we could generate the following mechanistic hypotheses: (i) AD poor response to dupilumab is associated with a potential upregulation of IFNG, IL22, TSLP, IL-17A and IL25 signalling pathways in keratinocytes and/or single nucleotide polymorphisms (SNPs) in genes encoding regulators of IFNG expression in Th1 cells and (ii) PsO resistance to cytokine-induced apoptosis is associated with SNPs in IFNG signalling genes regulating SOCS1 in keratinocytes. Finally, the IL4/IL13 pathway in the AD submap of the ISD map was converted into a probabilistic Boolean model to simulate the effects of IFNG in sensory perception of itching after treatment with dupilumab. Our findings suggest that inhibiting both IFNG and IL4R may improve the therapeutic management of itching. ConclusionThe ISD map provides a significant interactive, computationally accessible resource of molecular knowledge on AD and PsO that can be used to graphically review known AD and PsO mechanisms and generate mechanistic hypotheses.

bioinformatics↗

bioRxiv2025

TRF2 Non-Telomeric Function is Indispensable for Neural stemness

Depletion of TRF2 from chromosome ends results in telomeric fusions and genome instability in mammals. Here we show that although TRF2 is indispensable for the proliferation and survival of mouse neural stem cells (mNSCs), surprisingly, this is due to non-telomeric transcriptional function of TRF2, and not telomere protection. Complementing recent work showing TRF2 is dispensable for telomere protection in pluripotent stem cells. Deletion of TRF2 in adult mNSCs (TRF2fl/fl, Nestin-Cre) resulted in markedly reduced proliferation and impaired differentiation into neurons. However, telomere dysregulation-induced DNA damage was not observed, as indicated by the unaltered DNA damage response. Similarly, in SH-SY5Y cells, TRF2 depletion induced differentiation without causing telomere dysfunction. Mechanistically, non-telomeric TRF2 directly binds to the promoters of key genes that regulate differentiation. TRF2-dependent recruitment of the polycomb repressor complex (PRC2) and subsequent H3K27 trimethylation repress differentiation-associated genes, thereby maintaining NSC identity. Interestingly, G-quadruplex (G4) motifs are necessary for TRF2 binding. Disrupting the TRF2-G4 interaction-- either through G4-binding ligands or the G4-specific helicase DHX36--induces differentiation genes, thereby promoting neurogenesis. These findings reveal a pivotal non-telomeric role of TRF2 in NSC survival, providing key mechanistic insights into neurogenesis with implications for aging-related neurodegeneration.

molecular biology↗