Biology subjects

Majumder, A.

Publications and source records attributed to Majumder, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Osmotic Coupling of Mechanics and Epigenetics Regulates Chromatin Phase Organization

Cells experience epigenetic, osmotic, and mechanical perturbations that reorganize chromatin, yet how these distinct cues are integrated into a common physical response of the nucleus remains unclear. Here, we identify nuclear hydration as a central state variable that links microenvironmental perturbations to chromatin phase organization and nuclear mechanics. We develop a non-equilibrium mesoscale model that couples chromatin elasticity, water transport, and epigenetic reaction-diffusion kinetics. In this framework, chromatin behaves as a deformable polymer that segregates into coexisting water-rich euchromatic and water-poor heterochromatic phases, whose compositions and morphologies are regulated by hydration-dependent swelling, elastic strain, and histone-mark interconversion. The model predicts that epigenetic perturbations, osmotic shocks, and volume-changing mechanical loads reorganize chromatin by shifting intranuclear water content, nuclear volume, and euchromatin-heterochromatin phase balance. It further predicts that anisotropic forces impose directional strain, driving heterochromatin elongation, alignment, and lamellar transitions. Quantitative comparisons with super-resolution imaging, AFM and chromatin-accessibility measurement - across pharmacological, osmotic, and mechanical perturbations including confinement and micropatterning - support these predictions. Together, our results establish a chemo-mechano-osmotic framework in which nuclear hydration integrates biochemical and biophysical cues to regulate chromatin organization across scales.

biophysics↗

bioRxiv2026

Going beyond labels: Semi-supervised learning for enzyme kinetic parameter prediction

Enzyme kinetic parameters, such as the turnover number (kcat), underpin enzyme engineering and metabolic modeling. Machine learning models can predict these parameters from sequence and substrate representations, but their accuracy is limited by the scarcity and narrow coverage of experimentally labeled data, particularly for out-of-distribution enzymes. Existing strategies to exploit unlabeled data rely on homologous sequences, pseudo-labels or synthetic perturbations of labeled samples, limiting their potential to fully leverage unlabeled data for model improvement. Here, we show that regularization-based semi-supervised learning improves model performance by leveraging biologically meaningful unlabeled samples alongside labeled data during task-specific training, without assigning pseudo-labels to the unlabeled samples. Specifically, enzyme-substrate pairs lacking kcat, but characterized for other kinetic parameters, can serve as unlabeled data that improve kcat prediction. Using the clustered CataPro dataset at 40% sequence identity as a stringent benchmark, neural consistency regularization and graph-Laplacian regularization each performed better when unlabeled records were added, beyond the gains from regularization on labeled data alone. The benefit required sufficient labeled data, saturated at a few thousand unlabeled records for the neural model, and depended on the density of the unlabeled data in the feature space rather than on their proximity to labeled data. Gains extended to wild-type and mutant enzymes and to a local low-data adenylate kinase landscape. These findings show that incomplete kinetic records specifically, and unlabeled data points generally, are a valuable resource for enzyme kinetics prediction.

bioinformatics↗

bioRxiv2026

Nanoparticle Albumin-Bound Paclitaxel Targets Pulmonary Neutrophils

Nanoparticle albumin-bound paclitaxel (Abraxane) was among the first clinically approved nanomedicines and is a first-line chemotherapeutic. It enhances therapeutic efficacy and reduces side effects of paclitaxel. Despite its extensive clinical use, mechanisms of Abraxane's therapeutic effects are the subject of ongoing study. This work posits a new mechanism for Abraxane's effects in lung cancers and metastasis. Tracing the albumin component of Abraxane with radioisotopes or fluorophores, we find that Abraxane homes to the lungs. Abraxane's lung tropism is elevated by inflammation and is eliminated in complement protein C3 knockout mice, showing that complement pathway drives the uptake. Flow cytometry and histology show that neutrophils are the dominant cell type taking up Abraxane in the lungs. We demonstrate Abraxane's tropism to pulmonary neutrophils in mice and in human donor lungs. We note previously undocumented side effects associated with Abraxane's lung tropism, including pro-thrombotic and pro-inflammatory responses in acute lung inflammation. We show that Abraxane's efficacy against lung metastases is affected when lung uptake is eliminated by C3 knockout. Our results provide insight into why Abraxane is effective in lung cancer and metastases. These findings may be used to improve outcomes in patients receiving Abraxane and help design next-generation cancer nanomedicines.

