Biology subjects

Sil, P.

Publications and source records attributed to Sil, P..

16 recordsLinked to original sources

bioRxiv2026

An integrated resource for systems-level analysis of aging hallmarks and associated genes

Aging is a complex biological process involving progressive cellular dysfunction, tissue decline, and increased susceptibility to multiple chronic diseases. A systemic view of aging through its established hallmarks provides a structured framework to understand this complexity and drive therapeutic discovery. To this end, we present AgingHallmarksDB, an interactive web platform that enables systems-level analysis of hallmark-associated gene sets. Aging-related genes were first curated from seven established resources, and those present in at least two of these resources were considered as consensus aging-related genes. Using functional annotations derived from GO, KEGG, and Reactome, a total of 3111 genes were mapped to the 11 aging hallmarks, of which 2593 were supported by additional experimental or manually curated evidence, with 1089 of these forming the consensus set. Further, AgingHallmarksDB supplements hallmarks and gene annotations with tissue or cell-type class specificity, exosomal profiles, and regulatory interactions, enabling users to perform hallmark enrichment, protein-protein and regulatory interaction-based analysis. To elucidate the interconnectedness of hallmarks, network separation and proximity analyses of hallmark-associated modules were performed, revealing functional overlap between hallmarks on the human interactome. Furthermore, the utility of AgingHallmarksDB was demonstrated through network topological and regulatory interaction analyses of common hallmark genes, hallmark enrichment and network proximity analyses of eight chronic age-related diseases and seven developmental and congenital diseases, and gene set enrichment analysis of a PM2.5-associated skin transcriptome. Together, these analyses highlight the utility of AgingHallmarksDB for aging hallmark-centred systems biology research. The resource is accessible at https://cb.imsc.res.in/aginghallmarksdb/.

bioinformatics↗

bioRxiv2026

Dishevelled-mediated clustering stabilizes Frizzled6 and Vangl2 to establish planar cell polarity in the mammalian skin

Planar cell polarity (PCP) in epithelia is characterized by the polarized distribution of two opposing, membrane-associated PCP complexes across cell junctions. Transmembrane components of the PCP complex bridge cell junctions and organize into punctate, intercellular assemblies that exhibit a high degree of stability. Here, we define the contributions of the cytoplasmic PCP protein, Dishevelled (Dvl), in the sub-micron scale organization and stability of PCP complexes. Using endogenously-tagged fluorescent PCP reporters in the embryonic mouse epidermis, we quantify PCP protein mobility and clustering during polarization. We find that as transmembrane proteins immobilize into puncta, Dishevelled (Dvl2/3) co-accumulates with its transmembrane partner Frizzled (Fz6) in a polarized manner and stabilizes clusters of PCP complexes. We identify a previously unknown function for the oligomerizing DIX domain of Dvl3, typically associated with Wnt signaling, in Dvl3 asymmetric localization. These observations underscore a role for Dvl oligomerization in assembly and stabilization of asymmetric PCP puncta.

developmental biology↗

bioRxiv2026

Cell cycle-dependent transitions in PCP protein mobility erase and restore planar cell polarity in mitosis

Central to our understanding of how cells establish polarity is deciphering how polarity proteins are transported to and retained at asymmetric positions. Here, in the context of planar cell polarity (PCP) remodeling in mitosis where asymmetry is transiently lost and restored, we show that PCP proteins transition between mobile and stable states in coordination with cell cycle progression. Live imaging and FRAP analyses reveal that, in addition to becoming internalized into endocytic vesicles, membrane-associated PCP proteins dramatically increase their lateral mobility upon mitotic entry in a Plk1-dependent manner. Unexpectedly, asymmetry is not restored in cytokinesis via polarized delivery of PCP-protein containing vesicles. Rather, PCP proteins continue to diffuse laterally during cytokinesis where they are captured and stabilized non-cell autonomously through adhesive interactions with neighbors. We propose that a transient, laterally diffusive state in mitosis allows for flexibility and robustness in planar polarity as dividing cells change shape and rearrange.

cell biology↗

bioRxiv2025

Diverse ancestral myosin motors generate and segregate distinct types of nanocluster-rich domains at the plasma membrane