bioengineering↗

bioRxiv2026

A Versatile Microfluidic Device for High-throughput Combinatorial Drug Screening

Combination therapies can improve anticancer efficacy, but identifying effective drug pairs and dose combinations requires systematic exploration of multidimensional concentration spaces. Here, we extend a diffusion-driven, flowless microfluidic concentration gradient generator (CGG) to enable quantitative combinatorial drug screening without external pumps or continuous flow. The platform comprises a 5 x 5 array of interconnected culture nodes coupled to four peripheral reservoirs, in which overlapping diffusion fields generate spatially defined single- and multidrug exposures. Computational modelling was used to assign local drug concentrations to individual nodes, enabling direct correlation of the predicted exposure landscape with cellular response. Using MCF-7 breast cancer cells and 5-fluorouracil (5-FU) and doxorubicin (DOX) as model therapeutics, the platform resolved concentration-dependent single-agent responses, yielding IC50 values of 3.46 M for 5-FU and 1.22 M for DOX. Combinatorial loading generated 25 spatially defined 5-FU-DOX concentration pairs within a single device, which were resolved into two-dimensional concentration-response landscapes. Bliss independence analysis revealed concentration-specific drug interactions, with synergy predominating at low-to-intermediate concentrations and a transition towards additive and antagonistic responses at higher exposures. These findings establish a pump-free microfluidic strategy that integrates computational concentration mapping with spatially resolved pharmacological analysis to identify effective drug-combination windows within a single platform.

cancer biology↗

bioRxiv2026

Integrated in silico identification of fungal-derived dual-target inhibitors for anti-schistosomal drug discovery

Praziquantel, which has limited efficacy against young parasites and reduces susceptibility, is the principal therapy for schistosomiasis, a neglected tropical illness. This work identified fungal-derived compounds with potential dual inhibitory action against Schistosoma mansoni DHODH and cathepsin B1 using an integrated computational method. From 1,831 fungal metabolites, 120 were selected for molecular docking after structure standardisation, drug-likeness evaluation, ADMET, and toxicity screening. Ganoderlactone B (CID_122184973) and Spiroapplanatumine F (CID_132962217) strongly bound to DHODH and CB1, with docking affinities of -10.6 and -10.0 kcal/mol and -9.0 and -8.9, respectively. Docking validation showed good discrimination between active compounds and decoys with area-under-the-curve values of 0.98 for DHODH and 0.96 for CB1. The protein-ligand interaction study showed hydrogen bonding, hydrophobic interactions, and van der Waals contacts at the binding sites. In 100 ns molecular dynamics simulations, protein complexes exhibited modest backbone deviations and maintained compactness, although CID_132962217 showed sustained binding and a constrained conformation. MM-PBSA analysis identified CID_122184973 as the best common ligand for both targets. At the B3LYP/6-31G level, density functional theory calculations showed that CID_139584993 had the lowest HOMO-LUMO energy gap and hardness values of 3.552 and 1.776 eV, respectively, and the highest softness value of 0.282 eV-1, indicating greater electronic reactivity. Electrostatic potential mapping and QSAR predictions supported their interaction and antiparasitic potential. Overall, CID_122184973 and CID_132962217 are promising fungal scaffolds for dual-target anti-schistosomal drug development. Experimental enzyme inhibition, parasite viability, toxicity, and in vivo research are needed to confirm computational findings.

bioinformatics↗

bioRxiv2026

Bio-mimicked Leaf-Imprinted Topographies: Pattern Characterization and Cell Response

Proper alignment of cells is crucial for functioning of various tissues such as skeletal muscle tissues, neural cells, adipose-derived stem cells, etc. Current in-vitro fabrication methods to replicate the cellular environment, e.g., photolithography and 3D printing, are not cost-effective and cannot capture the complexity of the surfaces to which these cells are exposed to. In this work, we used bio-mimicked leaf templates to closely resemble the in-vivo environment the muscle cells and cultured C2C12 cells, myoblast cell lines, on modified PDMS substrates fabricated using these leaf templates. Using image analysis software, we analyzed the degree of alignment of cells, aspect ratio and the area projected by individual cells cultured on these surfaces. The C2C12 cells cultured on the PDMS substrates formed utilizing the front and back sides of the leaves of Musaceae Banana were found to have an Aspect Ratio of 6.3 and 8.3, the highest among the surfaces studied in this paper. C2C12 cells cultured had the highest degree of alignment on the negative replica of the back side of Dracaena Sanderiana. Due to the availability of a wide range of leaf templates and bio-mimicked surface structures to measure cell response, it is difficult to find the optimal design. Hence, we have also tried to create a catalog using 15 different leaf surfaces and characterized these surfaces into various categories based on the grooves on the surfaces to provide a more comprehensive set of surface designs for studying cell behavior. To quantitatively analyze the groove pattern, 2D FFT analysis was also performed to find the dominant wavelength of the grooves. In surface characterization, hydrophobicity is also a parameter that needs to be considered; hence, the water contact angle of these surfaces was also measured. Our findings highlight the importance of surface topography and hydrophobicity in influencing cell alignment and can contribute to developing biomimetic surfaces for tissue engineering applications.

bioengineering↗

bioRxiv2026

Shape, Shrink, Spheroid: A DIY High-throughput Spheroid Generation Device

3D spheroids, which closely replicate three-dimensional cell-cell and cell-extracellular matrix interactions, offer superior predictive capabilities compared to conventional 2D monolayer cultures, positioning them as forward-looking platforms in drug testing, cancer biology, and regenerative medicine. However, high-throughput generation of uniform sized spheroids is still a technological challenge. In one hand, the use of conventional ultra-low attachment (ULA) multiwell plates for this purpose is labour intensive and complex. On the other hand, the use of microfabricated facilities demands cutting-edge infrastructure such as clean room, photolithography, and microfluidic setup which are often unavailable for the resource constrained laboratories. In this study, we addressed these problems by developing a low-cost Do-It-Yourself (DIY), polydimethylsiloxane (PDMS) and agarose-based spheroid generation device, capable of producing and maintaining hundreds of spheroids with minimal user intervention. We have demonstrated two variants based on their size, termed here as S1 and S2 devices which fit into 6-well and 12-well plates, and can generate 600 and 1200 uniform-sized spheroids respectively. We validated our device with various cell lines including primary and cancerous cell lines. We further demonstrated the drug testing capabilities of the device by estimating the IC50 value of the anticancer drug Temozolomide on U87-MG. The value was comparable with the same obtained from the spheroids generated using conventional ULA plates. Additional attachment of a perfusion system made the device suitable for long-term spheroid culture without much user intervention. Furthermore, the devices can also be used for the production of spheroids with gradually changing diameters in a controlled manner, resembling a size gradient. This feature is useful for checking the effect of drugs on different-sized spheroids and for co-culturing spheroids with varying cell densities, mimicking the disease architecture. We have co-cultured two types of the placental trophoblast cells, i.e., extravillous trophoblast (HTR-8) and syncytiotrophoblast (BeWo) with varying densities. In summary, this paper demonstrates a unique DIY method for a high-throughput uniform-sized spheroid generation at a fraction of cost which can be deployed to resource-constrained labs.