Molecular organization of the plasma membrane (PM) at nano and micron scales is critical for its function in all living cells. This emerges not only from the self-assembly of lipids and proteins but also from active forces originating in the underlying cytoskeletal cortex. These forces drive membrane molecules into non-equilibrium steady state patterns such as nanoclusters. However, the molecular agents connecting membrane organization with cytoskeletal dynamics and stresses have remained unknown. Here we show that two classes of ubiquitous ancestral non-muscle myosins are deployed for the organization of different types of membrane components. Inner-leaflet localized Class I myosins link outer-leaflet GPI-anchored molecules to juxta-membrane actin-filaments, whereas the more cortically-localized Class II myosins operate on transmembrane proteins endowed with actin-binding capacity. Consistent with an active Flory Huggins theory for phase separation, these observations show that the distinct motor-driven membrane molecules generate spatially segregated mesoscale domains, enriched in nanoclusters derived from different myosin classes. Moreover, chemically reversible post-translational modifications such as palmitoylation enable concatenation of these domains by enhancing affinity of the membrane domain constituents for each other. We anticipate that the segregation potential of the ATP-fueled cell membrane is made available for the crucial purpose of modulating information transduction because it can be regulated in space and time during the construction of signaling cascades, underpinning functional plasma membrane organization.

cell biology↗

bioRxiv2025

Dynamic and atypical E-cadherin-based attachments mediate melanoblast migration through confined epithelial spaces

Epithelial tissues are populated with accessory cells such as immune cells, sensory cells, and pigment-producing melanocytes, which must migrate through and intercalate between tightly adherent epithelial cells. Although much is known about how cells migrate through interstitial spaces consisting of predominantly of collagen-rich ECM and mesenchyme, how cells migrate through confined epithelial spaces without impairing barrier function is far less understood. Here, using live imaging of the mouse epidermis, we captured the migration of embryonic melanocytes (melanoblasts) while simultaneously visualizing the basement membrane or epithelial surfaces. We show that melanoblasts migrate through both basal and suprabasal layers of the epidermis and hair follicles where they use keratinocyte surfaces, as well as the basement membrane, as substrates for migration. We show that melanoblasts form atypical and dynamic E-cadherin based attachments to surrounding keratinocytes that largely lack the cytoplasmic catenins known to anchor E-cadherin to the actin cytoskeleton. We show E-cadherin is needed in both melanoblasts and keratinocytes to stabilize migratory protrusions, and that depleting E-cadherin in melanoblasts results in reduced motility and ventral depigmentation in adult mice. These findings illustrate how migratory cells co-opt the cell-cell adhesion machinery connecting adjacent epithelial cells to invade between and migrate through them without interrupting the skin barrier.

cell biology↗

bioRxiv2025

Simple threshold-based Boolean rules fall short in capturing biological regulatory network dynamics

Among the various frameworks for modeling gene regulatory network (GRN) dynamics, Boolean modeling remains both powerful and accessible. Nevertheless, selecting update rules so that they capture the combinatorial control of various targets remains challenging due to limited quantitative data. Threshold majority rules (TMRs), a subtype of threshold functions (ThFs), update a genes state based on the signed sum of its regulators and its own activity, offering an elegant simplification. However, does the use of TMRs come at the cost of biological realism? Here, we rigorously evaluate the two standard TMR variants regarding their suitability in GRN modeling. We find that they provide limited canalyzation, exhibit discordant bias patterns, and often eliminate self-inhibitions. They are also underrepresented in empirical datasets, the opposite of what is expected for biologically relevant rules. Compared to nested canalyzing functions (NCFs), another class of ThFs but known to be preponderant in empirical datasets, TMRs exhibit heightened complexity and sensitivity to perturbations. At the network level, TMRs frequently fail to recover biological attractors and the associated basin size distributions. Using ensembles of random Boolean networks, we also show that one TMR type drives the network dynamics toward the chaotic regime. These findings invite a thoughtful reevaluation of TMRs as an appropriate logic for modeling GRNs despite their theoretical appeal.

systems biology↗

bioRxiv2024

Choices of regulatory logic class modulate the dynamical regime in random Boolean networks

Random Boolean networks (RBNs) have been widely explored as models for understanding complex systems, in particular gene regulatory networks (GRNs). Stability (order) and instability (chaos), critical characteristics of any dynamic system, have naturally been a central focus in RBN research. Several measures have previously been introduced to assess stability, e.g., via damage spreading or via statistical properties of attractors such as their number, lengths or basin sizes. Undoubtedly, network topology plays an important role in shaping the dynamics of RBN. Another key factor influencing the dynamics is the Boolean functions (BFs) assigned to each node. In this work, we conduct a systematic investigation to examine the influence of five different classes of BFs on the dynamics of RBNs. By employing various dynamical stability measures, we show that biologically meaningful BFs consistently drive the dynamics toward the stable regime compared to random BFs. This observation holds across networks with varying size, connectivity, and degree distributions. Additionally, we show that the change in the values of our stability measures with increasing connectivity or size of RBNs is different across the BF classes. For most observables, random BFs change the values significantly, pushing the dynamics toward a more chaotic regime with increasing connectivity or network size. In contrast, biologically meaningful BFs show very minimal fluctuations for most stability measures. These findings emphasize the advantage of restricting to biologically meaningful classes in the reconstruction and modeling of biological systems within Boolean framework.

systems biology↗

bioRxiv2023

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

Boolean networks (BNs) have been extensively used to model the dynamics of gene regulatory networks (GRNs) that underlie cellular decisions. The dynamics of BNs depend on the network architecture and regulatory logic rules (or Boolean functions (BFs)) associated with nodes, both of which have been shown to be far from random in large-scale studies of reconstructed Boolean models. At the level of the BFs, nested canalyzing functions (NCFs) have been shown to be strongly enriched in such GRN models. The central question we address here is whether that enrichment is due to certain sub-types of NCFs. To answer this, we build on one sub-type of NCFs, the chain functions (or chain-0 functions) proposed by Gat-Viks and Shamir. First, we propose 2 other sub-types of NCFs, namely, the class of chain-1 functions which is the dual of the class of chain-0 functions, and generalized chain functions, the union of the chain-0 and chain-1 types. Next, we find that the fraction of NCFs that are chain-0 functions decays exponentially with the number of inputs, and exhibits a fractal-like behaviour as a function of the bias for a fixed number of inputs. Moreover, we explain several of these observations analytically. Then, by analyzing 5990 BFs extracted from a large dataset of reconstructed Boolean models, and 2 other datasets, we find that generalized chain functions are significantly enriched within the NCFs. Lastly, we illustrate the severe restriction imposed by generalized chain functions compared to NCFs for 3 biological models and perform model selection on them using known relative stability constraints.

systems biology↗

bioRxiv2023

A Window into Mammalian Basement Membrane Development: Insights from the mTurq2-Col4a1 Mouse Model

Basement membranes (BMs) are specialized sheets of extracellular matrix that underlie epithelial and endothelial tissues. BMs regulate traffic of cells and molecules between compartments, and participate in signaling, cell migration and organogenesis. The dynamics of mammalian BMs, however, are poorly understood, largely due to a lack of models in which core BM components are endogenously labelled. Here, we describe the mTurquoise2-Col4a1 mouse, in which we fluorescently tag collagen IV, the main component of BMs. Using an innovative Planar-Sagittal live imaging technique to visualize the BM of developing skin, we directly observe BM deformation during hair follicle budding and basal progenitor cell divisions. The BMs inherent pliability enables dividing cells to remain attached to and deform the BM, rather than lose adhesion as generally thought. Using FRAP, we show BM collagen IV is extremely stable, even during periods of rapid epidermal growth. These findings demonstrate the utility of the mTurq2-Col4a1 mouse to shed new light on mammalian BM developmental dynamics.