bioengineering↗

bioRxiv2026

Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope

HIV-1 buds from infected cells as immature virion particles with a scattered envelope glycoprotein (Env) distribution on their envelope. It then undergoes maturation, during which the viral protease cleaves the Gag polyprotein at multiple sites, leading to structural reorganization of the viral particle and lateral redistribution of Env proteins, ultimately rendering the virion infectious. However, the underlying mechanism of maturation-induced Env reorganization remains elusive. In this study, we combine microsecond-long all-atom (AA), bottom-up coarse-grained (CG) molecular dynamics simulations, and diffusion model-based backmapping to investigate the structural organization and key interactions of Env in viral membranes. AA simulations of fully glycosylated Env embedded in HIV-1 mimetic asymmetric bilayers were first performed to characterize its conformational dynamics and Env-lipid interactions. We then developed a bottom-up CG model of glycosylated Env from that AA data and simulated the mature HIV-1 virion envelope containing multiple Env proteins. The CG simulations predict that Env proteins form clusters through interactions mediated by the cytoplasmic tail domain (CTD) and adopt diverse tilted conformations within these clusters. These CG simulations were then backmapped to AA resolution and further AA simulations were carried out to identify, in detail, the specific interacting residues in the Env clusters. Additionally, analysis of epitope accessibility shows that broadly neutralizing antibodies (bnAbs) targeting the V1/V2 and V3 loops may efficiently interact with Env clusters on the mature virion surface. Together, these results provide a molecular mechanism for Env oligomerization during viral maturation and offer new insights into the accessibility of bnAb epitopes on Env clusters.

biophysics↗

bioRxiv2026

A Functional Placenta-On-Chip Model For Maternal-Fetal Transport

The human placenta functions as a highly specialised barrier that integrates trophoblast differentiation, endocrine activity, and regulated transport of molecules to sustain fetal development. Experimental interrogation of placental barrier function remains challenging due to limited access to human placental tissue and the complexity of existing in vitro models. Here, we report a static, two-chamber placenta-on-chip platform designed to recapitulate key structural and functional attributes of the human placental barrier within an experimentally accessible format. The device design prioritises open maternal compartmentalisation and diffusion-dominated transport, reflecting the haemochorial nature of human placentation. It also remains compatible with standard multi-well plate formats for parallel experimentation. In this two-chambered device, separated by an extracellular matrix-loaded/coated microporous membrane, the trophoblast supports trophoblast syncytialisation, sustained {beta}-human chorionic gonadotropin secretion, and selective barrier function. The engineered barrier restricts macromolecular transport while permitting controlled diffusion of small solutes. Glucose transport across the device is strongly dependent on cellular configuration, with inclusion of the endothelial layer significantly modulating nutrient flux and yielding fetal-to-maternal glucose ratios comparable to those reported in vivo. The platform further supports directional transfer of urea from the fetal to the maternal compartment, demonstrating bidirectional metabolite exchange relevant to placental waste clearance. Under hyperglycemic conditions, glucose transport across the barrier increases without evidence of barrier breakdown, indicating sensitivity to metabolic perturbation. This scalable design of a placenta-on-chip platform provides a robust framework for studying placental transport, metabolic regulation, and barrier integrity. It offers broad application in placental biology, pregnancy-associated pathologies, and screening for pregnancy-safe drugs.

bioengineering↗

bioRxiv2025

Exploring the effect of dynamic deformation on the tight junctions of endothelial cells

Atherosclerosis (Ath) is a leading cause of cardiovascular deaths, accounting for approximately 17.1 million fatalities annually. This condition arises from plaque-induced arterial narrowing, which obstructs blood flow. Traditional animal models face ethical, economic, and translational limitations, while current in vitro models often oversimplify plaque formation by using fixed channels and neglecting the dynamic effects of narrowing on endothelial junctions. The study addresses the limitations by developing a microfluidic device that mimics human-relevant stenosis with dynamic channel narrowing under continuous perfusion. Endothelial cells, which are crucial for maintaining barrier integrity through tight junctions, are subjected to physiological shear stress and hyperlipidaemic conditions by administering free fatty acids. The model evaluates cell alignment, junctional stability, and disease progression under mechanically deformed static conditions. To validate the translational potential of this system, ROS scavenging drug, quercetin is tested for its ability to reverse oxidative stress and barrier dysfunction. This innovative microphysiological system offers a robust platform for investigating endothelial dysfunction in Ath and provides a valuable alternative to animal models for cardiovascular drug testing. By integrating both biochemical and mechanical cues in a controllable environment, this model aims to enhance our understanding of Ath and facilitate the development of more effective therapeutic strategies.

bioengineering↗

bioRxiv2025

High-Fidelity Simulation of Cell Adhesion and Flow with Coarse Grain Modelling: A Numerical and Experimental Approach

A coupled CFD-DEM framework was developed to investigate red blood cell (RBC) transport and cellular adhesion in constricted microchannels, with a primary objective of reducing computational cost while preserving physiological accuracy. Initially, numerical softening factors were implemented, allowing greater overlap between particles to expedite computations, with an optimal value of 0.03 selected. Adhesion forces between RBCs and the channel wall were incorporated, with a minimum effective distance of 0.4{square}{micro}m identified as computationally feasible. However, RBC-RBC adhesion led to artificial clustering and was therefore omitted. Coarse-graining methods were applied up to a factor of 2 to further reduce simulation time, with a value of 1.8 chosen based on consistent cell-free layer (CFL) thickness and drag force characteristics. To correct for the increased drag in coarse-grained models, rolling resistance (Type C) with a coefficient of 0.8 was employed, bringing deviations within 10%. The validated model was then extended to simulate the detachment of adherent C2C12 myoblasts under physiological flow. Experimental validation showed increasing cell retention with seeding time, and simulations reproduced this trend with <5% deviation. The resulting Detachment Force Ratio (DFR) at 6 hours indicates near-equivalence between adhesion and hydrodynamic forces, establishing the models robustness for cell-substrate interaction studies in microfluidics.

cell biology↗

bioRxiv2025

Structural Heterogeneity of the Membrane-Interacting Region of the HIV-1 Envelope Glycoprotein

The HIV-1 envelope glycoprotein (Env) trimer (gp120/gp41)3 forms the key functional envelope spike and is the target of neutralizing antibodies. The glycoprotein gp41 component mediates the fusion of viral and host cell membranes. In addition to its ectodomain, the membrane-interacting C-terminal domain of gp41 plays a crucial role in maintaining the fusogenicity and antigenic characteristics of Env. The membrane-interacting domain of gp41 consists of the highly conserved membrane proximal external region (MPER), which contains epitopes for broadly neutralizing antibodies, the transmembrane domain (TMD), which anchors Env in the membrane and mediates trimer formation, and the cytoplasmic tail (CT) domain, which plays an important role in Env trafficking to HIV-1 assembly sites. Previous experimental studies have extensively characterized the structure of the C-terminal domain of gp41; however, they reported different conformational states of the MPER and TMD. In this study, we used all-atom molecular dynamics simulations to investigate the structure and function of the membrane-interacting domain of gp41 in an HIV-1 mimetic membrane bilayer. The basic residues in the CT domain were found to interact favorably with PIP2, leading to lateral demixing of lipids and the accumulation of PIP2 in the cytofacial leaflet around the CT baseplate. Additionally, analysis based on an artificial intelligence (AI) machine learning based protocol revealed a diverse conformational ensemble of MPER-TMD, consistent with previous experimental observations. The MPER-TMD adopts both helix-turn-helix and extended helical conformations. We propose that the inherent flexibility of the MPER and the N-terminal region of TMD can play an important role in facilitating the late stages of membrane fusion. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/676619v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1ca7fc0org.highwire.dtl.DTLVardef@1894c82org.highwire.dtl.DTLVardef@fe22fcorg.highwire.dtl.DTLVardef@aaf7ee_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Mechanism-aware inference of response to targeted cancer therapies