cell biology↗

bioRxiv2023

Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph

Boolean network (BN) models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. The overall dynamics of such models are embodied in the systems state transition graph (STG) which is highly informative. Indeed, even if two BN models have the same network structure and recover the same attractors, their STGs can be drastically different depending on the type of regulatory logic rules or Boolean functions (BFs) employed. A key objective of the present work is to systematically delineate the effects of different classes of regulatory logic rules on the structural features of the STG of reconstructed Boolean GRNs, while keeping BN structure and biological attractors fixed. Furthermore, we ask how such global features might be driven by characteristics of the underlying BFs. For that, we draw from ideas and concepts proposed in cellular automata for both the structural features and their associated proxies. We use the network of 10 reconstructed Boolean GRNs to generate ensembles that differ in the type of logic used while keeping their structure fixed and recovering their biological attractors, and compute quantities associated with the structural features of the STG: bushiness and convergence, that are based on the number of garden-of-Eden (GoE) states and transient times to reach attractor states when originating at them. We find that ensembles employing biologically meaningful BFs have higher bushiness and convergence than those employing random ones. Computing these global measures gets expensive with larger network sizes, stressing the need for more feasible proxies. We thus adapt Wuensches Z-parameter to BFs in BNs and provide 4 natural variants, which along with the network sensitivity, comprise our descriptors of local dynamics. One variant of the network Z-parameter as well as the network sensitivity correlate particularly very well with the bushiness, serving as a good proxy for the same. Finally, we provide an excellent proxy for the convergence based on computing transient lengths originating at random states rather than GoE states.

systems biology↗

bioRxiv2023

Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks

Boolean models are a well-established framework to model developmental gene regulatory networks (DGRN) for acquisition of cellular identity. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a very large number of combinations of Boolean functions (BFs) that will reproduce the different cell fates (biological attractors). Here we leverage the developmental landscape to enable model selection on such ensembles using the relative stability of the attractors. First we show that 5 previously proposed measures of relative stability are strongly correlated and we stress the usefulness of the one that captures best the cell state transitions via the mean first passage time (MFPT) as it also allows the construction of a cellular lineage tree. A property of great computational convenience is the relative insensitivity of the different measures to changes in noise intensities. That allows us to use stochastic approaches to estimate the MFPT and thus to scale up the computations to large networks. Given this methodology, we study the landscape of 3 Boolean models of Arabidopsis thaliana root development and find that the latest one (a 2020 model) does not respect the biologically expected hierarchy of cell states based on their relative stabilities. Therefore we developed an iterative greedy algorithm that searches for models which satisfy the expected hierarchy of cell states. By applying our algorithm to the 2020 model, we find many Boolean models that do satisfy the expected hierarchy. Our methodology thus provides new tools that can enable reconstruction of more realistic and accurate Boolean models of DGRNs.

systems biology↗

bioRxiv2022

Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling

The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered GPI-anchored proteins (GPI-APs) form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drive the creation of active emulsions, mesoscale liquid ordered (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid-phase segregation. To test these ideas we use spatial imaging of homo-FRET combined with local membrane order and demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions, and exhibit significant lipid order, consistent with predictions of the active composite model.

cell biology↗

bioRxiv2020

Niclosamide inhibits SARS-CoV2 entry by blocking internalization through pH-dependent CLIC/GEEC endocytic pathway

Many viruses utilize the host endo-lysosomal network to infect cells. Tracing the endocytic itinerary of SARS-CoV2 can provide insights into viral trafficking and aid in designing new therapeutic targets. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV2 is internalized via the clathrin and dynamin-independent, pH-dependent CLIC/GEEC (CG) endocytic pathway. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, strongly block the uptake of RBD. Using transduction assays with SARS-CoV2 Spike-pseudovirus, we confirmed that these acidification inhibitors also impede viral infection. By contrast, Chloroquine neither affects RBD uptake nor extensively alters the endosomal pH, yet attenuates Spike-pseudovirus entry, indicating a pH-independent mechanism of intervention. We screened a subset of FDA-approved acidification inhibitors and found Niclosamide to be a potential SARS-CoV2 entry inhibitor. Niclosamide, thus, could provide broader applicability in subverting infection of similar category viruses entering host cells via this pH-dependent endocytic pathway.

cell biology↗

bioRxiv2019

Non-canonical autophagy in dendritic cells restricts cross-presentation and anti-tumor immunity