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

cancer biology↗

bioRxiv2025

Tracking Chemotherapy-Induced Oxidative Stressin Glioblastoma Cells Using NV-Based QuantumSensors

Glioblastoma (GBM) is a highly aggressive cancer with poor prognosis despite temozolomide(TMZ) treatment. TMZ induces oxidative stress, causing persistent redox alterations. We report the first use of nitrogen-vacancy centers in nanodiamonds as quantum sensors for T1 relaxometry in fixed GBM cells, detecting stable paramagnetic signatures linked to chemotherapy-induced persistent oxidative damage. U87-MG cells treated with TMZ show dose-dependent T1 shortening, consistent with conventional ROS fluorescence assays. TBHP studies confirm that the T1 response reflects accumulated redox adducts. Measurements remain robust across fixation and permeabilization protocols. Since drug-resistant GBM cells preserve antioxidant signatures, unchanged T1 times after treatment may indicate early resistance phenotypes. This fixed-tissue compatible readout could stratify patient response, guide adaptive therapy, and support biopsy-based diagnostics and post-treatment drug analysis in routinely preserved clinical specimens enabling retrospective studies and better outcomes for future personalized oncology decision making pathways.

biophysics↗

bioRxiv2025

Targeting DNA-LNPs to Endothelial Cells Improves Expression Magnitude, Duration, and Specificity

DNA-lipid nanoparticles (DNA-LNPs) loaded with inhibitors of the cGAS-STING pathway enable safe and effective delivery of DNA in vivo. Herein, we report the first instances of extrahepatic DNA-LNP targeting. DNA-LNPs conjugated to antibodies against PECAM-1 or VCAM-1 target the endothelium of the lungs and brain/spleen, respectively. These LNPs drive robust transgene expression in their target organs, with greater magnitude and duration than untargeted LNPs. Lung specificity of PECAM-targeted transgene expression increases over two weeks, resulting in markedly higher lung-to-liver expression ratios than our previous PECAM-targeted mRNA-LNPs. Off-target liver DNA expression declines to undetectable levels but persists in the lungs, while mRNA expression uniformly decreases due to its short half-life. We further improve this expression specificity by replacing full-length antibodies with Fab fragments. Single-cell analysis reveals a key mechanism underlying the improvements in organ-specificity: target organ expression is dominated by long-lived endothelial cells, while off-target liver delivery and expression are in non-endothelial cells with shorter half-lives. Collectively, these studies demonstrate that targeted DNA-LNPs achieve high levels of organ- and cell-type-specific transgene expression and thus provide a therapeutic platform for dozens of endothelial-centric diseases.

bioengineering↗

bioRxiv2025

Histone acetylation alters nuclear morphology and architecture of human mesenchymal stem cells in rigidity dependent manner

Nuclear morphology which is closely linked to various cell functions and disease states, is known to be modulated by mechanical stimuli and chromatin modifications. However, the combined effects of substrate rigidity and chromatin modifications remain largely unexplored. In this study, we investigated the interplay between substrate rigidity and histone acetylation, mediated by the histone deacetylase inhibitor (HDACi) valproic acid (VA), in modulating nuclear morphology in human mesenchymal stem cells (hMSCs) cultured on substrates with varying rigidities. We found that VA-induced chromatin decondensation diminished the effects of soft substrates on nuclear morphological parameters, a change not observed on stiff substrates. Furthermore, we showed that the reduction in nuclear stiffness with VA treatment on both substrates was independent of lamin expression, highlighting chromatin decondensation as a key determinant of the observed change in nuclear stiffness. In addition, we demonstrated that soft substrates induced significant nuclear wrinkling, which was alleviated by HDACi treatment, while no such effect of VA was observed on stiff substrates. Together, our findings suggest that chromatin remodeling via HDACi can override substrate-dependent nuclear mechanotransduction on soft substrates, offering new insights into the epigenetic regulation of nuclear mechanics with potential implications for pathologies associated with nuclear morphology.