Major Histocompatibility Complex I (MHC-I) molecules classically present peptides derived from endogenous antigens, but exogenous antigens can also gain access to the MHC-I machinery in dendritic cells (DCs), which can activate antigen-specific CD8+ T cells. This process, termed cross-presentation, can be triggered by the uptake of dying autologous cells, including tumor cells, by DCs. The molecular mechanisms that underlie efficient cross-presentation remain largely uncharacterized, and an improved understanding of these mechanisms might reveal novel strategies for anti-tumor therapies. Rubicon (RUBCN) is a molecule required for LC3-associated phagocytosis (LAP), but dispensable for canonical autophagy, and mice lacking this protein develop an autoimmune inflammatory pathology with age. Here, we demonstrate that Rubcn-deficient DCs have increased retention of engulfed cellular cargo in immature phagosomes resulting in increased phagosome-to-cytosol escape and antigen access to proteasome-mediated degradation. As a result, mice selectively lacking Rubcn in DCs mount stronger tumor antigen-specific CD8+ T cell responses and exhibit decreased tumor burden compared to wild type littermates. These findings identify LAP as a key regulator of cross-presentation and suggest that targeting RUBCN might represent a novel strategy for anti-tumor therapy.

immunology↗

bioRxiv2019

Dynamic actin-mediated nano-scale clustering of CD44 regulates its meso-scale organization at the plasma membrane

Transmembrane adhesion receptors at the cell surface, such as CD44, are often equipped with modules to interact with the extracellular-matrix(ECM) and the intra-cellular cytoskeletal machinery. CD44 has been recently shown to compartmentalize the membrane into domains by acting as membrane pickets, facilitating the function of signaling receptors. While spatial organization and diffusion studies of membrane proteins are usually conducted separately, here we combine observations of organization and diffusion by using high spatio-temporal resolution imaging on living cells to reveal a hierarchical organization of CD44. CD44 is present in a meso-scale meshwork pattern where it exhibits enhanced confinement and is enriched in nano-clusters of CD44 along its boundaries. This nanoclustering is orchestrated by the underlying cortical actin dynamics. Interaction with actin is mediated by specific segments of the intracellular-domain(ICD). This influences the organization of the protein at the nano-scale, generating a selective requirement for formin over Arp2/3-based actin-nucleation machinery. The extracellular-domain(ECD) and its interaction with elements of ECM do not influence the meso-scale organization, but may serve to reposition the meshwork with respect to the ECM. Taken together, our results capture the hierarchical nature of CD44 organization at the cell surface, with active cytoskeleton-templated nano-clusters localized to a meso-scale meshwork pattern.

cell biology↗

bioRxiv2019

Heme minimizes Parkinson’s disease-associated toxicity by inducing a conformational distortion in the oligomers of alpha-Synuclein

Aggregation of the intrinsically disordered protein alpha-Synuclein (-Syn) into insoluble fibrils with a cross-{beta} sheet amyloid structure plays a key role in the neuronal pathology of Parkinsons disease (PD). The fibrillation pathway of -Syn encompasses a multitude of transient oligomeric forms differing in size, secondary structure, hydrophobic exposure and toxicity. According to a recent solid state NMR study, the fibrillating unit of -Syn contains the core residues of the protein arranged into in-register parallel {beta} sheets with a unique Greek key topology. Here, we have shown that the physiologically available small molecule heme (hemin chloride) when added at sub-stoichiometric ratios to either monomeric or aggregated -Syn, arrests its aggregation in an oligomeric state, which is minimally toxic. Using cryo-EM, we observed that these heme-induced oligomers are mace-shaped and consist of approximately four monomers. However, the presence of a crucial twist or contortion in their Greek key structural architecture prevents further hierarchical appending into annular oligomers and protofilament formation. We confirm using a His50Gln mutant that the binding of heme onto His50 is crucial in inflicting the structural distortion and is responsible for the stabilization of the non-toxic and off-pathway -Syn oligomers. We believe that this study provides a novel strategy of developing a therapeutic solution of PD, which has been elusive so far.

biophysics↗