cell biology↗

bioRxiv2025

IFT20 regulates lymphatic endothelial cell-cell junctions via endocytic trafficking of VE-cadherin

Intraflagellar transport (IFT) proteins are required for the assembly and function of primary cilia. They also regulate non-ciliary polarized vesicular traffic, such as T cell receptor recycling. We recently reported that lymphatic endothelial cells assemble primary cilia and express IFT proteins. Here, we report that IFT20 regulates vascular endothelial cadherin (VE-cadherin) localization at adherens junctions. IFT20 deletion caused discontinuous, button-like interendothelial junctions. This resulted in excessive lymphangiogenesis and impaired lymph drainage in mice. In vitro, VEGF-C treatment of IFT20 KD primary human dermal lymphatic endothelial cells caused accumulation of VE-cadherin in RAB5+ endosomes and enhanced and sustained VEGFR-3 signaling. Our findings are consistent with a model in which IFT20 promotes recycling of VE-cadherin to the adherens junction where it sequesters VEGFR-3 at the cell surface, thereby limiting pro-lymphangiogenic signaling. In the absence of IFT20, intercellular junctions are destabilized, pro-lymphangiogenic VEGFR-3 signaling is enhanced, and lymph transport is impaired by intracellular sequestration of VE-cadherin. This study elucidates the function of an IFT protein in lymphatic endothelial cells and provides mechanistic insight into the processes that regulate lymphatic endothelial cell-cell junctions and lymphangiogenic signaling.

cell biology↗

bioRxiv2024

Mechano-sensing role of oncogenic lncRNA NEAT1 on soft vs. stiff substrates and its implications for glioblastoma progression

Long non-coding RNAs (lncRNAs) have gained increasing recognition as key regulators of cancer biology, overturning their earlier classification as non-functional genomic elements. Among them, NEAT1 (Nuclear-Enriched Abundant Transcript 1) has emerged as a prominent oncogenic lncRNA involved in multiple solid tumors, including liver, prostate, and gastric cancers, as well as gliomas. Although the role of NEAT1 in cancer has been extensively studied, most of these investigations have focused on biochemical factors, leaving the mechano-sensitivity of NEAT1 to mechanical alterations in the tumor microenvironment (TME) largely unexplored. As tumors progress, the TME undergoes significant mechanical changes, particularly extracellular matrix (ECM) stiffening, which modulates cellular behavior through mechano-transduction pathways. While much research has focused on how these mechanical cues influence protein-coding gene expression, their impact on lncRNAs such as NEAT1 remains understudied. This study aims to address this gap by investigating the mechano-sensitivity of NEAT1 in glioblastoma (GBM) cells cultured on polyacrylamide (PAA) gels that mimic the brains physiological stiffness (0.5 kPa) versus conventional, stiff tissue culture plastic (TCP). NEAT1 expression, quantified using qRT-PCR, revealed a significant increase on softer, brain-mimicking substrates compared to stiffer TCP. Overexpression of NEAT1 in brain-mimicking stiffness also showed higher expression levels of cancer progression markers, quantified by qRT-PCR. To further explore NEAT1s role in oncogenesis due to its mechano-sensing capabilities, siRNA-mediated downregulation of NEAT1 in GBM cells cultured on soft PAA gels was performed to reduce NEAT1 levels to those comparable to TCP. The results showed reduced cancer aggressiveness, characterized by decreased expression of invasion, stemness, and epithelial-mesenchymal transition (EMT) markers, further supported by migration and invasion assays. These findings highlight NEAT1 as a mechanosensitive regulator in response to substrate stiffness, underscoring its role in tumor progression.

cancer biology↗